Starting phenix.real_space_refine on Wed Sep 25 04:13:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vba_43118/09_2024/8vba_43118.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vba_43118/09_2024/8vba_43118.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vba_43118/09_2024/8vba_43118.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vba_43118/09_2024/8vba_43118.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vba_43118/09_2024/8vba_43118.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vba_43118/09_2024/8vba_43118.cif" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 5660 2.51 5 N 1638 2.21 5 O 2098 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 9416 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 7293 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 8, 'TRANS': 1029} Chain: "H" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 887 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "L" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 807 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Chain: "A" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 429 Unusual residues: {'BGC': 39} Classifications: {'undetermined': 39} Link IDs: {None: 38} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 39 Time building chain proxies: 6.32, per 1000 atoms: 0.67 Number of scatterers: 9416 At special positions: 0 Unit cell: (63.075, 95.7, 187.775, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 2098 8.00 N 1638 7.00 C 5660 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=39, symmetry=0 Number of additional bonds: simple=39, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.59 Conformation dependent library (CDL) restraints added in 1.2 seconds 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2182 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 12 sheets defined 3.7% alpha, 29.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 175 through 181 Processing helix chain 'A' and resid 366 through 370 Processing helix chain 'A' and resid 481 through 485 removed outlier: 3.810A pdb=" N PHE A 484 " --> pdb=" O HIS A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 504 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.718A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.603A pdb=" N PHE L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 76 removed outlier: 6.609A pdb=" N VAL A 99 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N MET A 98 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N ARG A 127 " --> pdb=" O MET A 98 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ALA A 100 " --> pdb=" O ARG A 127 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 123 through 128 current: chain 'A' and resid 400 through 411 removed outlier: 6.432A pdb=" N ALA A 401 " --> pdb=" O GLU A 430 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N SER A 432 " --> pdb=" O ALA A 401 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LEU A 403 " --> pdb=" O SER A 432 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 428 through 433 current: chain 'A' and resid 507 through 511 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 562 through 565 current: chain 'A' and resid 634 through 648 removed outlier: 6.648A pdb=" N ASN A 635 " --> pdb=" O THR A 661 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N ASN A 663 " --> pdb=" O ASN A 635 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU A 637 " --> pdb=" O ASN A 663 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N THR A 665 " --> pdb=" O LEU A 637 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N ALA A 639 " --> pdb=" O THR A 665 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ASN A 667 " --> pdb=" O ALA A 639 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ASN A 641 " --> pdb=" O ASN A 667 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N THR A 669 " --> pdb=" O ASN A 641 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ALA A 643 " --> pdb=" O THR A 669 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N THR A 671 " --> pdb=" O ALA A 643 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N THR A 645 " --> pdb=" O THR A 671 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N SER A 673 " --> pdb=" O THR A 645 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ASN A 647 " --> pdb=" O SER A 673 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ALA A 660 " --> pdb=" O ASN A 686 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N LEU A 688 " --> pdb=" O ALA A 660 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU A 662 " --> pdb=" O LEU A 688 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ALA A 690 " --> pdb=" O LEU A 662 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ALA A 664 " --> pdb=" O ALA A 690 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ASN A 692 " --> pdb=" O ALA A 664 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ASN A 666 " --> pdb=" O ASN A 692 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N THR A 694 " --> pdb=" O ASN A 666 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE A 668 " --> pdb=" O THR A 694 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N THR A 696 " --> pdb=" O ILE A 668 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N LEU A 670 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N GLU A 698 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLY A 672 " --> pdb=" O GLU A 698 " (cutoff:3.500A) removed outlier: 9.935A pdb=" N THR A 687 " --> pdb=" O ASN A 717 " (cutoff:3.500A) removed outlier: 12.184A pdb=" N THR A 719 " --> pdb=" O THR A 687 " (cutoff:3.500A) removed outlier: 11.751A pdb=" N THR A 689 " --> pdb=" O THR A 719 " (cutoff:3.500A) removed outlier: 10.858A pdb=" N ASN A 721 " --> pdb=" O THR A 689 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N SER A 691 " --> pdb=" O ASN A 721 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N THR A 723 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ILE A 693 " --> pdb=" O THR A 723 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N GLN A 725 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N LEU A 695 " --> pdb=" O GLN A 725 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N THR A 714 " --> pdb=" O ASN A 735 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N THR A 737 " --> pdb=" O THR A 714 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LEU A 716 " --> pdb=" O THR A 737 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 734 through 738 current: chain 'A' and resid 808 through 823 removed outlier: 6.493A pdb=" N VAL A 809 " --> pdb=" O ARG A 838 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N THR A 840 " --> pdb=" O VAL A 809 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N LEU A 811 " --> pdb=" O THR A 840 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N SER A 842 " --> pdb=" O LEU A 811 " (cutoff:3.500A) removed outlier: 9.011A pdb=" N ALA A 813 " --> pdb=" O SER A 842 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N ILE A 844 " --> pdb=" O ALA A 813 " (cutoff:3.500A) removed outlier: 12.813A pdb=" N ASN A 815 " --> pdb=" O ILE A 844 " (cutoff:3.500A) removed outlier: 16.093A pdb=" N LEU A 846 " --> pdb=" O ASN A 815 " (cutoff:3.500A) removed outlier: 13.675A pdb=" N ARG A 817 " --> pdb=" O LEU A 846 " (cutoff:3.500A) removed outlier: 15.046A pdb=" N GLY A 848 " --> pdb=" O ARG A 817 " (cutoff:3.500A) removed outlier: 13.748A pdb=" N LYS A 819 " --> pdb=" O GLY A 848 " (cutoff:3.500A) removed outlier: 15.675A pdb=" N SER A 850 " --> pdb=" O LYS A 819 " (cutoff:3.500A) removed outlier: 14.261A pdb=" N THR A 821 " --> pdb=" O SER A 850 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 861 through 866 current: chain 'A' and resid 1036 through 1052 removed outlier: 6.452A pdb=" N VAL A1037 " --> pdb=" O ARG A1066 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N THR A1068 " --> pdb=" O VAL A1037 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LEU A1039 " --> pdb=" O THR A1068 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N SER A1070 " --> pdb=" O LEU A1039 " (cutoff:3.500A) removed outlier: 9.230A pdb=" N ALA A1041 " --> pdb=" O SER A1070 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ILE A1072 " --> pdb=" O ALA A1041 " (cutoff:3.500A) removed outlier: 13.210A pdb=" N ASN A1043 " --> pdb=" O ILE A1072 " (cutoff:3.500A) removed outlier: 16.211A pdb=" N LEU A1074 " --> pdb=" O ASN A1043 " (cutoff:3.500A) removed outlier: 13.957A pdb=" N ARG A1045 " --> pdb=" O LEU A1074 " (cutoff:3.500A) removed outlier: 14.946A pdb=" N GLY A1076 " --> pdb=" O ARG A1045 " (cutoff:3.500A) removed outlier: 13.707A pdb=" N LYS A1047 " --> pdb=" O GLY A1076 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 85 removed outlier: 6.810A pdb=" N GLN A 88 " --> pdb=" O PRO A 84 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N VAL A 162 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU A 202 " --> pdb=" O ARG A 224 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE A 223 " --> pdb=" O SER A 268 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL A 267 " --> pdb=" O GLU A 296 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N VAL A 295 " --> pdb=" O GLN A 324 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 184 through 187 removed outlier: 4.315A pdb=" N TYR A 184 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ASP A 243 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N LEU A 247 " --> pdb=" O ASP A 243 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 387 through 389 removed outlier: 6.528A pdb=" N ILE A 415 " --> pdb=" O SER A 444 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 491 through 494 Processing sheet with id=AA6, first strand: chain 'A' and resid 531 through 533 removed outlier: 6.383A pdb=" N ILE A 531 " --> pdb=" O THR A 556 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 575 through 578 removed outlier: 3.554A pdb=" N ASN A 607 " --> pdb=" O ILE A 578 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE A 604 " --> pdb=" O LEU A 630 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ALA A 632 " --> pdb=" O ILE A 604 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ILE A 606 " --> pdb=" O ALA A 632 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N SER A 627 " --> pdb=" O ALA A 653 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASN A 655 " --> pdb=" O SER A 627 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE A 629 " --> pdb=" O ASN A 655 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ASN A 681 " --> pdb=" O ASN A 652 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ILE A 654 " --> pdb=" O ASN A 681 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 705 through 706 removed outlier: 7.370A pdb=" N ILE A 705 " --> pdb=" O GLN A 730 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N LYS A 732 " --> pdb=" O ILE A 705 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL A 729 " --> pdb=" O GLU A 751 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N SER A 753 " --> pdb=" O VAL A 729 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE A 731 " --> pdb=" O SER A 753 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N SER A 750 " --> pdb=" O TYR A 777 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N LYS A 779 " --> pdb=" O SER A 750 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ILE A 752 " --> pdb=" O LYS A 779 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N THR A 803 " --> pdb=" O LEU A 832 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE A 831 " --> pdb=" O ASN A 857 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE A 933 " --> pdb=" O GLN A 958 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N LYS A 960 " --> pdb=" O ILE A 933 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LEU A 935 " --> pdb=" O LYS A 960 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL A 957 " --> pdb=" O GLU A 979 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N SER A 981 " --> pdb=" O VAL A 957 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE A 959 " --> pdb=" O SER A 981 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N SER A 978 " --> pdb=" O TYR A1005 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N LYS A1007 " --> pdb=" O SER A 978 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE A 980 " --> pdb=" O LYS A1007 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL A1004 " --> pdb=" O HIS A1032 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ASP A1034 " --> pdb=" O VAL A1004 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N LEU A1006 " --> pdb=" O ASP A1034 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N THR A1031 " --> pdb=" O LEU A1060 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE A1059 " --> pdb=" O ASN A1085 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.841A pdb=" N GLU H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N TRP H 47 " --> pdb=" O GLU H 38 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ARG H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N LEU H 45 " --> pdb=" O ARG H 40 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 18 through 19 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 18 through 19 current: chain 'H' and resid 77 through 82 No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.508A pdb=" N VAL L 13 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 134 hydrogen bonds defined for protein. 339 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.65 Time building geometry restraints manager: 2.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2661 1.33 - 1.45: 1783 1.45 - 1.58: 4962 1.58 - 1.70: 66 1.70 - 1.82: 35 Bond restraints: 9507 Sorted by residual: bond pdb=" N ILE H 34 " pdb=" CA ILE H 34 " ideal model delta sigma weight residual 1.459 1.504 -0.045 1.19e-02 7.06e+03 1.45e+01 bond pdb=" C2 BGC A1614 " pdb=" C3 BGC A1614 " ideal model delta sigma weight residual 1.522 1.598 -0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" C2 BGC A1638 " pdb=" C3 BGC A1638 " ideal model delta sigma weight residual 1.522 1.595 -0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" C2 BGC A1605 " pdb=" C3 BGC A1605 " ideal model delta sigma weight residual 1.522 1.593 -0.071 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C2 BGC A1630 " pdb=" C3 BGC A1630 " ideal model delta sigma weight residual 1.522 1.593 -0.071 2.00e-02 2.50e+03 1.26e+01 ... (remaining 9502 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 11971 2.31 - 4.62: 773 4.62 - 6.92: 101 6.92 - 9.23: 81 9.23 - 11.54: 1 Bond angle restraints: 12927 Sorted by residual: angle pdb=" N ASN A 580 " pdb=" CA ASN A 580 " pdb=" C ASN A 580 " ideal model delta sigma weight residual 111.17 122.71 -11.54 1.41e+00 5.03e-01 6.70e+01 angle pdb=" C ALA H 78 " pdb=" N TYR H 79 " pdb=" CA TYR H 79 " ideal model delta sigma weight residual 122.87 114.33 8.54 1.61e+00 3.86e-01 2.81e+01 angle pdb=" N TRP L 92 " pdb=" CA TRP L 92 " pdb=" C TRP L 92 " ideal model delta sigma weight residual 113.38 106.89 6.49 1.23e+00 6.61e-01 2.79e+01 angle pdb=" N THR A 171 " pdb=" CA THR A 171 " pdb=" C THR A 171 " ideal model delta sigma weight residual 113.17 107.14 6.03 1.26e+00 6.30e-01 2.29e+01 angle pdb=" N THR A 558 " pdb=" CA THR A 558 " pdb=" C THR A 558 " ideal model delta sigma weight residual 113.30 106.94 6.36 1.34e+00 5.57e-01 2.26e+01 ... (remaining 12922 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 5672 17.85 - 35.70: 291 35.70 - 53.55: 67 53.55 - 71.40: 39 71.40 - 89.25: 3 Dihedral angle restraints: 6072 sinusoidal: 2612 harmonic: 3460 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual 93.00 60.43 32.57 1 1.00e+01 1.00e-02 1.51e+01 dihedral pdb=" C CYS H 92 " pdb=" N CYS H 92 " pdb=" CA CYS H 92 " pdb=" CB CYS H 92 " ideal model delta harmonic sigma weight residual -122.60 -114.11 -8.49 0 2.50e+00 1.60e-01 1.15e+01 dihedral pdb=" CA ASP A 255 " pdb=" CB ASP A 255 " pdb=" CG ASP A 255 " pdb=" OD1 ASP A 255 " ideal model delta sinusoidal sigma weight residual -30.00 -85.07 55.07 1 2.00e+01 2.50e-03 1.03e+01 ... (remaining 6069 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 1373 0.101 - 0.202: 165 0.202 - 0.303: 43 0.303 - 0.404: 36 0.404 - 0.505: 37 Chirality restraints: 1654 Sorted by residual: chirality pdb=" C3 BGC A1629 " pdb=" C2 BGC A1629 " pdb=" C4 BGC A1629 " pdb=" O3 BGC A1629 " both_signs ideal model delta sigma weight residual False 2.44 2.95 -0.51 2.00e-01 2.50e+01 6.38e+00 chirality pdb=" C3 BGC A1626 " pdb=" C2 BGC A1626 " pdb=" C4 BGC A1626 " pdb=" O3 BGC A1626 " both_signs ideal model delta sigma weight residual False 2.44 2.95 -0.51 2.00e-01 2.50e+01 6.38e+00 chirality pdb=" C3 BGC A1636 " pdb=" C2 BGC A1636 " pdb=" C4 BGC A1636 " pdb=" O3 BGC A1636 " both_signs ideal model delta sigma weight residual False 2.44 2.95 -0.50 2.00e-01 2.50e+01 6.35e+00 ... (remaining 1651 not shown) Planarity restraints: 1634 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 704 " -0.018 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C ALA A 704 " 0.064 2.00e-02 2.50e+03 pdb=" O ALA A 704 " -0.025 2.00e-02 2.50e+03 pdb=" N ILE A 705 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 721 " -0.017 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" CG ASN A 721 " 0.060 2.00e-02 2.50e+03 pdb=" OD1 ASN A 721 " -0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN A 721 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 491 " 0.013 2.00e-02 2.50e+03 2.62e-02 6.87e+00 pdb=" C SER A 491 " -0.045 2.00e-02 2.50e+03 pdb=" O SER A 491 " 0.017 2.00e-02 2.50e+03 pdb=" N ALA A 492 " 0.015 2.00e-02 2.50e+03 ... (remaining 1631 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 945 2.74 - 3.28: 9298 3.28 - 3.82: 16314 3.82 - 4.36: 20403 4.36 - 4.90: 34595 Nonbonded interactions: 81555 Sorted by model distance: nonbonded pdb=" O GLY A 853 " pdb=" OG SER A 876 " model vdw 2.200 3.040 nonbonded pdb=" OD1 ASN A 666 " pdb=" O2 BGC A1611 " model vdw 2.202 3.040 nonbonded pdb=" ND2 ASN A 735 " pdb=" OG1 THR A 756 " model vdw 2.210 3.120 nonbonded pdb=" O ALA A 569 " pdb=" ND2 ASN A 600 " model vdw 2.218 3.120 nonbonded pdb=" ND2 ASN A 717 " pdb=" O2 BGC A1621 " model vdw 2.227 2.496 ... (remaining 81550 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.630 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.080 9507 Z= 0.583 Angle : 1.309 11.541 12927 Z= 0.704 Chirality : 0.117 0.505 1654 Planarity : 0.004 0.049 1634 Dihedral : 12.480 89.246 3884 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.48 % Allowed : 4.63 % Favored : 94.90 % Rotamer: Outliers : 0.51 % Allowed : 10.15 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.24), residues: 1254 helix: -1.64 (0.98), residues: 25 sheet: 0.33 (0.19), residues: 758 loop : -0.66 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 33 HIS 0.009 0.002 HIS A 804 PHE 0.026 0.003 PHE H 29 TYR 0.019 0.003 TYR L 30 ARG 0.015 0.002 ARG A 728 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 160 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 678 ASN cc_start: 0.7677 (m-40) cc_final: 0.7402 (m-40) REVERT: A 705 ILE cc_start: 0.7964 (mm) cc_final: 0.7598 (mt) REVERT: A 823 ASN cc_start: 0.7917 (m-40) cc_final: 0.7427 (m-40) REVERT: A 953 GLN cc_start: 0.5653 (tt0) cc_final: 0.5169 (tm-30) REVERT: A 989 ASN cc_start: 0.7449 (m-40) cc_final: 0.6954 (t0) REVERT: L 52 THR cc_start: 0.8579 (m) cc_final: 0.8306 (t) outliers start: 5 outliers final: 2 residues processed: 162 average time/residue: 0.2171 time to fit residues: 49.1012 Evaluate side-chains 107 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 105 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain H residue 98 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.5954 > 50: distance: 7 - 14: 3.252 distance: 14 - 15: 3.097 distance: 15 - 18: 3.843 distance: 16 - 17: 13.887 distance: 18 - 19: 3.548 distance: 19 - 20: 10.061 distance: 19 - 21: 3.605 distance: 22 - 23: 15.568 distance: 23 - 24: 17.415 distance: 23 - 26: 12.126 distance: 24 - 25: 21.807 distance: 24 - 30: 20.662 distance: 26 - 27: 7.592 distance: 27 - 28: 14.579 distance: 28 - 29: 18.981 distance: 30 - 31: 39.694 distance: 31 - 32: 14.574 distance: 31 - 34: 27.981 distance: 32 - 33: 11.178 distance: 32 - 39: 17.848 distance: 34 - 35: 5.008 distance: 35 - 36: 15.294 distance: 36 - 37: 28.267 distance: 37 - 38: 6.085 distance: 39 - 40: 13.486 distance: 39 - 45: 32.531 distance: 40 - 41: 24.963 distance: 40 - 43: 19.580 distance: 41 - 42: 26.681 distance: 41 - 46: 16.107 distance: 43 - 44: 12.379 distance: 44 - 45: 51.807 distance: 46 - 47: 23.670 distance: 47 - 48: 31.702 distance: 48 - 49: 14.075 distance: 48 - 50: 49.079 distance: 50 - 51: 20.136 distance: 51 - 52: 25.453 distance: 51 - 54: 13.150 distance: 52 - 53: 15.572 distance: 52 - 55: 15.708 distance: 55 - 56: 18.103 distance: 56 - 57: 11.011 distance: 56 - 59: 10.421 distance: 57 - 58: 12.919 distance: 57 - 61: 40.144 distance: 59 - 60: 16.221 distance: 61 - 62: 14.770 distance: 62 - 63: 16.557 distance: 62 - 65: 11.110 distance: 63 - 64: 7.196 distance: 63 - 68: 8.702 distance: 65 - 66: 8.210 distance: 65 - 67: 16.030 distance: 68 - 69: 11.551 distance: 69 - 70: 4.799 distance: 69 - 72: 4.714 distance: 70 - 71: 6.393 distance: 70 - 77: 9.074 distance: 73 - 74: 6.411 distance: 74 - 75: 3.509 distance: 75 - 76: 5.825 distance: 77 - 78: 4.002 distance: 78 - 79: 3.444 distance: 78 - 81: 4.280 distance: 81 - 82: 6.484 distance: 82 - 83: 5.007