testing with greg testing with greg currently we are here: /netscr/pemsley/autobuild/hal.lmb.internal_2021-07-27__T03_14_14/test-tar/coot-Linux-x86_64-scientific-linux-7.9-pre-release-gtk2-python Tue 27 Jul 04:28:41 BST 2021 WARNING:: ccp4 setup file setup-ccp4 does not exist. /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/bin/coot --no-graphics --script command-line-greg.scm INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/ There are 142 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/list/mon_lib_list.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/a/ALA.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/a/ASP.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/a/ASN.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/c/CYS.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/g/GLN.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/g/GLY.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/g/GLU.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/p/PHE.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/h/HIS.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/i/ILE.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/l/LYS.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/l/LEU.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/m/MET.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/m/MSE.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/p/PRO.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/a/ARG.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/s/SER.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/t/THR.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/v/VAL.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/t/TRP.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/t/TYR.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/p/PO4.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/s/SO4.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/g/GOL.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/c/CIT.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/e/EDO.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/a/A.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/c/C.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/g/G.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/u/U.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/d/DA.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/d/DC.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/d/DG.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/d/DT.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/h/HOH.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/n/NA.cif Spacegroup: P 1 (filter-fileselection-filenames-state) (get-active-map-drag-flag) (use-graphics-interface-state) INFO:: coot.py imported Running python script /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/lib/python2.7/site-packages/coot/coot_load_modules.py Good Morning Paul, Welcome to Coot version 0.9.6.1-pre (set-display-intro-string "Good Morning Paul, Welcome to Coot version 0.9.6.1-pre") (use-graphics-interface-state) Running python script /lmb/home/pemsley/.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 44.00) (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) Running python script /lmb/home/pemsley/.coot-preferences/coot_probe_dots.py Running python script /lmb/home/pemsley/.coot-preferences/coot_toolbuttons.py Traceback (most recent call last): File "", line 1, in File "/lmb/home/pemsley/.coot-preferences/coot_toolbuttons.py", line 1, in coot_toolbar_button("My-refine", "sphere_refine_plus(9)", icon_name="gtk-zoom-in") NameError: name 'coot_toolbar_button' is not defined Running python script /lmb/home/pemsley/.coot-preferences/maps_configure.py (set-display-lists-for-maps 1) Running python script /lmb/home/pemsley/.coot-preferences/pepflip-new.py Running python script /lmb/home/pemsley/.coot-preferences/rama-plot.py Running python script /lmb/home/pemsley/.coot-preferences/refine.py (filter-fileselection-filenames-state) (get-active-map-drag-flag) (use-graphics-interface-state) Good morning Paul Emsley PI Garib Murshudov added 28092012. Welcome to Coot 0.9.6.1-pre. (set-display-intro-string "Good morning Paul. Welcome to Coot 0.9.6.1-pre") (set-display-lists-for-maps 1) load /lmb/home/pemsley/.coot-preferences/angle-factor.scm (set-hardware-stereo-angle-factor 1.50) load /lmb/home/pemsley/.coot-preferences/chain-refine-all.scm load /lmb/home/pemsley/.coot-preferences/chain-refine.scm load /lmb/home/pemsley/.coot-preferences/coot-preferences.scm (set-filter-fileselection-filenames 0) (unset-sticky-sort-by-date) (set-colour-map-rotation-on-read-pdb 21.00) (set-colour-map-rotation-on-read-pdb-c-only-flag 1) (set-density-size 44.00) (set-swap-difference-map-colours 0) (set-colour-map-rotation-for-map 14.00) (set-active-map-drag-flag 1) (set-idle-function-rotate-angle 1.00) load /lmb/home/pemsley/.coot-preferences/enhanced-ligand.scm load /lmb/home/pemsley/.coot-preferences/key-bindings.scm (set-add-terminal-residue-do-post-refine 1) (set-terminal-residue-do-rigid-body-refine 0) load /lmb/home/pemsley/.coot-preferences/kill-side-chain.scm load /lmb/home/pemsley/.coot-preferences/morph-march.scm load /lmb/home/pemsley/.coot-preferences/refine-utils.scm load /lmb/home/pemsley/.coot-preferences/startup.scm load /lmb/home/pemsley/.coot-preferences/template-key-bindings.scm (filter-fileselection-filenames-state) (get-active-map-drag-flag) INFO:: There are 1 command line scripts to run command-line-greg.scm INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb INFO:: file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 0 read successfully Molecule number -5 is not a valid model molecule INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/2WF6.cif INFO:: file /lmb/home/pemsley/data/greg-data/2WF6.cif has been read. Spacegroup: P 21 21 21 INFO:: using standard CCP4 Refmac dictionary to search for "ALF" There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/a/ALF.cif INFO:: using standard CCP4 Refmac dictionary to search for "MG" There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/m/MG.cif INFO:: using standard CCP4 Refmac dictionary to search for "BG6" There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/b/BG6.cif INFO:: Found 1 models Model 1 had 0 links Molecule 1 read successfully in new_molecule_by_atom_selection Something bad happened - No atoms selected INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/ins-code-fragment-pre.pdb INFO:: file /lmb/home/pemsley/data/greg-data/ins-code-fragment-pre.pdb has been read. INFO:: Found 1 models Model 1 had 0 links WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model Molecule 2 read successfully INFO:: Creating directory coot-backup INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_ins-code-fragment-pre.pdb_Tue_Jul_27_04:28:41_2021_modification_0.pdb.gz INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_ins-code-fragment-pre.pdb_Tue_Jul_27_04:28:41_2021_modification_1.pdb.gz INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_ins-code-fragment-pre.pdb_Tue_Jul_27_04:28:41_2021_modification_2.pdb.gz WARNING:: Error reading bogus.map Read map bogus.map failed WARNING:: Can't find file bogus.mtz INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz INFO:: Number of observed reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.84 INFO:: grid sampling...Nuvw = ( 132, 160, 80) INFO:: 0.032 seconds to read MTZ file INFO:: 0.015 seconds to initialize map INFO:: 0.024 seconds for FFT Pre-filter Map statistics: mean: 9.91697e-10 st.d: 0.311501 Pre-filter Map statistics: min: -0.903367 max: 2.9681 INFO:: 0.003 seconds for statistics Map extents: ..... 132 160 80 Map mean: ........ 9.91697e-10 Map sigma: ....... 0.311501 Map maximum: ..... 2.9681 Map minimum: ..... -0.903367 INFO:: 0.014 seconds for contour map INFO:: 0.088 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: /lmb/home/pemsley/data/greg-data/broken.mtz INFO:: not an mtz file: /lmb/home/pemsley/data/greg-data/broken.mtz INFO:: making conventional map from MTZ filename /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz using FWT PHWT INFO:: Number of observed reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.84 INFO:: grid sampling...Nuvw = ( 132, 160, 80) INFO:: 0.027 seconds to read MTZ file INFO:: 0.001 seconds to initialize map INFO:: 0.023 seconds for FFT Pre-filter Map statistics: mean: 9.91697e-10 st.d: 0.311501 Pre-filter Map statistics: min: -0.903367 max: 2.9681 INFO:: 0.002 seconds for statistics Map extents: ..... 132 160 80 Map mean: ........ 9.91697e-10 Map sigma: ....... 0.311501 Map maximum: ..... 2.9681 Map minimum: ..... -0.903367 INFO:: 0.01 seconds for contour map INFO:: 0.063 seconds in total INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/3hfl_sigmaa.mtz INFO:: Number of observed reflections: 17920 INFO:: finding ASU unique map points with sampling rate 1.84 INFO:: grid sampling...Nuvw = ( 80, 108, 112) INFO:: 0.024 seconds to read MTZ file INFO:: 0.007 seconds to initialize map INFO:: 0.022 seconds for FFT Pre-filter Map statistics: mean: 2.84654e-11 st.d: 0.260405 Pre-filter Map statistics: min: -1.04352 max: 1.77976 INFO:: 0.003 seconds for statistics Map extents: ..... 80 108 112 Map mean: ........ 2.84654e-11 Map sigma: ....... 0.260405 Map maximum: ..... 1.77976 Map minimum: ..... -1.04352 INFO:: 0.008 seconds for contour map INFO:: 0.064 seconds in total INFO:: map file type was determined to be CCP4 type INFO:: attempting to read CCP4 map: test-3hfl.map -1.00823 1 -0.937649 11 -0.867067 54 -0.796485 170 -0.725903 489 -0.655321 1325 -0.584739 2872 -0.514157 5479 -0.443575 9698 -0.372993 14930 -0.302411 21908 -0.231829 31992 -0.161247 47486 -0.0906649 66447 -0.0200828 78970 0.0504992 69453 0.121081 44331 0.191663 23720 0.262245 13306 0.332827 9760 0.403409 8451 0.473991 7319 0.544574 6417 0.615156 5389 0.685738 4277 0.75632 3285 0.826902 2374 0.897484 1623 0.968066 1031 1.03865 584 1.10923 314 1.17981 172 1.25039 84 1.32098 53 1.39156 30 1.46214 11 1.53272 13 1.6033 6 1.67389 2 1.74447 3 1.81505 0 Pre-filter Map statistics: mean: 2.84654e-11 st.d: 0.260405 Pre-filter Map statistics: min: -1.04352 max: 1.77976 INFO:: n grid points: 483840 INFO:: mean before filtering: 2.84654e-11 INFO:: variance before filtering: 0.0678109 INFO:: filter by ignoring 376 of 483840 counts ( = 0.07771%) with values around -0.04253 bounds -0.04267 -0.04239 from bin-number 3545 of 10000 Post-filter Map statistics: mean: 3.34e-05 st.d: 0.2605 Post-filter Map statistics: min: -1.044 max: 1.78 INFO:: map_density_distribution() took 4 milliseconds ------------------------- em 0 contour_level 0.4 Map extents: ..... 80 108 112 Map mean: ........ 3.34e-05 Map rmsd: ........ 0.2605 Map maximum: ..... 1.78 Map minimum: ..... -1.044 WARNING:: Error reading . . is a directory. INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb INFO:: file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 7 read successfully /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures successfully opened Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1g6x.pdb 23 fragments garnered from /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1g6x.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1c75.pdb 0 fragments garnered from /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1c75.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1gmx.pdb 33 fragments garnered from /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1gmx.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1hbn.pdb 543 fragments garnered from /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1hbn.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i27.pdb 68 fragments garnered from /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i27.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1ejg.pdb There was an error reading /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1ejg.pdb. ERROR 42 READ: Duplicate sequence number and insertion code. LINE #868 ATOM 414 CA BSER A 22 6.034 13.399 -2.687 0.21 1.55 C Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1e29.pdb 129 fragments garnered from /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1e29.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1g66.pdb 171 fragments garnered from /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1g66.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1g61.pdb 218 fragments garnered from /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1g61.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1f94.pdb 56 fragments garnered from /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1f94.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i12.pdb 45 fragments garnered from /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i12.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i8o.pdb 108 fragments garnered from /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i8o.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1e9g.pdb 52 fragments garnered from /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1e9g.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1fye.pdb 155 fragments garnered from /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1fye.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1ga6.pdb 364 fragments garnered from /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1ga6.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1g4i.pdb 13 fragments garnered from /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1g4i.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1ka1.pdb 349 fragments garnered from /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1ka1.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1koi.pdb 35 fragments garnered from /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1koi.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1jl1.pdb 145 fragments garnered from /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1jl1.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1jk3.pdb 72 fragments garnered from /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1jk3.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1g2y.pdb 24 fragments garnered from /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1g2y.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1et1.pdb 29 fragments garnered from /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1et1.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1g2b.pdb 0 fragments garnered from /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1g2b.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i4u.pdb 174 fragments garnered from /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i4u.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1euw.pdb 9 fragments garnered from /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1euw.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1k7c.pdb 228 fragments garnered from /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1k7c.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1fsg.pdb 226 fragments garnered from /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1fsg.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1fn8.pdb 4 fragments garnered from /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1fn8.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1hyo.pdb 411 fragments garnered from /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1hyo.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i0d.pdb 326 fragments garnered from /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i0d.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1gk9.pdb 0 fragments garnered from /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1gk9.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1hdh.pdb 520 fragments garnered from /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1hdh.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1hdo.pdb 137 fragments garnered from /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1hdo.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i0v.pdb 64 fragments garnered from /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i0v.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1e4m.pdb 494 fragments garnered from /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1e4m.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1ird.pdb 136 fragments garnered from /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1ird.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1jcl.pdb 247 fragments garnered from /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1jcl.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1iqz.pdb 75 fragments garnered from /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1iqz.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1h97.pdb 142 fragments garnered from /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1h97.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1c7k.pdb 127 fragments garnered from /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1c7k.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1jf8.pdb 123 fragments garnered from /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1jf8.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1h4x.pdb 106 fragments garnered from /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1h4x.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1heu.pdb 0 fragments garnered from /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1heu.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1f9v.pdb 143 fragments garnered from /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1f9v.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1j98.pdb 149 fragments garnered from /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1j98.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1es9.pdb 205 fragments garnered from /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1es9.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1f4p.pdb 140 fragments garnered from /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1f4p.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1kth.pdb 51 fragments garnered from /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1kth.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1ds1.pdb 318 fragments garnered from /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1ds1.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1g7a.pdb 14 fragments garnered from /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1g7a.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1dy5.pdb 119 fragments garnered from /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1dy5.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1jg1.pdb 208 fragments garnered from /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1jg1.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1hg7.pdb 20 fragments garnered from /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1hg7.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1eb6.pdb 172 fragments garnered from /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1eb6.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1f86.pdb 108 fragments garnered from /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1f86.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i40.pdb 0 fragments garnered from /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i40.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1jfb.pdb 0 fragments garnered from /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1jfb.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i2t.pdb 54 fragments garnered from /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i2t.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1jbe.pdb 68 fragments garnered from /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1jbe.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1j9b.pdb 131 fragments garnered from /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1j9b.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1hvb.pdb 294 fragments garnered from /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1hvb.pdb INFO:: 8375 fragments found in total of which 0 were 5 peptides not backwards A contains 94 residues from 1 to 93 target fragment start res: 10 had 29 db fragment hits, ilength=6 target fragment start res: 13 had 1772 db fragment hits, ilength=6 breaking out of match_target_fragment 6 with iresno= 16 merge fragments 10 to 20 with 2 fit sets to merge The merging is complete mainchain_fragment from 10 to 20 done mainchain_fragment successfully set cell and symmetry INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb INFO:: file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 9 read successfully INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:28:42_2021_modification_0.pdb.gz not backwards A contains 114 residues from -19 to 93 target fragment start res: -19 had 0 db fragment hits, ilength=6 retrying with ilength = 5 produces 14 hits. 2nd part with ilength = 5, iresno=-18 produces 9 hits. target fragment start res: -16 had 22 db fragment hits, ilength=6 target fragment start res: -13 had 48 db fragment hits, ilength=6 target fragment start res: -10 had 29 db fragment hits, ilength=6 target fragment start res: -7 had 1772 db fragment hits, ilength=6 target fragment start res: -4 had 2040 db fragment hits, ilength=6 target fragment start res: -1 had 2021 db fragment hits, ilength=6 breaking out of match_target_fragment 6 with iresno= 2 merge fragments -19 to 6 with 8 fit sets to merge The merging is complete mainchain_fragment from -19 to 6 done mainchain_fragment successfully set cell and symmetry short target_ca 0 with iresno 1, trying 0 short target_ca 0 with iresno 0, trying -1 WARNING:: short target at start - bailing out now. merge fragments 1 to 96 with 0 fit sets to merge The merging is complete mainchain_fragment from 1 to 96 done mainchain_fragment (process:319856): Gtk-CRITICAL **: 04:28:42.801: IA__gtk_widget_show: assertion 'GTK_IS_WIDGET (widget)' failed INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-add-terminal-1-test.pdb INFO:: file /lmb/home/pemsley/data/greg-data/tutorial-add-terminal-1-test.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 83/90 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 11 read successfully INFO:: fitting terminal residue with 5000 random trials WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model INFO:: done mutating residue [spec: 1 "A" 0 ""] in add_cb_to_terminal_res INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-add-terminal-1-test.pdb_Tue_Jul_27_04:28:43_2021_modification_0.pdb.gz INFO:: backup file name coot-backup/atom_selection_from_tutorial-add-terminal-1-test.pdb_Tue_Jul_27_04:28:43_2021_modification_0.pdb.gz INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/frag-2wot.pdb INFO:: file /lmb/home/pemsley/data/greg-data/frag-2wot.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Molecule 13 read successfully WARNING:: add_terminal_residue_using_phi_psi() residue not found for "XX" 276 INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb INFO:: file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 14 read successfully INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz INFO:: Number of observed reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.84 INFO:: grid sampling...Nuvw = ( 132, 160, 80) INFO:: 0.027 seconds to read MTZ file INFO:: 0 seconds to initialize map INFO:: 0.022 seconds for FFT Pre-filter Map statistics: mean: 9.917e-10 st.d: 0.3115 Pre-filter Map statistics: min: -0.9034 max: 2.968 INFO:: 0.003 seconds for statistics Map extents: ..... 132 160 80 Map mean: ........ 9.917e-10 Map sigma: ....... 0.3115 Map maximum: ..... 2.968 Map minimum: ..... -0.9034 INFO:: 0.008 seconds for contour map INFO:: 0.06 seconds in total INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:28:43_2021_modification_0.pdb.gz INFO:: fitting terminal residue with 5000 random trials WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model INFO:: done mutating residue [spec: 1 "A" 94 ""] in add_cb_to_terminal_res 0 N :: xyz = ( 58.61, 2.868, -1.743) occ: 1 b-fact: 45 1 C :: xyz = ( 60.07, 2.035, -3.48) occ: 1 b-fact: 45 2 CA :: xyz = ( 59.93, 2.304, -1.985) occ: 1 b-fact: 45 3 O :: xyz = ( 61.12, 1.595, -3.938) occ: 1 b-fact: 45 ------------------ add_view_raw() B11 View INFO:: backup file name coot-backup/atom_selection_from_tutorial-modern.pdb_Tue_Jul_27_04:28:44_2021_modification_0.pdb.gz INFO:: backup file name coot-backup/atom_selection_from_tutorial-modern.pdb_Tue_Jul_27_04:28:44_2021_modification_1.pdb.gz INFO:: backup file name coot-backup/atom_selection_from_tutorial-modern.pdb_Tue_Jul_27_04:28:44_2021_modification_2.pdb.gz INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/rotamer-test-fragment.pdb INFO:: file /lmb/home/pemsley/data/greg-data/rotamer-test-fragment.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Molecule 18 read successfully INFO:: Reading rotamer probability tables... INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/eleanor-HIS.pdb INFO:: file /lmb/home/pemsley/data/greg-data/eleanor-HIS.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Molecule 19 read successfully INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/res098.pdb INFO:: file /lmb/home/pemsley/data/greg-data/res098.pdb has been read. Spacegroup: P 41 21 2 INFO:: Found 1 models Model 1 had 0 links Molecule 20 read successfully ----------------- in create_mmdbmanager_from_res_vector() alt_conf is "" ----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0"" returning an atom selection for all moving atoms 11 atoms debug:: on creation last_restraints is 0x741ca50 INFO:: from_res_vec() created 19 monomer restraints created 10 bond restraints created 8 angle restraints created 0 plane restraints created 1 chiral vol restraints created 0 improper dihedral restraints Made 0 CHO-SS-and-other bond restraints Made 0 CHO-SS-and-other angle restraints Made 0 CHO-SS-and-other plane restraints Made 0 CHO-SS-and-other trans-peptide restraints INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "X" 15 "" " CG " ""] LYS to [spec: model 1 "X" 15 "" " CE " "A"] LYS delta -1.33 target 3.84 distortion 1.19e+03 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "X" 15 "" " CG " ""] LYS to [spec: model 1 "X" 15 "" " CE " "B"] LYS delta -1.32 target 3.84 distortion 1.14e+03 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "X" 15 "" " CG " ""] LYS to [spec: model 1 "X" 15 "" " NZ " "B"] LYS delta -0.547 target 3.52 distortion 38.7 debug:: restraints results 1 0 Minimum found (iteration number 16) at -84.4 Final Estimated RMS Z Scores: bonds: 0.553 angles: 0.503 improper-dihedrals: N/A torsions: N/A trans-peptide: 1.37 (non-sqrt) planes: 0.636 from 5 restraints parallel planes: N/A non-bonded: -0.746 chiral vol: 0.633 rama plot: N/A start_pos: N/A TargetPos: N/A GemanMcCl: N/A -------- Results --------- INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "X" 15 "" " CG " ""] LYS to [spec: model 1 "X" 15 "" " CE " "B"] LYS delta -0.755 target 3.84 distortion 81 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "X" 15 "" " CG " ""] LYS to [spec: model 1 "X" 15 "" " CE " "A"] LYS delta -0.755 target 3.84 distortion 80.9 Final Estimated RMS Z Scores bonds: 0.553 angles: 0.503 improper-dihedrals: N/A torsions: N/A trans-peptide: 1.37 (non-sqrt) planes: 0.636 from 5 restraints parallel planes: N/A non-bonded: -0.746 chiral vol: 0.633 rama plot: N/A start_pos: N/A TargetPos: N/A GemanMcCl: N/A INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_res098.pdb_Tue_Jul_27_04:29:09_2021_modification_0.pdb.gz INFO:: replace_coords: 11 atoms updated. debug:: in clear_all_atom_pull_restraints() 0 INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb INFO:: file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 21 read successfully INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz INFO:: Number of observed reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.84 INFO:: grid sampling...Nuvw = ( 132, 160, 80) INFO:: 0.027 seconds to read MTZ file INFO:: 0.001 seconds to initialize map INFO:: 0.023 seconds for FFT Pre-filter Map statistics: mean: 9.92e-10 st.d: 0.312 Pre-filter Map statistics: min: -0.903 max: 2.97 INFO:: 0.002 seconds for statistics Map extents: ..... 132 160 80 Map mean: ........ 9.92e-10 Map sigma: ....... 0.312 Map maximum: ..... 2.97 Map minimum: ..... -0.903 INFO:: 0.009 seconds for contour map INFO:: 0.062 seconds in total DEBUG:: split_residue table 0 N :: INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:29:09_2021_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! ------------------- debug:: in clear_all_atom_pull_restraints() 0 INFO:: fitting 1 ligands into cluster 0 INFO:: fitting 1 ligands into cluster 0 INFO:: fitting 1 ligands into cluster 0 INFO:: fitting 1 ligands into cluster 0 INFO:: fitting 1 ligands into cluster 0 INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:29:09_2021_modification_1.pdb.gz INFO:: replace_coords: 8 atoms updated. Fitting score for best rotamer: 5.99 INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/pdb3knw.ent INFO:: file /lmb/home/pemsley/data/greg-data/pdb3knw.ent has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 30 links INFO:: NCS chain comparison 185/199 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 23 read successfully INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_pdb3knw.ent_Tue_Jul_27_04:29:09_2021_modification_0.pdb.gz INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/pdb1py3.ent INFO:: file /lmb/home/pemsley/data/greg-data/pdb1py3.ent has been read. Spacegroup: C 1 2 1 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 91/204 INFO:: NCS chain comparison 90/204 INFO:: NCS chain comparison 175/179 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain C onto Chain B" Molecule 24 read successfully INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_pdb1py3.ent_Tue_Jul_27_04:29:10_2021_modification_0.pdb.gz INFO:: (result) TYR swapped atoms in [spec: 1 "A" 30 ""] TYR INFO:: (result) ASP swapped atoms in [spec: 1 "A" 35 ""] ASP INFO:: (result) PHE swapped atoms in [spec: 1 "A" 39 ""] PHE INFO:: (result) TYR swapped atoms in [spec: 1 "A" 54 ""] TYR INFO:: (result) PHE swapped atoms in [spec: 1 "A" 57 ""] PHE INFO:: (result) ASP swapped atoms in [spec: 1 "A" 66 ""] ASP INFO:: (result) PHE swapped atoms in [spec: 1 "A" 90 ""] PHE INFO:: (result) ASP swapped atoms in [spec: 1 "B" 2 ""] ASP INFO:: (result) TYR swapped atoms in [spec: 1 "B" 30 ""] TYR INFO:: (result) ASP swapped atoms in [spec: 1 "B" 35 ""] ASP INFO:: (result) PHE swapped atoms in [spec: 1 "B" 39 ""] PHE INFO:: (result) TYR swapped atoms in [spec: 1 "B" 54 ""] TYR INFO:: (result) TYR swapped atoms in [spec: 1 "B" 77 ""] TYR INFO:: (result) ASP swapped atoms in [spec: 1 "B" 85 ""] ASP INFO:: (result) PHE swapped atoms in [spec: 1 "B" 90 ""] PHE INFO:: (result) TYR swapped atoms in [spec: 1 "C" 30 ""] TYR INFO:: (result) TYR swapped atoms in [spec: 1 "C" 32 ""] TYR INFO:: (result) ASP swapped atoms in [spec: 1 "C" 35 ""] ASP INFO:: (result) PHE swapped atoms in [spec: 1 "C" 39 ""] PHE WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion() WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion() INFO:: (result) TYR swapped atoms in [spec: 1 "C" 54 ""] TYR INFO:: (result) PHE swapped atoms in [spec: 1 "C" 57 ""] PHE INFO:: (result) TYR swapped atoms in [spec: 1 "C" 81 ""] TYR INFO:: (result) ASP swapped atoms in [spec: 1 "C" 85 ""] ASP INFO:: (result) PHE swapped atoms in [spec: 1 "C" 90 ""] PHE INFO:: (result) ASP swapped atoms in [spec: 1 "C" 94 ""] ASP === 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: #() got status: #() PASS: Auto-read bad MTZ test Entered testcase - Map Sigma INFO:: map sigmas 0.311501026153564 #f PASS: Map Sigma Entered testcase - Another Level Test PASS: Another Level Test Entered testcase - Sharpen map from map PASS: Sharpen map from map Entered testcase - db-main makes mainchain PASS: db-main makes mainchain Entered testcase - Negative Residues in db-mainchain don't cause a crash PASS: Negative Residues in db-mainchain don't cause a crash Entered testcase - Set Atom Attribute Test PASS: Set Atom Attribute Test Entered testcase - Add Terminal Residue Test PASS: Add Terminal Residue Test Entered testcase - Adding residue by phi psi, no crash PASS: Adding residue by phi psi, no crash Entered testcase - Add Terminal Residue O Position Add terminal residue bond check dd-1: 0.230426588221248 Add terminal residue bond check dd-2: 2.2382103217575 PASS: Add Terminal Residue O Position Entered testcase - Select by Sphere Sphere mol: there are 4 residues in chain "B" Found 20 sphere atoms PASS: Select by Sphere Entered testcase - Test Views PASS: Test Views Entered testcase - Label Atoms and Delete PASS: Label Atoms and Delete Entered testcase - Rotamer outliers PASS: Rotamer outliers Entered testcase - HIS with unusual atom order rotates correct fragment for 180 sidechain flip dd-1: 0.0 dd-2: 2.36045066887977 PASS: HIS with unusual atom order rotates correct fragment for 180 sidechain flip Entered testcase - Alt Conf Occ Sum Reset For atom " CE " "A" returning occ 0.699999988079071 For atom " CE " "B" returning occ 0.200000002980232 For atom " NZ " "A" returning occ 0.699999988079071 For atom " NZ " "B" returning occ 0.200000002980232 For atom " CE " "A" returning occ 0.699999988079071 For atom " CE " "B" returning occ 0.200000002980232 For atom " NZ " "A" returning occ 0.699999988079071 For atom " NZ " "B" returning occ 0.200000002980232 test for closeness: 1.79999998211861 1.79999998211861 PASS: Alt Conf Occ Sum Reset Entered testcase - Correct occupancies after auto-fit rotamer on alt-confed residue PASS: Correct occupancies after auto-fit rotamer on alt-confed residue Entered testcase - Rotamers work on MSE se-1: (("SE " "") (0.699999988079071 2.0 "SE" "") (58.7999992370605 66.5329971313477 0.0469999983906746)) se-2: (("SE " "") (0.699999988079071 2.0 "SE" "") (60.1311187744141 69.3484802246094 -0.673518776893616)) PASS: Rotamers work on MSE Entered testcase - Hs are correctly swapped on a TYR bond-length-within-tolerance? bond-length 0.93069991132425 with target 0.93 and tolerance 0.02 for atoms ((" CD1" "") (1.0 (22.3700008392334 0.288300007581711 0.351099997758865 0.210400000214577 0.0551000013947487 0.0124000003561378 0.00350000010803342) " C" "") (61.2610015869141 -13.2200002670288 1.25)) and ((" HD1" "") (1.0 22.7800006866455 " H" "") (61.4099998474121 -12.8690004348755 2.09899997711182)) bond-length-within-tolerance? bond-length 0.930136198469449 with target 0.93 and tolerance 0.02 for atoms ((" CD2" "") (1.0 (24.4099998474121 0.258899986743927 0.405699998140335 0.262800008058548 0.0627999976277351 -0.0269000008702278 -0.00970000028610229) " C" "") (59.9500007629395 -13.3459997177124 -0.740000009536743)) and ((" HD2" "") (1.0 24.3099994659424 " H" "") (59.2050018310547 -13.0869998931885 -1.23300004005432)) bond-length-within-tolerance? bond-length 0.930888837109095 with target 0.93 and tolerance 0.02 for atoms ((" CE1" "") (1.0 (22.1599998474121 0.280600011348724 0.314999997615814 0.246199995279312 0.0603000000119209 -0.0186000000685453 -0.0172000005841255) " C" "") (62.1650009155273 -14.1079998016357 0.726000010967255)) and ((" HE1" "") (1.0 22.1200008392334 " H" "") (62.9140014648438 -14.3520002365112 1.22200000286102)) bond-length-within-tolerance? bond-length 0.929591631283786 with target 0.93 and tolerance 0.02 for atoms ((" CE2" "") (1.0 (23.9099998474121 0.281399995088577 0.359200000762939 0.267500013113022 0.0529999993741512 -0.0285000000149012 -0.0131999999284744) " C" "") (60.8559989929199 -14.2670001983643 -1.29900002479553)) and ((" HE2" "") (1.0 23.5400009155273 " H" "") (60.7249984741211 -14.6049995422363 -2.15499997138977)) INFO:: 25 residues had their atoms swapped INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb INFO:: file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 25 read successfully INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz INFO:: Number of observed reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.84 INFO:: grid sampling...Nuvw = ( 132, 160, 80) INFO:: 0.026 seconds to read MTZ file INFO:: 0.001 seconds to initialize map INFO:: 0.022 seconds for FFT Pre-filter Map statistics: mean: 9.92e-10 st.d: 0.312 Pre-filter Map statistics: min: -0.903 max: 2.97 INFO:: 0.002 seconds for statistics Map extents: ..... 132 160 80 Map mean: ........ 9.92e-10 Map sigma: ....... 0.312 Map maximum: ..... 2.97 Map minimum: ..... -0.903 INFO:: 0.009 seconds for contour map INFO:: 0.06 seconds in total DEBUG:: split_residue table 0 N :: INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:29:10_2021_modification_0.pdb.gz split_residue(int atom_index, int alt_conf_split_type) returns 0 debug:: split_residue() returned 0 "" INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/alt-conf-pepflip-test.pdb INFO:: file /lmb/home/pemsley/data/greg-data/alt-conf-pepflip-test.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Molecule 27 read successfully INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_alt-conf-pepflip-test.pdb_Tue_Jul_27_04:29:10_2021_modification_0.pdb.gz INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb INFO:: file /lmb/home/pemsley/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 28 read successfully ------------------ add_view_raw() CIS-TRANS cispep View INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Tue_Jul_27_04:29:10_2021_modification_0.pdb.gz INFO:: omega: 1 12.8 degrees INFO:: This is a CIS peptide - making it TRANS INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Tue_Jul_27_04:29:10_2021_modification_1.pdb.gz INFO:: Removing CIS peptide from PDB header: A 11 A 12 INFO:: mutate 11 A to a GLY INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Tue_Jul_27_04:29:10_2021_modification_2.pdb.gz ----------------- in create_mmdbmanager_from_res_vector() alt_conf is "" ----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0"" returning an atom selection for all moving atoms 11 atoms debug:: on creation last_restraints is 0x7c7a1f0 INFO:: from_res_vec() created 21 monomer restraints created 10 bond restraints created 10 angle restraints created 0 plane restraints created 1 chiral vol restraints created 0 improper dihedral restraints Made 1 link bond restraints Made 4 link angle restraints Made 3 link plane restraints Made 1 link trans-peptide restraints Made 0 CHO-SS-and-other bond restraints Made 0 CHO-SS-and-other angle restraints Made 0 CHO-SS-and-other plane restraints Made 0 CHO-SS-and-other trans-peptide restraints INFO:: added 0 helical restraints INFO:: Model: Bad Chiral Volume: [spec: model 1 "A" 12 "" " CA " ""] delta 0.609 target -2.73 sigma 0.1 distortion 37.1 INFO:: Model: Bad Bond: [spec: model 1 "A" 12 "" " CD " ""] to [spec: model 1 "A" 12 "" " N " ""] nZ 53.65 delta 0.751 target 1.473 sigma 0.014 distortion 2878.792 INFO:: Model: Bad Bond: [spec: model 1 "A" 11 "" " N " ""] to [spec: model 1 "A" 11 "" " CA " ""] nZ 12.30 delta -0.197 target 1.451 sigma 0.016 distortion 151.397 INFO:: Model: Bad Bond: [spec: model 1 "A" 12 "" " CA " ""] to [spec: model 1 "A" 12 "" " CB " ""] nZ 6.97 delta -0.139 target 1.530 sigma 0.020 distortion 48.548 INFO:: Model: Bad Bond: [spec: model 1 "A" 12 "" " CB " ""] to [spec: model 1 "A" 12 "" " CG " ""] nZ 4.91 delta 0.123 target 1.492 sigma 0.025 distortion 24.082 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 11 "" " O " ""] GLY to [spec: model 1 "A" 12 "" " C " ""] PRO delta -0.691 target 2.840 distortion 184.624 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 11 "" " C " ""] GLY to [spec: model 1 "A" 12 "" " O " ""] PRO delta -0.723 target 3.270 distortion 124.590 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 11 "" " O " ""] GLY to [spec: model 1 "A" 12 "" " O " ""] PRO delta -0.579 target 3.040 distortion 72.409 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 11 "" " O " ""] GLY to [spec: model 1 "A" 13 "" " N " ""] PRO delta -0.538 target 3.120 distortion 52.575 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 11 "" " C " ""] GLY to [spec: model 1 "A" 12 "" " C " ""] PRO delta -0.474 target 2.820 distortion 48.508 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 12 "" " N " ""] PRO to [spec: model 1 "A" 12 "" " O " ""] PRO delta -0.288 target 2.820 distortion 13.807 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 11 "" " CA " ""] GLY to [spec: model 1 "A" 8 "" " O " ""] LEU delta -0.334 target 3.440 distortion 12.438 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 12 "" " CA " ""] PRO to [spec: model 1 "A" 13 "" " CD " ""] PRO delta -0.244 target 3.100 distortion 8.311 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 11 "" " N " ""] GLY to [spec: model 1 "A" 10 "" " N " ""] ALA delta -0.222 target 2.820 distortion 8.264 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 12 "" " CB " ""] PRO to [spec: model 1 "A" 13 "" " CD " ""] PRO delta -0.262 target 3.840 distortion 6.407 Minimum found (iteration number 9) at -3886.738 Final Estimated RMS Z Scores: bonds: 0.574 angles: 0.707 improper-dihedrals: N/A torsions: N/A trans-peptide: 3.972 (non-sqrt) planes: 2.000 from 8 restraints parallel planes: N/A non-bonded: -0.397 chiral vol: 0.372 rama plot: N/A start_pos: N/A TargetPos: N/A GemanMcCl: N/A -------- Results --------- INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 11 "" " C " ""] GLY to [spec: model 1 "A" 12 "" " O " ""] PRO delta -0.212 target 3.270 distortion 5.907 Final Estimated RMS Z Scores bonds: 0.574 angles: 0.707 improper-dihedrals: N/A torsions: N/A trans-peptide: 3.972 (non-sqrt) planes: 2.000 from 8 restraints parallel planes: N/A non-bonded: -0.397 chiral vol: 0.372 rama plot: N/A start_pos: N/A TargetPos: N/A GemanMcCl: N/A INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Tue_Jul_27_04:29:10_2021_modification_3.pdb.gz INFO:: replace_coords: 11 atoms updated. debug:: in clear_all_atom_pull_restraints() 0 INFO:: mutate 11 A to a LEU INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Tue_Jul_27_04:29:10_2021_modification_4.pdb.gz INFO:: fitting 1 ligands into cluster 0 INFO:: fitting 1 ligands into cluster 0 INFO:: fitting 1 ligands into cluster 0 INFO:: fitting 1 ligands into cluster 0 INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Tue_Jul_27_04:29:10_2021_modification_5.pdb.gz INFO:: replace_coords: 8 atoms updated. Fitting score for best rotamer: 8.632 ----------------- in create_mmdbmanager_from_res_vector() alt_conf is "" ----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0"" returning an atom selection for all moving atoms 15 atoms debug:: on creation last_restraints is 0x7d6e700 INFO:: from_res_vec() created 32 monomer restraints created 14 bond restraints created 16 angle restraints created 0 plane restraints created 2 chiral vol restraints created 0 improper dihedral restraints Made 1 link bond restraints Made 4 link angle restraints Made 3 link plane restraints Made 1 link trans-peptide restraints Made 0 CHO-SS-and-other bond restraints Made 0 CHO-SS-and-other angle restraints Made 0 CHO-SS-and-other plane restraints Made 0 CHO-SS-and-other trans-peptide restraints INFO:: added 0 helical restraints INFO:: Model: Bad Bond: [spec: model 1 "A" 11 "" " C " ""] to [spec: model 1 "A" 12 "" " N " ""] nZ 2.30 delta -0.037 target 1.341 sigma 0.016 distortion 5.289 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 11 "" " CB " ""] LEU to [spec: model 1 "A" 12 "" " CD " ""] PRO delta -0.504 target 3.840 distortion 24.621 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 11 "" " C " ""] LEU to [spec: model 1 "A" 12 "" " O " ""] PRO delta -0.238 target 3.270 distortion 7.170 Minimum found (iteration number 5) at -4486.066 Final Estimated RMS Z Scores: bonds: 0.526 angles: 0.691 improper-dihedrals: N/A torsions: N/A trans-peptide: 7.361 (non-sqrt) planes: 2.054 from 8 restraints parallel planes: N/A non-bonded: -0.424 chiral vol: 0.410 rama plot: N/A start_pos: N/A TargetPos: N/A GemanMcCl: N/A -------- Results --------- INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 11 "" " CB " ""] LEU to [spec: model 1 "A" 12 "" " CD " ""] PRO delta -0.601 target 3.840 distortion 39.419 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 11 "" " C " ""] LEU to [spec: model 1 "A" 12 "" " O " ""] PRO delta -0.207 target 3.270 distortion 5.648 Final Estimated RMS Z Scores bonds: 0.526 angles: 0.691 improper-dihedrals: N/A torsions: N/A trans-peptide: 7.361 (non-sqrt) planes: 2.054 from 8 restraints parallel planes: N/A non-bonded: -0.424 chiral vol: 0.410 rama plot: N/A start_pos: N/A TargetPos: N/A GemanMcCl: N/A INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Tue_Jul_27_04:29:10_2021_modification_6.pdb.gz INFO:: replace_coords: 15 atoms updated. debug:: in clear_all_atom_pull_restraints() 0 INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb INFO:: file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 29 read successfully INFO:: backup file name coot-backup/atom_selection_from_tutorial-modern.pdb_Tue_Jul_27_04:29:21_2021_modification_0.pdb.gz cliquize 13 spinables for altconf --------------------------- 13 cliques ---------------- INFO:: omega: 1 -177.748 degrees INFO:: This is a TRANS peptide - making it CIS INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb INFO:: file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 31 read successfully INFO:: backup file name coot-backup/atom_selection_from_tutorial-modern.pdb_Tue_Jul_27_04:29:21_2021_modification_0.pdb.gz cliquize 12 spinables for altconf --------------------------- 11 cliques ---------------- 3 --- [spec: model 1 "A" 6 "" " CG1" ""] [spec: model 1 "A" 11 "" " CD2" ""] INFO:: mutate 10 A to a GLY INFO:: backup file name coot-backup/atom_selection_from_tutorial-modern.pdb_Tue_Jul_27_04:29:21_2021_modification_1.pdb.gz INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb INFO:: file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 33 read successfully INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz INFO:: Number of observed reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.840 INFO:: grid sampling...Nuvw = ( 132, 160, 80) INFO:: 0.026 seconds to read MTZ file INFO:: 0.001 seconds to initialize map INFO:: 0.022 seconds for FFT Pre-filter Map statistics: mean: 0.000 st.d: 0.312 Pre-filter Map statistics: min: -0.903 max: 2.968 INFO:: 0.003 seconds for statistics Map extents: ..... 132 160 80 Map mean: ........ 0.000 Map sigma: ....... 0.312 Map maximum: ..... 2.968 Map minimum: ..... -0.903 INFO:: 0.008 seconds for contour map INFO:: 0.060 seconds in total ----------------- in create_mmdbmanager_from_res_vector() alt_conf is "B" ----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 1"B" returning an atom selection for all moving atoms 6 atoms debug:: on creation last_restraints is 0x3047ff0 INFO:: from_res_vec() created 10 monomer restraints created 5 bond restraints created 4 angle restraints created 0 plane restraints created 1 chiral vol restraints created 0 improper dihedral restraints Made 0 CHO-SS-and-other bond restraints Made 0 CHO-SS-and-other angle restraints Made 0 CHO-SS-and-other plane restraints Made 0 CHO-SS-and-other trans-peptide restraints INFO:: Model: Bad Chiral Volume: [spec: model 1 "B" 72 "" " CA " ""] delta -0.292 target -2.503 sigma 0.100 distortion 8.550 INFO:: Model: Bad Bond: [spec: model 1 "B" 72 "" " CB " ""] to [spec: model 1 "B" 72 "" " SG " "B"] nZ 3.60 delta -0.072 target 1.808 sigma 0.020 distortion 12.963 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 72 "" " CA " ""] CYS to [spec: model 1 "B" 72 "" " SG " "B"] CYS delta -1.039 target 3.830 distortion 303.234 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 72 "" " SG " "B"] CYS to [spec: model 1 "B" 79 "" " OD2" ""] ASP delta -0.357 target 3.400 distortion 14.710 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 72 "" " O " ""] CYS to [spec: model 1 "B" 52 "" " CA " ""] TYR delta -0.287 target 3.470 distortion 9.060 Minimum found (iteration number 4) at -2034.595 Final Estimated RMS Z Scores: bonds: 0.591 angles: 0.627 improper-dihedrals: N/A torsions: N/A trans-peptide: 2.096 (non-sqrt) planes: 0.641 from 4 restraints parallel planes: N/A non-bonded: -0.310 chiral vol: 0.734 rama plot: N/A start_pos: N/A TargetPos: N/A GemanMcCl: N/A -------- Results --------- INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 72 "" " CA " ""] CYS to [spec: model 1 "B" 72 "" " SG " "B"] CYS delta -0.775 target 3.830 distortion 89.653 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 72 "" " SG " "B"] CYS to [spec: model 1 "B" 22 "" " CG2" ""] ILE delta -0.372 target 3.820 distortion 12.555 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 72 "" " O " ""] CYS to [spec: model 1 "B" 52 "" " CA " ""] TYR delta -0.299 target 3.470 distortion 9.829 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 72 "" " N " ""] CYS to [spec: model 1 "B" 71 "" " CG2" ""] ILE delta -0.240 target 3.540 distortion 6.356 Final Estimated RMS Z Scores bonds: 0.591 angles: 0.627 improper-dihedrals: N/A torsions: N/A trans-peptide: 2.096 (non-sqrt) planes: 0.641 from 4 restraints parallel planes: N/A non-bonded: -0.310 chiral vol: 0.734 rama plot: N/A start_pos: N/A TargetPos: N/A GemanMcCl: N/A INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:29:29_2021_modification_0.pdb.gz INFO:: replace_coords: 6 atoms updated. debug:: in clear_all_atom_pull_restraints() 0 INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-add-terminal-1-test.pdb INFO:: file /lmb/home/pemsley/data/greg-data/tutorial-add-terminal-1-test.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 83/90 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 35 read successfully DEBUG:: split_residue table 0 N :: INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-add-terminal-1-test.pdb_Tue_Jul_27_04:29:29_2021_modification_0.pdb.gz split_residue(int atom_index, int alt_conf_split_type) returns 0 debug:: split_residue() returned 0 "" ----------------- in create_mmdbmanager_from_res_vector() alt_conf is "" ----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0"" returning an atom selection for all moving atoms 39 atoms debug:: on creation last_restraints is 0x7e9cd70 INFO:: from_res_vec() created 81 monomer restraints created 34 bond restraints created 39 angle restraints created 2 plane restraints created 6 chiral vol restraints created 0 improper dihedral restraints Made 2 link bond restraints Made 6 link angle restraints Made 0 link plane restraints Made 4 link trans-peptide restraints Made 0 CHO-SS-and-other bond restraints Made 0 CHO-SS-and-other angle restraints Made 0 CHO-SS-and-other plane restraints Made 0 CHO-SS-and-other trans-peptide restraints INFO:: added 0 helical restraints INFO:: Model: Bad Chiral Volume: [spec: model 1 "A" 93 "" " CA " "A"] delta -0.245 target -2.503 sigma 0.100 distortion 6.019 INFO:: Model: Bad Chiral Volume: [spec: model 1 "A" 93 "" " CA " "B"] delta -0.245 target -2.503 sigma 0.100 distortion 6.019 INFO:: Model: Bad Chiral Volume: [spec: model 1 "A" 5 "" " CA " ""] delta -0.245 target -2.503 sigma 0.100 distortion 6.006 INFO:: Model: Bad Bond: [spec: model 1 "A" 92 "" " CB " ""] to [spec: model 1 "A" 92 "" " CG2" ""] nZ 5.93 delta 0.119 target 1.521 sigma 0.020 distortion 35.136 INFO:: Model: Bad Bond: [spec: model 1 "A" 92 "" " CG1" ""] to [spec: model 1 "A" 92 "" " CD1" ""] nZ 3.64 delta 0.073 target 1.513 sigma 0.020 distortion 13.227 INFO:: Model: Bad Bond: [spec: model 1 "A" 92 "" " C " ""] to [spec: model 1 "A" 92 "" " O " ""] nZ 3.12 delta 0.062 target 1.231 sigma 0.020 distortion 9.732 INFO:: Model: Bad Bond: [spec: model 1 "A" 92 "" " C " ""] to [spec: model 1 "A" 93 "" " N " "B"] nZ 3.11 delta 0.044 target 1.329 sigma 0.014 distortion 9.662 INFO:: Model: Bad Bond: [spec: model 1 "A" 92 "" " C " ""] to [spec: model 1 "A" 93 "" " N " "B"] nZ 3.11 delta 0.044 target 1.329 sigma 0.014 distortion 9.662 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 93 "" " OD2" "A"] ASP to [spec: model 1 "A" 93 "" " C " "A"] ASP delta -0.522 target 3.270 distortion 41.691 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 93 "" " OD2" "B"] ASP to [spec: model 1 "A" 93 "" " C " "B"] ASP delta -0.522 target 3.270 distortion 41.691 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 3 "" " CG1" ""] VAL to [spec: model 1 "A" 3 "" " O " ""] VAL delta -0.404 target 3.460 distortion 18.566 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 92 "" " CG2" ""] ILE to [spec: model 1 "A" 93 "" " N " "B"] ASP delta -0.283 target 3.540 distortion 8.503 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 3 "" " CG2" ""] VAL to [spec: model 1 "A" 4 "" " N " ""] CYS delta -0.260 target 3.540 distortion 7.315 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 92 "" " CG2" ""] ILE to [spec: model 1 "A" 93 "" " N " "A"] ASP delta -0.217 target 3.540 distortion 5.353 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 3 "" " N " ""] VAL to [spec: model 1 "A" 2 "" " CG2" ""] THR delta -0.208 target 3.540 distortion 5.015 Minimum found (iteration number 9) at -10964.861 Final Estimated RMS Z Scores: bonds: 0.516 angles: 0.631 improper-dihedrals: N/A torsions: N/A trans-peptide: 0.954 (non-sqrt) planes: 0.653 from 12 restraints parallel planes: N/A non-bonded: -0.382 chiral vol: 0.437 rama plot: N/A start_pos: N/A TargetPos: N/A GemanMcCl: N/A -------- Results --------- INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 93 "" " OD2" "A"] ASP to [spec: model 1 "A" 93 "" " C " "A"] ASP delta -0.446 target 3.270 distortion 27.225 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 93 "" " OD2" "B"] ASP to [spec: model 1 "A" 93 "" " C " "B"] ASP delta -0.446 target 3.270 distortion 27.184 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 3 "" " CG1" ""] VAL to [spec: model 1 "A" 3 "" " O " ""] VAL delta -0.358 target 3.460 distortion 14.204 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 3 "" " CG2" ""] VAL to [spec: model 1 "A" 4 "" " N " ""] CYS delta -0.338 target 3.540 distortion 12.054 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 92 "" " CG2" ""] ILE to [spec: model 1 "A" 93 "" " N " "B"] ASP delta -0.305 target 3.540 distortion 9.837 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 92 "" " CG2" ""] ILE to [spec: model 1 "A" 93 "" " N " "A"] ASP delta -0.305 target 3.540 distortion 9.825 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 5 "" " CG " ""] LEU to [spec: model 1 "A" 5 "" " O " ""] LEU delta -0.208 target 3.470 distortion 5.178 Final Estimated RMS Z Scores bonds: 0.516 angles: 0.631 improper-dihedrals: N/A torsions: N/A trans-peptide: 0.954 (non-sqrt) planes: 0.653 from 12 restraints parallel planes: N/A non-bonded: -0.382 chiral vol: 0.437 rama plot: N/A start_pos: N/A TargetPos: N/A GemanMcCl: N/A INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-add-terminal-1-test.pdb_Tue_Jul_27_04:29:29_2021_modification_1.pdb.gz INFO:: replace_coords: 39 atoms updated. debug:: in clear_all_atom_pull_restraints() 0 ----------------- in create_mmdbmanager_from_res_vector() alt_conf is "" ----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0"" returning an atom selection for all moving atoms 41 atoms debug:: on creation last_restraints is 0x7edc830 INFO:: from_res_vec() created 84 monomer restraints created 36 bond restraints created 40 angle restraints created 3 plane restraints created 5 chiral vol restraints created 0 improper dihedral restraints Made 4 link bond restraints Made 12 link angle restraints Made 7 link plane restraints Made 3 link trans-peptide restraints Made 0 CHO-SS-and-other bond restraints Made 0 CHO-SS-and-other angle restraints Made 0 CHO-SS-and-other plane restraints Made 0 CHO-SS-and-other trans-peptide restraints INFO:: added 0 helical restraints INFO:: Model: Bad Chiral Volume: [spec: model 1 "A" 41 "" " CA " ""] delta 4.587 target -2.503 sigma 0.100 distortion 2103.992 INFO:: Model: Bad Bond: [spec: model 1 "A" 41 "" " CG " ""] to [spec: model 1 "A" 41 "" " CD " ""] nZ 2.46 delta -0.049 target 1.516 sigma 0.020 distortion 6.055 INFO:: Model: Bad Bond: [spec: model 1 "A" 41 "" " N " ""] to [spec: model 1 "A" 41 "" " CA " ""] nZ 2.37 delta -0.045 target 1.458 sigma 0.019 distortion 5.633 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 39 "" " C " ""] ASN to [spec: model 1 "A" 41 "" " CA " ""] GLU delta -1.168 target 3.700 distortion 681.444 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 40 "" " N " ""] ARG to [spec: model 1 "A" 41 "" " CA " ""] GLU delta -1.114 target 3.550 distortion 658.604 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 41 "" " O " ""] GLU to [spec: model 1 "A" 43 "" " N " ""] VAL delta -0.791 target 2.880 distortion 321.280 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 39 "" " O " ""] ASN to [spec: model 1 "A" 41 "" " CA " ""] GLU delta -0.753 target 3.470 distortion 116.196 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 40 "" " N " ""] ARG to [spec: model 1 "A" 41 "" " CB " ""] GLU delta -0.750 target 3.520 distortion 107.899 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 41 "" " C " ""] GLU to [spec: model 1 "A" 43 "" " N " ""] VAL delta -0.653 target 3.350 distortion 78.508 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 39 "" " C " ""] ASN to [spec: model 1 "A" 41 "" " CB " ""] GLU delta -0.582 target 3.670 distortion 40.860 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 39 "" " CG " ""] ASN to [spec: model 1 "A" 39 "" " O " ""] ASN delta -0.415 target 3.270 distortion 22.685 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 39 "" " CB " ""] ASN to [spec: model 1 "A" 38 "" " O " ""] GLN delta -0.433 target 3.440 distortion 22.234 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 39 "" " CA " ""] ASN to [spec: model 1 "A" 41 "" " CB " ""] GLU delta -0.390 target 3.870 distortion 13.484 Minimum found (iteration number 7) at -11176.852 Final Estimated RMS Z Scores: bonds: 1.196 angles: 1.293 improper-dihedrals: N/A torsions: N/A trans-peptide: 2.936 (non-sqrt) planes: 0.515 from 14 restraints parallel planes: N/A non-bonded: -0.333 chiral vol: 0.909 rama plot: N/A start_pos: N/A TargetPos: N/A GemanMcCl: N/A -------- Results --------- INFO:: Model: Bad Bond: [spec: model 1 "A" 41 "" " C " ""] to [spec: model 1 "A" 42 "" " N " ""] nZ 5.76 delta -0.081 target 1.329 sigma 0.014 distortion 33.226 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 39 "" " O " ""] ASN to [spec: model 1 "A" 41 "" " O " ""] GLU delta -0.557 target 3.040 distortion 63.609 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 41 "" " N " ""] GLU to [spec: model 1 "A" 41 "" " CD " ""] GLU delta -0.576 target 3.350 distortion 52.121 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 41 "" " N " ""] GLU to [spec: model 1 "A" 41 "" " O " ""] GLU delta -0.431 target 2.820 distortion 36.754 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 41 "" " O " ""] GLU to [spec: model 1 "A" 42 "" " CA " ""] SER delta -0.404 target 2.820 distortion 30.946 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 39 "" " C " ""] ASN to [spec: model 1 "A" 41 "" " O " ""] GLU delta -0.423 target 3.270 distortion 23.713 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 39 "" " CB " ""] ASN to [spec: model 1 "A" 38 "" " O " ""] GLN delta -0.441 target 3.440 distortion 23.230 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 40 "" " C " ""] ARG to [spec: model 1 "A" 41 "" " O " ""] GLU delta -0.379 target 3.270 distortion 18.336 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 39 "" " CG " ""] ASN to [spec: model 1 "A" 39 "" " O " ""] ASN delta -0.338 target 3.270 distortion 14.207 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 40 "" " NH2" ""] ARG to [spec: model 1 "A" 38 "" " OE1" ""] GLN delta -0.256 target 2.880 distortion 10.421 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 40 "" " CG " ""] ARG to [spec: model 1 "A" 40 "" " O " ""] ARG delta -0.268 target 3.440 distortion 8.127 Final Estimated RMS Z Scores bonds: 1.196 angles: 1.293 improper-dihedrals: N/A torsions: N/A trans-peptide: 2.936 (non-sqrt) planes: 0.515 from 14 restraints parallel planes: N/A non-bonded: -0.333 chiral vol: 0.909 rama plot: N/A start_pos: N/A TargetPos: N/A GemanMcCl: N/A INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-add-terminal-1-test.pdb_Tue_Jul_27_04:29:29_2021_modification_2.pdb.gz INFO:: replace_coords: 41 atoms updated. debug:: in clear_all_atom_pull_restraints() 0 INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb INFO:: file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 36 read successfully ----------------- in create_mmdbmanager_from_res_vector() alt_conf is "" ----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0"" returning an atom selection for all moving atoms 27 atoms debug:: on creation last_restraints is 0x5f27950 INFO:: from_res_vec() created 52 monomer restraints created 23 bond restraints created 25 angle restraints created 0 plane restraints created 4 chiral vol restraints created 0 improper dihedral restraints Made 2 link bond restraints Made 6 link angle restraints Made 4 link plane restraints Made 2 link trans-peptide restraints Made 1 CHO-SS-and-other bond restraints Made 2 CHO-SS-and-other angle restraints Made 0 CHO-SS-and-other plane restraints Made 0 CHO-SS-and-other trans-peptide restraints INFO:: added 0 helical restraints INFO:: Model: Bad Bond: [spec: model 1 "B" 8 "" " CG " ""] to [spec: model 1 "B" 8 "" " CD1" ""] nZ 3.71 delta 0.074 target 1.521 sigma 0.020 distortion 13.746 INFO:: Model: Bad Bond: [spec: model 1 "B" 6 "" " CB " ""] to [spec: model 1 "B" 6 "" " CG2" ""] nZ 3.28 delta 0.066 target 1.521 sigma 0.020 distortion 10.747 INFO:: Model: Bad Bond: [spec: model 1 "B" 6 "" " CA " ""] to [spec: model 1 "B" 6 "" " CB " ""] nZ 3.02 delta 0.060 target 1.540 sigma 0.020 distortion 9.145 INFO:: Model: Bad Bond: [spec: model 1 "B" 7 "" " SG " ""] to [spec: model 1 "B" 96 "" " SG " ""] nZ 2.35 delta -0.047 target 2.031 sigma 0.020 distortion 5.536 INFO:: Model: Bad Bond: [spec: model 1 "B" 7 "" " N " ""] to [spec: model 1 "B" 7 "" " CA " ""] nZ 2.31 delta -0.044 target 1.458 sigma 0.019 distortion 5.357 INFO:: Model: Bad Bond: [spec: model 1 "B" 96 "" " N " ""] to [spec: model 1 "B" 96 "" " CA " ""] nZ 2.31 delta 0.044 target 1.458 sigma 0.019 distortion 5.352 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 6 "" " N " ""] VAL to [spec: model 1 "B" 5 "" " CG2" ""] THR delta -0.367 target 3.540 distortion 14.323 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 6 "" " CG1" ""] VAL to [spec: model 1 "B" 6 "" " O " ""] VAL delta -0.358 target 3.460 distortion 14.198 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 8 "" " CG " ""] LEU to [spec: model 1 "B" 8 "" " O " ""] LEU delta -0.283 target 3.470 distortion 8.821 Minimum found (iteration number 10) at -9531.067 Final Estimated RMS Z Scores: bonds: 0.686 angles: 0.584 improper-dihedrals: N/A torsions: N/A trans-peptide: 1.546 (non-sqrt) planes: 0.587 from 10 restraints parallel planes: N/A non-bonded: -0.413 chiral vol: 0.539 rama plot: N/A start_pos: N/A TargetPos: N/A GemanMcCl: N/A -------- Results --------- INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 6 "" " CG1" ""] VAL to [spec: model 1 "B" 6 "" " O " ""] VAL delta -0.466 target 3.460 distortion 26.345 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 6 "" " N " ""] VAL to [spec: model 1 "B" 5 "" " CG2" ""] THR delta -0.360 target 3.540 distortion 13.724 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 6 "" " CG2" ""] VAL to [spec: model 1 "B" 7 "" " N " ""] CYS delta -0.274 target 3.540 distortion 8.010 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 8 "" " CG " ""] LEU to [spec: model 1 "B" 8 "" " O " ""] LEU delta -0.259 target 3.470 distortion 7.516 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 7 "" " CB " ""] CYS to [spec: model 1 "B" 96 "" " C " ""] CYS delta -0.241 target 3.670 distortion 6.022 Final Estimated RMS Z Scores bonds: 0.686 angles: 0.584 improper-dihedrals: N/A torsions: N/A trans-peptide: 1.546 (non-sqrt) planes: 0.587 from 10 restraints parallel planes: N/A non-bonded: -0.413 chiral vol: 0.539 rama plot: N/A start_pos: N/A TargetPos: N/A GemanMcCl: N/A INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:29:54_2021_modification_0.pdb.gz INFO:: replace_coords: 27 atoms updated. debug:: in clear_all_atom_pull_restraints() 0 results: (#t #t #t #t) PASS: Hs are correctly swapped on a TYR Entered testcase - Splitting residue leaves no atoms with negative occupancy PASS: Splitting residue leaves no atoms with negative occupancy Entered testcase - Pepflip flips the correct alt confed atoms PASS: Pepflip flips the correct alt confed atoms Entered testcase - Correction of CISPEP test PASS: Correction of CISPEP test Entered testcase - H on a N moves on cis-trans convert dd: 3.29414331487717 PASS: H on a N moves on cis-trans convert Entered testcase - HA on a ALA exists after mutation to GLY PASS: HA on a ALA exists after mutation to GLY Entered testcase - Refine Zone with Alt conf refined moved: d=0.450293150125631 PASS: Refine Zone with Alt conf Entered testcase - Sphere Refine ======= got bond length 1.3118533722206 PASS: Sphere Refine Entered testcase - Neighbour-Refine doesn't destroy disulfide bonds bond-length-within-tolerance? bond-length 2.02857794181719 with target 2.0 and tolerance 0.05 for atoms ((" SG " "") (1.0 17.4099998474121 " S" "") (25.6135120391846 27.4804801940918 11.207314491272)) and ((" SG " "") (1.0 17.4899997711182 " S" "") (24.7830333709717 27.026216506958 9.41313552856445)) ----------------- in create_mmdbmanager_from_res_vector() alt_conf is "" ----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0"" returning an atom selection for all moving atoms 27 atoms debug:: on creation last_restraints is 0x5fc2c10 INFO:: from_res_vec() created 52 monomer restraints created 23 bond restraints created 25 angle restraints created 0 plane restraints created 4 chiral vol restraints created 0 improper dihedral restraints Made 2 link bond restraints Made 6 link angle restraints Made 4 link plane restraints Made 2 link trans-peptide restraints Made 1 CHO-SS-and-other bond restraints Made 2 CHO-SS-and-other angle restraints Made 0 CHO-SS-and-other plane restraints Made 0 CHO-SS-and-other trans-peptide restraints INFO:: added 0 helical restraints INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 6 "" " CG1" ""] VAL to [spec: model 1 "B" 6 "" " O " ""] VAL delta -0.466 target 3.460 distortion 26.345 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 6 "" " N " ""] VAL to [spec: model 1 "B" 5 "" " CG2" ""] THR delta -0.360 target 3.540 distortion 13.724 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 6 "" " CG2" ""] VAL to [spec: model 1 "B" 7 "" " N " ""] CYS delta -0.274 target 3.540 distortion 8.010 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 8 "" " CG " ""] LEU to [spec: model 1 "B" 8 "" " O " ""] LEU delta -0.259 target 3.470 distortion 7.516 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 7 "" " CB " ""] CYS to [spec: model 1 "B" 96 "" " C " ""] CYS delta -0.241 target 3.670 distortion 6.022 Minimum found (iteration number 1) at -9532.235 Final Estimated RMS Z Scores: bonds: 0.686 angles: 0.584 improper-dihedrals: N/A torsions: N/A trans-peptide: 1.546 (non-sqrt) planes: 0.587 from 10 restraints parallel planes: N/A non-bonded: -0.409 chiral vol: 0.539 rama plot: N/A start_pos: N/A TargetPos: N/A GemanMcCl: N/A -------- Results --------- INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 6 "" " CG1" ""] VAL to [spec: model 1 "B" 6 "" " O " ""] VAL delta -0.466 target 3.460 distortion 26.345 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 6 "" " N " ""] VAL to [spec: model 1 "B" 5 "" " CG2" ""] THR delta -0.360 target 3.540 distortion 13.724 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 6 "" " CG2" ""] VAL to [spec: model 1 "B" 7 "" " N " ""] CYS delta -0.274 target 3.540 distortion 8.010 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 8 "" " CG " ""] LEU to [spec: model 1 "B" 8 "" " O " ""] LEU delta -0.259 target 3.470 distortion 7.516 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 7 "" " CB " ""] CYS to [spec: model 1 "B" 96 "" " C " ""] CYS delta -0.241 target 3.670 distortion 6.022 Final Estimated RMS Z Scores bonds: 0.686 angles: 0.584 improper-dihedrals: N/A torsions: N/A trans-peptide: 1.546 (non-sqrt) planes: 0.587 from 10 restraints parallel planes: N/A non-bonded: -0.409 chiral vol: 0.539 rama plot: N/A start_pos: N/A TargetPos: N/A GemanMcCl: N/A INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:29:54_2021_modification_1.pdb.gz INFO:: replace_coords: 27 atoms updated. debug:: in clear_all_atom_pull_restraints() 0 bond-length-within-tolerance? bond-length 2.02857794181719 with target 2.0 and tolerance 0.05 for atoms ((" SG " "") (1.0 17.4099998474121 " S" "") (25.6135120391846 27.4804801940918 11.207314491272)) and ((" SG " "") (1.0 17.4899997711182 " S" "") (24.7830333709717 27.026216506958 9.41313552856445)) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/alt-conf-waters.pdb INFO:: file /lmb/home/pemsley/data/greg-data/alt-conf-waters.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Molecule 37 read successfully ----------------- in create_mmdbmanager_from_res_vector() alt_conf is "A" ----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 1"A" returning an atom selection for all moving atoms 1 atoms debug:: on creation last_restraints is 0x5f0d070 INFO:: from_res_vec() created 0 monomer restraints created 0 bond restraints created 0 angle restraints created 0 plane restraints created 0 chiral vol restraints created 0 improper dihedral restraints Made 0 CHO-SS-and-other bond restraints Made 0 CHO-SS-and-other angle restraints Made 0 CHO-SS-and-other plane restraints Made 0 CHO-SS-and-other trans-peptide restraints Final Estimated RMS Z Scores bonds: N/A angles: N/A improper-dihedrals: N/A torsions: N/A trans-peptide: N/A planes: N/A parallel planes: N/A non-bonded: N/A chiral vol: N/A rama plot: N/A start_pos: N/A TargetPos: N/A GemanMcCl: N/A INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_alt-conf-waters.pdb_Tue_Jul_27_04:29:55_2021_modification_0.pdb.gz INFO:: replace_coords: 1 atoms updated. debug:: in clear_all_atom_pull_restraints() 0 ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- debug:: in clear_all_atom_pull_restraints() 0 INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:29:55_2021_modification_0.pdb.gz INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:29:55_2021_modification_1.pdb.gz INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/backrub-fragment.pdb INFO:: file /lmb/home/pemsley/data/greg-data/backrub-fragment.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 38 read successfully INFO:: backup file name coot-backup/Copy_of__lmb_home_pemsley_data_greg-data_backrub-fragment.pdb_Tue_Jul_27_04:29:56_2021_modification_0.pdb.gz INFO:: backup file name coot-backup/Copy_of__lmb_home_pemsley_data_greg-data_backrub-fragment.pdb_Tue_Jul_27_04:29:56_2021_modification_1.pdb.gz INFO:: replace_coords: 14 atoms updated. INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/coords-B3A.pdb INFO:: file /lmb/home/pemsley/data/greg-data/coords-B3A.pdb has been read. Spacegroup: P 1 INFO:: using standard CCP4 Refmac dictionary to search for "B3A" There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/b/B3A.cif INFO:: Found 1 models Model 1 had 0 links Molecule 40 read successfully ----------------- in create_mmdbmanager_from_res_vector() alt_conf is "" ----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0"" returning an atom selection for all moving atoms 6 atoms debug:: on creation last_restraints is 0x6124c60 INFO:: from_res_vec() created 11 monomer restraints created 5 bond restraints created 5 angle restraints created 0 plane restraints created 1 chiral vol restraints created 0 improper dihedral restraints Made 0 CHO-SS-and-other bond restraints Made 0 CHO-SS-and-other angle restraints Made 0 CHO-SS-and-other plane restraints Made 0 CHO-SS-and-other trans-peptide restraints debug:: restraints results 1 0 Minimum found (iteration number 19) at -7.194 Final Estimated RMS Z Scores: bonds: 0.016 angles: 0.027 improper-dihedrals: N/A torsions: N/A trans-peptide: N/A planes: N/A parallel planes: N/A non-bonded: -1.440 chiral vol: 0.002 rama plot: N/A start_pos: N/A TargetPos: N/A GemanMcCl: N/A -------- Results --------- Final Estimated RMS Z Scores bonds: 0.016 angles: 0.027 improper-dihedrals: N/A torsions: N/A trans-peptide: N/A planes: N/A parallel planes: N/A non-bonded: -1.440 chiral vol: 0.002 rama plot: N/A start_pos: N/A TargetPos: N/A GemanMcCl: N/A INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_coords-B3A.pdb_Tue_Jul_27_04:29:58_2021_modification_0.pdb.gz INFO:: replace_coords: 6 atoms updated. debug:: in clear_all_atom_pull_restraints() 0 WARNING: in init_refmac_mon_lib, file "/lmb/home/pemsley/data/greg-data/lib-B3A.cif" not found. init_refmac_mon_lib /lmb/home/pemsley/data/greg-data/lib-B3A.cif had no bond restraints ----------------- in create_mmdbmanager_from_res_vector() alt_conf is "" ----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0"" returning an atom selection for all moving atoms 6 atoms debug:: on creation last_restraints is 0x6115ca0 INFO:: from_res_vec() created 11 monomer restraints created 5 bond restraints created 5 angle restraints created 0 plane restraints created 1 chiral vol restraints created 0 improper dihedral restraints Made 0 CHO-SS-and-other bond restraints Made 0 CHO-SS-and-other angle restraints Made 0 CHO-SS-and-other plane restraints Made 0 CHO-SS-and-other trans-peptide restraints debug:: restraints results 1 0 Minimum found (iteration number 20) at -7.360 Final Estimated RMS Z Scores: bonds: 0.016 angles: 0.019 improper-dihedrals: N/A torsions: N/A trans-peptide: N/A planes: N/A parallel planes: N/A non-bonded: -1.473 chiral vol: 0.005 rama plot: N/A start_pos: N/A TargetPos: N/A GemanMcCl: N/A -------- Results --------- Final Estimated RMS Z Scores bonds: 0.016 angles: 0.019 improper-dihedrals: N/A torsions: N/A trans-peptide: N/A planes: N/A parallel planes: N/A non-bonded: -1.473 chiral vol: 0.005 rama plot: N/A start_pos: N/A TargetPos: N/A GemanMcCl: N/A INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_coords-B3A.pdb_Tue_Jul_27_04:29:58_2021_modification_1.pdb.gz INFO:: replace_coords: 6 atoms updated. debug:: in clear_all_atom_pull_restraints() 0 There are 3 data in /lmb/home/pemsley/data/greg-data/lib-both.cif Welcome to Coot ----------------- in create_mmdbmanager_from_res_vector() alt_conf is "" ----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0"" returning an atom selection for all moving atoms 6 atoms debug:: on creation last_restraints is 0x7dbe030 INFO:: from_res_vec() created 11 monomer restraints created 5 bond restraints created 5 angle restraints created 0 plane restraints created 1 chiral vol restraints created 0 improper dihedral restraints Made 0 CHO-SS-and-other bond restraints Made 0 CHO-SS-and-other angle restraints Made 0 CHO-SS-and-other plane restraints Made 0 CHO-SS-and-other trans-peptide restraints debug:: restraints results 1 0 Minimum found (iteration number 17) at -7.423 Final Estimated RMS Z Scores: bonds: 0.014 angles: 0.017 improper-dihedrals: N/A torsions: N/A trans-peptide: N/A planes: N/A parallel planes: N/A non-bonded: -1.485 chiral vol: 0.005 rama plot: N/A start_pos: N/A TargetPos: N/A GemanMcCl: N/A -------- Results --------- Final Estimated RMS Z Scores bonds: 0.014 angles: 0.017 improper-dihedrals: N/A torsions: N/A trans-peptide: N/A planes: N/A parallel planes: N/A non-bonded: -1.485 chiral vol: 0.005 rama plot: N/A start_pos: N/A TargetPos: N/A GemanMcCl: N/A INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_coords-B3A.pdb_Tue_Jul_27_04:29:58_2021_modification_2.pdb.gz INFO:: replace_coords: 6 atoms updated. debug:: in clear_all_atom_pull_restraints() 0 INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz INFO:: Number of observed reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.840 INFO:: grid sampling...Nuvw = ( 132, 160, 80) INFO:: 0.027 seconds to read MTZ file INFO:: 0.001 seconds to initialize map INFO:: 0.022 seconds for FFT Pre-filter Map statistics: mean: 0.000 st.d: 0.312 Pre-filter Map statistics: min: -0.903 max: 2.968 INFO:: 0.002 seconds for statistics Map extents: ..... 132 160 80 Map mean: ........ 0.000 Map sigma: ....... 0.312 Map maximum: ..... 2.968 Map minimum: ..... -0.903 INFO:: 0.018 seconds for contour map INFO:: 0.070 seconds in total INFO:: Stored refmac parameters: /RNASE3GMP/COMPLEX/FGMP18 /RNASE3GMP/COMPLEX/SIGFGMP18 /RNASE/NATIVE/FreeR_flag is sensible. INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/test-TER-OXT.pdb INFO:: file /lmb/home/pemsley/data/greg-data/test-TER-OXT.pdb has been read. INFO:: Found 1 models Model 1 had 0 links WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model Molecule 42 read successfully INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_test-TER-OXT.pdb_Tue_Jul_27_04:30:02_2021_modification_0.pdb.gz Added OXT at 1/A/14 {ASP}/ OXT altLoc :: segid :: pos: (33.129,-9.090,14.916) B-factor: 45.000 debug:: add_OXT_to_residue() returns istat 1 WARNING:: This residue already has an OXT - aborting debug:: add_OXT_to_residue() returns istat 0 INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/val.pdb INFO:: file /lmb/home/pemsley/data/greg-data/val.pdb has been read. INFO:: Found 1 models Model 1 had 0 links WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model Molecule 43 read successfully INFO:: mutate 3 C to a HIS INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_val.pdb_Tue_Jul_27_04:30:02_2021_modification_0.pdb.gz INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/2yie-frag.pdb INFO:: file /lmb/home/pemsley/data/greg-data/2yie-frag.pdb has been read. INFO:: Found 1 models Model 1 had 0 links WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model Molecule 44 read successfully INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_2yie-frag.pdb_Tue_Jul_27_04:30:02_2021_modification_0.pdb.gz INFO:: 6 matched atoms had: mean devi: 0.040 rms devi: 0.047 max devi: 0.083 min devi: 0.013 INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/4f8g.pdb INFO:: file /lmb/home/pemsley/data/greg-data/4f8g.pdb has been read. Spacegroup: I 2 2 2 INFO:: using standard CCP4 Refmac dictionary to search for "NCO" There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/n/NCO.cif INFO:: Found 1 models Model 1 had 0 links Molecule 45 read successfully INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_4f8g.pdb_Tue_Jul_27_04:30:02_2021_modification_0.pdb.gz INFO:: 6 matched atoms had: mean devi: 0.043 rms devi: 0.048 max devi: 0.074 min devi: 0.015 INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/4f8g.pdb INFO:: file /lmb/home/pemsley/data/greg-data/4f8g.pdb has been read. Spacegroup: I 2 2 2 INFO:: Found 1 models Model 1 had 0 links Molecule 46 read successfully INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_4f8g.pdb_Tue_Jul_27_04:30:02_2021_modification_0.pdb.gz INFO:: 6 matched atoms had: mean devi: 0.039 rms devi: 0.044 max devi: 0.069 min devi: 0.015 INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/monomer-VAL.pdb INFO:: file /lmb/home/pemsley/data/greg-data/monomer-VAL.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links Molecule 47 read successfully ----------------- in create_mmdbmanager_from_res_vector() alt_conf is "" ----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0"" returning an atom selection for all moving atoms 15 atoms debug:: on creation last_restraints is 0x644a270 INFO:: from_res_vec() created 40 monomer restraints created 14 bond restraints created 25 angle restraints created 0 plane restraints created 1 chiral vol restraints created 0 improper dihedral restraints Made 0 CHO-SS-and-other bond restraints Made 0 CHO-SS-and-other angle restraints Made 0 CHO-SS-and-other plane restraints Made 0 CHO-SS-and-other trans-peptide restraints debug:: restraints results 1 0 Minimum found (iteration number 5) at -65.473 Final Estimated RMS Z Scores: bonds: 0.125 angles: 0.140 improper-dihedrals: N/A torsions: N/A trans-peptide: N/A planes: N/A parallel planes: N/A non-bonded: -1.003 chiral vol: 0.105 rama plot: N/A start_pos: N/A TargetPos: N/A GemanMcCl: N/A -------- Results --------- Final Estimated RMS Z Scores bonds: 0.125 angles: 0.140 improper-dihedrals: N/A torsions: N/A trans-peptide: N/A planes: N/A parallel planes: N/A non-bonded: -1.003 chiral vol: 0.105 rama plot: N/A start_pos: N/A TargetPos: N/A GemanMcCl: N/A INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_monomer-VAL.pdb_Tue_Jul_27_04:30:05_2021_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. debug:: in clear_all_atom_pull_restraints() 0 INFO:: undo molecule number set to: 47 INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_monomer-VAL.pdb_Tue_Jul_27_04:30:05_2021_modification_1.pdb.gz restoring from backup 2 2 INFO:: Reading coordinate file: coot-backup/_lmb_home_pemsley_data_greg-data_monomer-VAL.pdb_Tue_Jul_27_04:30:05_2021_modification_0.pdb.gz INFO:: file coot-backup/_lmb_home_pemsley_data_greg-data_monomer-VAL.pdb_Tue_Jul_27_04:30:05_2021_modification_0.pdb.gz has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links DEBUG:: apply_undo: (end) history_index: 0 max_history_index: 2 ----------------- in create_mmdbmanager_from_res_vector() alt_conf is "" ----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0"" returning an atom selection for all moving atoms 15 atoms debug:: on creation last_restraints is 0x6435d20 INFO:: from_res_vec() created 40 monomer restraints created 14 bond restraints created 25 angle restraints created 0 plane restraints created 1 chiral vol restraints created 0 improper dihedral restraints Made 0 CHO-SS-and-other bond restraints Made 0 CHO-SS-and-other angle restraints Made 0 CHO-SS-and-other plane restraints Made 0 CHO-SS-and-other trans-peptide restraints debug:: restraints results 1 0 Minimum found (iteration number 5) at -65.473 Final Estimated RMS Z Scores: bonds: 0.125 angles: 0.140 improper-dihedrals: N/A torsions: N/A trans-peptide: N/A planes: N/A parallel planes: N/A non-bonded: -1.003 chiral vol: 0.105 rama plot: N/A start_pos: N/A TargetPos: N/A GemanMcCl: N/A -------- Results --------- Final Estimated RMS Z Scores bonds: 0.125 angles: 0.140 improper-dihedrals: N/A torsions: N/A trans-peptide: N/A planes: N/A parallel planes: N/A non-bonded: -1.003 chiral vol: 0.105 rama plot: N/A start_pos: N/A TargetPos: N/A GemanMcCl: N/A INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_monomer-VAL.pdb_Tue_Jul_27_04:30:05_2021_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. debug:: in clear_all_atom_pull_restraints() 0 PASS: Neighbour-Refine doesn't destroy disulfide bonds Entered testcase - Rigid Body Refine Alt Conf Waters PASS: Rigid Body Refine Alt Conf Waters Entered testcase - Setting multiple atom attributes PASS: Setting multiple atom attributes Entered testcase - Tweak Alt Confs on Active Residue PASS: Tweak Alt Confs on Active Residue Entered testcase - Backrub rotamer PASS: Backrub rotamer Entered testcase - Libcif horne PASS: Libcif horne Entered testcase - Refmac Parameters Storage PASS: Refmac Parameters Storage Entered testcase - OXT is added before TER record - add only one found TER "TER 25 ASP A 14 " PASS: OXT is added before TER record - add only one Entered testcase - The position of the oxygen after a mutation PASS: The position of the oxygen after a mutation Entered testcase - TER is at the end of a nucleotide after mutation PASS: TER is at the end of a nucleotide after mutation Entered testcase - C7 is removed on mutation from a DC PASS: C7 is removed on mutation from a DC Entered testcase - C7 is added on mutation to a DC DEBUG:: atoms is (" P " " OP1" " OP2" " O5'" " C5'" " C4'" " O4'" " C3'" " O3'" " C2'" " C1'" " N1 " " C2 " " N3 " " C4 " " C5 " " C6 " " O2 " " O4 " " C7 ") PASS: C7 is added on mutation to a DC Entered testcase - Test for flying hydrogens on undo bond-length-within-tolerance? bond-length 0.959095262689385 with target 1.0 and tolerance 0.2 for atoms (("HG11" "") (1.0 20.0 " H" "") (3.49080801010132 -0.155079126358032 -1.95124411582947)) and ((" CG1" "") (1.0 20.0 " C" "") (2.86674046516418 -0.197896704077721 -1.22421586513519)) INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz INFO:: Number of observed reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.840 INFO:: grid sampling...Nuvw = ( 132, 160, 80) INFO:: 0.026 seconds to read MTZ file INFO:: 0.001 seconds to initialize map INFO:: 0.023 seconds for FFT Pre-filter Map statistics: mean: 0.000 st.d: 0.312 Pre-filter Map statistics: min: -0.903 max: 2.968 INFO:: 0.002 seconds for statistics Map extents: ..... 132 160 80 Map mean: ........ 0.000 Map sigma: ....... 0.312 Map maximum: ..... 2.968 Map minimum: ..... -0.903 INFO:: 0.028 seconds for contour map INFO:: 0.080 seconds in total INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz INFO:: Number of observed reflections: 17939 INFO:: finding ASU unique map points with sampling rate 2.200 INFO:: grid sampling...Nuvw = ( 160, 192, 96) INFO:: 0.027 seconds to read MTZ file INFO:: 0.024 seconds to initialize map INFO:: 0.030 seconds for FFT Pre-filter Map statistics: mean: 0.000 st.d: 0.312 Pre-filter Map statistics: min: -0.922 max: 3.052 INFO:: 0.004 seconds for statistics Map extents: ..... 160 192 96 Map mean: ........ 0.000 Map sigma: ....... 0.312 Map maximum: ..... 3.052 Map minimum: ..... -0.922 INFO:: 0.012 seconds for contour map INFO:: 0.097 seconds in total INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb INFO:: file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 50 read successfully INFO:: Masking around 64 atoms -0.856 6 -0.763 49 -0.669 357 -0.575 2059 -0.481 8405 -0.387 23284 -0.293 40481 -0.199 54095 -0.106 67817 -0.012 81890 0.082 54565 0.176 28724 0.270 14192 0.364 9162 0.458 7309 0.552 6314 0.645 5336 0.739 4653 0.833 3736 0.927 3043 1.021 2157 1.115 1562 1.209 1193 1.302 801 1.396 490 1.490 326 1.584 188 1.678 95 1.772 58 1.866 23 1.959 8 2.053 7 2.147 7 2.241 5 2.335 0 2.429 0 2.523 1 2.616 1 2.710 0 2.804 1 2.898 0 Pre-filter Map statistics: mean: -0.001 st.d: 0.306 Pre-filter Map statistics: min: -0.903 max: 2.851 PASS: Test for flying hydrogens on undo Entered testcase - Mask and difference map high-values: (0.941535592079163 0.906727492809296 0.926628708839417 0.631902277469635 0.639082372188568 0.804228544235229 0.741870164871216 1.07694554328918 1.00265049934387 0.962995290756226 0.780390620231628) low values: (0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0) -2.873 2 -2.782 0 -2.690 3 -2.598 0 -2.507 1 -2.415 1 -2.323 2 -2.232 2 -2.140 3 -2.048 3 -1.957 2 -1.865 3 -1.773 2 -1.682 8 -1.590 7 -1.499 13 -1.407 23 -1.315 34 -1.224 46 -1.132 51 -1.040 86 -0.949 117 -0.857 166 -0.765 166 -0.674 215 -0.582 250 -0.490 275 -0.399 316 -0.307 420 -0.215 496 -0.124 624 -0.032 413039 0.060 2311 0.151 1268 0.243 1057 0.335 766 0.426 423 0.518 146 0.610 44 0.701 8 0.793 1 Pre-filter Map statistics: mean: -0.001 st.d: 0.060 Pre-filter Map statistics: min: -2.919 max: 0.747 diff-high-values: (0.00532386638224125 0.0035001253709197 0.00468975584954023 0.00284230033867061 0.00178477843292058 0.00330947712063789 0.00646401522681117 0.00306889740750194 0.00498544052243233 0.00268250983208418 0.00498699676245451) diff-low-values: (-0.877030432224274 -0.886813521385193 -1.18278336524963 -1.14161944389343 -1.07821106910706 -0.84401935338974 -0.820745944976807 -0.712483763694763 -0.943061709403992 -0.538995862007141) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb INFO:: file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 53 read successfully INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz INFO:: Number of observed reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.840 INFO:: grid sampling...Nuvw = ( 132, 160, 80) INFO:: 0.027 seconds to read MTZ file INFO:: 0.000 seconds to initialize map INFO:: 0.021 seconds for FFT Pre-filter Map statistics: mean: 0.000 st.d: 0.312 Pre-filter Map statistics: min: -0.903 max: 2.968 INFO:: 0.003 seconds for statistics Map extents: ..... 132 160 80 Map mean: ........ 0.000 Map sigma: ....... 0.312 Map maximum: ..... 2.968 Map minimum: ..... -0.903 INFO:: 0.009 seconds for contour map INFO:: 0.060 seconds in total INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz INFO:: Number of observed reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.840 INFO:: grid sampling...Nuvw = ( 132, 160, 80) INFO:: 0.027 seconds to read MTZ file INFO:: 0.000 seconds to initialize map INFO:: 0.021 seconds for FFT Pre-filter Map statistics: mean: 0.000 st.d: 0.312 Pre-filter Map statistics: min: -0.903 max: 2.968 INFO:: 0.003 seconds for statistics Map extents: ..... 132 160 80 Map mean: ........ 0.000 Map sigma: ....... 0.312 Map maximum: ..... 2.968 Map minimum: ..... -0.903 INFO:: 0.008 seconds for contour map INFO:: 0.059 seconds in total INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz INFO:: Number of observed reflections: 17939 INFO:: finding ASU unique map points with sampling rate 2.500 INFO:: grid sampling...Nuvw = ( 180, 216, 108) INFO:: 0.028 seconds to read MTZ file INFO:: 0.035 seconds to initialize map INFO:: 0.039 seconds for FFT Pre-filter Map statistics: mean: 0.000 st.d: 0.312 Pre-filter Map statistics: min: -0.878 max: 3.071 INFO:: 0.006 seconds for statistics Map extents: ..... 180 216 108 Map mean: ........ 0.000 Map sigma: ....... 0.312 Map maximum: ..... 3.071 Map minimum: ..... -0.878 INFO:: 0.010 seconds for contour map INFO:: 0.118 seconds in total INFO:: multiplying map (function index) 0 Nuvw = ( 132, 160, 80) by 1.000 INFO:: multiplying map (function index) 1 Nuvw = ( 180, 216, 108) by 1.000 -0.852 7 -0.756 56 -0.659 450 -0.563 2678 -0.466 10692 -0.370 27878 -0.274 45478 -0.177 60675 -0.081 73526 0.016 72865 0.112 48030 0.208 23266 0.305 12333 0.401 8938 0.498 7248 0.594 6244 0.690 5449 0.787 4463 0.883 3656 0.980 2625 1.076 1944 1.172 1389 1.269 967 1.365 642 1.462 386 1.558 242 1.654 121 1.751 69 1.847 28 1.944 16 2.040 8 2.136 11 2.233 7 2.329 2 2.426 2 2.522 2 2.618 1 2.715 2 2.811 2 2.908 2 3.004 0 Pre-filter Map statistics: mean: 0.000 st.d: 0.311 Pre-filter Map statistics: min: -0.900 max: 2.956 -0.009 2 -0.009 0 -0.008 0 -0.008 4 -0.007 7 -0.007 19 -0.006 39 -0.005 93 -0.005 258 -0.004 553 -0.004 1116 -0.003 2340 -0.003 4973 -0.002 10090 -0.001 21790 -0.001 52744 -0.000 113768 0.000 117526 0.001 53953 0.001 20965 0.002 9678 0.003 5146 0.003 2974 0.004 1793 0.004 1049 0.005 620 0.005 383 0.006 217 0.006 129 0.007 74 0.008 52 0.008 15 0.009 7 0.009 6 0.010 1 0.010 6 0.011 2 0.012 4 0.012 2 0.013 2 0.013 0 Pre-filter Map statistics: mean: -0.000 st.d: 0.001 Pre-filter Map statistics: min: -0.010 max: 0.013 INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/pdb2qc1-sans-cho.pdb INFO:: file /lmb/home/pemsley/data/greg-data/pdb2qc1-sans-cho.pdb has been read. Spacegroup: P 21 21 21 INFO:: using standard CCP4 Refmac dictionary to search for "MAN" There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/m/MAN.cif INFO:: Found 1 models Model 1 had 3 links INFO:: NCS chain comparison 4/110 Molecule 59 read successfully INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz INFO:: Number of observed reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.500 INFO:: grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.027 seconds to read MTZ file INFO:: 0.007 seconds to initialize map INFO:: 0.016 seconds for FFT Pre-filter Map statistics: mean: 0.000 st.d: 0.312 Pre-filter Map statistics: min: -0.875 max: 2.978 INFO:: 0.001 seconds for statistics Map extents: ..... 108 132 64 Map mean: ........ 0.000 Map sigma: ....... 0.312 Map maximum: ..... 2.978 Map minimum: ..... -0.875 INFO:: 0.009 seconds for contour map INFO:: 0.060 seconds in total INFO:: dictionary does not already have NAG dynamic add it now INFO:: using standard CCP4 Refmac dictionary to search for "NAG" There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/n/NAG.cif ......... checking for /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/link-by-torsion-to-NAG-core-NAG-ASN.tab ..that failed - trying /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/link-by-torsion-to-pyranose-core-NAG-ASN.tab reading /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/link-by-torsion-to-pyranose-core-NAG-ASN.tab reading /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-pre-release-gtk2-python/share/coot/NAG-decorations.tab INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_pdb2qc1-sans-cho.pdb_Tue_Jul_27_04:30:10_2021_modification_0.pdb.gz INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_pdb2qc1-sans-cho.pdb_Tue_Jul_27_04:30:10_2021_modification_1.pdb.gz INFO:: link torsion generated from link bond restraint ---- contact_info() constructor added link bond contact 8 7 INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_pdb2qc1-sans-cho.pdb_Tue_Jul_27_04:30:10_2021_modification_2.pdb.gz INFO:: replace_coords: 22 atoms updated. ----------------- in create_mmdbmanager_from_res_vector() alt_conf is "" ----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0"" returning an atom selection for all moving atoms 22 atoms debug:: on creation last_restraints is 0x94dc840 INFO:: from_res_vec() created 55 monomer restraints created 21 bond restraints created 27 angle restraints created 2 plane restraints created 5 chiral vol restraints created 0 improper dihedral restraints Made 0 link bond restraints Made 0 link angle restraints Made 0 link plane restraints Made 0 link trans-peptide restraints Made 1 CHO-SS-and-other bond restraints Made 2 CHO-SS-and-other angle restraints Made 1 CHO-SS-and-other plane restraints Made 0 CHO-SS-and-other trans-peptide restraints INFO:: added 0 helical restraints INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 464 "" " O6 " ""] NAG to [spec: model 1 "B" 204 "" " CD2" ""] HIS delta -1.784 target 3.260 distortion 106666.781 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 464 "" " O6 " ""] NAG to [spec: model 1 "B" 204 "" " CG " ""] HIS delta -1.781 target 3.260 distortion 104448.664 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 464 "" " O6 " ""] NAG to [spec: model 1 "B" 204 "" " CB " ""] HIS delta -1.732 target 3.440 distortion 35029.703 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 464 "" " C6 " ""] NAG to [spec: model 1 "B" 204 "" " CB " ""] HIS delta -1.600 target 3.840 distortion 4962.521 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 141 "" " ND2" ""] ASN to [spec: model 1 "B" 464 "" " C2 " ""] NAG delta -1.195 target 3.550 distortion 1005.315 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 464 "" " C1 " ""] NAG to [spec: model 1 "B" 464 "" " O7 " ""] NAG delta -1.040 target 3.470 distortion 506.457 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 464 "" " C6 " ""] NAG to [spec: model 1 "B" 204 "" " CG " ""] HIS delta -1.038 target 3.660 distortion 377.742 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 464 "" " C7 " ""] NAG to [spec: model 1 "B" 418 "" " O " ""] HOH delta -0.873 target 3.270 distortion 281.432 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 464 "" " C6 " ""] NAG to [spec: model 1 "B" 204 "" " CD2" ""] HIS delta -0.900 target 3.660 distortion 192.925 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 464 "" " C6 " ""] NAG to [spec: model 1 "B" 353 "" " O " ""] HOH delta -0.729 target 3.440 distortion 106.123 Minimum found (iteration number 6) at -1296.568 Final Estimated RMS Z Scores: bonds: 1.572 angles: 1.717 improper-dihedrals: N/A torsions: N/A trans-peptide: 16.210 (non-sqrt) planes: 1.760 from 7 restraints parallel planes: N/A non-bonded: -0.275 chiral vol: 1.021 rama plot: N/A start_pos: N/A TargetPos: N/A GemanMcCl: N/A -------- Results --------- INFO:: Model: Bad Bond: [spec: model 1 "B" 141 "" " C " ""] to [spec: model 1 "B" 142 "" " N " ""] nZ 4.72 delta 0.066 target 1.329 sigma 0.014 distortion 22.271 INFO:: Model: Bad Bond: [spec: model 1 "B" 141 "" " CA " ""] to [spec: model 1 "B" 141 "" " CB " ""] nZ 2.85 delta 0.057 target 1.530 sigma 0.020 distortion 8.146 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 141 "" " ND2" ""] ASN to [spec: model 1 "B" 464 "" " C2 " ""] NAG delta -0.818 target 3.550 distortion 146.608 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 464 "" " C6 " ""] NAG to [spec: model 1 "B" 143 "" " CB " ""] SER delta -0.827 target 3.840 distortion 112.365 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 464 "" " C8 " ""] NAG to [spec: model 1 "B" 418 "" " O " ""] HOH delta -0.630 target 3.460 distortion 62.445 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 464 "" " O6 " ""] NAG to [spec: model 1 "B" 204 "" " CB " ""] HIS delta -0.569 target 3.440 distortion 46.358 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 141 "" " O " ""] ASN to [spec: model 1 "B" 411 "" " O " ""] HOH delta -0.460 target 3.040 distortion 35.925 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 141 "" " O " ""] ASN to [spec: model 1 "B" 141 "" " CG " ""] ASN delta -0.478 target 3.270 distortion 32.542 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 464 "" " O6 " ""] NAG to [spec: model 1 "B" 353 "" " O " ""] HOH delta -0.355 target 2.800 distortion 22.570 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 464 "" " C6 " ""] NAG to [spec: model 1 "B" 349 "" " O " ""] HOH delta -0.388 target 3.440 distortion 17.203 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 464 "" " C6 " ""] NAG to [spec: model 1 "B" 204 "" " CB " ""] HIS delta -0.359 target 3.840 distortion 11.542 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 141 "" " ND2" ""] ASN to [spec: model 1 "B" 418 "" " O " ""] HOH delta -0.262 target 2.880 distortion 10.945 Final Estimated RMS Z Scores bonds: 1.572 angles: 1.717 improper-dihedrals: N/A torsions: N/A trans-peptide: 16.210 (non-sqrt) planes: 1.760 from 7 restraints parallel planes: N/A non-bonded: -0.275 chiral vol: 1.021 rama plot: N/A start_pos: N/A TargetPos: N/A GemanMcCl: N/A INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_pdb2qc1-sans-cho.pdb_Tue_Jul_27_04:30:10_2021_modification_3.pdb.gz INFO:: replace_coords: 22 atoms updated. debug:: in clear_all_atom_pull_restraints() 0 ----------------- in create_mmdbmanager_from_res_vector() alt_conf is "" ----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0"" returning an atom selection for all moving atoms 22 atoms debug:: on creation last_restraints is 0x98cc0a0 INFO:: from_res_vec() created 55 monomer restraints created 21 bond restraints created 27 angle restraints created 2 plane restraints created 5 chiral vol restraints created 0 improper dihedral restraints Made 0 link bond restraints Made 0 link angle restraints Made 0 link plane restraints Made 0 link trans-peptide restraints Made 1 CHO-SS-and-other bond restraints Made 2 CHO-SS-and-other angle restraints Made 1 CHO-SS-and-other plane restraints Made 0 CHO-SS-and-other trans-peptide restraints INFO:: added 0 helical restraints INFO:: Model: Bad Bond: [spec: model 1 "B" 141 "" " C " ""] to [spec: model 1 "B" 142 "" " N " ""] nZ 4.72 delta 0.066 target 1.329 sigma 0.014 distortion 22.271 INFO:: Model: Bad Bond: [spec: model 1 "B" 141 "" " CA " ""] to [spec: model 1 "B" 141 "" " CB " ""] nZ 2.85 delta 0.057 target 1.530 sigma 0.020 distortion 8.146 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 141 "" " ND2" ""] ASN to [spec: model 1 "B" 464 "" " C2 " ""] NAG delta -0.818 target 3.550 distortion 146.608 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 464 "" " C6 " ""] NAG to [spec: model 1 "B" 143 "" " CB " ""] SER delta -0.827 target 3.840 distortion 112.365 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 464 "" " C8 " ""] NAG to [spec: model 1 "B" 418 "" " O " ""] HOH delta -0.630 target 3.460 distortion 62.445 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 464 "" " O6 " ""] NAG to [spec: model 1 "B" 204 "" " CB " ""] HIS delta -0.569 target 3.440 distortion 46.358 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 141 "" " O " ""] ASN to [spec: model 1 "B" 411 "" " O " ""] HOH delta -0.460 target 3.040 distortion 35.925 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 141 "" " O " ""] ASN to [spec: model 1 "B" 141 "" " CG " ""] ASN delta -0.478 target 3.270 distortion 32.542 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 464 "" " O6 " ""] NAG to [spec: model 1 "B" 353 "" " O " ""] HOH delta -0.355 target 2.800 distortion 22.570 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 464 "" " C6 " ""] NAG to [spec: model 1 "B" 349 "" " O " ""] HOH delta -0.388 target 3.440 distortion 17.203 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 464 "" " C6 " ""] NAG to [spec: model 1 "B" 204 "" " CB " ""] HIS delta -0.359 target 3.840 distortion 11.542 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 141 "" " ND2" ""] ASN to [spec: model 1 "B" 418 "" " O " ""] HOH delta -0.262 target 2.880 distortion 10.945 Minimum found (iteration number 11) at -1297.052 Final Estimated RMS Z Scores: bonds: 1.572 angles: 1.717 improper-dihedrals: N/A torsions: N/A trans-peptide: 16.211 (non-sqrt) planes: 1.760 from 7 restraints parallel planes: N/A non-bonded: -0.283 chiral vol: 1.021 rama plot: N/A start_pos: N/A TargetPos: N/A GemanMcCl: N/A -------- Results --------- INFO:: Model: Bad Bond: [spec: model 1 "B" 141 "" " C " ""] to [spec: model 1 "B" 142 "" " N " ""] nZ 4.72 delta 0.066 target 1.329 sigma 0.014 distortion 22.278 INFO:: Model: Bad Bond: [spec: model 1 "B" 141 "" " CA " ""] to [spec: model 1 "B" 141 "" " CB " ""] nZ 2.85 delta 0.057 target 1.530 sigma 0.020 distortion 8.144 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 141 "" " ND2" ""] ASN to [spec: model 1 "B" 464 "" " C2 " ""] NAG delta -0.818 target 3.550 distortion 146.613 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 464 "" " C6 " ""] NAG to [spec: model 1 "B" 143 "" " CB " ""] SER delta -0.827 target 3.840 distortion 112.368 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 464 "" " C8 " ""] NAG to [spec: model 1 "B" 418 "" " O " ""] HOH delta -0.630 target 3.460 distortion 62.446 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 464 "" " O6 " ""] NAG to [spec: model 1 "B" 204 "" " CB " ""] HIS delta -0.569 target 3.440 distortion 46.354 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 141 "" " O " ""] ASN to [spec: model 1 "B" 411 "" " O " ""] HOH delta -0.460 target 3.040 distortion 35.924 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 141 "" " O " ""] ASN to [spec: model 1 "B" 141 "" " CG " ""] ASN delta -0.478 target 3.270 distortion 32.540 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 464 "" " O6 " ""] NAG to [spec: model 1 "B" 353 "" " O " ""] HOH delta -0.355 target 2.800 distortion 22.567 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 464 "" " C6 " ""] NAG to [spec: model 1 "B" 349 "" " O " ""] HOH delta -0.388 target 3.440 distortion 17.205 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 464 "" " C6 " ""] NAG to [spec: model 1 "B" 204 "" " CB " ""] HIS delta -0.359 target 3.840 distortion 11.541 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "B" 141 "" " ND2" ""] ASN to [spec: model 1 "B" 418 "" " O " ""] HOH delta -0.262 target 2.880 distortion 10.944 Final Estimated RMS Z Scores bonds: 1.572 angles: 1.717 improper-dihedrals: N/A torsions: N/A trans-peptide: 16.211 (non-sqrt) planes: 1.760 from 7 restraints parallel planes: N/A non-bonded: -0.283 chiral vol: 1.021 rama plot: N/A start_pos: N/A TargetPos: N/A GemanMcCl: N/A INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_pdb2qc1-sans-cho.pdb_Tue_Jul_27_04:30:10_2021_modification_4.pdb.gz INFO:: replace_coords: 22 atoms updated. debug:: in clear_all_atom_pull_restraints() 0 PASS: Mask and difference map Entered testcase - Skeletonize a map PASS: Skeletonize a map Entered testcase - Simple Averaged maps INFO:: map sigmas: normal 0.31107833981514 and diff-map: 0.00107747386209667 PASS: Simple Averaged maps Entered testcase - Refine an NAG-ASN Link bond-length-within-tolerance? bond-length 1.46970796888831 with target 1.43 and tolerance 0.2 for atoms ((" ND2" "") (1.0 16.9300003051758 " N" "") (-14.3709716796875 -0.320891350507736 -7.33248519897461)) and ((" C1 " "") (1.0 45.0 " C" "") (-13.3689279556274 -0.83086097240448 -6.38597536087036)) ----------------- in create_mmdbmanager_from_res_vector() alt_conf is "" ----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0"" returning an atom selection for all moving atoms 12 atoms debug:: on creation last_restraints is 0x98be550 INFO:: from_res_vec() created 28 monomer restraints created 11 bond restraints created 15 angle restraints created 1 plane restraints created 1 chiral vol restraints created 0 improper dihedral restraints Made 0 CHO-SS-and-other bond restraints Made 0 CHO-SS-and-other angle restraints Made 0 CHO-SS-and-other plane restraints Made 0 CHO-SS-and-other trans-peptide restraints INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 30 "" " CB " ""] TYR to [spec: model 1 "A" 30 "" " CG " ""] TYR delta -1.310 target 2.820 distortion 14102.203 Minimum found (iteration number 14) at -2061.997 Final Estimated RMS Z Scores: bonds: 0.933 angles: 0.382 improper-dihedrals: N/A torsions: N/A trans-peptide: N/A planes: 0.411 from 1 restraints parallel planes: N/A non-bonded: -0.112 chiral vol: 0.698 rama plot: N/A start_pos: N/A TargetPos: N/A GemanMcCl: N/A -------- Results --------- INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 30 "" " CB " ""] TYR to [spec: model 1 "A" 30 "" " CG " ""] TYR delta -0.598 target 2.820 distortion 106.029 Final Estimated RMS Z Scores bonds: 0.933 angles: 0.382 improper-dihedrals: N/A torsions: N/A trans-peptide: N/A planes: 0.411 from 1 restraints parallel planes: N/A non-bonded: -0.112 chiral vol: 0.698 rama plot: N/A start_pos: N/A TargetPos: N/A GemanMcCl: N/A INFO:: backup file name coot-backup/atom_selection_from_tutorial-modern.pdb_Tue_Jul_27_04:30:39_2021_modification_0.pdb.gz INFO:: replace_coords: 12 atoms updated. debug:: in clear_all_atom_pull_restraints() 0 ----------------- in create_mmdbmanager_from_res_vector() alt_conf is "" ----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0"" returning an atom selection for all moving atoms 12 atoms debug:: on creation last_restraints is 0x94dd290 INFO:: from_res_vec() created 29 monomer restraints created 12 bond restraints created 15 angle restraints created 1 plane restraints created 1 chiral vol restraints created 0 improper dihedral restraints Made 0 CHO-SS-and-other bond restraints Made 0 CHO-SS-and-other angle restraints Made 0 CHO-SS-and-other plane restraints Made 0 CHO-SS-and-other trans-peptide restraints INFO:: Model: Bad Bond: [spec: model 1 "A" 30 "" " CB " ""] to [spec: model 1 "A" 30 "" " CG " ""] nZ 32.29 delta 0.710 target 1.512 sigma 0.022 distortion 1042.390 Minimum found (iteration number 17) at -2122.142 Final Estimated RMS Z Scores: bonds: 0.681 angles: 0.535 improper-dihedrals: N/A torsions: N/A trans-peptide: N/A planes: 1.088 from 1 restraints parallel planes: N/A non-bonded: -0.788 chiral vol: 0.761 rama plot: N/A start_pos: N/A TargetPos: N/A GemanMcCl: N/A -------- Results --------- Final Estimated RMS Z Scores bonds: 0.681 angles: 0.535 improper-dihedrals: N/A torsions: N/A trans-peptide: N/A planes: 1.088 from 1 restraints parallel planes: N/A non-bonded: -0.788 chiral vol: 0.761 rama plot: N/A start_pos: N/A TargetPos: N/A GemanMcCl: N/A INFO:: backup file name coot-backup/atom_selection_from_tutorial-modern.pdb_Tue_Jul_27_04:30:39_2021_modification_1.pdb.gz INFO:: replace_coords: 12 atoms updated. debug:: in clear_all_atom_pull_restraints() 0 PASS: Refine an NAG-ASN Link Entered testcase - correct matching dictionary names from test name PASS: correct matching dictionary names from test name Entered testcase - update monomer restraints Bond-length: 2.22229592410733: OK plane atom " CB " Bond-length: 1.51909453450828: bond-length-within-tolerance? bond-length 1.51909453450828 with target 1.512 and tolerance 0.04 for atoms ((" CB " "") (1.0 21.75 " C" "") (67.518798828125 4.88922309875488 19.4903774261475)) and ((" CG " "") (1.0 21.9699993133545 " C" "") (68.2945098876953 6.1531777381897 19.1612281799316)) INFO:: wrote mmCIF "coot-test-ala.cif" INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/monomer-ACT.pdb INFO:: file /lmb/home/pemsley/data/greg-data/monomer-ACT.pdb has been read. Spacegroup: P 1 INFO:: using standard CCP4 Refmac dictionary to search for "ACT" There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/a/ACT.cif INFO:: Found 1 models Model 1 had 0 links Molecule 62 read successfully There are 2 data in /lmb/home/pemsley/data/greg-data/libcheck_ACT.cif Welcome to Coot WARNING:: bond_restraint_length 4 should be 5 ----------------- in create_mmdbmanager_from_res_vector() alt_conf is "" ----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0"" returning an atom selection for all moving atoms 7 atoms debug:: on creation last_restraints is 0x4b6d210 INFO:: from_res_vec() created 15 monomer restraints created 5 bond restraints created 9 angle restraints created 1 plane restraints created 0 chiral vol restraints created 0 improper dihedral restraints Made 0 CHO-SS-and-other bond restraints Made 0 CHO-SS-and-other angle restraints Made 0 CHO-SS-and-other plane restraints Made 0 CHO-SS-and-other trans-peptide restraints INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 1 "" " C " ""] ACT to [spec: model 1 "A" 1 "" " O " ""] ACT delta -1.570 target 2.820 distortion 137846.359 Minimum found (iteration number 12) at -680.043 Final Estimated RMS Z Scores: bonds: 1.071 angles: 0.389 improper-dihedrals: N/A torsions: N/A trans-peptide: N/A planes: 0.619 from 1 restraints parallel planes: N/A non-bonded: -0.561 chiral vol: N/A rama plot: N/A start_pos: N/A TargetPos: N/A GemanMcCl: N/A -------- Results --------- INFO:: Model: Bad Bond: [spec: model 1 "A" 1 "" " C " ""] to [spec: model 1 "A" 1 "" " OXT" ""] nZ 2.39 delta -0.048 target 1.250 sigma 0.020 distortion 5.716 Final Estimated RMS Z Scores bonds: 1.071 angles: 0.389 improper-dihedrals: N/A torsions: N/A trans-peptide: N/A planes: 0.619 from 1 restraints parallel planes: N/A non-bonded: -0.561 chiral vol: N/A rama plot: N/A start_pos: N/A TargetPos: N/A GemanMcCl: N/A INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_monomer-ACT.pdb_Tue_Jul_27_04:31:04_2021_modification_0.pdb.gz INFO:: replace_coords: 7 atoms updated. debug:: in clear_all_atom_pull_restraints() 0 INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb INFO:: file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 63 read successfully INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:04_2021_modification_0.pdb.gz INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:04_2021_modification_1.pdb.gz INFO:: Removing CIS peptide from PDB header: A 26 A 27 INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:04_2021_modification_2.pdb.gz INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:04_2021_modification_3.pdb.gz INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:04_2021_modification_4.pdb.gz INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:04_2021_modification_5.pdb.gz INFO:: Removing CIS peptide from PDB header: B 26 B 27 INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:04_2021_modification_6.pdb.gz INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:04_2021_modification_7.pdb.gz INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb INFO:: file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 64 read successfully INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:05_2021_modification_0.pdb.gz INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:05_2021_modification_1.pdb.gz INFO:: NCS chain comparison 93/93 First atom of 720 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.878,12.955,8.761) B-factor: 30.170 First atom of 745 in second selection 1/B/1 {ASP}/ N altLoc :: segid :: pos: (13.876,16.167,23.033) B-factor: 20.030 INFO:: LSQ matched 93 atoms INFO:: 93 matched atoms had: mean devi: 1.179 rms devi: 4.859 max devi: 46.259 min devi: 0.125 find_ncs_matrix returns (LSQ) | 0.9637, -0.07462, -0.2563| | 0.2651, 0.3804, 0.886| | 0.0314, -0.9218, 0.3864| ( 38.09, -17.87, 14.32) INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" INFO:: backup file name coot-backup/atom_selection_from_tutorial-modern.pdb_Tue_Jul_27_04:31:05_2021_modification_0.pdb.gz INFO:: backup file name coot-backup/Copy_of__lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:05_2021_modification_0.pdb.gz INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb INFO:: file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 67 read successfully 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 name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:29:55_2021_modification_2.pdb.gz oops! in rotamer::GetResidue() No tree in restraint oops! in rotamer::GetResidue() No tree in restraint INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb INFO:: file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 68 read successfully INFO:: [spec: 1 "A" 28 ""] [state: 1 name: "m-85" prob: 44.000%] INFO:: [spec: 1 "A" 28 ""] [state: 1 name: "t80" prob: 33.000%] INFO:: [spec: 1 "A" 28 ""] [state: 1 name: "p90" prob: 13.000%] INFO:: [spec: 1 "A" 28 ""] [state: 1 name: "m -30 " prob: 9.000%] INFO:: [spec: 1 "A" 28 ""] [state: 1 name: "m -30 " prob: 9.000%] INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/rnase-A-needs-an-insertion.pdb INFO:: file /lmb/home/pemsley/data/greg-data/rnase-A-needs-an-insertion.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 50/87 Molecule 69 read successfully INFO:: aligning to mol number 69 chain: A ----- input to align_on_chain() ----------------- chain A target DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID wgap -3.000 is_nucleic_acid_flag 0 console_output 1 --------------------------------------------------- INFO:: input model sequence: GTVCLSAEATDTLNLIAASDGPFPYSSQDGVVFQNRESVLPTQSYGYYHEYTVITARTRGTRRIICGEATQEDYYTGDHYATFSLID INFO:: input target sequence: DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID Alignment model vs. target aligned: ---GTVCLSA---EATDTLNLIAASDGPFPYSSQDGVVFQNRESVLPTQSYGYYHEYTVIT--ARTRGTRRIICGEATQE ||||||| |||||||||| ||||||| ||||||||||||||||||||||||||| ||||||||||||||||| target: DVSGTVCLSALPPEATDTLNLIAS-DGPFPYSQ-DGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQE aligned: DYYTGDHYATFSLID ||||||||||||||| target: DYYTGDHYATFSLID INFO:: alignment score 150 INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_rnase-A-needs-an-insertion.pdb_Tue_Jul_27_04:31:06_2021_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: -1 "A" 1 ""] -> ASP [spec: -1 "A" 2 ""] -> VAL [spec: -1 "A" 3 ""] -> SER [spec: -1 "A" 11 ""] -> LEU [spec: -1 "A" 12 ""] -> PRO [spec: -1 "A" 13 ""] -> PRO [spec: -1 "A" 62 ""] -> PRO [spec: -1 "A" 63 ""] -> GLY Deletions: [spec: -1 "A" 25 ""] [spec: -1 "A" 34 ""] Mutations: [spec: -1 "A" 24 ""] -> SER [spec: -1 "A" 33 ""] -> GLN INFO:: mutate 24 A to a SER INFO:: mutate 33 A to a GLN apply resno updates... Applied 3 insertions Applied 2 mutations Applied 2 deletions INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb INFO:: file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 70 read successfully INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:06_2021_modification_0.pdb.gz INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb INFO:: file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 71 read successfully INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:06_2021_modification_0.pdb.gz INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/pdb3hfl.ent INFO:: file /lmb/home/pemsley/data/greg-data/pdb3hfl.ent has been read. INFO:: using standard CCP4 Refmac dictionary to search for "PCA" There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/p/PCA.cif INFO:: Found 1 models Model 1 had 0 links WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model INFO:: NCS chain comparison 15/212 INFO:: NCS chain comparison 7/212 INFO:: NCS chain comparison 10/215 Molecule 72 read successfully INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/3hfl_sigmaa.mtz INFO:: Number of observed reflections: 17920 INFO:: finding ASU unique map points with sampling rate 1.500 INFO:: grid sampling...Nuvw = ( 64, 96, 90) INFO:: 0.021 seconds to read MTZ file INFO:: 0.004 seconds to initialize map INFO:: 0.012 seconds for FFT Pre-filter Map statistics: mean: 0.000 st.d: 0.260 Pre-filter Map statistics: min: -1.034 max: 1.718 INFO:: 0.002 seconds for statistics Map extents: ..... 64 96 90 Map mean: ........ 0.000 Map sigma: ....... 0.260 Map maximum: ..... 1.718 Map minimum: ..... -1.034 INFO:: 0.011 seconds for contour map INFO:: 0.050 seconds in total INFO:: fitting 1 ligands into cluster 0 INFO:: fitting 1 ligands into cluster 0 INFO:: fitting 1 ligands into cluster 0 INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_pdb3hfl.ent_Tue_Jul_27_04:31:07_2021_modification_0.pdb.gz INFO:: replace_coords: 7 atoms updated. Fitting score for best rotamer: 5.834 INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_pdb3hfl.ent_Tue_Jul_27_04:31:07_2021_modification_1.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.000 rms devi: 0.000 max devi: 0.000 min devi: 0.000 INFO:: 5 matched atoms had: mean devi: 0.012 rms devi: 0.013 max devi: 0.021 min devi: 0.004 INFO:: 5 matched atoms had: mean devi: 0.270 rms devi: 0.335 max devi: 0.536 min devi: 0.085 INFO:: 5 matched atoms had: mean devi: 0.267 rms devi: 0.323 max devi: 0.495 min devi: 0.112 INFO:: 5 matched atoms had: mean devi: 0.270 rms devi: 0.335 max devi: 0.536 min devi: 0.085 INFO:: 5 matched atoms had: mean devi: 0.267 rms devi: 0.323 max devi: 0.495 min devi: 0.112 INFO:: 5 matched atoms had: mean devi: 0.012 rms devi: 0.013 max devi: 0.021 min devi: 0.004 INFO:: 5 matched atoms had: mean devi: 0.000 rms devi: 0.000 max devi: 0.000 min devi: 0.000 INFO:: 5 matched atoms had: mean devi: 0.270 rms devi: 0.335 max devi: 0.536 min devi: 0.085 INFO:: 5 matched atoms had: mean devi: 0.267 rms devi: 0.323 max devi: 0.495 min devi: 0.112 INFO:: 5 matched atoms had: mean devi: 0.000 rms devi: 0.000 max devi: 0.000 min devi: 0.000 INFO:: 5 matched atoms had: mean devi: 0.012 rms devi: 0.013 max devi: 0.021 min devi: 0.004 INFO:: 5 matched atoms had: mean devi: 0.000 rms devi: 0.000 max devi: 0.000 min devi: 0.000 INFO:: 5 matched atoms had: mean devi: 0.012 rms devi: 0.013 max devi: 0.021 min devi: 0.004 INFO:: 5 matched atoms had: mean devi: 0.267 rms devi: 0.323 max devi: 0.495 min devi: 0.112 INFO:: 5 matched atoms had: mean devi: 0.270 rms devi: 0.335 max devi: 0.536 min devi: 0.085 WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model INFO:: NCS chain comparison 0/8 INFO:: backup file name coot-backup/Ideal-A-form-RNA_Tue_Jul_27_04:31:07_2021_modification_0.pdb.gz INFO:: backup file name coot-backup/Ideal-A-form-RNA_Tue_Jul_27_04:31:07_2021_modification_1.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.269 rms devi: 0.337 max devi: 0.548 min devi: 0.082 INFO:: 5 matched atoms had: mean devi: 0.000 rms devi: 0.000 max devi: 0.000 min devi: 0.000 INFO:: 5 matched atoms had: mean devi: 0.012 rms devi: 0.013 max devi: 0.021 min devi: 0.004 INFO:: 5 matched atoms had: mean devi: 0.270 rms devi: 0.335 max devi: 0.536 min devi: 0.085 INFO:: 5 matched atoms had: mean devi: 0.267 rms devi: 0.323 max devi: 0.495 min devi: 0.112 INFO:: 5 matched atoms had: mean devi: 0.270 rms devi: 0.335 max devi: 0.536 min devi: 0.085 INFO:: 5 matched atoms had: mean devi: 0.267 rms devi: 0.323 max devi: 0.495 min devi: 0.112 INFO:: 5 matched atoms had: mean devi: 0.012 rms devi: 0.013 max devi: 0.021 min devi: 0.004 INFO:: 5 matched atoms had: mean devi: 0.000 rms devi: 0.000 max devi: 0.000 min devi: 0.000 INFO:: 5 matched atoms had: mean devi: 0.270 rms devi: 0.335 max devi: 0.536 min devi: 0.085 INFO:: 5 matched atoms had: mean devi: 0.267 rms devi: 0.323 max devi: 0.495 min devi: 0.112 INFO:: 5 matched atoms had: mean devi: 0.000 rms devi: 0.000 max devi: 0.000 min devi: 0.000 INFO:: 5 matched atoms had: mean devi: 0.012 rms devi: 0.013 max devi: 0.021 min devi: 0.004 INFO:: 5 matched atoms had: mean devi: 0.000 rms devi: 0.000 max devi: 0.000 min devi: 0.000 INFO:: 5 matched atoms had: mean devi: 0.012 rms devi: 0.013 max devi: 0.021 min devi: 0.004 INFO:: 5 matched atoms had: mean devi: 0.267 rms devi: 0.323 max devi: 0.495 min devi: 0.112 INFO:: 5 matched atoms had: mean devi: 0.270 rms devi: 0.335 max devi: 0.536 min devi: 0.085 WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model INFO:: NCS chain comparison 0/8 INFO:: backup file name coot-backup/Ideal-A-form-RNA_Tue_Jul_27_04:31:07_2021_modification_0.pdb.gz INFO:: backup file name coot-backup/Ideal-A-form-RNA_Tue_Jul_27_04:31:07_2021_modification_1.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.269 rms devi: 0.337 max devi: 0.548 min devi: 0.082 INFO:: 5 matched atoms had: mean devi: 0.006 rms devi: 0.007 max devi: 0.010 min devi: 0.003 INFO:: 5 matched atoms had: mean devi: 0.007 rms devi: 0.008 max devi: 0.013 min devi: 0.005 INFO:: 5 matched atoms had: mean devi: 0.272 rms devi: 0.336 max devi: 0.534 min devi: 0.088 INFO:: 5 matched atoms had: mean devi: 0.268 rms devi: 0.327 max devi: 0.506 min devi: 0.105 INFO:: 5 matched atoms had: mean devi: 0.272 rms devi: 0.336 max devi: 0.534 min devi: 0.088 INFO:: 5 matched atoms had: mean devi: 0.268 rms devi: 0.327 max devi: 0.506 min devi: 0.105 INFO:: 5 matched atoms had: mean devi: 0.007 rms devi: 0.008 max devi: 0.012 min devi: 0.005 INFO:: 5 matched atoms had: mean devi: 0.006 rms devi: 0.007 max devi: 0.010 min devi: 0.002 INFO:: 5 matched atoms had: mean devi: 0.272 rms devi: 0.336 max devi: 0.534 min devi: 0.088 INFO:: 5 matched atoms had: mean devi: 0.268 rms devi: 0.326 max devi: 0.506 min devi: 0.105 INFO:: 5 matched atoms had: mean devi: 0.006 rms devi: 0.007 max devi: 0.010 min devi: 0.003 INFO:: 5 matched atoms had: mean devi: 0.007 rms devi: 0.008 max devi: 0.013 min devi: 0.005 INFO:: 5 matched atoms had: mean devi: 0.006 rms devi: 0.007 max devi: 0.010 min devi: 0.002 INFO:: 5 matched atoms had: mean devi: 0.007 rms devi: 0.008 max devi: 0.012 min devi: 0.005 INFO:: 5 matched atoms had: mean devi: 0.268 rms devi: 0.327 max devi: 0.506 min devi: 0.104 INFO:: 5 matched atoms had: mean devi: 0.272 rms devi: 0.336 max devi: 0.534 min devi: 0.088 WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model INFO:: NCS chain comparison 0/8 INFO:: backup file name coot-backup/Ideal-A-form-DNA_Tue_Jul_27_04:31:07_2021_modification_0.pdb.gz INFO:: backup file name coot-backup/Ideal-A-form-DNA_Tue_Jul_27_04:31:07_2021_modification_1.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.270 rms devi: 0.336 max devi: 0.538 min devi: 0.085 INFO:: backup file name coot-backup/Ideal-A-form-DNA_Tue_Jul_27_04:31:07_2021_modification_2.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.272 rms devi: 0.336 max devi: 0.534 min devi: 0.092 INFO:: backup file name coot-backup/Ideal-A-form-DNA_Tue_Jul_27_04:31:07_2021_modification_3.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.004 rms devi: 0.005 max devi: 0.007 min devi: 0.002 INFO:: backup file name coot-backup/Ideal-A-form-DNA_Tue_Jul_27_04:31:07_2021_modification_4.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.266 rms devi: 0.326 max devi: 0.502 min devi: 0.093 INFO:: 5 matched atoms had: mean devi: 0.006 rms devi: 0.007 max devi: 0.010 min devi: 0.003 INFO:: 5 matched atoms had: mean devi: 0.007 rms devi: 0.008 max devi: 0.013 min devi: 0.005 INFO:: 5 matched atoms had: mean devi: 0.272 rms devi: 0.336 max devi: 0.534 min devi: 0.088 INFO:: 5 matched atoms had: mean devi: 0.268 rms devi: 0.327 max devi: 0.506 min devi: 0.105 INFO:: 5 matched atoms had: mean devi: 0.272 rms devi: 0.336 max devi: 0.534 min devi: 0.088 INFO:: 5 matched atoms had: mean devi: 0.268 rms devi: 0.327 max devi: 0.506 min devi: 0.105 INFO:: 5 matched atoms had: mean devi: 0.007 rms devi: 0.008 max devi: 0.012 min devi: 0.005 INFO:: 5 matched atoms had: mean devi: 0.006 rms devi: 0.007 max devi: 0.010 min devi: 0.002 INFO:: 5 matched atoms had: mean devi: 0.272 rms devi: 0.336 max devi: 0.534 min devi: 0.088 INFO:: 5 matched atoms had: mean devi: 0.268 rms devi: 0.326 max devi: 0.506 min devi: 0.105 INFO:: 5 matched atoms had: mean devi: 0.006 rms devi: 0.007 max devi: 0.010 min devi: 0.003 INFO:: 5 matched atoms had: mean devi: 0.007 rms devi: 0.008 max devi: 0.013 min devi: 0.005 INFO:: 5 matched atoms had: mean devi: 0.006 rms devi: 0.007 max devi: 0.010 min devi: 0.002 INFO:: 5 matched atoms had: mean devi: 0.007 rms devi: 0.008 max devi: 0.012 min devi: 0.005 INFO:: 5 matched atoms had: mean devi: 0.268 rms devi: 0.327 max devi: 0.506 min devi: 0.104 INFO:: 5 matched atoms had: mean devi: 0.272 rms devi: 0.336 max devi: 0.534 min devi: 0.088 WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model INFO:: NCS chain comparison 0/8 INFO:: backup file name coot-backup/Ideal-A-form-DNA_Tue_Jul_27_04:31:07_2021_modification_0.pdb.gz INFO:: backup file name coot-backup/Ideal-A-form-DNA_Tue_Jul_27_04:31:07_2021_modification_1.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.270 rms devi: 0.336 max devi: 0.538 min devi: 0.085 INFO:: backup file name coot-backup/Ideal-A-form-DNA_Tue_Jul_27_04:31:07_2021_modification_2.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.272 rms devi: 0.336 max devi: 0.534 min devi: 0.092 INFO:: backup file name coot-backup/Ideal-A-form-DNA_Tue_Jul_27_04:31:07_2021_modification_3.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.004 rms devi: 0.005 max devi: 0.007 min devi: 0.002 INFO:: backup file name coot-backup/Ideal-A-form-DNA_Tue_Jul_27_04:31:07_2021_modification_4.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.266 rms devi: 0.326 max devi: 0.502 min devi: 0.093 INFO:: backup file name coot-backup/Copy_of__lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_0.pdb.gz INFO:: mutate 32 A to a LYS INFO:: backup file name coot-backup/Copy_of__lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_1.pdb.gz INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/some-waters-with-ter.pdb INFO:: file /lmb/home/pemsley/data/greg-data/some-waters-with-ter.pdb has been read. INFO:: Found 1 models Model 1 had 0 links WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model Molecule 79 read successfully INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_some-waters-with-ter.pdb_Tue_Jul_27_04:31:08_2021_modification_0.pdb.gz 1/D/79 {HOH}/ O altLoc :: segid :: pos: (3.000,4.000,5.000) B-factor: 45.000 added to molecule INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tm+some-waters.pdb INFO:: file /lmb/home/pemsley/data/greg-data/tm+some-waters.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 80 read successfully INFO:: Protein centre at: xyz = ( 41.57, 8.745, 12.89) using sigma cut off 2.000 Calling lig.water_fit() INFO:: find_clusters map_rms is 0.312 INFO:: Using density cut-off: 0.623 (2.000 sigma) (mean -0.034 stdev: 0.146) INFO:: Blobs with volume larger than 11.000 A^3 are too big to be considered waters. INFO:: Using water to protein distance limits: 2.400 3.200 INFO:: Finding clusters...done ------------------------------------------------------------- INFO:: cluster at xyz = ( 59.9, 3.001, -4.25) is too big to be water INFO:: cluster at xyz = ( 70.03, 19.07, 18.64) is too big to be water INFO:: cluster at xyz = ( 52.94, 9.091, 20.14) is too big to be water INFO:: found 57 waters in water fitting Done - back from lig.water_fit() DEBUG:: new_waters_mol_flag: 0 INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tm+some-waters.pdb_Tue_Jul_27_04:31:08_2021_modification_0.pdb.gz INFO:: Adding to solvent chain: D INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb INFO:: file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 81 read successfully INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_0.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_1.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_2.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_3.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_4.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_5.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_6.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_7.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_8.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_9.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_10.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_11.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_12.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_13.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_14.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_15.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_16.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_17.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_18.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_19.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_20.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_21.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_22.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_23.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_24.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_25.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_26.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_27.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_28.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_29.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_30.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_31.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_32.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_33.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_34.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_35.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_36.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_37.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_38.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_39.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_40.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_41.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_42.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_43.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_44.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_45.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_46.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_47.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_48.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_49.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_50.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_51.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_52.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_53.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_54.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_55.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_56.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_57.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_58.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_59.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_60.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_61.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_62.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_63.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_64.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_65.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_66.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_67.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_68.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_69.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_70.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_71.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_72.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_73.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_74.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_75.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_76.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_77.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_78.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_79.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_80.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_81.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_82.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_83.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_84.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_85.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_86.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_87.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_88.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_89.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_90.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_91.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_92.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_93.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_94.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_95.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_96.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_97.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_98.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:08_2021_modification_99.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/water-test-no-cell.pdb INFO:: file /lmb/home/pemsley/data/greg-data/water-test-no-cell.pdb has been read. INFO:: Found 1 models Model 1 had 0 links WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model Molecule 82 read successfully INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_water-test-no-cell.pdb_Tue_Jul_27_04:31:16_2021_modification_0.pdb.gz No symmetry available INFO:: moved 0 water molecules INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/pathological-water-test.pdb INFO:: file /lmb/home/pemsley/data/greg-data/pathological-water-test.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 83 read successfully INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_pathological-water-test.pdb_Tue_Jul_27_04:31:16_2021_modification_0.pdb.gz INFO:: moved 181 water molecules INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz INFO:: Number of observed reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.500 INFO:: grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.026 seconds to read MTZ file INFO:: 0.001 seconds to initialize map INFO:: 0.017 seconds for FFT Pre-filter Map statistics: mean: 0.000 st.d: 0.312 Pre-filter Map statistics: min: -0.875 max: 2.978 INFO:: 0.001 seconds for statistics Map extents: ..... 108 132 64 Map mean: ........ 0.000 Map sigma: ....... 0.312 Map maximum: ..... 2.978 Map minimum: ..... -0.875 INFO:: 0.027 seconds for contour map INFO:: 0.072 seconds in total INFO:: backup file name coot-backup/Copy_of__lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:16_2021_modification_0.pdb.gz INFO:: fitting terminal residue with 5000 random trials WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model INFO:: done mutating residue [spec: 1 "A" 94 ""] in add_cb_to_terminal_res INFO:: backup file name coot-backup/Copy_of__lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:16_2021_modification_1.pdb.gz 0 N :: xyz = ( 58.52, 2.839, -1.766) occ: 1.000 b-fact: 45.000 1 C :: xyz = ( 60.16, 1.94, -3.445) occ: 1.000 b-fact: 45.000 2 CA :: xyz = ( 59.81, 2.193, -1.983) occ: 1.000 b-fact: 45.000 3 O :: xyz = ( 61.3, 1.603, -3.756) occ: 1.000 b-fact: 45.000 INFO:: backup file name coot-backup/Copy_of__lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:17_2021_modification_0.pdb.gz INFO:: backup file name coot-backup/Copy_of__lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:17_2021_modification_1.pdb.gz INFO:: backup file name coot-backup/Copy_of__lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:17_2021_modification_2.pdb.gz INFO:: backup file name coot-backup/Copy_of__lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:17_2021_modification_3.pdb.gz INFO:: backup file name coot-backup/Copy_of__lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:17_2021_modification_4.pdb.gz INFO:: backup file name coot-backup/Copy_of__lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:17_2021_modification_5.pdb.gz INFO:: backup file name coot-backup/Copy_of__lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:17_2021_modification_6.pdb.gz INFO:: backup file name coot-backup/Copy_of__lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:17_2021_modification_7.pdb.gz INFO:: backup file name coot-backup/Copy_of__lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:17_2021_modification_8.pdb.gz INFO:: backup file name coot-backup/Copy_of__lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:17_2021_modification_9.pdb.gz 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: 30.170 First atom of 745 in second selection 1/B/1 {ASP}/ N altLoc :: segid :: pos: (13.876,16.167,23.033) B-factor: 20.030 INFO:: LSQ matched 93 atoms INFO:: 93 matched atoms had: mean devi: 1.179 rms devi: 4.859 max devi: 46.259 min devi: 0.125 find_ncs_matrix returns (LSQ) | 0.9637, -0.07462, -0.2563| | 0.2651, 0.3804, 0.886| | 0.0314, -0.9218, 0.3864| ( 38.09, -17.87, 14.32) INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" DEBUG ncs_control_change_ncs_master_to_chain_update_widget imol: 86 and ichain: 0 DEBUG:: ncs_control_change_ncs_master_to_chain imol: 86 and ichain: 0 %%%%%% add_ncs_ghosts_using_ncs_master %%%%%% imaster: 0 Checking chains for NCS matching to chain A INFO:: NCS chain comparison 93/93 First atom of 720 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.878,12.955,8.761) B-factor: 30.170 First atom of 745 in second selection 1/B/1 {ASP}/ N altLoc :: segid :: pos: (13.876,16.167,23.033) B-factor: 20.030 INFO:: LSQ matched 93 atoms INFO:: 93 matched atoms had: mean devi: 1.179 rms devi: 4.859 max devi: 46.259 min devi: 0.125 find_ncs_matrix returns (LSQ) | 0.9637, -0.07462, -0.2563| | 0.2651, 0.3804, 0.886| | 0.0314, -0.9218, 0.3864| ( 38.09, -17.87, 14.32) Adding ghost with name: NCS found from matching Chain B onto Chain A INFO:: set_ncs_master_chain Constructed 1 ghosts Ghost info:: NCS found from matching Chain B onto Chain A INFO:: backup file name coot-backup/Copy_of__lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:17_2021_modification_10.pdb.gz INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb INFO:: file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 87 read successfully 0//-32767 {HOH}/ O altLoc :: segid :: pos: (41.595,8.687,12.909) B-factor: 45.000 added to molecule (and new chain) 1/C/2 {HOH}/ O altLoc :: segid :: pos: (43.595,8.687,12.909) B-factor: 45.000 added to molecule 1/C/3 {HOH}/ O altLoc :: segid :: pos: (45.595,8.687,12.909) B-factor: 45.000 added to molecule 1/C/4 {HOH}/ O altLoc :: segid :: pos: (47.595,8.687,12.909) B-factor: 45.000 added to molecule 1/C/5 {HOH}/ O altLoc :: segid :: pos: (49.595,8.687,12.909) B-factor: 45.000 added to molecule 1/D/16 {HOH}/ O altLoc :: segid :: pos: (51.595,8.687,12.909) B-factor: 45.000 added to molecule 1/D/17 {HOH}/ O altLoc :: segid :: pos: (53.595,8.687,12.909) B-factor: 45.000 added to molecule 1/D/18 {HOH}/ O altLoc :: segid :: pos: (55.595,8.687,12.909) B-factor: 45.000 added to molecule 1/D/19 {HOH}/ O altLoc :: segid :: pos: (57.595,8.687,12.909) B-factor: 45.000 added to molecule 1/D/20 {HOH}/ O altLoc :: segid :: pos: (59.595,8.687,12.909) B-factor: 45.000 added to molecule 1/D/21 {HOH}/ O altLoc :: segid :: pos: (61.595,8.687,12.909) B-factor: 45.000 added to molecule 1/D/22 {HOH}/ O altLoc :: segid :: pos: (63.595,8.687,12.909) B-factor: 45.000 added to molecule 1/D/23 {HOH}/ O altLoc :: segid :: pos: (65.595,8.687,12.909) B-factor: 45.000 added to molecule 1/D/24 {HOH}/ O altLoc :: segid :: pos: (67.595,8.687,12.909) B-factor: 45.000 added to molecule 1/D/25 {HOH}/ O altLoc :: segid :: pos: (69.595,8.687,12.909) B-factor: 45.000 added to molecule INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/pdb1hvv.ent INFO:: file /lmb/home/pemsley/data/greg-data/pdb1hvv.ent has been read. Spacegroup: P 31 2 1 INFO:: using standard CCP4 Refmac dictionary to search for "TAR" There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/t/TAR.cif INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 62/67 INFO:: NCS chain comparison 66/67 INFO:: NCS chain comparison 61/67 INFO:: NCS chain comparison 0/67 INFO:: fill_ghost_info Constructed 3 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Ghost 1 name: "NCS found from matching Chain C onto Chain A" Ghost 2 name: "NCS found from matching Chain D onto Chain A" Molecule 88 read successfully INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/monomer-ACT.pdb INFO:: file /lmb/home/pemsley/data/greg-data/monomer-ACT.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links Molecule 89 read successfully INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/monomer-NPO.pdb INFO:: file /lmb/home/pemsley/data/greg-data/monomer-NPO.pdb has been read. Spacegroup: P 1 INFO:: using standard CCP4 Refmac dictionary to search for "NPO" There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/n/NPO.cif INFO:: Found 1 models Model 1 had 0 links Molecule 90 read successfully INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_pdb1hvv.ent_Tue_Jul_27_04:31:18_2021_modification_0.pdb.gz 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: 45.260 First atom of 506 in second selection 1/B/193 {SER}/ N altLoc :: segid :: pos: (0.570,-74.720,-82.848) B-factor: 88.520 INFO:: LSQ matched 62 atoms INFO:: 62 matched atoms had: mean devi: 2.499 rms devi: 2.796 max devi: 6.686 min devi: 0.440 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: 45.260 First atom of 535 in second selection 1/C/190 {GLN}/ N altLoc :: segid :: pos: (63.726,-15.709,-72.885) B-factor: 50.760 INFO:: LSQ matched 66 atoms INFO:: 66 matched atoms had: mean devi: 1.971 rms devi: 2.173 max devi: 4.541 min devi: 0.430 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: 45.260 First atom of 497 in second selection 1/D/193 {SER}/ N altLoc :: segid :: pos: (62.917,-35.989,-55.929) B-factor: 78.350 INFO:: LSQ matched 61 atoms INFO:: 61 matched atoms had: mean devi: 3.704 rms devi: 4.086 max devi: 9.438 min devi: 0.286 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:: NCS chain comparison 0/67 INFO:: NCS chain comparison 0/54 INFO:: fill_ghost_info Constructed 3 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Ghost 1 name: "NCS found from matching Chain C onto Chain A" Ghost 2 name: "NCS found from matching Chain D onto Chain A" ------- resulting_merge_info has size 2 -------- resulting_merge_info[0] {residue-spec-not-set} -X,-X+Y,-Z+1/3 -> -1 0 0 -1 1 0 0 0 -1 translations: 0.000 0.000 0.333 pre-trans: 0 0 0 INFO:: NCS chain comparison 62/67 First atom of 540 in first selection 1/A/190 {GLN}/ N altLoc :: segid :: pos: (62.572,-20.497,95.468) B-factor: 45.260 First atom of 506 in second selection 1/B/193 {SER}/ N altLoc :: segid :: pos: (64.424,-37.854,121.388) B-factor: 88.520 INFO:: LSQ matched 62 atoms INFO:: 62 matched atoms had: mean devi: 2.499 rms devi: 2.796 max devi: 6.686 min devi: 0.440 find_ncs_matrix returns (LSQ) | 0.8045, 0.069, 0.59| | 0.5435, 0.315, -0.778| | -0.2395, 0.9466, 0.2159| ( -57.32, 43.57, 131.4) INFO:: NCS chain comparison 66/67 First atom of 540 in first selection 1/A/190 {GLN}/ N altLoc :: segid :: pos: (62.572,-20.497,95.468) B-factor: 45.260 First atom of 535 in second selection 1/C/190 {GLN}/ N altLoc :: segid :: pos: (-18.259,-63.043,111.425) B-factor: 50.760 INFO:: LSQ matched 66 atoms INFO:: 66 matched atoms had: mean devi: 1.971 rms devi: 2.173 max devi: 4.541 min devi: 0.430 find_ncs_matrix returns (LSQ) | -0.5596, -0.8266, 0.06065| | -0.8239, 0.5468, -0.1492| | 0.09015, -0.1334, -0.9869| ( -4.436, 16.92, 204.3) INFO:: NCS chain comparison 61/67 First atom of 540 in first selection 1/A/190 {GLN}/ N altLoc :: segid :: pos: (62.572,-20.497,95.468) B-factor: 45.260 First atom of 497 in second selection 1/D/193 {SER}/ N altLoc :: segid :: pos: (-0.291,-72.482,94.469) B-factor: 78.350 INFO:: LSQ matched 61 atoms INFO:: 61 matched atoms had: mean devi: 3.704 rms devi: 4.086 max devi: 9.438 min devi: 0.286 find_ncs_matrix returns (LSQ) | -0.4782, -0.7381, -0.476| | -0.7473, 0.05733, 0.662| | -0.4613, 0.6723, -0.579| ( 53.45, -87.51, 210.2) INFO:: NCS chain comparison 0/67 INFO:: NCS chain comparison 0/67 INFO:: NCS chain comparison 0/54 INFO:: fill_ghost_info Constructed 3 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Ghost 1 name: "NCS found from matching Chain C onto Chain A" Ghost 2 name: "NCS found from matching Chain D onto Chain A" INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_pdb1hvv.ent_Tue_Jul_27_04:31:18_2021_modification_1.pdb.gz 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: 45.260 First atom of 506 in second selection 1/B/193 {SER}/ N altLoc :: segid :: pos: (0.570,-74.720,-82.848) B-factor: 88.520 INFO:: LSQ matched 62 atoms INFO:: 62 matched atoms had: mean devi: 2.499 rms devi: 2.796 max devi: 6.686 min devi: 0.440 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: 45.260 First atom of 535 in second selection 1/C/190 {GLN}/ N altLoc :: segid :: pos: (63.726,-15.709,-72.885) B-factor: 50.760 INFO:: LSQ matched 66 atoms INFO:: 66 matched atoms had: mean devi: 1.971 rms devi: 2.173 max devi: 4.541 min devi: 0.430 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: 45.260 First atom of 497 in second selection 1/D/193 {SER}/ N altLoc :: segid :: pos: (62.917,-35.989,-55.929) B-factor: 78.350 INFO:: LSQ matched 61 atoms INFO:: 61 matched atoms had: mean devi: 3.704 rms devi: 4.086 max devi: 9.438 min devi: 0.286 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:: NCS chain comparison 0/67 INFO:: NCS chain comparison 67/67 First atom of 540 in first selection 1/A/190 {GLN}/ N altLoc :: segid :: pos: (-13.535,-64.438,-56.928) B-factor: 45.260 First atom of 540 in second selection 1/F/190 {GLN}/ N altLoc :: segid :: pos: (62.572,-20.497,95.468) B-factor: 45.260 INFO:: LSQ matched 67 atoms INFO:: 67 matched atoms had: mean devi: 0.000 rms devi: 0.000 max devi: 0.000 min devi: 0.000 find_ncs_matrix returns (LSQ) | -0.5, -0.866, 2.047e-15| | -0.866, 0.5,-2.401e-15| | 1.056e-15,-2.974e-15, -1| (-1.954e-13, 2.345e-13, 38.54) 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: 45.260 First atom of 506 in second selection 1/G/193 {SER}/ N altLoc :: segid :: pos: (64.424,-37.854,121.388) B-factor: 88.520 INFO:: LSQ matched 62 atoms INFO:: 62 matched atoms had: mean devi: 2.499 rms devi: 2.796 max devi: 6.686 min devi: 0.440 find_ncs_matrix returns (LSQ) | -0.873, -0.3073, 0.3788| | -0.4249, 0.09775, -0.8999| | 0.2395, -0.9466, -0.2159| ( -9.072, 71.43, -92.86) 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: 45.260 First atom of 535 in second selection 1/H/190 {GLN}/ N altLoc :: segid :: pos: (-18.259,-63.043,111.425) B-factor: 50.760 INFO:: LSQ matched 66 atoms INFO:: 66 matched atoms had: mean devi: 1.971 rms devi: 2.173 max devi: 4.541 min devi: 0.430 find_ncs_matrix returns (LSQ) | 0.9933, -0.06025, 0.09887| | 0.07266, 0.9892, -0.1271| | -0.09015, 0.1334, 0.9869| ( -12.43, 12.3, -165.7) 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: 45.260 First atom of 497 in second selection 1/I/193 {SER}/ N altLoc :: segid :: pos: (-0.291,-72.482,94.469) B-factor: 78.350 INFO:: LSQ matched 61 atoms INFO:: 61 matched atoms had: mean devi: 3.704 rms devi: 4.086 max devi: 9.438 min devi: 0.286 find_ncs_matrix returns (LSQ) | 0.8863, 0.3194, -0.3353| | 0.0405, 0.6679, 0.7432| | 0.4613, -0.6723, 0.579| ( 49.07, -90.04, -171.6) INFO:: NCS chain comparison 0/67 INFO:: NCS chain comparison 0/67 INFO:: NCS chain comparison 0/54 INFO:: NCS chain comparison 0/54 INFO:: NCS chain comparison 0/54 INFO:: NCS chain comparison 0/54 INFO:: NCS chain comparison 0/54 INFO:: NCS chain comparison 54/54 First atom of 63 in first selection 1//1352 {TAR}/ O1 altLoc :: segid :: pos: (28.993,-30.241,-68.921) B-factor: 80.230 First atom of 63 in second selection 1/J/1352 {TAR}/ O1 altLoc :: segid :: pos: (11.693,-40.229,107.461) B-factor: 80.230 WARNING:: no points to do matching find_ncs_matrix returns (LSQ) | 0, 0, 0| | 0, 0, 0| | 0, 0, 0| ( 0, 0, 0) WARNING:: Junk NCS matrix No NCS matrix defined INFO:: NCS chain comparison 0/2 INFO:: NCS chain comparison 0/2 INFO:: NCS chain comparison 0/2 INFO:: NCS chain comparison 0/2 INFO:: NCS chain comparison 0/2 INFO:: NCS chain comparison 2/2 First atom of 22 in first selection 1/E/1 {ACT}/ OXT altLoc :: segid :: pos: (0.000,0.000,0.000) B-factor: 20.000 First atom of 22 in second selection 1/K/1 {ACT}/ OXT altLoc :: segid :: pos: (0.000,0.000,38.540) B-factor: 20.000 WARNING:: residue is not amino acid or nucleotide! Assuming non-standard nucleotide. WARNING:: no P in this reference residue 1 WARNING:: no P in this reference residue 1 WARNING:: residue is not amino acid or nucleotide! Assuming non-standard nucleotide. WARNING:: no P in this reference residue 101 WARNING:: no P in this reference residue 101 WARNING:: - no residue for reference molecule residue number 2 for reference chain-id: "E" WARNING:: - no residue for moving molecule residue number 2 for reference chain-id: "E" WARNING:: - no residue for reference molecule residue number 3 for reference chain-id: "E" WARNING:: - no residue for moving molecule residue number 3 for reference chain-id: "E" WARNING:: - no residue for reference molecule residue number 4 for reference chain-id: "E" WARNING:: - no residue for moving molecule residue number 4 for reference chain-id: "E" WARNING:: - no residue for reference molecule residue number 5 for reference chain-id: "E" WARNING:: - no residue for moving molecule residue number 5 for reference chain-id: "E" WARNING:: - no residue for reference molecule residue number 6 for reference chain-id: "E" WARNING:: - no residue for moving molecule residue number 6 for reference chain-id: "E" WARNING:: ... and others... WARNING:: no points to do matching find_ncs_matrix returns (LSQ) | 0, 0, 0| | 0, 0, 0| | 0, 0, 0| ( 0, 0, 0) WARNING:: Junk NCS matrix No NCS matrix defined INFO:: fill_ghost_info Constructed 7 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" Ghost 3 name: "NCS found from matching Chain F onto Chain A" Ghost 4 name: "NCS found from matching Chain G onto Chain A" Ghost 5 name: "NCS found from matching Chain H onto Chain A" Ghost 6 name: "NCS found from matching Chain I onto Chain A" ------- resulting_merge_info has size 6 -------- resulting_merge_info[0] {residue-spec-not-set} INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb INFO:: file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 92 read successfully INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:19_2021_modification_0.pdb.gz INFO:: backup file name coot-backup/atom_selection_from_tutorial-modern.pdb_Tue_Jul_27_04:31:19_2021_modification_0.pdb.gz INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:19_2021_modification_1.pdb.gz INFO:: Removing CIS peptide from PDB header: A 26 A 27 INFO:: NCS chain comparison 93/93 First atom of 720 in first selection 1/AAA/1 {ASP}/ N altLoc :: segid :: pos: (44.878,12.955,8.761) B-factor: 30.170 First atom of 745 in second selection 1/B/1 {ASP}/ N altLoc :: segid :: pos: (13.876,16.167,23.033) B-factor: 20.030 INFO:: LSQ matched 93 atoms INFO:: 93 matched atoms had: mean devi: 0.359 rms devi: 0.452 max devi: 2.134 min devi: 0.084 find_ncs_matrix returns (LSQ) | 0.9705, -0.0469, -0.2365| | 0.2359, 0.3887, 0.8907| | 0.05015, -0.9202, 0.3883| ( 37.8, -17.18, 13.83) INFO:: NCS chain comparison 90/93 First atom of 720 in first selection 1/AAA/1 {ASP}/ N altLoc :: segid :: pos: (44.878,12.955,8.761) B-factor: 30.170 First atom of 699 in second selection 1/B-chain/1 {ASP}/ N altLoc :: segid :: pos: (13.876,16.167,23.033) B-factor: 20.030 INFO:: LSQ matched 90 atoms INFO:: 90 matched atoms had: mean devi: 0.360 rms devi: 0.454 max devi: 2.133 min devi: 0.085 find_ncs_matrix returns (LSQ) | 0.9705, -0.04705, -0.2365| | 0.2358, 0.3892, 0.8904| | 0.05015, -0.9199, 0.3889| ( 37.8, -17.18, 13.81) INFO:: fill_ghost_info Constructed 2 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain AAA" Ghost 1 name: "NCS found from matching Chain B-chain onto Chain AAA" ------- resulting_merge_info has size 1 -------- resulting_merge_info[0] {residue-spec-not-set} INFO:: backup file name coot-backup/atom_selection_from_tutorial-modern.pdb_Tue_Jul_27_04:31:19_2021_modification_1.pdb.gz INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:19_2021_modification_2.pdb.gz INFO:: NCS chain comparison 93/93 First atom of 720 in first selection 1/AAA/1 {ASP}/ N altLoc :: segid :: pos: (44.878,12.955,8.761) B-factor: 30.170 First atom of 745 in second selection 1/B/1 {ASP}/ N altLoc :: segid :: pos: (13.876,16.167,23.033) B-factor: 20.030 INFO:: LSQ matched 93 atoms INFO:: 93 matched atoms had: mean devi: 0.359 rms devi: 0.452 max devi: 2.134 min devi: 0.084 find_ncs_matrix returns (LSQ) | 0.9705, -0.0469, -0.2365| | 0.2359, 0.3887, 0.8907| | 0.05015, -0.9202, 0.3883| ( 37.8, -17.18, 13.83) INFO:: NCS chain comparison 90/93 First atom of 720 in first selection 1/AAA/1 {ASP}/ N altLoc :: segid :: pos: (44.878,12.955,8.761) B-factor: 30.170 First atom of 699 in second selection 1/B-chain/1 {ASP}/ N altLoc :: segid :: pos: (13.876,16.167,23.033) B-factor: 20.030 INFO:: LSQ matched 90 atoms INFO:: 90 matched atoms had: mean devi: 0.360 rms devi: 0.454 max devi: 2.133 min devi: 0.085 find_ncs_matrix returns (LSQ) | 0.9705, -0.04705, -0.2365| | 0.2358, 0.3892, 0.8904| | 0.05015, -0.9199, 0.3889| ( 37.8, -17.18, 13.81) INFO:: NCS chain comparison 90/93 First atom of 720 in first selection 1/AAA/1 {ASP}/ N altLoc :: segid :: pos: (44.878,12.955,8.761) B-factor: 30.170 First atom of 699 in second selection 1/AAA2/1 {ASP}/ N altLoc :: segid :: pos: (13.876,16.167,23.033) B-factor: 20.030 INFO:: LSQ matched 90 atoms INFO:: 90 matched atoms had: mean devi: 0.360 rms devi: 0.454 max devi: 2.133 min devi: 0.085 find_ncs_matrix returns (LSQ) | 0.9705, -0.04705, -0.2365| | 0.2358, 0.3892, 0.8904| | 0.05015, -0.9199, 0.3889| ( 37.8, -17.18, 13.81) INFO:: fill_ghost_info Constructed 3 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain AAA" Ghost 1 name: "NCS found from matching Chain B-chain onto Chain AAA" Ghost 2 name: "NCS found from matching Chain AAA2 onto Chain AAA" ------- resulting_merge_info has size 1 -------- resulting_merge_info[0] {residue-spec-not-set} INFO:: Matching/moving molecule number 95 to 94 INFO:: LSQ matched 4 atoms INFO:: 4 matched atoms had: mean devi: 0.035 rms devi: 0.038 max devi: 0.055 min devi: 0.017 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 name coot-backup/Copy_of__lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:19_2021_modification_0.pdb.gz INFO:: coordinates transformed by orthogonal matrix: | 0.9737, 0.007115, -0.2278| | 0.2062, 0.3981, 0.8939| | 0.09703, -0.9173, 0.3861| ( 37.45, -16.6, 12.88) INFO:: fractional coordinates matrix: | 0.9737, 0.008587, -0.1361| | 0.1708, 0.3981, 0.4427| | 0.1623, -1.852, 0.3861| ( 0.577, -0.2119, 0.3319) PASS: update monomer restraints Entered testcase - Write mmCIF restraints correctly PASS: Write mmCIF restraints correctly Entered testcase - Refinement OK with zero bond esd PASS: Refinement OK with zero bond esd Entered testcase - Change Chain IDs and Chain Sorting PASS: Change Chain IDs and Chain Sorting Entered testcase - Chain-ids in links change also on change chain id PASS: Chain-ids in links change also on change chain id Entered testcase - Replace Fragment distances: (20.8326663813327 20.8326666331108 20.8326661982214 20.8326666331108 20.8326663813327) PASS: Replace Fragment Entered testcase - Residues in Region of Residue found 6 neighbours (("B" 60 "") ("A" 42 "") ("B" 61 "") ("A" 38 "") ("A" 41 "") ("A" 39 "")) found 0 neighbours () PASS: Residues in Region of Residue Entered testcase - Residues in region of a point PASS: Residues in region of a point Entered testcase - Empty molecule on type selection PASS: Empty molecule on type selection Entered testcase - Set Rotamer PASS: Set Rotamer Entered testcase - Rotamer names and scores are correct Rotamer 0 : "m-85" 100.0 Rotamer 1 : "t80" 90.1668395996094 Rotamer 2 : "p90" 50.7077865600586 Rotamer 3 : "m -30 " 21.4231548309326 Rotamer 4 : "m -30 " 21.4231548309326 PASS: Rotamer names and scores are correct Entered testcase - Align and mutate a model with deletions ::::: (69 "A" 1 "") #f #f ::::: (69 "A" 4 "") #t #t ::::: (69 "A" 57 "") #t #t ::::: (69 "A" 60 "") #f #f ::::: (69 "A" 61 "") #f #f ::::: (69 "A" 92 "") #t #t ::::: (69 "A" 94 "") #f #f results: (#t #t #t #t #t #t #t) PASS: Align and mutate a model with deletions Entered testcase - renumbered residues should be in seqnum order PASS: renumbered residues should be in seqnum order Entered testcase - Autofit Rotamer on Residues with Insertion codes PASS: Autofit Rotamer on Residues with Insertion codes Entered testcase - RNA base has correct residue type after mutation mutated base to type "C" - was "A" mutated base to type "Cr" - was "A" PASS: RNA base has correct residue type after mutation Entered testcase - resname from serial number doesnt crash on silly input PASS: resname from serial number doesnt crash on silly input Entered testcase - DNA bases are the correct residue type after mutation mutated base to type "DC" mutated base to type "DG" mutated base to type "DA" mutated base to type "DT" mutated base to type "Cd" mutated base to type "Gd" mutated base to type "Ad" mutated base to type "Td" PASS: DNA bases are the correct residue type after mutation Entered testcase - SegIDs are correct after mutate PASS: SegIDs are correct after mutate Entered testcase - TER on water chain is removed on adding a water by hand PASS: TER on water chain is removed on adding a water by hand Entered testcase - TER on water chain is removed on adding waters automatically PASS: TER on water chain is removed on adding waters automatically Entered testcase - Adding atoms to Many-Chained Molecule PASS: Adding atoms to Many-Chained Molecule Entered testcase - Arrange waters round protein PASS: Arrange waters round protein Entered testcase - Correct Segid After Add Terminal Residue PASS: Correct Segid After Add Terminal Residue Entered testcase - Correct Segid after NCS residue range copy PASS: Correct Segid after NCS residue range copy Entered testcase - Merge Water Chains PASS: Merge Water Chains Entered testcase - Consolidated merge -------- starting chain list ----------- DEBUG:: (chain-ids imol) is ("A" "B" "C" "D" "") DEBUG:: chain-list is ("A" "B" "C" "D" "" "E" "F" "G" "H" "I" "J" "K") PASS: Consolidated merge Entered testcase - Test for good chain ids after a merge chain-ids: ("AAA" "B" "B-chain") --- chain-ids: ("AAA" "B" "B-chain" "AAA2") PASS: Test for good chain ids after a merge Entered testcase - LSQ by atom bond-length-within-tolerance? bond-length 0.110921496735531 with target 0.0 and tolerance 0.2 for atoms ((" C " "") (1.0 15.5799999237061 " C" "") (56.8940010070801 1.29299998283386 19.6700000762939)) and ((" C " "") (1.0 16.7800006866455 " C" "") (56.8856086730957 1.18242847919464 19.6726627349854)) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb INFO:: file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 96 read successfully INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/pdb1py3.ent INFO:: file /lmb/home/pemsley/data/greg-data/pdb1py3.ent has been read. Spacegroup: C 1 2 1 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 91/204 INFO:: NCS chain comparison 90/204 INFO:: NCS chain comparison 175/179 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain C onto Chain B" Molecule 97 read successfully INFO:: spacegroup: P 21 21 21 INFO:: spacegroup: C 1 2 1 INFO:: Matching/moving molecule number 96 to 97 INFO:: LSQ matched 164 atoms INFO:: 164 matched atoms had: mean devi: 0.502 rms devi: 0.594 max devi: 1.679 min devi: 0.043 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 name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:19_2021_modification_0.pdb.gz INFO:: coordinates transformed by orthogonal matrix: | 0.8273, 0.1661, 0.5366| | -0.3732, 0.8765, 0.3041| | -0.4199, -0.4519, 0.7871| ( 33.77, -3.902, -16.53) INFO:: fractional coordinates matrix: | 0.8273, 0.2005, 0.3208| | -0.3092, 0.8765, 0.1506| | -0.7024, -0.9123, 0.7871| ( 0.5204, -0.04982, -0.426) INFO:: spacegroup: C 1 2 1 INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb INFO:: file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 98 read successfully INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:20_2021_modification_0.pdb.gz INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb INFO:: file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 99 read successfully INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/2goz-manip.pdb INFO:: file /lmb/home/pemsley/data/greg-data/2goz-manip.pdb has been read. Spacegroup: C 1 2 1 INFO:: using standard CCP4 Refmac dictionary to search for "GDP" There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/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 /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/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 /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/c/CR.cif INFO:: using standard CCP4 Refmac dictionary to search for "OMC" There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/o/OMC.cif INFO:: using standard CCP4 Refmac dictionary to search for "5BU" There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/5/5BU.cif INFO:: Found 1 models Model 1 had 7 links INFO:: NCS chain comparison 10/85 Molecule 100 read successfully 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 /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/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 /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/c/CR.cif INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb INFO:: file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 101 read successfully INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz INFO:: Number of observed reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.500 INFO:: grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.030 seconds to read MTZ file INFO:: 0.001 seconds to initialize map INFO:: 0.016 seconds for FFT Pre-filter Map statistics: mean: 0.000 st.d: 0.312 Pre-filter Map statistics: min: -0.875 max: 2.978 INFO:: 0.001 seconds for statistics Map extents: ..... 108 132 64 Map mean: ........ 0.000 Map sigma: ....... 0.312 Map maximum: ..... 2.978 Map minimum: ..... -0.875 INFO:: 0.010 seconds for contour map INFO:: 0.058 seconds in total masking....masking done INFO:: fitting 1 ligands into cluster 0 INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:21_2021_modification_0.pdb.gz INFO:: replace_coords: 745 atoms updated. debug:: in clear_all_atom_pull_restraints() 0 SFAC LINE: SFAC C H N O S INFO:: CELL set to 5.903 13.698 9.237 90.000 98.211 90.000 READ-INS:: Spacegroup: "P 1 21/c 1" INFO:: read_file() chain with chain id has 2 residues Symmetry available for this molecule Molecule 103 read successfully LATT LINE: LATT -2 SFAC LINE: SFAC C H N O CO INFO:: CELL set to 34.324 34.324 11.089 90.000 90.000 90.000 READ-INS:: Spacegroup: "I 41 2 2" INFO:: read_file() chain with chain id has 2 residues Symmetry available for this molecule Molecule 104 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 90.000 90.000 90.000 READ-INS:: Spacegroup: "I 21 3" INFO:: read_file() chain with chain id has 121 residues Symmetry available for this molecule Molecule 105 read successfully -0.695 231 -0.524 4724 -0.352 24910 -0.181 55291 -0.009 95241 0.162 40930 0.334 7480 0.505 3968 0.677 2790 0.848 2117 1.020 1738 1.191 1221 1.363 888 1.534 595 1.706 355 1.877 240 2.049 137 2.220 97 2.392 62 2.563 46 2.735 17 2.906 17 3.078 13 3.249 10 3.421 7 3.592 1 3.764 3 3.935 7 4.107 2 4.278 5 4.450 1 4.621 2 4.793 2 4.964 0 5.136 1 5.307 0 5.479 0 5.650 0 5.822 0 5.993 1 6.165 0 Pre-filter Map statistics: mean: -0.000 st.d: 0.305 Pre-filter Map statistics: min: -0.781 max: 6.079 -0.201 7 -0.179 48 -0.158 209 -0.136 787 -0.115 2257 -0.093 5676 -0.072 12730 -0.050 24380 -0.029 38190 -0.007 46230 0.014 43880 0.036 32484 0.057 19420 0.079 9718 0.100 4120 0.122 1677 0.143 718 0.165 329 0.186 133 0.208 77 0.229 29 0.251 11 0.272 13 0.294 8 0.315 2 0.337 2 0.358 2 0.380 1 0.401 1 0.423 2 0.444 2 0.466 1 0.487 1 0.509 1 0.530 1 0.552 1 0.573 0 0.595 0 0.616 0 0.638 2 0.659 0 Pre-filter Map statistics: mean: -0.000 st.d: 0.047 Pre-filter Map statistics: min: -0.212 max: 0.649 INFO:: spacegroup: I 21 3 INFO:: spacegroup: I 21 3 INFO:: spacegroup: I 21 3 WARNING:: invalid molecule (204050) for write_shelx_ins_file WARNING:: failed to get AFIX handle for "A" 1 "ASP" " N " WARNING:: failed to get AFIX handle for "A" 1 "ASP" " CA " WARNING:: failed to get AFIX handle for "A" 1 "ASP" " CB " WARNING:: failed to get AFIX handle for "A" 1 "ASP" " CG " WARNING:: failed to get AFIX handle for "A" 1 "ASP" " OD1" WARNING:: failed to get AFIX handle for "A" 1 "ASP" " OD2" WARNING:: failed to get AFIX handle for "A" 1 "ASP" " C " WARNING:: failed to get AFIX handle for "A" 1 "ASP" " O " WARNING:: failed to get AFIX handle for "A" 2 "VAL" " N " WARNING:: failed to get AFIX handle for "A" 2 "VAL" " CA " INFO:: SHELXL file rnase.ins written. INFO:: fitting terminal residue with 5000 random trials WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model INFO:: done mutating residue [spec: 1 "B" 2021 ""] in add_cb_to_terminal_res INFO:: backup file name coot-backup/atom_selection_from_insulin.res_Tue_Jul_27_04:31:22_2021_modification_0.res.gz WARNING:: failed to get AFIX handle for "B" 2010 "HIS" " N " WARNING:: failed to get AFIX handle for "B" 2010 "HIS" " CA " WARNING:: failed to get AFIX handle for "B" 2010 "HIS" " C " WARNING:: failed to get AFIX handle for "B" 2010 "HIS" " O " WARNING:: failed to get AFIX handle for "B" 2010 "HIS" " CB " WARNING:: failed to get AFIX handle for "B" 2010 "HIS" " CG " WARNING:: failed to get AFIX handle for "B" 2010 "HIS" " ND1" WARNING:: failed to get AFIX handle for "B" 2010 "HIS" " CE1" WARNING:: failed to get AFIX handle for "B" 2010 "HIS" " NE2" WARNING:: failed to get AFIX handle for "B" 2010 "HIS" " CD2" 0 N :: xyz = ( -11.81, 18.53, 58.84) occ: 1.000 b-fact: 45.000 1 C :: xyz = ( -11.2, 19.72, 60.93) occ: 1.000 b-fact: 45.000 2 CA :: xyz = ( -12.08, 19.69, 59.68) occ: 1.000 b-fact: 45.000 3 O :: xyz = ( -10.87, 20.79, 61.44) occ: 1.000 b-fact: 45.000 INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_insulin.res_Tue_Jul_27_04:31:22_2021_modification_0.res.gz WARNING:: failed to get AFIX handle for "A" 1001 "GLY" " N " WARNING:: failed to get AFIX handle for "A" 1001 "GLY" " CA " WARNING:: failed to get AFIX handle for "A" 1001 "GLY" " C " WARNING:: failed to get AFIX handle for "A" 1001 "GLY" " O " WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " N " WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " CA " WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " CB " WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " CG2" WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " CG1" WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " CD1" 1/D/3069 {HOH}/ O altLoc :: segid :: pos: (3.000,-1.000,60.000) B-factor: 45.000 added to molecule INFO:: Protein centre at: xyz = ( -0.2998, 10.6, 57.56) using sigma cut off 0.600 Calling lig.water_fit() INFO:: find_clusters map_rms is 0.305 INFO:: Using density cut-off: 0.183 (0.600 sigma) (mean -0.020 stdev: 0.112) INFO:: Blobs with volume larger than 11.000 A^3 are too big to be considered waters. INFO:: Using water to protein distance limits: 2.400 3.200 INFO:: Finding clusters...done ------------------------------------------------------------- INFO:: cluster at xyz = ( -4.859, 20.8, 69.7) is too big to be water INFO:: cluster at xyz = ( 4.249, -1.354, 48.69) is too big to be water INFO:: cluster at xyz = ( 0.05491, 16.3, 69.67) is too big to be water INFO:: cluster at xyz = ( 15.59, 8.13, 53.24) is too big to be water INFO:: cluster at xyz = ( 20.55, 4.875, 65.84) is too big to be water INFO:: cluster at xyz = ( -5.054, 9.822, 69.12) is too big to be water INFO:: found 28 waters in water fitting Done - back from lig.water_fit() DEBUG:: new_waters_mol_flag: 0 INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_insulin.res_Tue_Jul_27_04:31:22_2021_modification_1.res.gz WARNING:: failed to get AFIX handle for "A" 1001 "GLY" " N " WARNING:: failed to get AFIX handle for "A" 1001 "GLY" " CA " WARNING:: failed to get AFIX handle for "A" 1001 "GLY" " C " WARNING:: failed to get AFIX handle for "A" 1001 "GLY" " O " WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " N " WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " CA " WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " CB " WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " CG2" WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " CG1" WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " CD1" INFO:: Adding to solvent chain: D LATT LINE: LATT -1 SFAC LINE: SFAC C H N O S SE CL WARNING:: BAD ATOM line 17 2 field(s) :DAMP 0.3: INFO:: CELL set to 42.140 83.030 89.790 90.000 90.000 90.000 READ-INS:: Spacegroup: "P 21 21 21" INFO:: read_file() chain with chain id has 5 residues Symmetry available for this molecule Molecule 110 read successfully LATT LINE: LATT -1 SFAC LINE: SFAC C H N O MG CL INFO:: CELL set to 14.080 32.760 18.660 90.000 101.730 90.000 READ-INS:: Spacegroup: "P 1 21 1" INFO:: read_file() chain with chain id has 23 residues Symmetry available for this molecule Molecule 111 read successfully WARNING:: failed to get AFIX handle for "A" 1 "CPC" " C1 " WARNING:: failed to get AFIX handle for "A" 1 "CPC" " O1 " WARNING:: failed to get AFIX handle for "A" 1 "CPC" " C2 " WARNING:: failed to get AFIX handle for "A" 1 "CPC" " C3 " WARNING:: failed to get AFIX handle for "A" 1 "CPC" " H3 " WARNING:: failed to get AFIX handle for "A" 1 "CPC" " C4 " WARNING:: failed to get AFIX handle for "A" 1 "CPC" " H4 " WARNING:: failed to get AFIX handle for "A" 1 "CPC" " C5 " WARNING:: failed to get AFIX handle for "A" 1 "CPC" "CL1 " WARNING:: failed to get AFIX handle for "A" 1 "CPC" " N1 " INFO:: SHELXL file new-horma.ins written. LATT LINE: LATT -1 SFAC LINE: SFAC C H N O MG CL debug:: ## new chain wiith chain-id A INFO:: CELL set to 14.080 32.760 18.660 90.000 101.730 90.000 READ-INS:: Spacegroup: "P 1 21 1" INFO:: read_file() chain with chain id A has 23 residues Symmetry available for this molecule Molecule 112 read successfully LATT LINE: LATT -2 SFAC LINE: SFAC S INFO:: CELL set to 108.999 108.999 107.555 90.000 90.000 90.000 READ-INS:: Spacegroup: "I 4 2 2" INFO:: read_file() chain with chain id has 4 residues Symmetry available for this molecule Molecule 113 read successfully INFO:: using standard CCP4 Refmac dictionary to search for "3GP" There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/3/3GP.cif WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model INFO:: backup file name coot-backup/3GP_from_dict_Tue_Jul_27_04:31:22_2021_modification_0.pdb.gz INFO:: backup file name coot-backup/3GP_from_dict_Tue_Jul_27_04:31:22_2021_modification_1.pdb.gz INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/monomer-3GP.pdb INFO:: file /lmb/home/pemsley/data/greg-data/monomer-3GP.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links Molecule 115 read successfully INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_monomer-3GP.pdb_Tue_Jul_27_04:31:22_2021_modification_0.pdb.gz INFO:: comp-id: LIG is marked for non-autoloading - stopping now INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/test-LIG.pdb INFO:: file /lmb/home/pemsley/data/greg-data/test-LIG.pdb has been read. INFO:: comp-id: LIG is marked for non-autoloading - stopping now INFO:: Found 1 models Model 1 had 0 links WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model Molecule 116 read successfully INFO:: comp-id: LIG is marked for non-autoloading - stopping now INFO:: comp-id: LIG is marked for non-autoloading - stopping now INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/test-LIG.pdb INFO:: file /lmb/home/pemsley/data/greg-data/test-LIG.pdb has been read. INFO:: using standard CCP4 Refmac dictionary to search for "LIG" There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/l/LIG.cif INFO:: Found 1 models Model 1 had 0 links WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model Molecule 117 read successfully INFO:: comp-id: LIG is marked for non-autoloading - stopping now INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb INFO:: file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 118 read successfully WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model INFO:: backup file name coot-backup/3GP_from_dict_Tue_Jul_27_04:31:23_2021_modification_0.pdb.gz INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:23_2021_modification_0.pdb.gz INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:31:23_2021_modification_1.pdb.gz INFO:: NCS chain comparison 93/93 First atom of 720 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.878,12.955,8.761) B-factor: 30.170 First atom of 745 in second selection 1/B/1 {ASP}/ N altLoc :: segid :: pos: (13.876,16.167,23.033) B-factor: 20.030 INFO:: LSQ matched 93 atoms INFO:: 93 matched atoms had: mean devi: 0.359 rms devi: 0.452 max devi: 2.134 min devi: 0.084 find_ncs_matrix returns (LSQ) | 0.9705, -0.0469, -0.2365| | 0.2359, 0.3887, 0.8907| | 0.05015, -0.9202, 0.3883| ( 37.8, -17.18, 13.83) INFO:: NCS chain comparison 0/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" ------- resulting_merge_info has size 1 -------- resulting_merge_info[0] [spec: mmdb::MinInt4 "L" 1 ""] INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/monomer-3GP.pdb INFO:: file /lmb/home/pemsley/data/greg-data/monomer-3GP.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links Molecule 120 read successfully ------------------ add_view_raw() ligand-view INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_monomer-3GP.pdb_Tue_Jul_27_04:31:24_2021_modification_0.pdb.gz ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- debug:: in clear_all_atom_pull_restraints() 0 INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/monomer-NPO.pdb INFO:: file /lmb/home/pemsley/data/greg-data/monomer-NPO.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links Molecule 121 read successfully INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb INFO:: file /lmb/home/pemsley/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb has been read. Spacegroup: C 2 2 21 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 10/113 INFO:: NCS chain comparison 107/113 INFO:: NCS chain comparison 10/113 INFO:: NCS chain comparison 107/113 INFO:: NCS chain comparison 10/113 INFO:: NCS chain comparison 107/113 INFO:: NCS chain comparison 10/113 INFO:: NCS chain comparison 0/113 INFO:: NCS chain comparison 10/117 INFO:: NCS chain comparison 112/117 INFO:: NCS chain comparison 10/117 INFO:: NCS chain comparison 112/117 INFO:: NCS chain comparison 10/117 INFO:: NCS chain comparison 112/117 INFO:: NCS chain comparison 0/117 INFO:: fill_ghost_info Constructed 6 ghosts Ghost 0 name: "NCS found from matching Chain C onto Chain A" Ghost 1 name: "NCS found from matching Chain E onto Chain A" Ghost 2 name: "NCS found from matching Chain G onto Chain A" Ghost 3 name: "NCS found from matching Chain D onto Chain B" Ghost 4 name: "NCS found from matching Chain F onto Chain B" Ghost 5 name: "NCS found from matching Chain H onto Chain B" Molecule 127 read successfully INFO:: making conventional map from MTZ filename /lmb/home/pemsley/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz using FWT PHWT INFO:: Number of observed reflections: 54440 INFO:: finding ASU unique map points with sampling rate 1.500 INFO:: grid sampling...Nuvw = ( 160, 160, 336) INFO:: 0.127 seconds to read MTZ file INFO:: 0.077 seconds to initialize map INFO:: 0.067 seconds for FFT Pre-filter Map statistics: mean: -0.000 st.d: 0.171 Pre-filter Map statistics: min: -0.695 max: 1.343 INFO:: 0.008 seconds for statistics Map extents: ..... 160 160 336 Map mean: ........ -0.000 Map sigma: ....... 0.171 Map maximum: ..... 1.343 Map minimum: ..... -0.695 INFO:: 0.014 seconds for contour map INFO:: 0.293 seconds in total INFO:: making difference map from MTZ filename /lmb/home/pemsley/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz using DELFWT PHDELWT INFO:: Number of observed reflections: 54440 INFO:: finding ASU unique map points with sampling rate 1.500 INFO:: grid sampling...Nuvw = ( 160, 160, 336) INFO:: 0.084 seconds to read MTZ file INFO:: 0.001 seconds to initialize map INFO:: 0.066 seconds for FFT Pre-filter Map statistics: mean: 0.000 st.d: 0.033 Pre-filter Map statistics: min: -0.192 max: 0.366 INFO:: 0.008 seconds for statistics Map extents: ..... 160 160 336 Map mean: ........ 0.000 Map sigma: ....... 0.033 Map maximum: ..... 0.366 Map minimum: ..... -0.192 INFO:: 0.014 seconds for contour map INFO:: 0.173 seconds in total INFO:: ligand number 0 is molecule number 121 with wiggly flag: 0 in execute_ligand_search_internal() import maps from mol 128 INFO:: Protein centre at: xyz = ( 58.29, 34.65, 30.63) -0.677 6 -0.641 8 -0.605 27 -0.569 116 -0.532 354 -0.496 977 -0.460 1943 -0.424 3356 -0.387 5156 -0.351 6576 -0.315 7850 -0.279 8875 -0.242 9742 -0.206 11742 -0.170 16950 -0.134 29805 -0.097 58214 -0.061 102889 -0.025 142998 0.011 471776 0.048 106846 0.084 56087 0.120 21597 0.156 6911 0.192 2135 0.229 920 0.265 467 0.301 346 0.337 216 0.374 118 0.410 117 0.446 80 0.482 50 0.519 28 0.555 33 0.591 15 0.627 14 0.664 11 0.700 2 0.736 7 0.772 0 Pre-filter Map statistics: mean: -0.022 st.d: 0.089 Pre-filter Map statistics: min: -0.695 max: 0.754 INFO:: find_clusters map_rms is 0.171 INFO:: Using density cut-off: 0.171 (1.000 sigma) (mean -0.022 stdev: 0.089) INFO:: Blobs with volume larger than 11.000 A^3 are too big to be considered waters. INFO:: Using water to protein distance limits: 2.400 3.200 INFO:: Finding clusters...done INFO:: fitting 1 ligands into cluster 0 INFO:: fitting 1 ligands into cluster 1 INFO:: fitting 1 ligands into cluster 2 INFO:: fitting 1 ligands into cluster 3 INFO:: fitting 1 ligands into cluster 4 INFO:: fitting 1 ligands into cluster 5 INFO:: fitting 1 ligands into cluster 6 INFO:: fitting 1 ligands into cluster 7 INFO:: fitting 1 ligands into cluster 8 INFO:: fitting 1 ligands into cluster 9 debug:: n_ligands_for_cluster() top_score 3.875 and 4 are decent out of 12 ----------------- in create_mmdbmanager_from_res_vector() alt_conf is "" ----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0"" returning an atom selection for all moving atoms 15 atoms debug:: on creation last_restraints is 0x95b24a0 INFO:: from_res_vec() created 39 monomer restraints created 15 bond restraints created 22 angle restraints created 2 plane restraints created 0 chiral vol restraints created 0 improper dihedral restraints Made 0 CHO-SS-and-other bond restraints Made 0 CHO-SS-and-other angle restraints Made 0 CHO-SS-and-other plane restraints Made 0 CHO-SS-and-other trans-peptide restraints INFO:: Model: Bad Bond: [spec: model 1 "A" 1 "" " O2 " ""] to [spec: model 1 "A" 1 "" " N1 " ""] nZ 8.98 delta -0.180 target 1.400 sigma 0.020 distortion 80.688 Refinement elapsed time: 0.031 Minimum found (iteration number 15) at -356.672 Final Estimated RMS Z Scores: bonds: 0.281 angles: 0.054 improper-dihedrals: N/A torsions: N/A trans-peptide: N/A planes: 0.130 from 2 restraints parallel planes: N/A non-bonded: -0.688 chiral vol: N/A rama plot: N/A start_pos: N/A TargetPos: N/A GemanMcCl: N/A -------- Results --------- Final Estimated RMS Z Scores bonds: 0.281 angles: 0.054 improper-dihedrals: N/A torsions: N/A trans-peptide: N/A planes: 0.130 from 2 restraints parallel planes: N/A non-bonded: -0.688 chiral vol: N/A rama plot: N/A start_pos: N/A TargetPos: N/A GemanMcCl: N/A INFO:: backup file name coot-backup/Fitted_ligand_#0-0_Tue_Jul_27_04:31:43_2021_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. debug:: in clear_all_atom_pull_restraints() 0 debug:: n_ligands_for_cluster() top_score 1.949 and 8 are decent out of 12 ----------------- in create_mmdbmanager_from_res_vector() alt_conf is "" ----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0"" returning an atom selection for all moving atoms 15 atoms debug:: on creation last_restraints is 0x9601120 INFO:: from_res_vec() created 39 monomer restraints created 15 bond restraints created 22 angle restraints created 2 plane restraints created 0 chiral vol restraints created 0 improper dihedral restraints Made 0 CHO-SS-and-other bond restraints Made 0 CHO-SS-and-other angle restraints Made 0 CHO-SS-and-other plane restraints Made 0 CHO-SS-and-other trans-peptide restraints INFO:: Model: Bad Bond: [spec: model 1 "A" 1 "" " O2 " ""] to [spec: model 1 "A" 1 "" " N1 " ""] nZ 8.98 delta -0.180 target 1.400 sigma 0.020 distortion 80.688 Refinement elapsed time: 0.020 Minimum found (iteration number 8) at -221.605 Final Estimated RMS Z Scores: bonds: 0.140 angles: 0.125 improper-dihedrals: N/A torsions: N/A trans-peptide: N/A planes: 0.127 from 2 restraints parallel planes: N/A non-bonded: -0.660 chiral vol: N/A rama plot: N/A start_pos: N/A TargetPos: N/A GemanMcCl: N/A -------- Results --------- INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 1 "" " O2 " ""] NPO to [spec: model 1 "A" 1 "" " H6 " ""] NPO delta -0.210 target 2.720 distortion 8.015 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 1 "" " O3 " ""] NPO to [spec: model 1 "A" 1 "" " H2 " ""] NPO delta -0.186 target 2.720 distortion 6.422 Final Estimated RMS Z Scores bonds: 0.140 angles: 0.125 improper-dihedrals: N/A torsions: N/A trans-peptide: N/A planes: 0.127 from 2 restraints parallel planes: N/A non-bonded: -0.660 chiral vol: N/A rama plot: N/A start_pos: N/A TargetPos: N/A GemanMcCl: N/A INFO:: backup file name coot-backup/Fitted_ligand_#1-0_Tue_Jul_27_04:32:30_2021_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. debug:: in clear_all_atom_pull_restraints() 0 debug:: n_ligands_for_cluster() top_score 2.090 and 4 are decent out of 12 ----------------- in create_mmdbmanager_from_res_vector() alt_conf is "" ----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0"" returning an atom selection for all moving atoms 15 atoms debug:: on creation last_restraints is 0x95edb00 INFO:: from_res_vec() created 39 monomer restraints created 15 bond restraints created 22 angle restraints created 2 plane restraints created 0 chiral vol restraints created 0 improper dihedral restraints Made 0 CHO-SS-and-other bond restraints Made 0 CHO-SS-and-other angle restraints Made 0 CHO-SS-and-other plane restraints Made 0 CHO-SS-and-other trans-peptide restraints INFO:: Model: Bad Bond: [spec: model 1 "A" 1 "" " O2 " ""] to [spec: model 1 "A" 1 "" " N1 " ""] nZ 8.98 delta -0.180 target 1.400 sigma 0.020 distortion 80.688 Refinement elapsed time: 0.028 Minimum found (iteration number 16) at -212.926 Final Estimated RMS Z Scores: bonds: 0.197 angles: 0.052 improper-dihedrals: N/A torsions: N/A trans-peptide: N/A planes: 0.075 from 2 restraints parallel planes: N/A non-bonded: -0.683 chiral vol: N/A rama plot: N/A start_pos: N/A TargetPos: N/A GemanMcCl: N/A -------- Results --------- Final Estimated RMS Z Scores bonds: 0.197 angles: 0.052 improper-dihedrals: N/A torsions: N/A trans-peptide: N/A planes: 0.075 from 2 restraints parallel planes: N/A non-bonded: -0.683 chiral vol: N/A rama plot: N/A start_pos: N/A TargetPos: N/A GemanMcCl: N/A INFO:: backup file name coot-backup/Fitted_ligand_#2-0_Tue_Jul_27_04:32:46_2021_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. debug:: in clear_all_atom_pull_restraints() 0 debug:: n_ligands_for_cluster() top_score -1.000 and 0 are decent out of 0 debug:: n_ligands_for_cluster() top_score -1.000 and 0 are decent out of 0 debug:: n_ligands_for_cluster() top_score -1.000 and 0 are decent out of 0 debug:: n_ligands_for_cluster() top_score -1.000 and 0 are decent out of 0 debug:: n_ligands_for_cluster() top_score -1.000 and 0 are decent out of 0 debug:: n_ligands_for_cluster() top_score -1.000 and 0 are decent out of 0 debug:: n_ligands_for_cluster() top_score -1.000 and 0 are decent out of 0 INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/monomer-3GP.pdb INFO:: file /lmb/home/pemsley/data/greg-data/monomer-3GP.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links Molecule 134 read successfully INFO:: backup file name coot-backup/Copy_of__lmb_home_pemsley_data_greg-data_monomer-3GP.pdb_Tue_Jul_27_04:32:47_2021_modification_0.pdb.gz INFO:: replace_coords: 36 atoms updated. INFO:: backup file name coot-backup/Copy_of__lmb_home_pemsley_data_greg-data_monomer-3GP.pdb_Tue_Jul_27_04:32:47_2021_modification_1.pdb.gz INFO:: replace_coords: 36 atoms updated. INFO:: backup file name coot-backup/Copy_of__lmb_home_pemsley_data_greg-data_monomer-3GP.pdb_Tue_Jul_27_04:32:47_2021_modification_2.pdb.gz INFO:: replace_coords: 36 atoms updated. INFO:: backup file name coot-backup/Copy_of__lmb_home_pemsley_data_greg-data_monomer-3GP.pdb_Tue_Jul_27_04:32:47_2021_modification_3.pdb.gz INFO:: replace_coords: 36 atoms updated. WARNING: in init_refmac_mon_lib, file "/lmb/home/pemsley/data/greg-data/libcheck_3GP.cif" not found. init_refmac_mon_lib /lmb/home/pemsley/data/greg-data/libcheck_3GP.cif had no bond restraints WARNING: in init_refmac_mon_lib, file "/lmb/home/pemsley/data/greg-data/libcheck_3GP.cif" not found. init_refmac_mon_lib /lmb/home/pemsley/data/greg-data/libcheck_3GP.cif had no bond restraints WARNING: in init_refmac_mon_lib, file "/lmb/home/pemsley/data/greg-data/libcheck_3GP.cif" not found. init_refmac_mon_lib /lmb/home/pemsley/data/greg-data/libcheck_3GP.cif had no bond restraints INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb INFO:: file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 136 read successfully debug:: assign_pir_sequence():: storing sequence: ACDEFGHIKLMNPQ for chain id: A in molecule number 136 input_sequence pushing back A ACDEFGHIKLMNPQ debug:: assign_pir_sequence():: storing sequence: ACDEFGHIKLMNPQRST for chain id: A in molecule number 136 INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/crashes_on_cootaneering-v2.pdb INFO:: file /lmb/home/pemsley/data/greg-data/crashes_on_cootaneering-v2.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 1/2 INFO:: NCS chain comparison 0/2 INFO:: NCS chain comparison 0/13 Molecule 137 read successfully INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz INFO:: Number of observed reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.500 INFO:: grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.026 seconds to read MTZ file INFO:: 0.001 seconds to initialize map INFO:: 0.019 seconds for FFT Pre-filter Map statistics: mean: 0.000 st.d: 0.312 Pre-filter Map statistics: min: -0.875 max: 2.978 INFO:: 0.002 seconds for statistics Map extents: ..... 108 132 64 Map mean: ........ 0.000 Map sigma: ....... 0.312 Map maximum: ..... 2.978 Map minimum: ..... -0.875 INFO:: 0.009 seconds for contour map INFO:: 0.057 seconds in total debug:: assign_pir_sequence():: storing sequence: DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID for chain id: A in molecule number 137 input_sequence pushing back A DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID Sequence: ?EYTVITPGARTR Confidence: 1.000 From : HEYTVITPGARTR Chain id: 0 Offset: 53 INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_crashes_on_cootaneering-v2.pdb_Tue_Jul_27_04:32:49_2021_modification_0.pdb.gz bypassing ? at 0 Mutating to GLU at 1 Mutating poly_ala residue number 58 Mutating to TYR at 2 Mutating poly_ala residue number 59 Mutating to THR at 3 Mutating poly_ala residue number 60 Mutating to VAL at 4 Mutating poly_ala residue number 61 Mutating to ILE at 5 Mutating poly_ala residue number 62 Mutating to THR at 6 Mutating poly_ala residue number 63 Mutating to PRO at 7 Mutating poly_ala residue number 64 Mutating to GLY at 8 Mutating poly_ala residue number 65 Mutating to ALA at 9 Mutating poly_ala residue number 66 Mutating to ARG at 10 Mutating poly_ala residue number 67 Mutating to THR at 11 Mutating poly_ala residue number 68 Mutating to ARG at 12 Mutating poly_ala residue number 69 DEBUG:: Creating a new chain B WARNING:: thrown Null previous residue WARNING:: no rotamers probabilities for residue type GLY INFO:: replace_coords: 12 atoms updated. oops! in rotamer::GetResidue() No tree in restraint oops! in rotamer::GetResidue() No tree in restraint oops! in rotamer::GetResidue() No tree in restraint oops! in rotamer::GetResidue() No tree in restraint oops! in rotamer::GetResidue() No tree in restraint oops! in rotamer::GetResidue() No tree in restraint oops! in rotamer::GetResidue() No tree in restraint oops! in rotamer::GetResidue() No tree in restraint INFO:: replace_coords: 15 atoms updated. INFO:: replace_coords: 10 atoms updated. INFO:: replace_coords: 10 atoms updated. INFO:: replace_coords: 11 atoms updated. INFO:: replace_coords: 10 atoms updated. INFO:: replace_coords: 10 atoms updated. WARNING:: thrown Failed to get a good fitting result WARNING:: no rotamers probabilities for residue type GLY WARNING:: thrown Failed to get a good fitting result WARNING:: no rotamers probabilities for residue type ALA INFO:: replace_coords: 14 atoms updated. INFO:: replace_coords: 10 atoms updated. WARNING:: thrown Null next residue INFO:: fitting 1 ligands into cluster 0 INFO:: fitting 1 ligands into cluster 0 INFO:: fitting 1 ligands into cluster 0 INFO:: fitting 1 ligands into cluster 0 INFO:: fitting 1 ligands into cluster 0 INFO:: fitting 1 ligands into cluster 0 INFO:: fitting 1 ligands into cluster 0 INFO:: fitting 1 ligands into cluster 0 INFO:: fitting 1 ligands into cluster 0 INFO:: fitting 1 ligands into cluster 0 INFO:: fitting 1 ligands into cluster 0 INFO:: fitting 1 ligands into cluster 0 INFO:: fitting 1 ligands into cluster 0 INFO:: fitting 1 ligands into cluster 0 INFO:: fitting 1 ligands into cluster 0 INFO:: fitting 1 ligands into cluster 0 INFO:: fitting 1 ligands into cluster 0 INFO:: fitting 1 ligands into cluster 0 INFO:: fitting 1 ligands into cluster 0 INFO:: fitting 1 ligands into cluster 0 INFO:: fitting 1 ligands into cluster 0 INFO:: fitting 1 ligands into cluster 0 INFO:: fitting 1 ligands into cluster 0 INFO:: fitting 1 ligands into cluster 0 INFO:: fitting 1 ligands into cluster 0 INFO:: fitting 1 ligands into cluster 0 INFO:: fitting 1 ligands into cluster 0 INFO:: fitting 1 ligands into cluster 0 INFO:: fitting 1 ligands into cluster 0 INFO:: fitting 1 ligands into cluster 0 INFO:: fitting 1 ligands into cluster 0 INFO:: fitting 1 ligands into cluster 0 INFO:: fitting 1 ligands into cluster 0 INFO:: replace_coords: 11 atoms updated. INFO:: 5 matched atoms had: mean devi: 0.000 rms devi: 0.000 max devi: 0.000 min devi: 0.000 INFO:: 5 matched atoms had: mean devi: 0.012 rms devi: 0.013 max devi: 0.021 min devi: 0.004 INFO:: 5 matched atoms had: mean devi: 0.270 rms devi: 0.335 max devi: 0.536 min devi: 0.085 INFO:: 5 matched atoms had: mean devi: 0.267 rms devi: 0.323 max devi: 0.495 min devi: 0.112 INFO:: 5 matched atoms had: mean devi: 0.270 rms devi: 0.335 max devi: 0.536 min devi: 0.085 INFO:: 5 matched atoms had: mean devi: 0.267 rms devi: 0.323 max devi: 0.495 min devi: 0.112 INFO:: 5 matched atoms had: mean devi: 0.012 rms devi: 0.013 max devi: 0.021 min devi: 0.004 INFO:: 5 matched atoms had: mean devi: 0.000 rms devi: 0.000 max devi: 0.000 min devi: 0.000 INFO:: 5 matched atoms had: mean devi: 0.270 rms devi: 0.335 max devi: 0.536 min devi: 0.085 INFO:: 5 matched atoms had: mean devi: 0.267 rms devi: 0.323 max devi: 0.495 min devi: 0.112 INFO:: 5 matched atoms had: mean devi: 0.000 rms devi: 0.000 max devi: 0.000 min devi: 0.000 INFO:: 5 matched atoms had: mean devi: 0.012 rms devi: 0.013 max devi: 0.021 min devi: 0.004 INFO:: 5 matched atoms had: mean devi: 0.000 rms devi: 0.000 max devi: 0.000 min devi: 0.000 INFO:: 5 matched atoms had: mean devi: 0.012 rms devi: 0.013 max devi: 0.021 min devi: 0.004 INFO:: 5 matched atoms had: mean devi: 0.267 rms devi: 0.323 max devi: 0.495 min devi: 0.112 INFO:: 5 matched atoms had: mean devi: 0.270 rms devi: 0.335 max devi: 0.536 min devi: 0.085 WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model INFO:: NCS chain comparison 0/8 INFO:: backup file name coot-backup/Ideal-A-form-RNA_Tue_Jul_27_04:32:49_2021_modification_0.pdb.gz ------------------ add_view_raw() RNA-builder-view INFO:: backup file name coot-backup/Copy_of_Ideal-A-form-RNA_Tue_Jul_27_04:32:49_2021_modification_0.pdb.gz INFO:: backup file name coot-backup/Ideal-A-form-RNA_Tue_Jul_27_04:32:49_2021_modification_1.pdb.gz INFO:: NCS chain comparison 0/8 INFO:: NCS chain comparison 8/8 First atom of 170 in first selection 1/A/1 {G}/ P altLoc :: segid :: pos: (67.803,-2.641,8.312) B-factor: 76.880 First atom of 170 in second selection 1/C/1 {G}/ P altLoc :: segid :: pos: (91.772,21.389,32.470) B-factor: 76.880 INFO:: LSQ matched 8 atoms INFO:: 8 matched atoms had: mean devi: 0.137 rms devi: 0.149 max devi: 0.236 min devi: 0.068 find_ncs_matrix returns (LSQ) | 1, -0.001328, -0.001388| | 0.001328, 1, 7.875e-05| | 0.001388, -8.06e-05, 1| ( -23.9, -24.18, -24.2) INFO:: NCS chain comparison 0/8 INFO:: NCS chain comparison 0/8 INFO:: NCS chain comparison 8/8 First atom of 170 in first selection 1/B/1 {C}/ P altLoc :: segid :: pos: (69.189,-2.009,20.544) B-factor: 76.880 First atom of 170 in second selection 1/D/1 {C}/ P altLoc :: segid :: pos: (93.316,22.212,44.709) B-factor: 76.880 INFO:: LSQ matched 8 atoms INFO:: 8 matched atoms had: mean devi: 0.092 rms devi: 0.099 max devi: 0.164 min devi: 0.058 find_ncs_matrix returns (LSQ) | 1, 0.00312,-0.0003107| | -0.003121, 1, -0.005678| | 0.000293, 0.005679, 1| ( -24.2, -23.62, -24.33) INFO:: fill_ghost_info Constructed 2 ghosts Ghost 0 name: "NCS found from matching Chain C onto Chain A" Ghost 1 name: "NCS found from matching Chain D onto Chain B" ------- resulting_merge_info has size 2 -------- resulting_merge_info[0] {residue-spec-not-set} INFO:: Matching/moving molecule number 141 to 141 ERROR:: No symmetry available INFO:: LSQ matched 125 atoms INFO:: 125 matched atoms had: mean devi: 0.142 rms devi: 0.149 max devi: 0.243 min devi: 0.028 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 name coot-backup/Copy_of_Ideal-A-form-RNA_Tue_Jul_27_04:32:49_2021_modification_0.pdb.gz INFO:: coordinates transformed by orthogonal matrix: | 1, 0.003218, -0.003497| | -0.003225, 1, -0.001985| | 0.003491, 0.001997, 1| ( -24.05, -23.7, -24.44) No unit cell for this molecule, hence no fractional matrix. ------------------ add_view_raw() RNA-ghots-view INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/1wly.pdb INFO:: file /lmb/home/pemsley/data/greg-data/1wly.pdb has been read. Spacegroup: C 1 2 1 INFO:: Found 1 models Model 1 had 0 links Molecule 142 read successfully INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/1yb5.pdb INFO:: file /lmb/home/pemsley/data/greg-data/1yb5.pdb has been read. Spacegroup: P 21 21 2 INFO:: using standard CCP4 Refmac dictionary to search for "CL" There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/c/CL.cif INFO:: using standard CCP4 Refmac dictionary to search for "NAP" There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/n/NAP.cif INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 324/324 INFO:: NCS chain comparison 0/324 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 143 read successfully INFO:: reference 142 has 750 atoms selected INFO:: moving 143 has 842 atoms selected superposing... number of Ca atoms in selections: 110 (moving) and 100 (reference) Another Go... Moving Reference Distance(/A) A 6 A 7 A 8 <---> A 2 : 0.7510 A 9 <---> A 3 : 0.9422 A 10 <---> A 4 : 0.6300 A 11 <---> A 5 : 0.7119 A 12 <---> A 6 : 0.6310 A 13 <---> A 7 : 0.4675 A 14 <---> A 8 : 0.4264 A 15 <---> A 9 : 0.9792 A 16 <---> A 10 : 0.7549 A 17 <---> A 11 : 0.4884 A 18 <---> A 12 : 0.7451 A 19 <---> A 13 : 0.4606 A 20 <---> A 14 : 1.2809 A 21 <---> A 15 : 1.2412 A 22 <---> A 16 : 1.0733 A 23 <---> A 17 : 0.9730 A 24 <---> A 18 : 0.4705 A 25 <---> A 19 : 0.3560 A 26 <---> A 20 : 3.1145 A 27 A 28 <---> A 21 : 1.5754 A 29 <---> A 22 : 1.6322 A 30 A 31 <---> A 23 : 1.9973 A 32 <---> A 25 : 1.8324 A 33 <---> A 26 : 0.9310 A 34 <---> A 27 : 0.6808 A 35 <---> A 28 : 0.2674 A 36 <---> A 29 : 0.5995 A 37 <---> A 30 : 0.6992 A 38 <---> A 31 : 0.8620 A 39 <---> A 32 : 0.8421 A 40 <---> A 33 : 0.7208 A 41 <---> A 34 : 0.8681 A 42 <---> A 35 : 0.7781 A 43 <---> A 36 : 0.6211 A 44 <---> A 37 : 0.4657 A 45 <---> A 38 : 0.7475 A 46 <---> A 39 : 0.5170 A 47 <---> A 40 : 0.5058 A 48 <---> A 41 : 0.8897 A 49 <---> A 42 : 0.5835 A 50 <---> A 43 : 0.4347 A 51 <---> A 44 : 0.6192 A 52 <---> A 45 : 0.2150 A 53 <---> A 46 : 0.7474 A 54 <---> A 47 : 1.0213 A 55 <---> A 48 : 0.9208 A 56 <---> A 49 : 0.9392 A 57 A 58 A 59 A 60 A 61 A 62 A 63 A 64 A 65 <---> A 60 : 0.4666 A 66 <---> A 61 : 0.0523 A 67 <---> A 62 : 1.0719 A 68 <---> A 63 : 0.7933 A 69 <---> A 64 : 0.8916 A 70 <---> A 65 : 1.2580 A 71 <---> A 66 : 0.6932 A 72 <---> A 67 : 1.0345 A 73 <---> A 68 : 1.4417 A 74 <---> A 69 : 0.9092 A 75 <---> A 70 : 1.6166 A 76 <---> A 71 : 0.8741 A 77 <---> A 72 : 0.2388 A 78 <---> A 73 : 0.3118 A 79 <---> A 74 : 0.3887 A 80 <---> A 75 : 0.7613 A 81 <---> A 76 : 0.9044 A 82 <---> A 77 : 0.6090 A 83 <---> A 78 : 1.7978 A 84 <---> A 79 : 1.9256 A 85 <---> A 80 : 1.3416 A 86 <---> A 81 : 0.5658 A 87 <---> A 82 : 0.4480 A 88 <---> A 83 : 0.9078 A 89 <---> A 84 : 0.3625 A 90 <---> A 85 : 0.4040 A 91 <---> A 86 : 0.4586 A 92 <---> A 87 : 0.4340 A 93 <---> A 88 : 0.3664 A 94 <---> A 89 : 0.4921 A 95 <---> A 90 : 0.6498 A 96 <---> A 91 : 1.5805 A 97 <---> A 92 : 2.8839 A 98 A 99 A 100 Moving: KLMRAVRVFEFGGPEVLKLRSDIAVPIPKDHQVLIKVHACGVNPVETYIRSGTYSRKPLLPYTPGSDVAG Target: --VMAAVIHKKGGPDNFVWEE-VK-VSPGPGQVRLRNTAIGVNFLDTYHRA--------PPIVVGFEAAA Moving: VIEAVGDNASAFKKGDRVFTSSTISGGYAEYALAADHTVY Target: VVEEVGPGVTDFTVGERVCTCL---GAYSQERLYPAEKLI INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_1yb5.pdb_Tue_Jul_27_04:32:50_2021_modification_0.pdb.gz INFO:: coordinates transformed by orthogonal matrix: | -0.9117, -0.3803, 0.1557| | -0.3625, 0.9227, 0.131| | -0.1935, 0.06299, -0.9791| ( 70.65, 7.793, 21.29) Rotation - polar (omega,phi,kappa) 87.1413 101.0220 169.7385 Rotation - euler (alpha,beta,gamma) 40.0716 168.2570 18.0277 Translation - Angstroms 70.6538 7.7930 21.2852 INFO: core rmsd achieved: 1.0199 Angstroems number of residues in reference structure: 322 number of residues in moving structure: 324 number of residues in aligned sections (reference): 100 number of residues in aligned sections (moving): 110 number of aligned residues: 95 number of gaps: 4 number of misdirections: 0 number of SSE combinations: 4.0000 sequence identity: 30.5263% ------------------ add_view_raw() SSM View WARNING:: Error reading /lmb/home/pemsley/data/greg-data/1pyd.pdb INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/2qd9.pdb INFO:: file /lmb/home/pemsley/data/greg-data/2qd9.pdb has been read. Spacegroup: P 21 21 21 INFO:: using standard CCP4 Refmac dictionary to search for "LGF" There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/l/LGF.cif INFO:: Found 1 models Model 1 had 0 links Molecule 144 read successfully INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/2gtn.pdb INFO:: file /lmb/home/pemsley/data/greg-data/2gtn.pdb has been read. Spacegroup: P 21 21 21 INFO:: using standard CCP4 Refmac dictionary to search for "LIE" There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/l/LIE.cif INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 0/337 Molecule 145 read successfully INFO:: reference 144 has 169 atoms selected INFO:: moving 145 has 169 atoms selected superposing... number of Ca atoms in selections: 21 (moving) and 21 (reference) Another Go... Moving Reference Distance(/A) A 140 <---> A 140 : 0.1804 A 141 <---> A 141 : 0.0760 A 142 <---> A 142 : 0.1052 A 143 <---> A 143 : 0.1246 A 144 <---> A 144 : 0.1370 A 145 <---> A 145 : 0.1380 A 146 <---> A 146 : 0.1662 A 147 <---> A 147 : 0.2744 A 148 <---> A 148 : 0.2728 A 149 <---> A 149 : 0.1173 A 150 <---> A 150 : 0.1684 A 151 <---> A 151 : 0.0928 A 152 <---> A 152 : 0.1200 A 153 <---> A 153 : 0.1281 A 154 <---> A 154 : 0.2539 A 155 <---> A 155 : 0.6351 A 156 <---> A 156 : 0.1300 A 157 <---> A 157 : 0.1478 A 158 <---> A 158 : 0.2238 A 159 <---> A 159 : 0.2271 A 160 <---> A 160 : 0.2372 Moving: YIHSADIIHRDLKPSNLAVNE Target: YIHSADIIHRDLKPSNLAVNE INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_2gtn.pdb_Tue_Jul_27_04:32:51_2021_modification_0.pdb.gz INFO:: coordinates transformed by orthogonal matrix: | 0.9998, 0.009845, -0.01938| | -0.009814, 1, 0.001689| | 0.0194, -0.001498, 0.9998| ( 0.3207, 0.6598, 0.8819) Rotation - polar (omega,phi,kappa) 116.8035 -94.6984 1.2491 Rotation - euler (alpha,beta,gamma) 175.0200 1.1149 -175.5832 Translation - Angstroms 0.3207 0.6598 0.8819 INFO: core rmsd achieved: 0.2210 Angstroems number of residues in reference structure: 330 number of residues in moving structure: 337 number of residues in aligned sections (reference): 21 number of residues in aligned sections (moving): 21 number of aligned residues: 21 number of gaps: 0 number of misdirections: 0 number of SSE combinations: 1.0000 sequence identity: 100.0000% LATT LINE: LATT -2 SFAC LINE: SFAC C H N O S INFO:: CELL set to 77.7260 77.7260 77.7260 90.0000 90.0000 90.0000 READ-INS:: Spacegroup: "I 21 3" INFO:: read_file() chain with chain id has 121 residues Symmetry available for this molecule Molecule 146 read successfully INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz INFO:: Number of observed reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.5000 INFO:: grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.0280 seconds to read MTZ file INFO:: 0.0000 seconds to initialize map INFO:: 0.0190 seconds for FFT Pre-filter Map statistics: mean: 0.0000 st.d: 0.3115 Pre-filter Map statistics: min: -0.8750 max: 2.9776 INFO:: 0.0010 seconds for statistics Map extents: ..... 108 132 64 Map mean: ........ 0.0000 Map sigma: ....... 0.3115 Map maximum: ..... 2.9776 Map minimum: ..... -0.8750 INFO:: 0.0180 seconds for contour map INFO:: 0.0660 seconds in total INFO:: NCS chain comparison 93/93 First atom of 720 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.8780,12.9550,8.7610) B-factor: 30.1700 First atom of 745 in second selection 1/B/1 {ASP}/ N altLoc :: segid :: pos: (13.8760,16.1670,23.0330) B-factor: 20.0300 INFO:: LSQ matched 93 atoms INFO:: 93 matched atoms had: mean devi: 1.1788 rms devi: 4.8592 max devi: 46.2590 min devi: 0.1254 find_ncs_matrix returns (LSQ) | 0.9637, -0.07462, -0.2563| | 0.2651, 0.3804, 0.886| | 0.0314, -0.9218, 0.3864| ( 38.09, -17.87, 14.32) INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" INFO:: installing ghost map with name :Map 3 NCS found from matching Chain B onto Chain A Pre-filter Map statistics: mean: 0.0000 st.d: 0.3115 Pre-filter Map statistics: min: -0.9034 max: 2.9681 Done install_ghost_map Reference matcher: 0 and 0 | 0.9637, -0.07462, -0.2563| | 0.2651, 0.3804, 0.886| | 0.0314, -0.9218, 0.3864| ( 38.09, -17.87, 14.32) inverse of reference matcher transformation: | 0.9637, 0.2651, 0.0314| | -0.07462, 0.3804, -0.9218| | -0.2563, 0.886, 0.3864| ( -32.42, 22.84, 20.06) boxing over uvw = ( -0.04469, -0.1739, -0.2816) to uvw = ( 1.228, 0.3332, 0.7985) INFO:: There were 2.0000 maps contributing to the average INFO:: rescaling by 0.5000 INFO:: 422400 out of 422400 (100.0000%) map points were masked out of NCS average target volume, chain A INFO:: made 1 averaged map(s) -1.4148 2 -1.3189 5 -1.2231 7 -1.1273 10 -1.0314 11 -0.9356 51 -0.8398 188 -0.7439 668 -0.6481 2188 -0.5523 6354 -0.4564 16289 -0.3606 32837 -0.2647 50991 -0.1689 60282 -0.0731 58847 0.0228 49343 0.1186 37766 0.2144 28486 0.3103 21907 0.4061 16329 0.5019 11846 0.5978 8631 0.6936 6238 0.7894 4429 0.8853 3065 0.9811 2054 1.0770 1348 1.1728 869 1.2686 563 1.3645 323 1.4603 222 1.5561 109 1.6520 59 1.7478 31 1.8436 21 1.9395 12 2.0353 8 2.1312 6 2.2270 3 2.3228 1 2.4187 1 Pre-filter Map statistics: mean: 0.0005 st.d: 0.3255 Pre-filter Map statistics: min: -1.4627 max: 2.3707 INFO:: installing ghost map with name :Map 147 NCS found from matching Chain B onto Chain A Pre-filter Map statistics: mean: 0.0000 st.d: 0.3115 Pre-filter Map statistics: min: -0.8750 max: 2.9776 Done install_ghost_map Reference matcher: 0 and 0 | 0.9637, -0.07462, -0.2563| | 0.2651, 0.3804, 0.886| | 0.0314, -0.9218, 0.3864| ( 38.09, -17.87, 14.32) inverse of reference matcher transformation: | 0.9637, 0.2651, 0.0314| | -0.07462, 0.3804, -0.9218| | -0.2563, 0.886, 0.3864| ( -32.42, 22.84, 20.06) boxing over uvw = ( -0.04469, -0.1739, -0.2816) to uvw = ( 1.228, 0.3332, 0.7985) INFO:: There were 2.0000 maps contributing to the average INFO:: rescaling by 0.5000 INFO:: 228096 out of 228096 (100.0000%) map points were masked out of NCS average target volume, chain A INFO:: made 1 averaged map(s) -1.4022 3 -1.3074 1 -1.2127 4 -1.1179 8 -1.0231 5 -0.9283 32 -0.8336 104 -0.7388 349 -0.6440 1163 -0.5493 3433 -0.4545 8783 -0.3597 17620 -0.2650 27133 -0.1702 32345 -0.0754 31462 0.0193 26827 0.1141 20587 0.2089 15419 0.3036 11965 0.3984 8787 0.4932 6637 0.5879 4777 0.6827 3343 0.7775 2426 0.8722 1733 0.9670 1142 1.0618 796 1.1565 469 1.2513 296 1.3461 188 1.4409 96 1.5356 80 1.6304 34 1.7252 20 1.8199 14 1.9147 6 2.0095 4 2.1042 3 2.1990 0 2.2938 2 2.3885 0 Pre-filter Map statistics: mean: 0.0004 st.d: 0.3236 Pre-filter Map statistics: min: -1.4496 max: 2.3411 no diffs NCS target chain has 93 peers. INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb INFO:: file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 152 read successfully INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:32:52_2021_modification_0.pdb.gz INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:32:52_2021_modification_1.pdb.gz INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:32:52_2021_modification_2.pdb.gz INFO:: NCS chain comparison 90/93 First atom of 720 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.8780,12.9550,8.7610) B-factor: 30.1700 First atom of 724 in second selection 1/B/4 {GLY}/ N altLoc :: segid :: pos: (18.1830,22.2640,18.9300) B-factor: 21.7100 INFO:: LSQ matched 90 atoms INFO:: 90 matched atoms had: mean devi: 0.3643 rms devi: 0.4571 max devi: 2.1351 min devi: 0.0881 find_ncs_matrix returns (LSQ) | 0.9705, -0.04634, -0.2366| | 0.2357, 0.3884, 0.8908| | 0.05061, -0.9203, 0.3878| ( 37.8, -17.18, 13.82) INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" DEBUG ncs_control_change_ncs_master_to_chain_update_widget imol: 152 and ichain: 0 DEBUG:: ncs_control_change_ncs_master_to_chain imol: 152 and ichain: 0 %%%%%% add_ncs_ghosts_using_ncs_master %%%%%% imaster: 0 Checking chains for NCS matching to chain A INFO:: NCS chain comparison 90/93 First atom of 720 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.8780,12.9550,8.7610) B-factor: 30.1700 First atom of 724 in second selection 1/B/4 {GLY}/ N altLoc :: segid :: pos: (18.1830,22.2640,18.9300) B-factor: 21.7100 INFO:: LSQ matched 90 atoms INFO:: 90 matched atoms had: mean devi: 0.3643 rms devi: 0.4571 max devi: 2.1351 min devi: 0.0881 find_ncs_matrix returns (LSQ) | 0.9705, -0.04634, -0.2366| | 0.2357, 0.3884, 0.8908| | 0.05061, -0.9203, 0.3878| ( 37.8, -17.18, 13.82) Adding ghost with name: NCS found from matching Chain B onto Chain A INFO:: set_ncs_master_chain Constructed 1 ghosts Ghost info:: NCS found from matching Chain B onto Chain A INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:32:52_2021_modification_3.pdb.gz INFO:: mutate 2 A to a TRP INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:32:52_2021_modification_4.pdb.gz DEBUG ncs_control_change_ncs_master_to_chain_update_widget imol: 152 and ichain: 0 DEBUG:: ncs_control_change_ncs_master_to_chain imol: 152 and ichain: 0 %%%%%% add_ncs_ghosts_using_ncs_master %%%%%% imaster: 0 Checking chains for NCS matching to chain A INFO:: NCS chain comparison 92/93 First atom of 727 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.8780,12.9550,8.7610) B-factor: 30.1700 First atom of 745 in second selection 1/B/1 {ASP}/ N altLoc :: segid :: pos: (13.7154,16.0316,23.2057) B-factor: 30.1700 INFO:: LSQ matched 93 atoms INFO:: 93 matched atoms had: mean devi: 0.3427 rms devi: 0.4454 max devi: 2.1352 min devi: 0.0124 find_ncs_matrix returns (LSQ) | 0.9705, -0.04643, -0.2365| | 0.2356, 0.3891, 0.8906| | 0.05068, -0.92, 0.3886| ( 37.8, -17.17, 13.81) Adding ghost with name: NCS found from matching Chain B onto Chain A INFO:: set_ncs_master_chain Constructed 1 ghosts Ghost info:: NCS found from matching Chain B onto Chain A INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Jul_27_04:32:52_2021_modification_5.pdb.gz INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/pdb1t6q.ent INFO:: file /lmb/home/pemsley/data/greg-data/pdb1t6q.ent has been read. Spacegroup: C 2 2 21 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 110/110 INFO:: NCS chain comparison 110/110 INFO:: fill_ghost_info Constructed 2 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Ghost 1 name: "NCS found from matching Chain C onto Chain A" Molecule 153 read successfully INFO:: mutate 50 A to a ASP INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_pdb1t6q.ent_Tue_Jul_27_04:32:53_2021_modification_0.pdb.gz INFO:: NCS chain comparison 109/110 First atom of 881 in first selection 1/A/7 {GLY}/ N altLoc :: segid :: pos: (31.7950,49.9730,50.8660) B-factor: 68.1800 First atom of 893 in second selection 1/B/6 {CYS}/ N altLoc :: segid :: pos: (45.3620,34.2400,30.6710) B-factor: 84.3600 INFO:: LSQ matched 110 atoms INFO:: 110 matched atoms had: mean devi: 0.2048 rms devi: 0.2651 max devi: 1.1707 min devi: 0.0160 find_ncs_matrix returns (LSQ) | 0.5407, 0.4775, 0.6926| | -0.4862, -0.4944, 0.7205| | 0.6865, -0.7263, -0.03511| ( -28.15, 65.89, 42.9) INFO:: NCS chain comparison 109/110 First atom of 881 in first selection 1/A/7 {GLY}/ N altLoc :: segid :: pos: (31.7950,49.9730,50.8660) B-factor: 68.1800 First atom of 881 in second selection 1/C/7 {GLY}/ N altLoc :: segid :: pos: (47.6640,58.9920,25.9960) B-factor: 67.7200 INFO:: LSQ matched 110 atoms INFO:: 110 matched atoms had: mean devi: 0.2275 rms devi: 0.3035 max devi: 1.6549 min devi: 0.0661 find_ncs_matrix returns (LSQ) | 0.5303, -0.4851, 0.6953| | 0.4758, -0.5085, -0.7177| | 0.7017, 0.7114, -0.03884| ( 18.19, 77.78, -25.69) INFO:: fill_ghost_info Constructed 2 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Ghost 1 name: "NCS found from matching Chain C onto Chain A" DEBUG ncs_control_change_ncs_master_to_chain_update_widget imol: 153 and ichain: 0 DEBUG:: ncs_control_change_ncs_master_to_chain imol: 153 and ichain: 0 %%%%%% add_ncs_ghosts_using_ncs_master %%%%%% imaster: 0 Checking chains for NCS matching to chain A INFO:: NCS chain comparison 109/110 First atom of 881 in first selection 1/A/7 {GLY}/ N altLoc :: segid :: pos: (31.7950,49.9730,50.8660) B-factor: 68.1800 First atom of 893 in second selection 1/B/6 {CYS}/ N altLoc :: segid :: pos: (45.3620,34.2400,30.6710) B-factor: 84.3600 INFO:: LSQ matched 110 atoms INFO:: 110 matched atoms had: mean devi: 0.2048 rms devi: 0.2651 max devi: 1.1707 min devi: 0.0160 find_ncs_matrix returns (LSQ) | 0.5407, 0.4775, 0.6926| | -0.4862, -0.4944, 0.7205| | 0.6865, -0.7263, -0.03511| ( -28.15, 65.89, 42.9) Adding ghost with name: NCS found from matching Chain B onto Chain A INFO:: NCS chain comparison 109/110 First atom of 881 in first selection 1/A/7 {GLY}/ N altLoc :: segid :: pos: (31.7950,49.9730,50.8660) B-factor: 68.1800 First atom of 881 in second selection 1/C/7 {GLY}/ N altLoc :: segid :: pos: (47.6640,58.9920,25.9960) B-factor: 67.7200 INFO:: LSQ matched 110 atoms INFO:: 110 matched atoms had: mean devi: 0.2275 rms devi: 0.3035 max devi: 1.6549 min devi: 0.0661 find_ncs_matrix returns (LSQ) | 0.5303, -0.4851, 0.6953| | 0.4758, -0.5085, -0.7177| | 0.7017, 0.7114, -0.03884| ( 18.19, 77.78, -25.69) Adding ghost with name: NCS found from matching Chain C onto Chain A INFO:: set_ncs_master_chain Constructed 2 ghosts Ghost info:: NCS found from matching Chain B onto Chain A Ghost info:: NCS found from matching Chain C onto Chain A INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_pdb1t6q.ent_Tue_Jul_27_04:32:53_2021_modification_1.pdb.gz INFO:: backup file name coot-backup/_lmb_home_pemsley_data_greg-data_pdb1t6q.ent_Tue_Jul_27_04:32:53_2021_modification_2.pdb.gz INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/pdb1hvv.ent INFO:: file /lmb/home/pemsley/data/greg-data/pdb1hvv.ent has been read. Spacegroup: P 31 2 1 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 62/67 INFO:: NCS chain comparison 66/67 INFO:: NCS chain comparison 61/67 INFO:: NCS chain comparison 0/67 INFO:: fill_ghost_info Constructed 3 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Ghost 1 name: "NCS found from matching Chain C onto Chain A" Ghost 2 name: "NCS found from matching Chain D onto Chain A" Molecule 154 read successfully DEBUG ncs_control_change_ncs_master_to_chain_id imol: 154 and chain_id: B %%%%%% add_ncs_ghosts_using_ncs_master %%%%%% imaster: 1 Checking chains for NCS matching to chain B INFO:: NCS chain comparison 62/62 First atom of 506 in first selection 1/B/193 {SER}/ N altLoc :: segid :: pos: (0.5700,-74.7200,-82.8480) B-factor: 88.5200 First atom of 540 in second selection 1/A/190 {GLN}/ N altLoc :: segid :: pos: (-13.5350,-64.4380,-56.9280) B-factor: 45.2600 INFO:: LSQ matched 62 atoms INFO:: 62 matched atoms had: mean devi: 2.4989 rms devi: 2.7962 max devi: 6.6860 min devi: 0.4401 find_ncs_matrix returns (LSQ) | 0.7026, 0.1278, 0.7| | 0.6024, 0.4169, -0.6807| | -0.3788, 0.8999, 0.2159| ( 62.25, -87.53, -9.128) Adding ghost with name: NCS found from matching Chain A onto Chain B INFO:: NCS chain comparison 62/62 First atom of 506 in first selection 1/B/193 {SER}/ N altLoc :: segid :: pos: (0.5700,-74.7200,-82.8480) B-factor: 88.5200 First atom of 535 in second selection 1/C/190 {GLN}/ N altLoc :: segid :: pos: (63.7260,-15.7090,-72.8850) B-factor: 50.7600 INFO:: LSQ matched 62 atoms INFO:: 62 matched atoms had: mean devi: 2.6728 rms devi: 2.9369 max devi: 6.1200 min devi: 0.2483 find_ncs_matrix returns (LSQ) | -0.3504, -0.8022, -0.4834| | -0.7587, -0.05952, 0.6488| | -0.5492, 0.594, -0.5878| ( -29.05, 14.61, -72.53) Adding ghost with name: NCS found from matching Chain C onto Chain B INFO:: NCS chain comparison 61/62 First atom of 506 in first selection 1/B/193 {SER}/ N altLoc :: segid :: pos: (0.5700,-74.7200,-82.8480) B-factor: 88.5200 First atom of 497 in second selection 1/D/193 {SER}/ N altLoc :: segid :: pos: (62.9170,-35.9890,-55.9290) B-factor: 78.3500 INFO:: LSQ matched 61 atoms INFO:: 61 matched atoms had: mean devi: 1.7317 rms devi: 1.9769 max devi: 7.9453 min devi: 0.5297 find_ncs_matrix returns (LSQ) | -0.3815, -0.9208, -0.08098| | -0.9191, 0.3685, 0.1396| | -0.09874, 0.1277, -0.9869| ( -11.18, 4.757, -127.2) Adding ghost with name: NCS found from matching Chain D onto Chain B INFO:: NCS chain comparison 0/62 INFO:: set_ncs_master_chain Constructed 3 ghosts Ghost info:: NCS found from matching Chain A onto Chain B Ghost info:: NCS found from matching Chain C onto Chain B Ghost info:: NCS found from matching Chain D onto Chain B INFO:: Matching/moving molecule number 155 to 154 INFO:: LSQ matched 44 atoms INFO:: 44 matched atoms had: mean devi: 0.2239 rms devi: 0.2350 max devi: 0.3369 min devi: 0.0588 INFO:: Axis orientation: ( 0.7368, 0.6481, 0.1925) INFO:: Rotation in CCP4 Polar Angles: Polar = (78.9031,41.336,116.426) INFO:: backup file name coot-backup/Copy_of__lmb_home_pemsley_data_greg-data_pdb1hvv.ent_Tue_Jul_27_04:32:54_2021_modification_0.pdb.gz INFO:: coordinates transformed by orthogonal matrix: | 0.3395, 0.5177, 0.7853| | 0.8624, 0.162, -0.4796| | -0.3755, 0.8401, -0.3915| ( 90.55, -91.12, -47.52) INFO:: fractional coordinates matrix: | 0.8374, 0.1106, 0.6656| | 0.9958, -0.3359, -0.7249| | -0.2868, 0.6992, -0.3915| ( 0.4296, -1.191, -0.411) INFO:: Matching/moving molecule number 156 to 154 INFO:: LSQ matched 44 atoms INFO:: 44 matched atoms had: mean devi: 0.1943 rms devi: 0.2112 max devi: 0.3583 min devi: 0.0329 INFO:: Axis orientation: ( -0.431, 0.3986, 0.8095) INFO:: Rotation in CCP4 Polar Angles: Polar = (144.051,-42.7613,171.905) INFO:: backup file name coot-backup/Copy_of__lmb_home_pemsley_data_greg-data_pdb1hvv.ent_Tue_Jul_27_04:32:54_2021_modification_0.pdb.gz INFO:: coordinates transformed by orthogonal matrix: | -0.6203, -0.2279, -0.7505| | -0.4559, -0.6739, 0.5814| | -0.6382, 0.7028, 0.3141| ( -22.14, -19.93, 1.626) INFO:: fractional coordinates matrix: | -0.8835, -0.09252, -0.543| | -0.5264, -0.4107, 0.8789| | -0.4875, 0.7087, 0.3141| ( -0.381, -0.2605, 0.01406) INFO:: Matching/moving molecule number 157 to 154 INFO:: LSQ matched 44 atoms INFO:: 44 matched atoms had: mean devi: 0.4174 rms devi: 0.4531 max devi: 0.7926 min devi: 0.0759 INFO:: Axis orientation: ( 0.6231, -0.7786, -0.07411) INFO:: Rotation in CCP4 Polar Angles: Polar = (85.7498,128.67,177.232) INFO:: backup file name coot-backup/Copy_of__lmb_home_pemsley_data_greg-data_pdb1hvv.ent_Tue_Jul_27_04:32:54_2021_modification_0.pdb.gz INFO:: coordinates transformed by orthogonal matrix: | -0.2227, -0.9733, -0.05471| | -0.9662, 0.2129, 0.1454| | -0.1299, 0.08525, -0.9879| ( -15.82, -0.3228, -130) INFO:: fractional coordinates matrix: | -0.7806, -0.3462, 0.03831| | -1.116, 0.7707, 0.2198| | -0.09924, 0.106, -0.9879| ( -0.1813, -0.00422, -1.125) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/pdb1hvv.ent INFO:: file /lmb/home/pemsley/data/greg-data/pdb1hvv.ent has been read. Spacegroup: P 31 2 1 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 62/67 INFO:: NCS chain comparison 66/67 INFO:: NCS chain comparison 61/67 INFO:: NCS chain comparison 0/67 INFO:: fill_ghost_info Constructed 3 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Ghost 1 name: "NCS found from matching Chain C onto Chain A" Ghost 2 name: "NCS found from matching Chain D onto Chain A" Molecule 158 read successfully INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/1hvv_sigmaa.mtz INFO:: Number of observed reflections: 20903 INFO:: finding ASU unique map points with sampling rate 1.5000 INFO:: grid sampling...Nuvw = ( 112, 112, 150) INFO:: 0.0320 seconds to read MTZ file INFO:: 0.0160 seconds to initialize map INFO:: 0.0280 seconds for FFT Pre-filter Map statistics: mean: -0.0000 st.d: 0.2241 Pre-filter Map statistics: min: -0.8818 max: 1.7219 INFO:: 0.0020 seconds for statistics Map extents: ..... 112 112 150 Map mean: ........ -0.0000 Map sigma: ....... 0.2241 Map maximum: ..... 1.7219 Map minimum: ..... -0.8818 INFO:: 0.0080 seconds for contour map INFO:: 0.0860 seconds in total INFO:: NCS chain comparison 62/67 First atom of 540 in first selection 1/A/190 {GLN}/ N altLoc :: segid :: pos: (-13.5350,-64.4380,-56.9280) B-factor: 45.2600 First atom of 506 in second selection 1/B/193 {SER}/ N altLoc :: segid :: pos: (0.5700,-74.7200,-82.8480) B-factor: 88.5200 INFO:: LSQ matched 62 atoms INFO:: 62 matched atoms had: mean devi: 2.4989 rms devi: 2.7962 max devi: 6.6860 min devi: 0.4401 find_ncs_matrix returns (LSQ) | 0.7026, 0.6024, -0.3788| | 0.1278, 0.4169, 0.8999| | 0.7, -0.6807, 0.2159| ( 5.528, 36.75, -101.2) INFO:: NCS chain comparison 66/67 First atom of 540 in first selection 1/A/190 {GLN}/ N altLoc :: segid :: pos: (-13.5350,-64.4380,-56.9280) B-factor: 45.2600 First atom of 535 in second selection 1/C/190 {GLN}/ N altLoc :: segid :: pos: (63.7260,-15.7090,-72.8850) B-factor: 50.7600 INFO:: LSQ matched 66 atoms INFO:: 66 matched atoms had: mean devi: 1.9713 rms devi: 2.1729 max devi: 4.5411 min devi: 0.4295 find_ncs_matrix returns (LSQ) | -0.4445, -0.8903, -0.09887| | -0.893, 0.4317, 0.1271| | -0.07049, 0.1448, -0.9869| ( -8.624, 7.402, -127.7) INFO:: NCS chain comparison 61/67 First atom of 540 in first selection 1/A/190 {GLN}/ N altLoc :: segid :: pos: (-13.5350,-64.4380,-56.9280) B-factor: 45.2600 First atom of 497 in second selection 1/D/193 {SER}/ N altLoc :: segid :: pos: (62.9170,-35.9890,-55.9290) B-factor: 78.3500 INFO:: LSQ matched 61 atoms INFO:: 61 matched atoms had: mean devi: 3.7042 rms devi: 4.0859 max devi: 9.4383 min devi: 0.2858 find_ncs_matrix returns (LSQ) | -0.7198, -0.6079, 0.3353| | -0.5986, 0.2989, -0.7432| | 0.3516, -0.7356, -0.579| ( 36.14, -61.4, -149.3) INFO:: NCS chain comparison 0/67 INFO:: fill_ghost_info Constructed 3 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Ghost 1 name: "NCS found from matching Chain C onto Chain A" Ghost 2 name: "NCS found from matching Chain D onto Chain A" INFO:: installing ghost map with name :Map 159 NCS found from matching Chain B onto Chain A Pre-filter Map statistics: mean: -0.0000 st.d: 0.2241 Pre-filter Map statistics: min: -0.8818 max: 1.7219 Done install_ghost_map INFO:: installing ghost map with name :Map 159 NCS found from matching Chain C onto Chain A Pre-filter Map statistics: mean: -0.0000 st.d: 0.2241 Pre-filter Map statistics: min: -0.8818 max: 1.7219 Done install_ghost_map INFO:: installing ghost map with name :Map 159 NCS found from matching Chain D onto Chain A Pre-filter Map statistics: mean: -0.0000 st.d: 0.2241 Pre-filter Map statistics: min: -0.8818 max: 1.7219 Done install_ghost_map Reference matcher: 0 and 0 | 0.7026, 0.6024, -0.3788| | 0.1278, 0.4169, 0.8999| | 0.7, -0.6807, 0.2159| ( 5.528, 36.75, -101.2) inverse of reference matcher transformation: | 0.7026, 0.1278, 0.7| | 0.6024, 0.4169, -0.6807| | -0.3788, 0.8999, 0.2159| ( 62.25, -87.53, -9.128) boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) Reference matcher: 0 and 1 | -0.4445, -0.8903, -0.09887| | -0.893, 0.4317, 0.1271| | -0.07049, 0.1448, -0.9869| ( -8.624, 7.402, -127.7) inverse of reference matcher transformation: | -0.4445, -0.893, -0.07049| | -0.8903, 0.4317, 0.1448| | -0.09887, 0.1271, -0.9869| ( -6.223, 7.613, -127.8) boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) Reference matcher: 0 and 2 | -0.7198, -0.6079, 0.3353| | -0.5986, 0.2989, -0.7432| | 0.3516, -0.7356, -0.579| ( 36.14, -61.4, -149.3) inverse of reference matcher transformation: | -0.7198, -0.5986, 0.3516| | -0.6079, 0.2989, -0.7356| | 0.3353, -0.7432, -0.579| ( 41.75, -69.53, -144.2) boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) INFO:: There were 4.0000 maps contributing to the average INFO:: rescaling by 0.2500 INFO:: 313712 out of 313712 (100.0000%) map points were masked out of NCS average target volume, chain A INFO:: made 1 averaged map(s) -0.9667 1 -0.9046 3 -0.8424 8 -0.7803 10 -0.7182 37 -0.6561 102 -0.5940 196 -0.5319 490 -0.4698 1190 -0.4077 2390 -0.3456 4703 -0.2835 8981 -0.2214 16028 -0.1593 27796 -0.0972 44285 -0.0351 60780 0.0271 53651 0.0892 32327 0.1513 21048 0.2134 14284 0.2755 9269 0.3376 5945 0.3997 3629 0.4618 2439 0.5239 1480 0.5860 942 0.6481 569 0.7102 378 0.7723 239 0.8344 166 0.8965 112 0.9587 94 1.0208 50 1.0829 35 1.1450 21 1.2071 17 1.2692 5 1.3313 4 1.3934 5 1.4555 3 1.5176 0 Pre-filter Map statistics: mean: -0.0008 st.d: 0.1767 Pre-filter Map statistics: min: -0.9977 max: 1.4866 INFO:: installing ghost map with name :Map 159 NCS found from matching Chain B onto Chain A Pre-filter Map statistics: mean: -0.0000 st.d: 0.2241 Pre-filter Map statistics: min: -0.8818 max: 1.7219 Done install_ghost_map INFO:: installing ghost map with name :Map 159 NCS found from matching Chain C onto Chain A Pre-filter Map statistics: mean: -0.0000 st.d: 0.2241 Pre-filter Map statistics: min: -0.8818 max: 1.7219 Done install_ghost_map INFO:: installing ghost map with name :Map 159 NCS found from matching Chain D onto Chain A Pre-filter Map statistics: mean: -0.0000 st.d: 0.2241 Pre-filter Map statistics: min: -0.8818 max: 1.7219 Done install_ghost_map Reference matcher: 0 and 0 | 0.7026, 0.6024, -0.3788| | 0.1278, 0.4169, 0.8999| | 0.7, -0.6807, 0.2159| ( 5.528, 36.75, -101.2) inverse of reference matcher transformation: | 0.7026, 0.1278, 0.7| | 0.6024, 0.4169, -0.6807| | -0.3788, 0.8999, 0.2159| ( 62.25, -87.53, -9.128) boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) Reference matcher: 0 and 1 | -0.4445, -0.8903, -0.09887| | -0.893, 0.4317, 0.1271| | -0.07049, 0.1448, -0.9869| ( -8.624, 7.402, -127.7) inverse of reference matcher transformation: | -0.4445, -0.893, -0.07049| | -0.8903, 0.4317, 0.1448| | -0.09887, 0.1271, -0.9869| ( -6.223, 7.613, -127.8) boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) Reference matcher: 0 and 2 | -0.7198, -0.6079, 0.3353| | -0.5986, 0.2989, -0.7432| | 0.3516, -0.7356, -0.579| ( 36.14, -61.4, -149.3) inverse of reference matcher transformation: | -0.7198, -0.5986, 0.3516| | -0.6079, 0.2989, -0.7356| | 0.3353, -0.7432, -0.579| ( 41.75, -69.53, -144.2) boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) INFO:: There were 4.0000 maps contributing to the average INFO:: rescaling by 0.2500 INFO:: 313712 out of 313712 (100.0000%) map points were masked out of NCS average target volume, chain A INFO:: made 1 averaged map(s) -0.9667 1 -0.9046 3 -0.8424 8 -0.7803 10 -0.7182 37 -0.6561 102 -0.5940 196 -0.5319 490 -0.4698 1190 -0.4077 2390 -0.3456 4703 -0.2835 8981 -0.2214 16028 -0.1593 27796 -0.0972 44285 -0.0351 60780 0.0271 53651 0.0892 32327 0.1513 21048 0.2134 14284 0.2755 9269 0.3376 5945 0.3997 3629 0.4618 2439 0.5239 1480 0.5860 942 0.6481 569 0.7102 378 0.7723 239 0.8344 166 0.8965 112 0.9587 94 1.0208 50 1.0829 35 1.1450 21 1.2071 17 1.2692 5 1.3313 4 1.3934 5 1.4555 3 1.5176 0 Pre-filter Map statistics: mean: -0.0008 st.d: 0.1767 Pre-filter Map statistics: min: -0.9977 max: 1.4866 INFO:: installing ghost map with name :Map 159 NCS found from matching Chain B onto Chain A Pre-filter Map statistics: mean: -0.0000 st.d: 0.2241 Pre-filter Map statistics: min: -0.8818 max: 1.7219 Done install_ghost_map INFO:: installing ghost map with name :Map 159 NCS found from matching Chain C onto Chain A Pre-filter Map statistics: mean: -0.0000 st.d: 0.2241 Pre-filter Map statistics: min: -0.8818 max: 1.7219 Done install_ghost_map INFO:: installing ghost map with name :Map 159 NCS found from matching Chain D onto Chain A Pre-filter Map statistics: mean: -0.0000 st.d: 0.2241 Pre-filter Map statistics: min: -0.8818 max: 1.7219 Done install_ghost_map Reference matcher: 0 and 0 | 0.7026, 0.6024, -0.3788| | 0.1278, 0.4169, 0.8999| | 0.7, -0.6807, 0.2159| ( 5.528, 36.75, -101.2) inverse of reference matcher transformation: | 0.7026, 0.1278, 0.7| | 0.6024, 0.4169, -0.6807| | -0.3788, 0.8999, 0.2159| ( 62.25, -87.53, -9.128) boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) Reference matcher: 0 and 1 | -0.4445, -0.8903, -0.09887| | -0.893, 0.4317, 0.1271| | -0.07049, 0.1448, -0.9869| ( -8.624, 7.402, -127.7) inverse of reference matcher transformation: | -0.4445, -0.893, -0.07049| | -0.8903, 0.4317, 0.1448| | -0.09887, 0.1271, -0.9869| ( -6.223, 7.613, -127.8) boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) Reference matcher: 0 and 2 | -0.7198, -0.6079, 0.3353| | -0.5986, 0.2989, -0.7432| | 0.3516, -0.7356, -0.579| ( 36.14, -61.4, -149.3) inverse of reference matcher transformation: | -0.7198, -0.5986, 0.3516| | -0.6079, 0.2989, -0.7356| | 0.3353, -0.7432, -0.579| ( 41.75, -69.53, -144.2) boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) INFO:: There were 4.0000 maps contributing to the average INFO:: rescaling by 0.2500 INFO:: 313712 out of 313712 (100.0000%) map points were masked out of NCS average target volume, chain A INFO:: made 1 averaged map(s) -0.9667 1 -0.9046 3 -0.8424 8 -0.7803 10 -0.7182 37 -0.6561 102 -0.5940 196 -0.5319 490 -0.4698 1190 -0.4077 2390 -0.3456 4703 -0.2835 8981 -0.2214 16028 -0.1593 27796 -0.0972 44285 -0.0351 60780 0.0271 53651 0.0892 32327 0.1513 21048 0.2134 14284 0.2755 9269 0.3376 5945 0.3997 3629 0.4618 2439 0.5239 1480 0.5860 942 0.6481 569 0.7102 378 0.7723 239 0.8344 166 0.8965 112 0.9587 94 1.0208 50 1.0829 35 1.1450 21 1.2071 17 1.2692 5 1.3313 4 1.3934 5 1.4555 3 1.5176 0 Pre-filter Map statistics: mean: -0.0008 st.d: 0.1767 Pre-filter Map statistics: min: -0.9977 max: 1.4866 error (syntax error) error (syntax error) error (not syntax error) Traceback (most recent call last): File "", line 1, in NameError: name 'rr_not_found_thing' is not defined INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/monomer-ACT.pdb INFO:: file /lmb/home/pemsley/data/greg-data/monomer-ACT.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links Molecule 168 read successfully Entering test: test COO modification INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/ There are 142 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/list/mon_lib_list.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/a/ALA.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/a/ASP.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/a/ASN.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/c/CYS.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/g/GLN.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/g/GLY.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/g/GLU.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/p/PHE.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/h/HIS.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/i/ILE.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/l/LYS.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/l/LEU.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/m/MET.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/m/MSE.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/p/PRO.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/a/ARG.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/s/SER.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/t/THR.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/v/VAL.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/t/TRP.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/t/TYR.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/p/PO4.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/s/SO4.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/g/GOL.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/c/CIT.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/e/EDO.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/a/A.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/c/C.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/g/G.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/u/U.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/d/DA.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/d/DC.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/d/DG.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/d/DT.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/h/HOH.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/n/NA.cif INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/hideous-OXT.pdb INFO:: file /lmb/home/pemsley/data/greg-data/hideous-OXT.pdb has been read. Spacegroup: P 21 21 21 read 9 atom ##################################### calling init_shared_post() A 0 created 7 bond restraints created 8 angle restraints created 1 plane restraints created 1 chiral vol restraints created 0 improper dihedral restraints created 2 torsion restraints INFO:: by_linear() created 23 restraints Minimum found (iteration number 351) at 0.0060 Final Estimated RMS Z Scores: bonds: 0.0007 angles: 0.0235 improper-dihedrals: N/A torsions: 0.0153 trans-peptide: N/A planes: 0.0014 from 2 restraints parallel planes: N/A non-bonded: N/A chiral vol: 0.0022 rama plot: N/A start_pos: N/A TargetPos: N/A GemanMcCl: N/A -------- Results --------- refinement_took 0.1420 seconds pushing back atom 0 [spec: model 1 "A" 93 "" " CA " ""] xyz = ( 56.96, 4.697, -1.903) pushing back atom 1 [spec: model 1 "A" 93 "" " C " ""] xyz = ( 58.38, 4.509, -2.436) pushing back atom 2 [spec: model 1 "A" 93 "" " O " ""] xyz = ( 59.28, 5.299, -2.144) OXT out of plane distance: 0.0000 OXT->O distance: 2.1103 PASS: test COO modification Entering test: OXT in restraints? INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/ There are 142 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/list/mon_lib_list.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/a/ALA.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/a/ASP.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/a/ASN.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/c/CYS.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/g/GLN.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/g/GLY.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/g/GLU.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/p/PHE.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/h/HIS.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/i/ILE.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/l/LYS.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/l/LEU.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/m/MET.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/m/MSE.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/p/PRO.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/a/ARG.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/s/SER.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/t/THR.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/v/VAL.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/t/TRP.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/t/TYR.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/p/PO4.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/s/SO4.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/g/GOL.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/c/CIT.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/e/EDO.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/a/A.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/c/C.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/g/G.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/u/U.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/d/DA.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/d/DC.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/d/DG.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/d/DT.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/h/HOH.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/n/NA.cif There are 2 data in /lmb/home/pemsley/data/greg-data/libcheck_BCS.cif PASS: OXT in restraints? Entering test: Relative file name PASS: Relative file name Entering test: geometry distortion comparision Good gdi < exception thrown Good gdi > exception thrown PASS: geometry distortion comparision Entering test: test symm trans to origin Got length 0.1414 PASS: test symm trans to origin Entering test: test lsq plane LSQ deviations: 0.0000 0.0000 PASS: test lsq plane Entering test: remove whitespace PASS: remove whitespace Entering test: New comp_ids are sane PASS: New comp_ids are sane Entering test: Remove Trailing Slash PASS: Remove Trailing Slash Entering test: Residues for phi,psi are close enough to be considered linked 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 State file 0-coot.state.scm written. State file 0-coot.state.py written. State file 0-coot-history.py written. State file 0-coot-history.scm written. PASS: LSQ by atom Entered testcase - LSQing changes the space-group and cell to that of the reference molecule PASS: LSQing changes the space-group and cell to that of the reference molecule Entered testcase - set-residue-name sets the correct residue PASS: set-residue-name sets the correct residue Entered testcase - fit-protein-make-specs makes all specs specs: 189 ((99 "A" 1 "") (99 "A" 2 "") (99 "A" 3 "") (99 "A" 4 "") (99 "A" 5 "") (99 "A" 6 "") (99 "A" 7 "") (99 "A" 8 "") (99 "A" 9 "") (99 "A" 10 "") (99 "A" 11 "") (99 "A" 12 "") (99 "A" 13 "") (99 "A" 14 "") (99 "A" 15 "") (99 "A" 16 "") (99 "A" 17 "") (99 "A" 18 "") (99 "A" 19 "") (99 "A" 20 "") (99 "A" 21 "") (99 "A" 22 "") (99 "A" 23 "") (99 "A" 24 "") (99 "A" 25 "") (99 "A" 26 "") (99 "A" 27 "") (99 "A" 28 "") (99 "A" 29 "") (99 "A" 30 "") (99 "A" 31 "") (99 "A" 32 "") (99 "A" 33 "") (99 "A" 34 "") (99 "A" 35 "") (99 "A" 36 "") (99 "A" 37 "") (99 "A" 38 "") (99 "A" 39 "") (99 "A" 40 "") (99 "A" 41 "") (99 "A" 42 "") (99 "A" 43 "") (99 "A" 44 "") (99 "A" 45 "") (99 "A" 46 "") (99 "A" 47 "") (99 "A" 48 "") (99 "A" 49 "") (99 "A" 50 "") (99 "A" 51 "") (99 "A" 52 "") (99 "A" 53 "") (99 "A" 54 "") (99 "A" 55 "") (99 "A" 56 "") (99 "A" 57 "") (99 "A" 58 "") (99 "A" 59 "") (99 "A" 60 "") (99 "A" 61 "") (99 "A" 62 "") (99 "A" 63 "") (99 "A" 64 "") (99 "A" 65 "") (99 "A" 66 "") (99 "A" 67 "") (99 "A" 68 "") (99 "A" 69 "") (99 "A" 70 "") (99 "A" 71 "") (99 "A" 72 "") (99 "A" 73 "") (99 "A" 74 "") (99 "A" 75 "") (99 "A" 76 "") (99 "A" 77 "") (99 "A" 78 "") (99 "A" 79 "") (99 "A" 80 "") (99 "A" 81 "") (99 "A" 82 "") (99 "A" 83 "") (99 "A" 84 "") (99 "A" 85 "") (99 "A" 86 "") (99 "A" 87 "") (99 "A" 88 "") (99 "A" 89 "") (99 "A" 90 "") (99 "A" 91 "") (99 "A" 92 "") (99 "A" 93 "") (99 "B" 1 "") (99 "B" 2 "") (99 "B" 3 "") (99 "B" 4 "") (99 "B" 5 "") (99 "B" 6 "") (99 "B" 7 "") (99 "B" 8 "") (99 "B" 9 "") (99 "B" 10 "") (99 "B" 11 "") (99 "B" 12 "") (99 "B" 13 "") (99 "B" 14 "") (99 "B" 15 "") (99 "B" 16 "") (99 "B" 17 "") (99 "B" 18 "") (99 "B" 19 "") (99 "B" 20 "") (99 "B" 21 "") (99 "B" 22 "") (99 "B" 23 "") (99 "B" 24 "") (99 "B" 25 "") (99 "B" 26 "") (99 "B" 27 "") (99 "B" 28 "") (99 "B" 29 "") (99 "B" 30 "") (99 "B" 31 "") (99 "B" 32 "") (99 "B" 33 "") (99 "B" 34 "") (99 "B" 35 "") (99 "B" 36 "") (99 "B" 37 "") (99 "B" 38 "") (99 "B" 39 "") (99 "B" 40 "") (99 "B" 41 "") (99 "B" 42 "") (99 "B" 43 "") (99 "B" 44 "") (99 "B" 45 "") (99 "B" 46 "") (99 "B" 47 "") (99 "B" 48 "") (99 "B" 49 "") (99 "B" 50 "") (99 "B" 51 "") (99 "B" 52 "") (99 "B" 53 "") (99 "B" 54 "") (99 "B" 55 "") (99 "B" 56 "") (99 "B" 57 "") (99 "B" 58 "") (99 "B" 59 "") (99 "B" 60 "") (99 "B" 61 "") (99 "B" 62 "") (99 "B" 63 "") (99 "B" 64 "") (99 "B" 65 "") (99 "B" 66 "") (99 "B" 67 "") (99 "B" 68 "") (99 "B" 69 "") (99 "B" 70 "") (99 "B" 71 "") (99 "B" 72 "") (99 "B" 73 "") (99 "B" 74 "") (99 "B" 75 "") (99 "B" 76 "") (99 "B" 77 "") (99 "B" 78 "") (99 "B" 79 "") (99 "B" 80 "") (99 "B" 81 "") (99 "B" 82 "") (99 "B" 83 "") (99 "B" 84 "") (99 "B" 85 "") (99 "B" 86 "") (99 "B" 87 "") (99 "B" 88 "") (99 "B" 89 "") (99 "B" 90 "") (99 "B" 91 "") (99 "B" 92 "") (99 "B" 93 "") (99 "B" 94 "") (99 "B" 95 "") (99 "B" 96 "")) PASS: fit-protein-make-specs makes all specs Entered testcase - Phosphate distance in pucker analysis is sane PASS: Phosphate distance in pucker analysis is sane Entered testcase - Fix for Oliver Clarke fit by atom selection bug bl: 0.0363726829001203 PASS: Fix for Oliver Clarke fit by atom selection bug Ended 01-pdb+mtz.scm Running 02-shelx.scm ... Entered testcase - Read small molecule .res file PASS: Read small molecule .res file Entered testcase - Read hollander small molecule .res file PASS: Read hollander small molecule .res file Entered testcase - read shelx insulin with fcf PASS: read shelx insulin with fcf Entered testcase - Write an INS from PDB test PASS: Write an INS from PDB test Entered 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 PASS: Get monomer test Entered testcase - Delete all-molecule Hydrogens here 1 PASS: Delete all-molecule Hydrogens Entered testcase - Non-Autoloads PASS: Non-Autoloads Entered testcase - Merge molecules of a ligand with a spec PASS: Merge molecules of a ligand with a spec Entered testcase - Move and Refine Ligand test PASS: Move and Refine Ligand test Entered testcase - Many Molecules - Ligand Fitting Fitting NPO gave these results: # PASS: Many Molecules - Ligand Fitting Entered testcase - flip residue (around eigen vectors) distance: 4.79714893189444 distance d2: 2.66560074985002e-7 PASS: flip residue (around eigen vectors) Entered testcase - Reading new dictionary restraints replaces PASS: Reading new dictionary restraints replaces 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 137 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 "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 2 "/lmb/home/pemsley/data/greg-data/ins-code-fragment-pre.pdb" 3 "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 4 "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 5 "/lmb/home/pemsley/data/greg-data/3hfl_sigmaa.mtz 2FOFCWT PH2FOFCWT" 6 "test-3hfl.map" 7 "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 8 "mainchain-forward" 9 "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 10 "mainchain-forwards" 11 "/lmb/home/pemsley/data/greg-data/tutorial-add-terminal-1-test.pdb" 12 "atom selection from tutorial-add-terminal-1-test.pdb" 13 "/lmb/home/pemsley/data/greg-data/frag-2wot.pdb" 14 "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 15 "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 16 "sphere selection from tutorial-modern.pdb" 18 "/lmb/home/pemsley/data/greg-data/rotamer-test-fragment.pdb" 19 "/lmb/home/pemsley/data/greg-data/eleanor-HIS.pdb" 20 "/lmb/home/pemsley/data/greg-data/res098.pdb" 21 "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 22 "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 23 "/lmb/home/pemsley/data/greg-data/pdb3knw.ent" 24 "/lmb/home/pemsley/data/greg-data/pdb1py3.ent" 27 "/lmb/home/pemsley/data/greg-data/alt-conf-pepflip-test.pdb" 28 "/lmb/home/pemsley/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb" 31 "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 32 "atom selection from tutorial-modern.pdb" 33 "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 34 "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 35 "/lmb/home/pemsley/data/greg-data/tutorial-add-terminal-1-test.pdb" 36 "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 37 "/lmb/home/pemsley/data/greg-data/alt-conf-waters.pdb" 38 "/lmb/home/pemsley/data/greg-data/backrub-fragment.pdb" 39 "Copy_of_/lmb/home/pemsley/data/greg-data/backrub-fragment.pdb" 40 "/lmb/home/pemsley/data/greg-data/coords-B3A.pdb" 41 "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz /RNASE3GMP/COMPLEX/FWT /RNASE3GMP/COMPLEX/PHWT" 42 "/lmb/home/pemsley/data/greg-data/test-TER-OXT.pdb" 43 "/lmb/home/pemsley/data/greg-data/val.pdb" 44 "/lmb/home/pemsley/data/greg-data/2yie-frag.pdb" 45 "/lmb/home/pemsley/data/greg-data/4f8g.pdb" 46 "/lmb/home/pemsley/data/greg-data/4f8g.pdb" 47 "/lmb/home/pemsley/data/greg-data/monomer-VAL.pdb" 48 "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 49 "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 50 "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 51 "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT Masked Map" 52 "difference-map" 55 "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 56 "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 57 "averaged-map" 58 "difference-map" 59 "/lmb/home/pemsley/data/greg-data/pdb2qc1-sans-cho.pdb" 60 "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 61 "atom selection from tutorial-modern.pdb" 62 "/lmb/home/pemsley/data/greg-data/monomer-ACT.pdb" 63 "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 64 "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 65 "Copy_of_/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 66 "atom selection from tutorial-modern.pdb" 67 "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 68 "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 69 "/lmb/home/pemsley/data/greg-data/rnase-A-needs-an-insertion.pdb" 70 "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 71 "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 72 "/lmb/home/pemsley/data/greg-data/pdb3hfl.ent" 73 "/lmb/home/pemsley/data/greg-data/3hfl_sigmaa.mtz 2FOFCWT PH2FOFCWT" 74 "Ideal-A-form-RNA" 75 "Ideal-A-form-RNA" 76 "Ideal-A-form-DNA" 77 "Ideal-A-form-DNA" 78 "Copy_of_/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 79 "/lmb/home/pemsley/data/greg-data/some-waters-with-ter.pdb" 80 "/lmb/home/pemsley/data/greg-data/tm+some-waters.pdb" 81 "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 82 "/lmb/home/pemsley/data/greg-data/water-test-no-cell.pdb" 83 "/lmb/home/pemsley/data/greg-data/pathological-water-test.pdb" 84 "Copy_of_/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 85 "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 86 "Copy_of_/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 87 "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 88 "/lmb/home/pemsley/data/greg-data/pdb1hvv.ent" 89 "/lmb/home/pemsley/data/greg-data/monomer-ACT.pdb" 90 "/lmb/home/pemsley/data/greg-data/monomer-NPO.pdb" 91 "SymOp_-X,-X+Y,-Z+1/3_Copy_of_88" 92 "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 93 "atom selection from tutorial-modern.pdb" 94 "Copy_of_/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 95 "Copy_of_/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 96 "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 97 "/lmb/home/pemsley/data/greg-data/pdb1py3.ent" 98 "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 99 "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 100 "/lmb/home/pemsley/data/greg-data/2goz-manip.pdb" 101 "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 102 "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 103 "/lmb/home/pemsley/data/greg-data/HOF.RES" 104 "/lmb/home/pemsley/data/greg-data/hollander.ins" 107 "/lmb/home/pemsley/data/greg-data/insulin.fcf Diff-SigmaA" 108 "atom selection from insulin.res" 109 "atom selection from insulin.res" 111 "/lmb/home/pemsley/data/greg-data/horma-p21.res" 112 "new-horma.ins" 113 "/lmb/home/pemsley/data/greg-data/crash.hat" 114 "3GP_from_dict" 115 "/lmb/home/pemsley/data/greg-data/monomer-3GP.pdb" 116 "/lmb/home/pemsley/data/greg-data/test-LIG.pdb" 117 "/lmb/home/pemsley/data/greg-data/test-LIG.pdb" 118 "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 119 "3GP_from_dict" 120 "/lmb/home/pemsley/data/greg-data/monomer-3GP.pdb" 121 "/lmb/home/pemsley/data/greg-data/monomer-NPO.pdb" 122 "Copy_of_/lmb/home/pemsley/data/greg-data/monomer-NPO.pdb" 123 "Copy_of_/lmb/home/pemsley/data/greg-data/monomer-NPO.pdb" 124 "Copy_of_/lmb/home/pemsley/data/greg-data/monomer-NPO.pdb" 125 "Copy_of_/lmb/home/pemsley/data/greg-data/monomer-NPO.pdb" 126 "Copy_of_/lmb/home/pemsley/data/greg-data/monomer-NPO.pdb" 127 "/lmb/home/pemsley/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb" 128 "/lmb/home/pemsley/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz FWT PHWT" 129 "/lmb/home/pemsley/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz DELFWT PHDELWT" 130 "Masked (by protein)" 131 "Fitted ligand #0-0" 132 "Fitted ligand #1-0" 133 "Fitted ligand #2-0" 134 "/lmb/home/pemsley/data/greg-data/monomer-3GP.pdb" 135 "Copy_of_/lmb/home/pemsley/data/greg-data/monomer-3GP.pdb" 136 "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 137 "/lmb/home/pemsley/data/greg-data/crashes_on_cootaneering-v2.pdb" 138 "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 139 "Ideal-A-form-RNA" 142 "/lmb/home/pemsley/data/greg-data/1wly.pdb" 143 "/lmb/home/pemsley/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 159 NCS found from matching Chain B onto Chain A" n-matchers: 2 ==== test-name: "Map 159 NCS found from matching Chain C onto Chain A" n-matchers: 2 ==== test-name: "Map 159 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 124 # of expected passes 124 # of expected failures 0 # of unexpected passes 0 # of unexpected failures 0 # of unresolved testcases 0 # of unsupported testcases 0 # of untested testcases 0 Loading greg-tests/end.grg ... Loaded greg-tests/end.grg === Summary of all tests === # of tools 1 # of testcases attempted 124 # of expected passes 124 # of expected failures 0 # of unexpected passes 0 # of unexpected failures 0 # of unresolved testcases 0 # of unsupported testcases 0 # of untested testcases 0 # of files abandoned 0 ObjectCache: Leaked 0003 refs to ObjectCache: Leaked 0003 refs to test_coot: coot test passed