Starting phenix.real_space_refine on Sat Dec 28 19:21:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xu1_33455/12_2024/7xu1_33455_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xu1_33455/12_2024/7xu1_33455.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xu1_33455/12_2024/7xu1_33455.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xu1_33455/12_2024/7xu1_33455.map" model { file = "/net/cci-nas-00/data/ceres_data/7xu1_33455/12_2024/7xu1_33455_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xu1_33455/12_2024/7xu1_33455_trim.cif" } resolution = 3.0 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= 0.006 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: 5 Type Number sf(0) Gaussians S 126 5.16 5 C 17134 2.51 5 N 4401 2.21 5 O 5256 1.98 5 H 25165 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 52082 Number of models: 1 Model: "" Number of chains: 19 Chain: "C" Number of atoms: 17102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1110, 17102 Classifications: {'peptide': 1110} Link IDs: {'PTRANS': 52, 'TRANS': 1057} Chain breaks: 2 Chain: "B" Number of atoms: 17063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1107, 17063 Classifications: {'peptide': 1107} Link IDs: {'PTRANS': 52, 'TRANS': 1054} Chain breaks: 3 Chain: "A" Number of atoms: 16846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1092, 16846 Classifications: {'peptide': 1092} Link IDs: {'PTRANS': 50, 'TRANS': 1041} Chain breaks: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 231 Unusual residues: {'BLA': 1, 'EIC': 1, 'NAG': 12} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 211 Unusual residues: {'BLA': 1, 'NAG': 12} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "A" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 265 Unusual residues: {'BLA': 1, 'EIC': 2, 'NAG': 13} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 19.81, per 1000 atoms: 0.38 Number of scatterers: 52082 At special positions: 0 Unit cell: (140.052, 152.784, 171.882, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 126 16.00 O 5256 8.00 N 4401 7.00 C 17134 6.00 H 25165 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.06 Simple disulfide: pdb=" SG CYS C 427 " - pdb=" SG CYS A 987 " distance=2.02 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.04 Simple disulfide: pdb=" SG CYS C 987 " - pdb=" SG CYS B 427 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.06 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B 987 " - pdb=" SG CYS A 427 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 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=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " NAG-ASN " NAG A1802 " - " ASN A 331 " " NAG A1803 " - " ASN A 603 " " NAG A1804 " - " ASN A 616 " " NAG A1805 " - " ASN A 657 " " NAG A1806 " - " ASN A 709 " " NAG A1807 " - " ASN A1074 " " NAG A1808 " - " ASN A1098 " " NAG A1809 " - " ASN A 165 " " NAG A1810 " - " ASN A 282 " " NAG A1811 " - " ASN A 343 " " NAG A1813 " - " ASN A 17 " " NAG A1814 " - " ASN A 61 " " NAG A1815 " - " ASN A 149 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 331 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B1074 " " NAG B1308 " - " ASN B1098 " " NAG B1309 " - " ASN B 165 " " NAG B1310 " - " ASN B 282 " " NAG B1311 " - " ASN B 343 " " NAG B1312 " - " ASN B 17 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C1074 " " NAG C1308 " - " ASN C1098 " " NAG C1309 " - " ASN C 165 " " NAG C1310 " - " ASN C 282 " " NAG C1311 " - " ASN C 343 " " NAG C1312 " - " ASN C 17 " " NAG D 1 " - " ASN C 234 " " NAG E 1 " - " ASN C 717 " " NAG F 1 " - " ASN C 801 " " NAG G 1 " - " ASN C1134 " " NAG H 1 " - " ASN B 234 " " NAG I 1 " - " ASN B 717 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN B1134 " " NAG L 1 " - " ASN A 717 " " NAG M 1 " - " ASN A 801 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN A 234 " " NAG P 1 " - " ASN A 122 " Time building additional restraints: 11.33 Conformation dependent library (CDL) restraints added in 3.1 seconds 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB VAL B 70 " Number of C-beta restraints generated: 6188 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 53 sheets defined 24.3% alpha, 25.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.22 Creating SS restraints... Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 366 through 371 removed outlier: 3.663A pdb=" N ASN C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.265A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 619 through 625 Processing helix chain 'C' and resid 626 through 629 Processing helix chain 'C' and resid 630 through 635 removed outlier: 3.669A pdb=" N VAL C 635 " --> pdb=" O PRO C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 753 Processing helix chain 'C' and resid 756 through 783 removed outlier: 3.634A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.574A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 836 through 843 Processing helix chain 'C' and resid 848 through 856 removed outlier: 3.787A pdb=" N ALA C 852 " --> pdb=" O ASP C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.602A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.680A pdb=" N GLU C 990 " --> pdb=" O LYS C 986 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N VAL C 991 " --> pdb=" O CYS C 987 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 removed outlier: 3.792A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 372 removed outlier: 4.290A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.228A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 619 through 625 Processing helix chain 'B' and resid 626 through 629 Processing helix chain 'B' and resid 630 through 635 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 753 removed outlier: 3.590A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 783 removed outlier: 3.603A pdb=" N CYS B 760 " --> pdb=" O TYR B 756 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 848 through 856 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 939 removed outlier: 3.602A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.888A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.052A pdb=" N GLU B 990 " --> pdb=" O LYS B 986 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N VAL B 991 " --> pdb=" O CYS B 987 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 367 through 372 removed outlier: 4.359A pdb=" N SER A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.662A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.574A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 756 through 783 Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.667A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 856 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.944A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.198A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.669A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.715A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 27 through 30 removed outlier: 4.115A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA C 263 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.341A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.658A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.902A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.669A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 9.300A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 10.221A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 10.718A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 84 through 85 removed outlier: 12.886A pdb=" N PHE C 238 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 12.847A pdb=" N PHE C 135 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 12.792A pdb=" N THR C 240 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 10.676A pdb=" N ASN C 137 " --> pdb=" O THR C 240 " (cutoff:3.500A) removed outlier: 10.491A pdb=" N LEU C 242 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 9.300A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 10.221A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 10.718A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 152 through 154 removed outlier: 3.565A pdb=" N MET C 153 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AA7, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.033A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.304A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'C' and resid 551 through 554 removed outlier: 4.166A pdb=" N GLU C 583 " --> pdb=" O ASP C 578 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.542A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.619A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.078A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'C' and resid 787 through 788 Processing sheet with id=AB8, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.922A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.473A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.473A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.226A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.799A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 9.540A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 10.166A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.509A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 12.914A pdb=" N PHE B 238 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 13.141A pdb=" N PHE B 135 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 12.976A pdb=" N THR B 240 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 10.787A pdb=" N ASN B 137 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 10.365A pdb=" N LEU B 242 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 9.540A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 10.166A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.509A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.066A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.275A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'B' and resid 539 through 543 removed outlier: 4.217A pdb=" N GLU B 583 " --> pdb=" O ASP B 578 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.592A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.868A pdb=" N ALA B 701 " --> pdb=" O ILE A 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 712 through 713 removed outlier: 3.861A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.915A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 718 through 728 Processing sheet with id=AD7, first strand: chain 'B' and resid 735 through 736 Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.717A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.540A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.012A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.181A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.875A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 9.261A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 311 through 315 removed outlier: 4.418A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 324 through 325 removed outlier: 7.139A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.865A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.580A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AF1, first strand: chain 'A' and resid 542 through 543 Processing sheet with id=AF2, first strand: chain 'A' and resid 551 through 554 removed outlier: 5.094A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.294A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AF5, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.105A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.470A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.701A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'A' and resid 1094 through 1097 1066 hydrogen bonds defined for protein. 2862 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: 20.54 Time building geometry restraints manager: 13.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.05: 25159 1.05 - 1.27: 4340 1.27 - 1.48: 11425 1.48 - 1.69: 11606 1.69 - 1.91: 156 Bond restraints: 52686 Sorted by residual: bond pdb=" C1C BLA B1313 " pdb=" NC BLA B1313 " ideal model delta sigma weight residual 1.368 1.533 -0.165 2.00e-02 2.50e+03 6.79e+01 bond pdb=" C4C BLA C1313 " pdb=" NC BLA C1313 " ideal model delta sigma weight residual 1.375 1.540 -0.165 2.00e-02 2.50e+03 6.79e+01 bond pdb=" C1C BLA A1816 " pdb=" NC BLA A1816 " ideal model delta sigma weight residual 1.368 1.533 -0.165 2.00e-02 2.50e+03 6.78e+01 bond pdb=" NB BLA C1313 " pdb=" C4B BLA C1313 " ideal model delta sigma weight residual 1.371 1.534 -0.163 2.00e-02 2.50e+03 6.65e+01 bond pdb=" C4C BLA B1313 " pdb=" NC BLA B1313 " ideal model delta sigma weight residual 1.375 1.538 -0.163 2.00e-02 2.50e+03 6.61e+01 ... (remaining 52681 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.03: 93985 4.03 - 8.07: 397 8.07 - 12.10: 12 12.10 - 16.14: 6 16.14 - 20.17: 6 Bond angle restraints: 94406 Sorted by residual: angle pdb=" CA CYS B 432 " pdb=" CB CYS B 432 " pdb=" SG CYS B 432 " ideal model delta sigma weight residual 114.40 134.57 -20.17 2.30e+00 1.89e-01 7.69e+01 angle pdb=" CA CYS C 432 " pdb=" CB CYS C 432 " pdb=" SG CYS C 432 " ideal model delta sigma weight residual 114.40 134.39 -19.99 2.30e+00 1.89e-01 7.56e+01 angle pdb=" CA ASP B 80 " pdb=" C ASP B 80 " pdb=" O ASP B 80 " ideal model delta sigma weight residual 121.47 113.98 7.49 1.15e+00 7.56e-01 4.24e+01 angle pdb=" N VAL B 70 " pdb=" CA VAL B 70 " pdb=" HA VAL B 70 " ideal model delta sigma weight residual 110.00 92.08 17.92 3.00e+00 1.11e-01 3.57e+01 angle pdb=" C11 EIC C1314 " pdb=" C10 EIC C1314 " pdb=" C9 EIC C1314 " ideal model delta sigma weight residual 127.32 109.40 17.92 3.00e+00 1.11e-01 3.57e+01 ... (remaining 94401 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 23561 17.82 - 35.65: 1924 35.65 - 53.47: 538 53.47 - 71.30: 149 71.30 - 89.12: 24 Dihedral angle restraints: 26196 sinusoidal: 14624 harmonic: 11572 Sorted by residual: dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual 93.00 149.95 -56.95 1 1.00e+01 1.00e-02 4.36e+01 dihedral pdb=" CA ASN B 165 " pdb=" C ASN B 165 " pdb=" N CYS B 166 " pdb=" CA CYS B 166 " ideal model delta harmonic sigma weight residual -180.00 -148.55 -31.45 0 5.00e+00 4.00e-02 3.96e+01 dihedral pdb=" CA VAL B 130 " pdb=" C VAL B 130 " pdb=" N CYS B 131 " pdb=" CA CYS B 131 " ideal model delta harmonic sigma weight residual 180.00 -151.03 -28.97 0 5.00e+00 4.00e-02 3.36e+01 ... (remaining 26193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.554: 4390 0.554 - 1.109: 0 1.109 - 1.663: 0 1.663 - 2.218: 0 2.218 - 2.772: 1 Chirality restraints: 4391 Sorted by residual: chirality pdb=" CA VAL B 70 " pdb=" N VAL B 70 " pdb=" C VAL B 70 " pdb=" CB VAL B 70 " both_signs ideal model delta sigma weight residual False 2.44 -0.33 2.77 2.00e-01 2.50e+01 1.92e+02 chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B 122 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" C1 NAG C1302 " pdb=" ND2 ASN C 122 " pdb=" C2 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 4388 not shown) Planarity restraints: 7939 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" ND BLA C1313 " 0.136 2.00e-02 2.50e+03 1.46e-01 5.34e+02 pdb=" C1A BLA C1313 " -0.333 2.00e-02 2.50e+03 pdb=" C1D BLA C1313 " 0.031 2.00e-02 2.50e+03 pdb=" C2D BLA C1313 " -0.034 2.00e-02 2.50e+03 pdb=" C3D BLA C1313 " 0.026 2.00e-02 2.50e+03 pdb=" C4D BLA C1313 " 0.133 2.00e-02 2.50e+03 pdb=" CAD BLA C1313 " -0.009 2.00e-02 2.50e+03 pdb=" CHA BLA C1313 " 0.207 2.00e-02 2.50e+03 pdb=" CHD BLA C1313 " -0.012 2.00e-02 2.50e+03 pdb=" CMD BLA C1313 " -0.144 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND BLA B1313 " 0.131 2.00e-02 2.50e+03 1.44e-01 5.17e+02 pdb=" C1A BLA B1313 " -0.331 2.00e-02 2.50e+03 pdb=" C1D BLA B1313 " 0.030 2.00e-02 2.50e+03 pdb=" C2D BLA B1313 " -0.035 2.00e-02 2.50e+03 pdb=" C3D BLA B1313 " 0.026 2.00e-02 2.50e+03 pdb=" C4D BLA B1313 " 0.131 2.00e-02 2.50e+03 pdb=" CAD BLA B1313 " -0.013 2.00e-02 2.50e+03 pdb=" CHA BLA B1313 " 0.201 2.00e-02 2.50e+03 pdb=" CHD BLA B1313 " 0.002 2.00e-02 2.50e+03 pdb=" CMD BLA B1313 " -0.140 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB BLA C1313 " 0.083 2.00e-02 2.50e+03 9.19e-02 2.11e+02 pdb=" OB BLA C1313 " -0.007 2.00e-02 2.50e+03 pdb=" C1B BLA C1313 " 0.086 2.00e-02 2.50e+03 pdb=" C2B BLA C1313 " 0.014 2.00e-02 2.50e+03 pdb=" C3B BLA C1313 " -0.027 2.00e-02 2.50e+03 pdb=" C4A BLA C1313 " -0.208 2.00e-02 2.50e+03 pdb=" C4B BLA C1313 " 0.015 2.00e-02 2.50e+03 pdb=" CAB BLA C1313 " -0.089 2.00e-02 2.50e+03 pdb=" CHB BLA C1313 " 0.133 2.00e-02 2.50e+03 pdb=" CMB BLA C1313 " 0.000 2.00e-02 2.50e+03 ... (remaining 7936 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.27: 7571 2.27 - 2.85: 114625 2.85 - 3.44: 131516 3.44 - 4.02: 190244 4.02 - 4.60: 285725 Nonbonded interactions: 729681 Sorted by model distance: nonbonded pdb="HH11 ARG A 346 " pdb=" O PHE A 347 " model vdw 1.691 2.450 nonbonded pdb=" OE2 GLU B 725 " pdb=" HE2 HIS B1064 " model vdw 1.694 2.450 nonbonded pdb=" O ASP A 253 " pdb=" H GLY A 257 " model vdw 1.695 2.450 nonbonded pdb=" OD2 ASP C 40 " pdb="HH12 ARG C 44 " model vdw 1.710 2.450 nonbonded pdb=" OG SER A1051 " pdb=" HD1 HIS A1064 " model vdw 1.711 2.450 ... (remaining 729676 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 69 or (resid 70 and (name N or name CA or name \ C or name O or name CB or name CG1 or name CG2 or name HA or name HB or name HG1 \ 1 or name HG12 or name HG13 or name HG21 or name HG22 or name HG23)) or resid 77 \ through 79 or (resid 80 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)) or resid \ 81 through 142 or (resid 143 and (name N or name CA or name C or name O or name \ CB or name CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or na \ me HG13 or name HG21 or name HG22 or name HG23)) or resid 144 through 152 or (re \ sid 153 and (name N or name CA or name C or name O or name CB or name CG or name \ SD or name CE or name HA or name HB2 or name HB3 or name HG2 or name HG3 or nam \ e HE1 or name HE2 or name HE3)) or resid 154 through 244 or (resid 245 and (name \ N or name CA or name C or name O or name CB or name CG or name ND1 or name CD2 \ or name CE1 or name NE2 or name HA or name HB2 or name HB3 or name HD1 or name H \ D2 or name HE1)) or resid 246 through 256 or (resid 257 and (name N or name CA o \ r name C or name O or name HA2 or name HA3)) or resid 258 through 1140 or resid \ 1804 through 1811 or resid 1813 through 1814)) selection = (chain 'B' and (resid 14 through 70 or (resid 77 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ or name HA or \ name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE \ 2 or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 78 through 148 or ( \ resid 149 and (name N or name CA or name C or name O or name CB or name CG or na \ me OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD21)) o \ r resid 150 through 226 or (resid 227 and (name N or name CA or name C or name O \ or name CB or name CG1 or name CG2 or name HA or name HB or name HG11 or name H \ G12 or name HG13 or name HG21 or name HG22 or name HG23)) or resid 228 through 6 \ 02 or (resid 603 and (name N or name CA or name C or name O or name CB or name C \ G or name OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name H \ D21)) or resid 604 through 618 or (resid 632 and (name N or name CA or name C or \ name O or name CB or name OG1 or name CG2 or name HA or name HB or name HG1 or \ name HG21 or name HG22 or name HG23)) or resid 633 through 829 or (resid 835 and \ (name N or name CA or name C or name O or name CB or name CG or name CD or name \ CE or name NZ or name HA or name HB2 or name HB3 or name HG2 or name HG3 or nam \ e HD2 or name HD3 or name HE2 or name HE3 or name HZ1 or name HZ2 or name HZ3)) \ or resid 836 through 1140 or resid 1301 through 1308 or resid 1310 through 1311) \ ) selection = (chain 'C' and (resid 14 through 70 or (resid 77 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ or name HA or \ name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE \ 2 or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 78 through 142 or ( \ resid 143 and (name N or name CA or name C or name O or name CB or name CG1 or n \ ame CG2 or name HA or name HB or name HG11 or name HG12 or name HG13 or name HG2 \ 1 or name HG22 or name HG23)) or resid 144 through 148 or (resid 149 and (name N \ or name CA or name C or name O or name CB or name CG or name OD1 or name ND2 or \ name H or name HA or name HB2 or name HB3 or name HD21)) or resid 150 through 2 \ 26 or (resid 227 and (name N or name CA or name C or name O or name CB or name C \ G1 or name CG2 or name HA or name HB or name HG11 or name HG12 or name HG13 or n \ ame HG21 or name HG22 or name HG23)) or resid 228 through 602 or (resid 603 and \ (name N or name CA or name C or name O or name CB or name CG or name OD1 or name \ ND2 or name H or name HA or name HB2 or name HB3 or name HD21)) or resid 604 th \ rough 618 or (resid 632 and (name N or name CA or name C or name O or name CB or \ name OG1 or name CG2 or name HA or name HB or name HG1 or name HG21 or name HG2 \ 2 or name HG23)) or resid 633 through 829 or (resid 835 and (name N or name CA o \ r name C or name O or name CB or name CG or name CD or name CE or name NZ or nam \ e HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or \ name HE2 or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 836 through \ 1140 or resid 1302 through 1309 or resid 1311 through 1312)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } 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=0.00 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: 2.060 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: 0.720 Extract box with map and model: 1.630 Check model and map are aligned: 0.310 Set scattering table: 0.380 Process input model: 90.030 Find NCS groups from input model: 2.020 Set up NCS constraints: 0.200 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: 0.010 Load rotamer database and sin/cos tables:10.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 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 : 0.012 0.165 27521 Z= 0.813 Angle : 0.881 20.175 37442 Z= 0.401 Chirality : 0.066 2.772 4391 Planarity : 0.005 0.146 4758 Dihedral : 13.723 89.124 10890 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.24 % Allowed : 0.38 % Favored : 99.38 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.92 (0.14), residues: 3285 helix: 0.57 (0.20), residues: 732 sheet: -0.33 (0.18), residues: 741 loop : -1.23 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 152 HIS 0.007 0.001 HIS B 207 PHE 0.014 0.001 PHE A 79 TYR 0.021 0.001 TYR A 365 ARG 0.015 0.001 ARG C 847 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 199 time to evaluate : 3.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 70 VAL cc_start: 0.6984 (OUTLIER) cc_final: 0.6679 (m) REVERT: C 1002 GLN cc_start: 0.7809 (tp-100) cc_final: 0.7566 (tp-100) REVERT: B 78 ARG cc_start: 0.6091 (ttp80) cc_final: 0.5805 (ttp80) REVERT: B 170 TYR cc_start: 0.7245 (t80) cc_final: 0.6966 (t80) REVERT: A 389 ASP cc_start: 0.7610 (m-30) cc_final: 0.7343 (m-30) REVERT: A 1101 HIS cc_start: 0.7927 (m90) cc_final: 0.7580 (m90) outliers start: 7 outliers final: 2 residues processed: 204 average time/residue: 2.1080 time to fit residues: 515.0619 Evaluate side-chains 121 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 118 time to evaluate : 3.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain A residue 227 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 278 optimal weight: 0.7980 chunk 250 optimal weight: 0.4980 chunk 138 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 168 optimal weight: 0.7980 chunk 133 optimal weight: 0.9990 chunk 258 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 192 optimal weight: 4.9990 chunk 299 optimal weight: 6.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 HIS B 607 GLN A 137 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 27521 Z= 0.207 Angle : 0.536 14.339 37442 Z= 0.278 Chirality : 0.053 1.979 4391 Planarity : 0.004 0.066 4758 Dihedral : 8.381 89.587 5008 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.42 % Allowed : 4.69 % Favored : 94.90 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % 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: -0.73 (0.14), residues: 3285 helix: 1.07 (0.20), residues: 765 sheet: -0.28 (0.18), residues: 731 loop : -1.29 (0.14), residues: 1789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 64 HIS 0.005 0.001 HIS B1064 PHE 0.014 0.001 PHE A 643 TYR 0.018 0.001 TYR B 365 ARG 0.006 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 3.190 Fit side-chains revert: symmetry clash REVERT: C 675 GLN cc_start: 0.7526 (OUTLIER) cc_final: 0.6957 (tt0) REVERT: C 869 MET cc_start: 0.8494 (mtp) cc_final: 0.8281 (mtp) REVERT: C 1002 GLN cc_start: 0.7759 (tp-100) cc_final: 0.7507 (tp-100) REVERT: B 170 TYR cc_start: 0.7408 (t80) cc_final: 0.7044 (t80) REVERT: B 212 LEU cc_start: 0.8097 (tp) cc_final: 0.7866 (tt) REVERT: A 389 ASP cc_start: 0.7603 (m-30) cc_final: 0.7341 (m-30) REVERT: A 1101 HIS cc_start: 0.7962 (m90) cc_final: 0.7620 (m90) outliers start: 12 outliers final: 2 residues processed: 137 average time/residue: 1.9057 time to fit residues: 321.0736 Evaluate side-chains 118 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 115 time to evaluate : 3.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain A residue 227 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 166 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 249 optimal weight: 1.9990 chunk 204 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 300 optimal weight: 10.0000 chunk 324 optimal weight: 3.9990 chunk 267 optimal weight: 0.0470 chunk 297 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 240 optimal weight: 0.0000 overall best weight: 1.0088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 969 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 27521 Z= 0.236 Angle : 0.517 14.348 37442 Z= 0.268 Chirality : 0.052 1.876 4391 Planarity : 0.003 0.054 4758 Dihedral : 7.502 78.767 5005 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.38 % Allowed : 5.49 % Favored : 94.13 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % 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: -0.69 (0.14), residues: 3285 helix: 1.12 (0.20), residues: 760 sheet: -0.19 (0.18), residues: 713 loop : -1.28 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 64 HIS 0.007 0.001 HIS C 146 PHE 0.015 0.001 PHE A 643 TYR 0.018 0.001 TYR B 365 ARG 0.004 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 3.148 Fit side-chains revert: symmetry clash REVERT: C 675 GLN cc_start: 0.7532 (OUTLIER) cc_final: 0.6956 (tt0) REVERT: C 1002 GLN cc_start: 0.7748 (tp-100) cc_final: 0.7475 (tp-100) REVERT: B 212 LEU cc_start: 0.8021 (tp) cc_final: 0.7742 (tt) REVERT: A 389 ASP cc_start: 0.7676 (m-30) cc_final: 0.7408 (m-30) REVERT: A 1101 HIS cc_start: 0.7984 (m90) cc_final: 0.7640 (m90) outliers start: 11 outliers final: 5 residues processed: 129 average time/residue: 1.8936 time to fit residues: 300.0086 Evaluate side-chains 124 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 118 time to evaluate : 3.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 987 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 296 optimal weight: 3.9990 chunk 225 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 143 optimal weight: 0.2980 chunk 201 optimal weight: 4.9990 chunk 301 optimal weight: 1.9990 chunk 318 optimal weight: 1.9990 chunk 157 optimal weight: 10.0000 chunk 285 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 969 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 27521 Z= 0.349 Angle : 0.551 14.970 37442 Z= 0.286 Chirality : 0.053 1.824 4391 Planarity : 0.004 0.047 4758 Dihedral : 7.089 70.746 5005 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.52 % Allowed : 7.08 % Favored : 92.40 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % 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: -0.74 (0.14), residues: 3285 helix: 0.98 (0.20), residues: 756 sheet: -0.17 (0.18), residues: 747 loop : -1.30 (0.14), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 64 HIS 0.003 0.001 HIS B 146 PHE 0.015 0.001 PHE B 86 TYR 0.025 0.001 TYR B 365 ARG 0.003 0.000 ARG C 765 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 3.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 675 GLN cc_start: 0.7491 (OUTLIER) cc_final: 0.6938 (tt0) REVERT: A 389 ASP cc_start: 0.7841 (m-30) cc_final: 0.7574 (m-30) REVERT: A 1101 HIS cc_start: 0.8023 (m90) cc_final: 0.7661 (m90) outliers start: 15 outliers final: 8 residues processed: 131 average time/residue: 1.7835 time to fit residues: 291.5484 Evaluate side-chains 122 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 3.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 987 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 265 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 237 optimal weight: 7.9990 chunk 131 optimal weight: 1.9990 chunk 272 optimal weight: 0.0870 chunk 220 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 162 optimal weight: 1.9990 chunk 286 optimal weight: 0.3980 chunk 80 optimal weight: 3.9990 overall best weight: 1.0964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 27521 Z= 0.246 Angle : 0.513 14.199 37442 Z= 0.266 Chirality : 0.052 1.806 4391 Planarity : 0.003 0.044 4758 Dihedral : 6.691 69.767 5005 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.56 % Allowed : 7.78 % Favored : 91.67 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % 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: -0.68 (0.14), residues: 3285 helix: 1.05 (0.20), residues: 754 sheet: -0.15 (0.18), residues: 741 loop : -1.27 (0.14), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 64 HIS 0.003 0.001 HIS B1064 PHE 0.010 0.001 PHE B 86 TYR 0.018 0.001 TYR B 365 ARG 0.002 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 3.154 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 675 GLN cc_start: 0.7530 (OUTLIER) cc_final: 0.6993 (tt0) REVERT: C 1002 GLN cc_start: 0.7800 (tp-100) cc_final: 0.7503 (tp-100) REVERT: A 389 ASP cc_start: 0.7804 (m-30) cc_final: 0.7547 (m-30) REVERT: A 1101 HIS cc_start: 0.8035 (m90) cc_final: 0.7680 (m90) outliers start: 16 outliers final: 8 residues processed: 131 average time/residue: 1.9101 time to fit residues: 313.8365 Evaluate side-chains 123 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 3.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 987 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 107 optimal weight: 1.9990 chunk 287 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 187 optimal weight: 0.3980 chunk 78 optimal weight: 2.9990 chunk 319 optimal weight: 1.9990 chunk 265 optimal weight: 0.8980 chunk 147 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 167 optimal weight: 0.0570 overall best weight: 0.8702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1106 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 27521 Z= 0.214 Angle : 0.505 13.977 37442 Z= 0.261 Chirality : 0.052 1.807 4391 Planarity : 0.003 0.042 4758 Dihedral : 6.381 68.320 5005 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.73 % Allowed : 8.02 % Favored : 91.25 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % 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: -0.62 (0.14), residues: 3285 helix: 1.14 (0.20), residues: 754 sheet: -0.12 (0.18), residues: 726 loop : -1.24 (0.14), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 64 HIS 0.004 0.001 HIS B 146 PHE 0.013 0.001 PHE A 643 TYR 0.016 0.001 TYR C1138 ARG 0.002 0.000 ARG C 765 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 3.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 675 GLN cc_start: 0.7516 (OUTLIER) cc_final: 0.6974 (tt0) REVERT: C 1002 GLN cc_start: 0.7821 (tp-100) cc_final: 0.7534 (tp-100) REVERT: A 389 ASP cc_start: 0.7799 (m-30) cc_final: 0.7547 (m-30) REVERT: A 1101 HIS cc_start: 0.8002 (m90) cc_final: 0.7635 (m90) outliers start: 21 outliers final: 11 residues processed: 139 average time/residue: 1.7753 time to fit residues: 307.8113 Evaluate side-chains 125 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 3.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 986 LYS Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 987 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 307 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 233 optimal weight: 5.9990 chunk 180 optimal weight: 0.6980 chunk 268 optimal weight: 1.9990 chunk 178 optimal weight: 4.9990 chunk 318 optimal weight: 1.9990 chunk 199 optimal weight: 2.9990 chunk 193 optimal weight: 0.9980 chunk 146 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1106 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 27521 Z= 0.288 Angle : 0.521 14.245 37442 Z= 0.270 Chirality : 0.052 1.803 4391 Planarity : 0.003 0.040 4758 Dihedral : 6.352 66.126 5005 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.83 % Allowed : 8.54 % Favored : 90.62 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % 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: -0.64 (0.14), residues: 3285 helix: 1.09 (0.20), residues: 756 sheet: -0.13 (0.18), residues: 734 loop : -1.25 (0.14), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 64 HIS 0.003 0.001 HIS B 146 PHE 0.014 0.001 PHE A 643 TYR 0.021 0.001 TYR B 365 ARG 0.003 0.000 ARG C 765 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 3.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 1002 GLN cc_start: 0.7798 (tp-100) cc_final: 0.7505 (tp-100) REVERT: A 389 ASP cc_start: 0.7839 (m-30) cc_final: 0.7591 (m-30) REVERT: A 1101 HIS cc_start: 0.8052 (m90) cc_final: 0.7686 (m90) outliers start: 24 outliers final: 13 residues processed: 135 average time/residue: 1.7641 time to fit residues: 296.9510 Evaluate side-chains 125 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 3.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 986 LYS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 987 CYS Chi-restraints excluded: chain A residue 994 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 196 optimal weight: 3.9990 chunk 127 optimal weight: 8.9990 chunk 189 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 202 optimal weight: 1.9990 chunk 216 optimal weight: 2.9990 chunk 157 optimal weight: 0.8980 chunk 29 optimal weight: 0.1980 chunk 250 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 HIS A1106 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 27521 Z= 0.230 Angle : 0.512 14.025 37442 Z= 0.265 Chirality : 0.052 1.893 4391 Planarity : 0.003 0.040 4758 Dihedral : 6.219 65.249 5005 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.73 % Allowed : 9.06 % Favored : 90.21 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % 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: -0.60 (0.14), residues: 3285 helix: 1.14 (0.20), residues: 756 sheet: -0.09 (0.19), residues: 726 loop : -1.22 (0.14), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 64 HIS 0.005 0.001 HIS B 69 PHE 0.013 0.001 PHE A 643 TYR 0.017 0.001 TYR B 365 ARG 0.002 0.000 ARG C 765 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 3.238 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 427 CYS cc_start: 0.3899 (m) cc_final: 0.3575 (m) REVERT: C 1002 GLN cc_start: 0.7824 (tp-100) cc_final: 0.7540 (tp-100) REVERT: A 389 ASP cc_start: 0.7828 (m-30) cc_final: 0.7580 (m-30) REVERT: A 902 MET cc_start: 0.8541 (mmt) cc_final: 0.8264 (mmt) REVERT: A 1101 HIS cc_start: 0.8041 (m90) cc_final: 0.7674 (m90) outliers start: 21 outliers final: 14 residues processed: 134 average time/residue: 1.7323 time to fit residues: 290.0981 Evaluate side-chains 124 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 3.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 986 LYS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 987 CYS Chi-restraints excluded: chain A residue 994 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 289 optimal weight: 0.9980 chunk 304 optimal weight: 0.7980 chunk 278 optimal weight: 0.9980 chunk 296 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 232 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 267 optimal weight: 2.9990 chunk 280 optimal weight: 1.9990 chunk 295 optimal weight: 0.7980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 HIS A1106 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 27521 Z= 0.231 Angle : 0.516 14.015 37442 Z= 0.268 Chirality : 0.053 1.985 4391 Planarity : 0.003 0.039 4758 Dihedral : 6.185 64.401 5005 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.66 % Allowed : 9.10 % Favored : 90.24 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % 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: -0.60 (0.14), residues: 3285 helix: 1.15 (0.20), residues: 756 sheet: -0.09 (0.18), residues: 726 loop : -1.23 (0.14), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 64 HIS 0.003 0.001 HIS B 146 PHE 0.013 0.001 PHE A 643 TYR 0.016 0.001 TYR B 365 ARG 0.002 0.000 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 3.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1002 GLN cc_start: 0.7824 (tp-100) cc_final: 0.7534 (tp-100) REVERT: A 389 ASP cc_start: 0.7811 (m-30) cc_final: 0.7569 (m-30) REVERT: A 902 MET cc_start: 0.8558 (mmt) cc_final: 0.8264 (mmt) REVERT: A 1101 HIS cc_start: 0.8053 (m90) cc_final: 0.7687 (m90) outliers start: 19 outliers final: 12 residues processed: 124 average time/residue: 1.7681 time to fit residues: 275.8950 Evaluate side-chains 121 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 3.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 987 CYS Chi-restraints excluded: chain A residue 994 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 194 optimal weight: 1.9990 chunk 313 optimal weight: 1.9990 chunk 191 optimal weight: 7.9990 chunk 148 optimal weight: 0.5980 chunk 217 optimal weight: 0.9980 chunk 328 optimal weight: 3.9990 chunk 302 optimal weight: 0.6980 chunk 261 optimal weight: 0.8980 chunk 27 optimal weight: 0.0980 chunk 202 optimal weight: 1.9990 chunk 160 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1002 GLN B 164 ASN A 836 GLN A1106 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 27521 Z= 0.180 Angle : 0.491 13.708 37442 Z= 0.254 Chirality : 0.051 1.764 4391 Planarity : 0.003 0.041 4758 Dihedral : 5.977 63.578 5005 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.49 % Allowed : 9.13 % Favored : 90.38 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % 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: -0.53 (0.14), residues: 3285 helix: 1.32 (0.20), residues: 747 sheet: -0.09 (0.18), residues: 726 loop : -1.20 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 64 HIS 0.003 0.001 HIS B1064 PHE 0.016 0.001 PHE A 133 TYR 0.015 0.001 TYR C1138 ARG 0.002 0.000 ARG C1014 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 3.155 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 1002 GLN cc_start: 0.7795 (tp40) cc_final: 0.7543 (tp-100) REVERT: B 170 TYR cc_start: 0.7481 (t80) cc_final: 0.7166 (t80) REVERT: A 389 ASP cc_start: 0.7726 (m-30) cc_final: 0.7470 (m-30) REVERT: A 1101 HIS cc_start: 0.8006 (m90) cc_final: 0.7642 (m90) outliers start: 14 outliers final: 11 residues processed: 129 average time/residue: 1.7433 time to fit residues: 285.4243 Evaluate side-chains 123 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 3.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 987 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 207 optimal weight: 0.9990 chunk 278 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 241 optimal weight: 0.4980 chunk 38 optimal weight: 0.9990 chunk 72 optimal weight: 0.4980 chunk 262 optimal weight: 0.6980 chunk 109 optimal weight: 5.9990 chunk 269 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.114527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.084018 restraints weight = 116420.879| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.46 r_work: 0.2931 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 27521 Z= 0.184 Angle : 0.489 13.819 37442 Z= 0.253 Chirality : 0.051 1.832 4391 Planarity : 0.003 0.041 4758 Dihedral : 5.863 62.573 5005 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.38 % Allowed : 9.44 % Favored : 90.17 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % 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: -0.47 (0.14), residues: 3285 helix: 1.37 (0.20), residues: 748 sheet: -0.06 (0.19), residues: 718 loop : -1.16 (0.14), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 64 HIS 0.003 0.000 HIS B 207 PHE 0.015 0.001 PHE C 140 TYR 0.014 0.001 TYR B 365 ARG 0.001 0.000 ARG A 983 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8552.12 seconds wall clock time: 149 minutes 15.71 seconds (8955.71 seconds total)