| Hi Paul, The version I am running in CCP4-8 is indeed 0.9.8.7 but I am still getting the errors. Attached is the log file. Thanks, Mark _____________________ Mark A. Saper, Ph.D. Visiting Professor Dept of Microbiology and Molecular Genetics Hebrew University Faculty of Medicine sa...@umich.edu | +972 52 815-0480 To unsubscribe from the COOT list, click the following link: |
Last login: Tue Apr 4 09:48:01 on ttys004 Inside .bash_profile The default interactive shell is now zsh. To update your account to use zsh, please run `chsh -s /bin/zsh`. For more details, please visit https://support.apple.com/kb/HT208050. msla0656:~ saper$ cd "/Users/saper/Research/SaNfo/230324_Diamond/Y33F_DNA_P023_X12/zn_above/xia2_3dii/phenix/Refine_12/" ; /Applications/ccp4-8.0/bin/coot INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: /Applications/ccp4-8.0/lib/data/monomers/ There are 225 data in /Applications/ccp4-8.0/lib/data/monomers/list/mon_lib_list.cif There are 2 data in /Applications/ccp4-8.0/lib/data/monomers/a/ALA.cif There are 2 data in /Applications/ccp4-8.0/lib/data/monomers/a/ASP.cif There are 2 data in /Applications/ccp4-8.0/lib/data/monomers/a/ASN.cif There are 2 data in /Applications/ccp4-8.0/lib/data/monomers/c/CYS.cif There are 2 data in /Applications/ccp4-8.0/lib/data/monomers/g/GLN.cif There are 2 data in /Applications/ccp4-8.0/lib/data/monomers/g/GLY.cif There are 2 data in /Applications/ccp4-8.0/lib/data/monomers/g/GLU.cif There are 2 data in /Applications/ccp4-8.0/lib/data/monomers/p/PHE.cif There are 2 data in /Applications/ccp4-8.0/lib/data/monomers/h/HIS.cif There are 2 data in /Applications/ccp4-8.0/lib/data/monomers/i/ILE.cif There are 2 data in /Applications/ccp4-8.0/lib/data/monomers/l/LYS.cif There are 2 data in /Applications/ccp4-8.0/lib/data/monomers/l/LEU.cif There are 2 data in /Applications/ccp4-8.0/lib/data/monomers/m/MET.cif There are 2 data in /Applications/ccp4-8.0/lib/data/monomers/m/MSE.cif There are 2 data in /Applications/ccp4-8.0/lib/data/monomers/p/PRO.cif There are 2 data in /Applications/ccp4-8.0/lib/data/monomers/a/ARG.cif There are 2 data in /Applications/ccp4-8.0/lib/data/monomers/s/SER.cif There are 2 data in /Applications/ccp4-8.0/lib/data/monomers/t/THR.cif There are 2 data in /Applications/ccp4-8.0/lib/data/monomers/v/VAL.cif There are 2 data in /Applications/ccp4-8.0/lib/data/monomers/t/TRP.cif There are 2 data in /Applications/ccp4-8.0/lib/data/monomers/t/TYR.cif There are 2 data in /Applications/ccp4-8.0/lib/data/monomers/p/PO4.cif There are 2 data in /Applications/ccp4-8.0/lib/data/monomers/s/SO4.cif There are 2 data in /Applications/ccp4-8.0/lib/data/monomers/g/GOL.cif There are 2 data in /Applications/ccp4-8.0/lib/data/monomers/c/CIT.cif There are 2 data in /Applications/ccp4-8.0/lib/data/monomers/e/EDO.cif There are 2 data in /Applications/ccp4-8.0/lib/data/monomers/a/A.cif There are 2 data in /Applications/ccp4-8.0/lib/data/monomers/c/C.cif There are 2 data in /Applications/ccp4-8.0/lib/data/monomers/g/G.cif There are 2 data in /Applications/ccp4-8.0/lib/data/monomers/u/U.cif There are 2 data in /Applications/ccp4-8.0/lib/data/monomers/d/DA.cif There are 2 data in /Applications/ccp4-8.0/lib/data/monomers/d/DC.cif There are 2 data in /Applications/ccp4-8.0/lib/data/monomers/d/DG.cif There are 2 data in /Applications/ccp4-8.0/lib/data/monomers/d/DT.cif There are 2 data in /Applications/ccp4-8.0/lib/data/monomers/h/HOH.cif There are 2 data in /Applications/ccp4-8.0/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
** (coot-bin:72466): WARNING **: Trying to register gtype 'GMountMountFlags' as
enum when in fact it is of type 'GFlags'
** (coot-bin:72466): WARNING **: Trying to register gtype 'GDriveStartFlags' as
enum when in fact it is of type 'GFlags'
** (coot-bin:72466): WARNING **: Trying to register gtype 'GSocketMsgFlags' as
enum when in fact it is of type 'GFlags'
INFO:: coot_python initialized
Running python script
/Applications/ccp4-8.0/coot_py2/lib/python2.7/site-packages/coot/coot_load_modules.py
Good Morning Mark, Welcome to Coot version 0.9.8.7
(set-display-intro-string "Good Morning Mark, Welcome to Coot version 0.9.8.7")
Coot Python Scripting GUI code found and loaded.
Coot Python Scripting GUI code found and loaded.
(use-graphics-interface-state)
Running python script /Users/saper/.coot-preferences/Bernhards_bindings.py
Running python script /Users/saper/.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 16.00)
(set-swap-difference-map-colours 0)
(set-colour-map-rotation-for-map 14.00)
(set-active-map-drag-flag 1)
(set-idle-function-rotate-angle 1.00)
(filter-fileselection-filenames-state)
(get-active-map-drag-flag)
(use-graphics-interface-state)
Coot Scheme Scripting GUI code found and loaded.
Good morning Mark Saper. Welcome to Coot 0.9.8.7.
(set-display-intro-string "Good morning Mark. Welcome to Coot 0.9.8.7")
(set-display-lists-for-maps 0)
load /Users/saper/.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 16.00)
(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 /Users/saper/.coot-preferences/curlew-refinement-tools.scm
(filter-fileselection-filenames-state)
(get-active-map-drag-flag)
(use-graphics-interface-state)
(filter-fileselection-filenames-state)
(filter-fileselection-filenames-state)
DEBUG:: filename:
/Users/saper/Research/SaNfo/230324_Diamond/Y33F_DNA_P023_X12/zn_above/xia2_3dii/phenix/Refine_12/Y33F_DNA_P023_X12_refine_12-coot-1.pdb
(handle-read-draw-molecule-with-recentre
"/Users/saper/Research/SaNfo/230324_Diamond/Y33F_DNA_P023_X12/zn_above/xia2_3dii/phenix/Refine_12/Y33F_DNA_P023_X12_refine_12-coot-1.pdb"
1)
INFO:: Reading coordinate file:
/Users/saper/Research/SaNfo/230324_Diamond/Y33F_DNA_P023_X12/zn_above/xia2_3dii/phenix/Refine_12/Y33F_DNA_P023_X12_refine_12-coot-1.pdb
INFO:: file
/Users/saper/Research/SaNfo/230324_Diamond/Y33F_DNA_P023_X12/zn_above/xia2_3dii/phenix/Refine_12/Y33F_DNA_P023_X12_refine_12-coot-1.pdb
has been read.
Spacegroup: P 41 21 2
INFO:: using standard CCP4 Refmac dictionary to search for "FE"
There are 2 data in /Applications/ccp4-8.0/lib/data/monomers/f/FE.cif
INFO:: using standard CCP4 Refmac dictionary to search for "ZN"
There are 2 data in /Applications/ccp4-8.0/lib/data/monomers/z/ZN.cif
INFO:: using standard CCP4 Refmac dictionary to search for "3DR"
There are 2 data in /Applications/ccp4-8.0/lib/data/monomers/3/3DR.cif
INFO:: Found 1 models
Model 1 had 2 links
INFO:: NCS chain comparison 0/299
INFO:: NCS chain comparison 0/299
INFO:: NCS chain comparison 0/299
INFO:: NCS chain comparison 0/5
INFO:: NCS chain comparison 0/5
INFO:: NCS chain comparison 0/7
debug:: g.safe_scheme_command() with command post-set-rotation-centre-hook
debug:: g.safe_scheme_command() with command post-read-model-hook
INFO:: in run_post_read_model_hook() pFunc 0x107f5ca68 is not callable
INFO:: in run_post_read_model_hook() pDict 0x7fce8f297168
INFO:: in run_post_read_model_hook() pModule 0x7fce8f282be8
Molecule 0 read successfully
(filter-fileselection-filenames-state)
(filter-fileselection-filenames-state)
INFO:: making conventional map from MTZ filename
/Users/saper/Research/SaNfo/230324_Diamond/Y33F_DNA_P023_X12/zn_above/xia2_3dii/phenix/Refine_12/Y33F_DNA_P023_X12_refine_12.mtz
using 2FOFCWT PH2FOFCWT
INFO:: Number of observed reflections: 21453
INFO:: finding ASU unique map points with sampling rate 1.8
INFO:: grid sampling...Nuvw = ( 120, 120, 320)
Pre-filter Map statistics: mean: 5.42665e-08 st.d: 0.175245
Pre-filter Map statistics: min: -0.563024 max: 1.24297
INFO:: n grid points: 576060
INFO:: mean before filtering: 5.42665e-08
INFO:: variance before filtering: 0.0307108
INFO:: filter by ignoring 413 of 576060 counts ( = 0.07169%) with values around
-0.02655 bounds -0.02664 -0.02646 from bin-number 2970 of 10000
Post-filter Map statistics: mean: 1.924e-05 st.d: 0.1753
Post-filter Map statistics: min: -0.563 max: 1.243
Map extents: ..... 120 120 320
Map mean: ........ 1.924e-05
Map sigma: ....... 0.1753
Map maximum: ..... 1.243
Map minimum: ..... -0.563
(make-and-draw-map-with-reso-with-refmac-params
"/Users/saper/Research/SaNfo/230324_Diamond/Y33F_DNA_P023_X12/zn_above/xia2_3dii/phenix/Refine_12/Y33F_DNA_P023_X12_refine_12.mtz"
"2FOFCWT" "PH2FOFCWT" "" 0 0 0 "Fobs:None-specified" "SigF:None-specified"
"RFree:None-specified" 0 0 0 0.00 0.00)
INFO:: making difference map from MTZ filename
/Users/saper/Research/SaNfo/230324_Diamond/Y33F_DNA_P023_X12/zn_above/xia2_3dii/phenix/Refine_12/Y33F_DNA_P023_X12_refine_12.mtz
using FOFCWT PHFOFCWT
INFO:: Number of observed reflections: 21453
INFO:: finding ASU unique map points with sampling rate 1.8
INFO:: grid sampling...Nuvw = ( 120, 120, 320)
Pre-filter Map statistics: mean: 1.917e-06 st.d: 0.0796
Pre-filter Map statistics: min: -0.4068 max: 0.661
INFO:: n grid points: 576060
INFO:: mean before filtering: 1.917e-06
INFO:: variance before filtering: 0.006337
INFO:: filter by ignoring 385 of 576060 counts ( = 0.06683%) with values around
-0.01509 bounds -0.01515 -0.01504 from bin-number 3668 of 10000
Post-filter Map statistics: mean: 1.203e-05 st.d: 0.07963
Post-filter Map statistics: min: -0.4068 max: 0.661
Map extents: ..... 120 120 320
Map mean: ........ 1.203e-05
Map sigma: ....... 0.07963
Map maximum: ..... 0.661
Map minimum: ..... -0.4068
(make-and-draw-map-with-reso-with-refmac-params
"/Users/saper/Research/SaNfo/230324_Diamond/Y33F_DNA_P023_X12/zn_above/xia2_3dii/phenix/Refine_12/Y33F_DNA_P023_X12_refine_12.mtz"
"FOFCWT" "PHFOFCWT" "" 0 1 0 "Fobs:None-specified" "SigF:None-specified"
"RFree:None-specified" 0 0 0 0.00 0.00)
(graphics-general-key-press-hook 65406)
debug:: g.safe_scheme_command() with command (graphics-general-key-press-hook
65406)
Key 65406 not found in (python) key bindings
Key 65406 not found in (scheme) key bindings
(graphics-general-key-press-hook 65406)
debug:: g.safe_scheme_command() with command (graphics-general-key-press-hook
65406)
Key 65406 not found in (python) key bindings
Key 65406 not found in (scheme) key bindings
(0) "HG12"/1/chainid="A"/67/VAL, occ: 1 with B-factor: 53.93 element: " H" at
(-3.824,28.35,-14.81) : 0.2953
(graphics-general-key-press-hook 65406)
debug:: g.safe_scheme_command() with command (graphics-general-key-press-hook
65406)
Key 65406 not found in (python) key bindings
Key 65406 not found in (scheme) key bindings
(graphics-general-key-press-hook 65406)
debug:: g.safe_scheme_command() with command (graphics-general-key-press-hook
65406)
Key 65406 not found in (python) key bindings
Key 65406 not found in (scheme) key bindings
(graphics-general-key-press-hook 65406)
debug:: g.safe_scheme_command() with command (graphics-general-key-press-hook
65406)
Key 65406 not found in (python) key bindings
Key 65406 not found in (scheme) key bindings
(0) " O "/1/chainid="A"/68/HIS, occ: 1 with B-factor: 44.59 element: " O" at
(-4.522,31.26,-13.21) : 0.3302
(graphics-general-key-press-hook 65406)
debug:: g.safe_scheme_command() with command (graphics-general-key-press-hook
65406)
Key 65406 not found in (python) key bindings
Key 65406 not found in (scheme) key bindings
(graphics-general-key-press-hook 65406)
debug:: g.safe_scheme_command() with command (graphics-general-key-press-hook
65406)
Key 65406 not found in (python) key bindings
Key 65406 not found in (scheme) key bindings
(0) " CB "/1/chainid="A"/5/SER, occ: 1 with B-factor: 40.19 element: " C" at
(6.226,29.9,-4.086) : 0.445
(graphics-general-key-press-hook 65406)
debug:: g.safe_scheme_command() with command (graphics-general-key-press-hook
65406)
Key 65406 not found in (python) key bindings
Key 65406 not found in (scheme) key bindings
(graphics-general-key-press-hook 65406)
debug:: g.safe_scheme_command() with command (graphics-general-key-press-hook
65406)
Key 65406 not found in (python) key bindings
Key 65406 not found in (scheme) key bindings
(graphics-general-key-press-hook 65406)
debug:: g.safe_scheme_command() with command (graphics-general-key-press-hook
65406)
Key 65406 not found in (python) key bindings
Key 65406 not found in (scheme) key bindings
(0) " CA "/1/chainid="A"/4/GLY, occ: 1 with B-factor: 37.2 element: " C" at
(7.213,25.48,-4.741) : 0.5732
(graphics-general-key-press-hook 65406)
debug:: g.safe_scheme_command() with command (graphics-general-key-press-hook
65406)
Key 65406 not found in (python) key bindings
Key 65406 not found in (scheme) key bindings
(graphics-general-key-press-hook 65406)
debug:: g.safe_scheme_command() with command (graphics-general-key-press-hook
65406)
Key 65406 not found in (python) key bindings
Key 65406 not found in (scheme) key bindings
(graphics-general-key-press-hook 65406)
debug:: g.safe_scheme_command() with command (graphics-general-key-press-hook
65406)
Key 65406 not found in (python) key bindings
Key 65406 not found in (scheme) key bindings
(0) " OE1"/1/chainid="A"/144/GLU, occ: 1 with B-factor: 52.13 element: " O" at
(-8.042,28.99,-5.379) : 0.438
(graphics-general-key-press-hook 65406)
debug:: g.safe_scheme_command() with command (graphics-general-key-press-hook
65406)
Key 65406 not found in (python) key bindings
Key 65406 not found in (scheme) key bindings
(graphics-general-key-press-hook 65406)
debug:: g.safe_scheme_command() with command (graphics-general-key-press-hook
65406)
Key 65406 not found in (python) key bindings
Key 65406 not found in (scheme) key bindings
(graphics-general-key-press-hook 65406)
debug:: g.safe_scheme_command() with command (graphics-general-key-press-hook
65406)
Key 65406 not found in (python) key bindings
Key 65406 not found in (scheme) key bindings
Model atom pick failed.
(graphics-general-key-press-hook 65406)
debug:: g.safe_scheme_command() with command (graphics-general-key-press-hook
65406)
Key 65406 not found in (python) key bindings
Key 65406 not found in (scheme) key bindings
(graphics-general-key-press-hook 65406)
debug:: g.safe_scheme_command() with command (graphics-general-key-press-hook
65406)
Key 65406 not found in (python) key bindings
Key 65406 not found in (scheme) key bindings
(0) " O "/1/chainid="A"/152/GLU, occ: 1 with B-factor: 37.82 element: " O" at
(-19.36,31.03,-1.321) : 0.2471
(graphics-general-key-press-hook 65406)
debug:: g.safe_scheme_command() with command (graphics-general-key-press-hook
65406)
Key 65406 not found in (python) key bindings
Key 65406 not found in (scheme) key bindings
(graphics-general-key-press-hook 65406)
debug:: g.safe_scheme_command() with command (graphics-general-key-press-hook
65406)
Key 65406 not found in (python) key bindings
Key 65406 not found in (scheme) key bindings
(0) " HB2"/1/chainid="A"/181/HIS, occ: 1 with B-factor: 49.18 element: " H" at
(-8.673,27.59,1.503) : 0.2776
(graphics-general-key-press-hook 65406)
debug:: g.safe_scheme_command() with command (graphics-general-key-press-hook
65406)
Key 65406 not found in (python) key bindings
Key 65406 not found in (scheme) key bindings
(graphics-general-key-press-hook 65406)
debug:: g.safe_scheme_command() with command (graphics-general-key-press-hook
65406)
Key 65406 not found in (python) key bindings
Key 65406 not found in (scheme) key bindings
(0) " CG "/1/chainid="A"/149/LYS, occ: 1 with B-factor: 56.68 element: " C" at
(-13.79,36.2,1.028) : 0.4713
(graphics-general-key-press-hook 65406)
debug:: g.safe_scheme_command() with command (graphics-general-key-press-hook
65406)
Key 65406 not found in (python) key bindings
Key 65406 not found in (scheme) key bindings
(graphics-general-key-press-hook 65406)
debug:: g.safe_scheme_command() with command (graphics-general-key-press-hook
65406)
Key 65406 not found in (python) key bindings
Key 65406 not found in (scheme) key bindings
(0) " C4'"/1/chainid="D"/938/DG, occ: 1 with B-factor: 118.1 element: " C" at
(-8.693,47.22,-17.45) : 0.4365
INFO:: recentre: clicked on imol: 0
debug:: g.safe_scheme_command() with command post-set-rotation-centre-hook
(graphics-general-key-press-hook 65406)
debug:: g.safe_scheme_command() with command (graphics-general-key-press-hook
65406)
Key 65406 not found in (python) key bindings
Key 65406 not found in (scheme) key bindings
(graphics-general-key-press-hook 65406)
debug:: g.safe_scheme_command() with command (graphics-general-key-press-hook
65406)
Key 65406 not found in (python) key bindings
Key 65406 not found in (scheme) key bindings
(graphics-general-key-press-hook 65406)
debug:: g.safe_scheme_command() with command (graphics-general-key-press-hook
65406)
Key 65406 not found in (python) key bindings
Key 65406 not found in (scheme) key bindings
(graphics-general-key-press-hook 65406)
debug:: g.safe_scheme_command() with command (graphics-general-key-press-hook
65406)
Key 65406 not found in (python) key bindings
Key 65406 not found in (scheme) key bindings
(0) " C2'"/1/chainid="D"/938/DG, occ: 1 with B-factor: 107.1 element: " C" at
(-9.721,46.28,-15.54) : 0.34
(graphics-general-key-press-hook 65406)
debug:: g.safe_scheme_command() with command (graphics-general-key-press-hook
65406)
Key 65406 not found in (python) key bindings
Key 65406 not found in (scheme) key bindings
(graphics-general-key-press-hook 65406)
debug:: g.safe_scheme_command() with command (graphics-general-key-press-hook
65406)
Key 65406 not found in (python) key bindings
Key 65406 not found in (scheme) key bindings
(graphics-general-key-press-hook 65406)
debug:: g.safe_scheme_command() with command (graphics-general-key-press-hook
65406)
Key 65406 not found in (python) key bindings
Key 65406 not found in (scheme) key bindings
(0) " C1'"/1/chainid="D"/939/DT, occ: 1 with B-factor: 106.5 element: " C" at
(-15.28,42.29,-18.74) : 0.1795
(graphics-general-key-press-hook 65406)
debug:: g.safe_scheme_command() with command (graphics-general-key-press-hook
65406)
Key 65406 not found in (python) key bindings
Key 65406 not found in (scheme) key bindings
(graphics-general-key-press-hook 65406)
debug:: g.safe_scheme_command() with command (graphics-general-key-press-hook
65406)
Key 65406 not found in (python) key bindings
Key 65406 not found in (scheme) key bindings
(0) " N9 "/1/chainid="D"/940/DG, occ: 1 with B-factor: 64.92 element: " N" at
(-13.87,40.47,-10.39) : 0.2743
INFO:: recentre: clicked on imol: 0
debug:: g.safe_scheme_command() with command post-set-rotation-centre-hook
(graphics-general-key-press-hook 65406)
debug:: g.safe_scheme_command() with command (graphics-general-key-press-hook
65406)
Key 65406 not found in (python) key bindings
Key 65406 not found in (scheme) key bindings
click on 2 atoms (in the same molecule)
(0) " C4'"/1/chainid="D"/940/DG, occ: 1 with B-factor: 72.77 element: " C" at
(-16.1,39.13,-12.71) : 0.1608
(0) " C3'"/1/chainid="D"/941/DG, occ: 1 with B-factor: 54.83 element: " C" at
(-18.08,39.42,-5.868) : 0.1805
----------------- 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 66 atoms
debug:: on creation last_restraints is 0x7fce92022a00
INFO:: from_res_vec() created 202 monomer restraints
created 70 bond restraints
created 122 angle restraints
created 4 plane restraints
created 6 chiral vol restraints
created 0 improper dihedral restraints
Made 1 link bond restraints
Made 4 link angle restraints
Made 0 link plane restraints
Made 0 link trans-peptide restraints
Made 9 CHO-SS-and-other bond restraints
Made 27 CHO-SS-and-other angle restraints
Made 9 CHO-SS-and-other plane restraints
Made 0 CHO-SS-and-other trans-peptide restraints
INFO:: added 0 helical restraints
INFO:: extra restraints origin: from
make_base_pairing_and_stacking_restraints_ng()
--------------------- in add_extra_restraints() we have 7335 standard
restraints
--------------------- in add_extra_restraints() adding 0 extra bond restraints
--------------------- in add_extra_restraints() adding 0 extra GM restraints
--------------------- in add_extra_restraints() adding 0 extra angle restraints
--------------------- in add_extra_restraints() par-plan adding 1 pp restraints
--------------------- in add_extra_restraints() target-position adding 0
position restraints
INFO:: -------------------------- made 0 extra bond restraints
INFO:: -------------------------- made 0 extra GM restraints
INFO:: Model: Bad Bond: [spec: model 1 "A" 83 "" " C " ""] to [spec: model 1
"D" 941 "" " O3'" ""] nZ 864.70 delta 11.068 target 1.334 sigma 0.013
distortion 747697.900
INFO:: Model: Bad Bond: [spec: model 1 "A" 77 "" " C " ""] to [spec: model 1
"D" 941 "" " O3'" ""] nZ 750.49 delta 9.606 target 1.334 sigma 0.013
distortion 563234.313
INFO:: Model: Bad Bond: [spec: model 1 "A" 74 "" " C " ""] to [spec: model 1
"D" 941 "" " O3'" ""] nZ 653.08 delta 8.359 target 1.334 sigma 0.013
distortion 426519.321
INFO:: Model: Bad Bond: [spec: model 1 "A" 71 "" " C " ""] to [spec: model 1
"D" 940 "" " O3'" ""] nZ 451.30 delta 5.777 target 1.334 sigma 0.013
distortion 203669.677
INFO:: Model: Bad Bond: [spec: model 1 "A" 114 "" " C " ""] to [spec: model 1
"D" 941 "" " O3'" ""] nZ 446.57 delta 5.716 target 1.334 sigma 0.013
distortion 199423.169
INFO:: Model: Bad Bond: [spec: model 1 "A" 83 "" " C " ""] to [spec: model 1
"D" 940 "" " O3'" ""] nZ 391.83 delta 5.015 target 1.334 sigma 0.013
distortion 153529.971
INFO:: Model: Bad Bond: [spec: model 1 "A" 112 "" " C " ""] to [spec: model 1
"D" 941 "" " O3'" ""] nZ 352.48 delta 4.512 target 1.334 sigma 0.013
distortion 124240.193
INFO:: Model: Bad Bond: [spec: model 1 "A" 72 "" " C " ""] to [spec: model 1
"D" 940 "" " O3'" ""] nZ 349.27 delta 4.471 target 1.334 sigma 0.013
distortion 121986.807
INFO:: Model: Bad Bond: [spec: model 1 "A" 74 "" " C " ""] to [spec: model 1
"D" 940 "" " O3'" ""] nZ 343.88 delta 4.402 target 1.334 sigma 0.013
distortion 118252.203
INFO:: Model: Bad Bond: [spec: model 1 "D" 941 "" " C3'" ""] to [spec: model 1
"D" 941 "" " O3'" ""] nZ 3.92 delta 0.039 target 1.424 sigma 0.010 distortion
15.356
INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "D" 941 "" " OP1" ""] DG
to [spec: model 1 "A" 74 "" "HD22" ""] ASN delta -1.171 target 2.920
distortion 3572.145
INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "D" 941 "" " OP1" ""] DG
to [spec: model 1 "A" 77 "" "HD22" ""] ASN delta -1.076 target 2.920
distortion 1857.266
INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "D" 941 "" " OP1" ""] DG
to [spec: model 1 "A" 74 "" " ND2" ""] ASN delta -0.741 target 3.270
distortion 137.361
INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "D" 940 "" " O5'" ""] DG
to [spec: model 1 "D" 939 "" " H3'" ""] DT delta -0.620 target 2.920
distortion 106.649
INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "D" 940 "" " P " ""] DG
to [spec: model 1 "D" 939 "" " H3'" ""] DT delta -0.630 target 3.200
distortion 81.419
INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "D" 940 "" " OP1" ""] DG
to [spec: model 1 "D" 940 "" " H3'" ""] DG delta -0.569 target 2.920
distortion 78.370
INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "D" 941 "" " O3'" ""] DG
to [spec: model 1 "D" 942 "" " H5'" ""] DA delta -0.551 target 2.920
distortion 70.230
INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "D" 941 "" " OP1" ""] DG
to [spec: model 1 "A" 77 "" " ND2" ""] ASN delta -0.611 target 3.270
distortion 67.894
INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "D" 940 "" " O4'" ""] DG
to [spec: model 1 "A" 72 "" " HA " ""] ILE delta -0.538 target 2.920
distortion 64.923
INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "D" 941 "" " H21" ""] DG
to [spec: model 1 "B" 905 "" " C2 " ""] DC delta -0.557 target 3.100
distortion 60.004
Refinement elapsed time: 0.145
Unexpected error from gsl_multimin_fdfminimizer_iterate at iter 7
Error:: in gsl_multimin_fdfminimizer_iterate() result was GSL_ENOPROG
Error:: iter: 7 f 1123094.675 1123094.675 pnorm 181.194 g0norm 181.194
parallel plane 7335 {restraint: } 38.323
Final Estimated RMS Z Scores (ENOPROG)
bonds: 114.925
angles: 12.805
improper-dihedrals: N/A
torsions: N/A
trans-peptide: N/A
planes: 16.235 from 13 restraints
parallel planes: 6.191 from 1 restraints
non-bonded: 1.438
chiral vol: 5.690
rama plot: N/A
start_pos: N/A
TargetPos: N/A
GemanMcCl: N/A
INFO:: Model: Bad Chiral Volume: [spec: model 1 "D" 941 "" " C3'" ""] delta
-1.270 target 2.657 sigma 0.100 distortion 161.350
INFO:: Model: Bad Chiral Volume: [spec: model 1 "D" 940 "" " C3'" ""] delta
-0.492 target 2.657 sigma 0.100 distortion 24.202
INFO:: Model: Bad Chiral Volume: [spec: model 1 "D" 940 "" " C1'" ""] delta
0.292 target -2.428 sigma 0.100 distortion 8.512
INFO:: Model: Bad Bond: [spec: model 1 "A" 83 "" " C " ""] to [spec: model 1
"D" 941 "" " O3'" ""] nZ 508.45 delta 6.508 target 1.334 sigma 0.013
distortion 258520.607
INFO:: Model: Bad Bond: [spec: model 1 "D" 941 "" " O3'" ""] to [spec: model 1
"D" 942 "" " P " ""] nZ 503.46 delta 5.035 target 1.607 sigma 0.010
distortion 253475.941
INFO:: Model: Bad Bond: [spec: model 1 "A" 74 "" " C " ""] to [spec: model 1
"D" 941 "" " O3'" ""] nZ 350.64 delta 4.488 target 1.334 sigma 0.013
distortion 122949.155
INFO:: Model: Bad Bond: [spec: model 1 "A" 114 "" " C " ""] to [spec: model 1
"D" 941 "" " O3'" ""] nZ 308.25 delta 3.946 target 1.334 sigma 0.013
distortion 95018.332
INFO:: Model: Bad Bond: [spec: model 1 "A" 83 "" " C " ""] to [spec: model 1
"D" 940 "" " O3'" ""] nZ 306.97 delta 3.929 target 1.334 sigma 0.013
distortion 94228.497
INFO:: Model: Bad Bond: [spec: model 1 "A" 77 "" " C " ""] to [spec: model 1
"D" 941 "" " O3'" ""] nZ 291.71 delta 3.734 target 1.334 sigma 0.013
distortion 85097.032
INFO:: Model: Bad Bond: [spec: model 1 "A" 71 "" " C " ""] to [spec: model 1
"D" 940 "" " O3'" ""] nZ 291.12 delta 3.726 target 1.334 sigma 0.013
distortion 84750.341
INFO:: Model: Bad Bond: [spec: model 1 "A" 74 "" " C " ""] to [spec: model 1
"D" 940 "" " O3'" ""] nZ 210.65 delta 2.696 target 1.334 sigma 0.013
distortion 44372.625
INFO:: Model: Bad Bond: [spec: model 1 "A" 112 "" " C " ""] to [spec: model 1
"D" 941 "" " O3'" ""] nZ 183.28 delta 2.346 target 1.334 sigma 0.013
distortion 33592.005
INFO:: Model: Bad Bond: [spec: model 1 "A" 72 "" " C " ""] to [spec: model 1
"D" 940 "" " O3'" ""] nZ 94.82 delta 1.214 target 1.334 sigma 0.013
distortion 8991.552
INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "D" 941 "" " O3'" ""] DG
to [spec: model 1 "A" 74 "" "HD21" ""] ASN delta -1.404 target 2.920
distortion 20397.832
INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "D" 940 "" " O3'" ""] DG
to [spec: model 1 "A" 74 "" " H " ""] ASN delta -1.278 target 2.920
distortion 7739.899
INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "D" 941 "" " O3'" ""] DG
to [spec: model 1 "A" 114 "" "HG23" ""] VAL delta -1.141 target 2.920
distortion 2898.290
INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "D" 940 "" " O3'" ""] DG
to [spec: model 1 "A" 74 "" " N " ""] ASN delta -1.217 target 3.270
distortion 2000.662
INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "D" 941 "" " C3'" ""] DG
to [spec: model 1 "A" 74 "" "HD22" ""] ASN delta -1.079 target 3.100
distortion 1251.585
INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "D" 940 "" " C3'" ""] DG
to [spec: model 1 "A" 72 "" " O " ""] ILE delta -1.185 target 3.420
distortion 1217.092
INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "D" 941 "" " P " ""] DG
to [spec: model 1 "A" 74 "" " HB2" ""] ASN delta -1.072 target 3.200
distortion 977.688
INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "D" 941 "" " O3'" ""] DG
to [spec: model 1 "A" 74 "" " ND2" ""] ASN delta -1.090 target 3.270
distortion 947.214
INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "D" 941 "" " C3'" ""] DG
to [spec: model 1 "A" 114 "" "HG11" ""] VAL delta -1.004 target 3.100
distortion 792.226
INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "D" 941 "" " OP2" ""] DG
to [spec: model 1 "A" 74 "" " HB3" ""] ASN delta -0.933 target 2.920
distortion 730.525
INFO:: Most dissatisfied restraint (refine no-progress): Bond C/83/A O3'/941/D
z = 508.46
----------------------- FAIL, ENOPROG ---------------
########################################################################
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