Starting phenix.real_space_refine on Sun Jan 26 12:13:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tp0_26043/01_2025/7tp0_26043.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tp0_26043/01_2025/7tp0_26043.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tp0_26043/01_2025/7tp0_26043.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tp0_26043/01_2025/7tp0_26043.map" model { file = "/net/cci-nas-00/data/ceres_data/7tp0_26043/01_2025/7tp0_26043.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tp0_26043/01_2025/7tp0_26043.cif" } resolution = 3.57 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= -0.004 sd= 0.138 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 15641 2.51 5 N 4020 2.21 5 O 4823 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 24589 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 7985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 7985 Classifications: {'peptide': 1022} Link IDs: {'PTRANS': 49, 'TRANS': 972} Chain breaks: 6 Chain: "B" Number of atoms: 7859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1007, 7859 Classifications: {'peptide': 1007} Link IDs: {'PTRANS': 48, 'TRANS': 958} Chain breaks: 7 Chain: "C" Number of atoms: 7891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 7891 Classifications: {'peptide': 1011} Link IDs: {'PTRANS': 48, 'TRANS': 962} Chain breaks: 7 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: "Q" 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: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 14.06, per 1000 atoms: 0.57 Number of scatterers: 24589 At special positions: 0 Unit cell: (128.52, 142.56, 177.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 105 16.00 O 4823 8.00 N 4020 7.00 C 15641 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 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=2.01 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=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 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=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 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 A1032 " - pdb=" SG CYS A1043 " distance=2.00 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.02 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " 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=2.01 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " 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=2.02 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 Q 1 " - " NAG Q 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG A1311 " - " ASN A 165 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 343 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 61 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 122 " " NAG B1307 " - " ASN B 282 " " NAG B1308 " - " ASN B 165 " " NAG B1309 " - " ASN B 616 " " NAG B1310 " - " ASN B 709 " " NAG B1311 " - " ASN B1074 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C1074 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 165 " " NAG C1309 " - " ASN C 657 " " NAG C1310 " - " ASN C 709 " " NAG C1311 " - " ASN C 122 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 234 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN B1134 " " NAG L 1 " - " ASN B 717 " " NAG M 1 " - " ASN B1098 " " NAG N 1 " - " ASN C 234 " " NAG O 1 " - " ASN C1098 " " NAG P 1 " - " ASN C1134 " " NAG Q 1 " - " ASN C 801 " Time building additional restraints: 6.28 Conformation dependent library (CDL) restraints added in 3.1 seconds 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5696 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 45 sheets defined 27.4% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.52 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.104A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.873A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 498 through 502 removed outlier: 3.899A pdb=" N GLY A 502 " --> pdb=" O PRO A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 625 Processing helix chain 'A' and resid 633 through 639 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.941A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.107A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.599A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.720A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.599A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.532A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (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 removed outlier: 3.689A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.129A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.045A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.094A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.478A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.565A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.896A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.927A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.612A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (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: 3.974A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (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 removed outlier: 3.829A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.575A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE B1013 " --> pdb=" O THR B1009 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1145 removed outlier: 3.683A pdb=" N LEU B1145 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.800A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.143A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.636A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.545A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.795A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.659A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.768A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.557A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.105A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.864A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 Processing helix chain 'C' and resid 941 through 944 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.541A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.755A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.253A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER C1021 " --> pdb=" O GLU C1017 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.998A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.857A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.807A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.564A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.883A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.592A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.766A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 451 through 454 removed outlier: 4.304A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 660 removed outlier: 6.128A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.510A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.117A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.855A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.918A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.893A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.001A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 85 removed outlier: 5.370A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.556A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.291A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.825A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.500A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.677A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.251A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AD2, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.569A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1123 removed outlier: 4.010A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.046A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.908A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.740A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 324 through 328 removed outlier: 6.011A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.402A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.617A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.655A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1123 removed outlier: 3.636A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1094 through 1097 1022 hydrogen bonds defined for protein. 2760 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: 11.18 Time building geometry restraints manager: 7.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6768 1.33 - 1.46: 4646 1.46 - 1.58: 13578 1.58 - 1.70: 0 1.70 - 1.83: 129 Bond restraints: 25121 Sorted by residual: bond pdb=" C5 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.413 1.492 -0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" CA PRO A 792 " pdb=" C PRO A 792 " ideal model delta sigma weight residual 1.514 1.536 -0.021 5.50e-03 3.31e+04 1.53e+01 bond pdb=" C5 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.413 1.490 -0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" C5 NAG C1302 " pdb=" O5 NAG C1302 " ideal model delta sigma weight residual 1.413 1.490 -0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" C5 NAG C1311 " pdb=" O5 NAG C1311 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.43e+01 ... (remaining 25116 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.81: 33880 4.81 - 9.63: 287 9.63 - 14.44: 6 14.44 - 19.26: 0 19.26 - 24.07: 1 Bond angle restraints: 34174 Sorted by residual: angle pdb=" CA VAL B 622 " pdb=" CB VAL B 622 " pdb=" CG1 VAL B 622 " ideal model delta sigma weight residual 110.40 134.47 -24.07 1.70e+00 3.46e-01 2.01e+02 angle pdb=" N CYS B 391 " pdb=" CA CYS B 391 " pdb=" C CYS B 391 " ideal model delta sigma weight residual 108.96 119.56 -10.60 1.49e+00 4.50e-01 5.06e+01 angle pdb=" N CYS C 391 " pdb=" CA CYS C 391 " pdb=" C CYS C 391 " ideal model delta sigma weight residual 109.07 119.45 -10.38 1.52e+00 4.33e-01 4.67e+01 angle pdb=" CA PRO A 631 " pdb=" N PRO A 631 " pdb=" CD PRO A 631 " ideal model delta sigma weight residual 112.00 102.92 9.08 1.40e+00 5.10e-01 4.20e+01 angle pdb=" N ARG B 457 " pdb=" CA ARG B 457 " pdb=" C ARG B 457 " ideal model delta sigma weight residual 111.24 118.23 -6.99 1.29e+00 6.01e-01 2.94e+01 ... (remaining 34169 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 14588 17.87 - 35.75: 908 35.75 - 53.62: 172 53.62 - 71.50: 58 71.50 - 89.37: 30 Dihedral angle restraints: 15756 sinusoidal: 6912 harmonic: 8844 Sorted by residual: dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -157.57 71.57 1 1.00e+01 1.00e-02 6.57e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -150.59 64.59 1 1.00e+01 1.00e-02 5.48e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -146.49 60.49 1 1.00e+01 1.00e-02 4.87e+01 ... (remaining 15753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.314: 4063 0.314 - 0.629: 9 0.629 - 0.943: 0 0.943 - 1.257: 0 1.257 - 1.572: 1 Chirality restraints: 4073 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.07e+02 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.06e+02 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 9.09e+01 ... (remaining 4070 not shown) Planarity restraints: 4387 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 657 " -0.141 2.00e-02 2.50e+03 1.48e-01 2.72e+02 pdb=" CG ASN B 657 " 0.090 2.00e-02 2.50e+03 pdb=" OD1 ASN B 657 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN B 657 " 0.223 2.00e-02 2.50e+03 pdb=" C1 NAG B1305 " -0.176 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A1074 " -0.138 2.00e-02 2.50e+03 1.46e-01 2.65e+02 pdb=" CG ASN A1074 " 0.081 2.00e-02 2.50e+03 pdb=" OD1 ASN A1074 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN A1074 " 0.223 2.00e-02 2.50e+03 pdb=" C1 NAG A1310 " -0.175 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 165 " 0.141 2.00e-02 2.50e+03 1.45e-01 2.63e+02 pdb=" CG ASN B 165 " -0.099 2.00e-02 2.50e+03 pdb=" OD1 ASN B 165 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN B 165 " -0.213 2.00e-02 2.50e+03 pdb=" C1 NAG B1308 " 0.173 2.00e-02 2.50e+03 ... (remaining 4384 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.00: 12853 3.00 - 3.48: 23945 3.48 - 3.95: 40143 3.95 - 4.43: 44164 4.43 - 4.90: 74750 Nonbonded interactions: 195855 Sorted by model distance: nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.527 3.040 nonbonded pdb=" OE1 GLU A 516 " pdb=" OH TYR B 200 " model vdw 2.530 3.040 nonbonded pdb=" OG1 THR A 109 " pdb=" OD1 ASP A 111 " model vdw 2.550 3.040 nonbonded pdb=" OH TYR A 200 " pdb=" OE1 GLU C 516 " model vdw 2.561 3.040 nonbonded pdb=" OG SER A 746 " pdb=" OE1 GLU A 748 " model vdw 2.562 3.040 ... (remaining 195850 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 27 through 623 or resid 639 through 1147 or resid 1301 thr \ ough 1311)) selection = chain 'B' selection = (chain 'C' and (resid 27 through 623 or resid 639 through 1147 or resid 1301 thr \ ough 1311)) } 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' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.990 Check model and map are aligned: 0.160 Set scattering table: 0.250 Process input model: 56.110 Find NCS groups from input model: 1.500 Set up NCS constraints: 0.120 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 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 : 0.014 0.079 25121 Z= 0.886 Angle : 1.757 24.073 34174 Z= 1.163 Chirality : 0.102 1.572 4073 Planarity : 0.014 0.207 4340 Dihedral : 13.118 89.372 9943 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 0.27 Ramachandran Plot: Outliers : 0.77 % Allowed : 6.65 % Favored : 92.59 % Rotamer: Outliers : 1.62 % Allowed : 3.01 % Favored : 95.37 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.07 % 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: -1.08 (0.14), residues: 2994 helix: -0.69 (0.17), residues: 689 sheet: 0.47 (0.21), residues: 544 loop : -1.11 (0.14), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.201 0.022 TRP C 886 HIS 0.015 0.003 HIS A1048 PHE 0.078 0.011 PHE A 58 TYR 0.146 0.021 TYR A 904 ARG 0.013 0.001 ARG C 466 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 56 time to evaluate : 3.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 ILE cc_start: 0.8144 (OUTLIER) cc_final: 0.7906 (mm) REVERT: B 210 ILE cc_start: 0.5132 (OUTLIER) cc_final: 0.4869 (mt) REVERT: B 328 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7800 (mmm-85) REVERT: B 455 LEU cc_start: 0.5615 (OUTLIER) cc_final: 0.5354 (mt) REVERT: C 869 MET cc_start: 0.8813 (mtt) cc_final: 0.8574 (mtm) outliers start: 43 outliers final: 9 residues processed: 99 average time/residue: 0.3936 time to fit residues: 63.8560 Evaluate side-chains 51 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 2.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 907 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 255 optimal weight: 10.0000 chunk 229 optimal weight: 7.9990 chunk 127 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 237 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 chunk 144 optimal weight: 6.9990 chunk 176 optimal weight: 0.9980 chunk 275 optimal weight: 0.8980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN A 625 HIS B 907 ASN C 207 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.054970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.038831 restraints weight = 143196.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.040506 restraints weight = 77752.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.040683 restraints weight = 40691.300| |-----------------------------------------------------------------------------| r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 25121 Z= 0.231 Angle : 0.688 15.778 34174 Z= 0.363 Chirality : 0.047 0.273 4073 Planarity : 0.005 0.179 4340 Dihedral : 7.213 58.831 4556 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.11 % Favored : 95.66 % Rotamer: Outliers : 1.02 % Allowed : 4.29 % Favored : 94.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.38 % 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: -0.26 (0.15), residues: 2994 helix: 1.01 (0.20), residues: 677 sheet: 0.20 (0.19), residues: 689 loop : -0.83 (0.15), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 353 HIS 0.009 0.001 HIS A 625 PHE 0.016 0.002 PHE C 392 TYR 0.018 0.002 TYR C 265 ARG 0.005 0.001 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 43 time to evaluate : 2.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 ARG cc_start: 0.8806 (OUTLIER) cc_final: 0.8568 (ptt-90) REVERT: A 468 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7931 (mm) REVERT: B 122 ASN cc_start: 0.2450 (OUTLIER) cc_final: 0.2136 (p0) REVERT: B 210 ILE cc_start: 0.5379 (OUTLIER) cc_final: 0.5159 (mt) REVERT: B 455 LEU cc_start: 0.6200 (OUTLIER) cc_final: 0.5973 (mt) REVERT: B 731 MET cc_start: 0.9223 (ptt) cc_final: 0.8868 (ptm) REVERT: C 456 PHE cc_start: 0.8260 (m-80) cc_final: 0.7993 (m-80) REVERT: C 869 MET cc_start: 0.8624 (mtt) cc_final: 0.8320 (mtm) outliers start: 27 outliers final: 10 residues processed: 70 average time/residue: 0.3562 time to fit residues: 43.5082 Evaluate side-chains 53 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 38 time to evaluate : 2.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 907 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 89 optimal weight: 5.9990 chunk 117 optimal weight: 7.9990 chunk 34 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 chunk 74 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 40 optimal weight: 0.4980 chunk 78 optimal weight: 6.9990 chunk 143 optimal weight: 7.9990 chunk 82 optimal weight: 0.2980 chunk 275 optimal weight: 0.5980 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 607 GLN A 625 HIS ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.054706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.038628 restraints weight = 143127.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.039992 restraints weight = 79976.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.040323 restraints weight = 44245.373| |-----------------------------------------------------------------------------| r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 25121 Z= 0.209 Angle : 0.586 11.859 34174 Z= 0.306 Chirality : 0.045 0.253 4073 Planarity : 0.004 0.162 4340 Dihedral : 6.273 62.090 4548 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.38 % Favored : 95.39 % Rotamer: Outliers : 1.21 % Allowed : 5.08 % Favored : 93.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.69 % 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: 0.08 (0.15), residues: 2994 helix: 1.44 (0.20), residues: 691 sheet: 0.39 (0.19), residues: 677 loop : -0.70 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 886 HIS 0.011 0.001 HIS A 625 PHE 0.014 0.001 PHE B 456 TYR 0.018 0.001 TYR A1067 ARG 0.003 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 40 time to evaluate : 3.061 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 408 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8437 (ptt-90) REVERT: A 468 ILE cc_start: 0.8232 (OUTLIER) cc_final: 0.7969 (mm) REVERT: A 519 HIS cc_start: 0.6724 (m90) cc_final: 0.6378 (p90) REVERT: B 122 ASN cc_start: 0.2392 (OUTLIER) cc_final: 0.2079 (p0) REVERT: B 731 MET cc_start: 0.9216 (ptt) cc_final: 0.8922 (ptm) REVERT: C 456 PHE cc_start: 0.8255 (m-80) cc_final: 0.8041 (m-80) REVERT: C 869 MET cc_start: 0.8633 (mtt) cc_final: 0.8326 (mtm) outliers start: 32 outliers final: 11 residues processed: 70 average time/residue: 0.3523 time to fit residues: 44.4619 Evaluate side-chains 48 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 34 time to evaluate : 3.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 907 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 47 optimal weight: 10.0000 chunk 268 optimal weight: 1.9990 chunk 138 optimal weight: 20.0000 chunk 275 optimal weight: 6.9990 chunk 290 optimal weight: 8.9990 chunk 65 optimal weight: 8.9990 chunk 193 optimal weight: 2.9990 chunk 141 optimal weight: 40.0000 chunk 85 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 136 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 625 HIS A 675 GLN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.054263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.038132 restraints weight = 148451.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.039666 restraints weight = 83944.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.039830 restraints weight = 45777.671| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.108 25121 Z= 0.382 Angle : 0.638 11.429 34174 Z= 0.330 Chirality : 0.046 0.252 4073 Planarity : 0.004 0.158 4340 Dihedral : 6.306 65.351 4546 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.48 % Favored : 95.26 % Rotamer: Outliers : 1.05 % Allowed : 6.10 % Favored : 92.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.69 % 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: -0.09 (0.15), residues: 2994 helix: 1.23 (0.20), residues: 709 sheet: 0.12 (0.18), residues: 721 loop : -0.72 (0.15), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 886 HIS 0.008 0.002 HIS B 519 PHE 0.022 0.002 PHE C 392 TYR 0.022 0.002 TYR A1067 ARG 0.003 0.000 ARG A 634 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 38 time to evaluate : 3.029 Fit side-chains revert: symmetry clash REVERT: A 408 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.8563 (ptt-90) REVERT: A 468 ILE cc_start: 0.8220 (OUTLIER) cc_final: 0.7925 (mm) REVERT: A 519 HIS cc_start: 0.6941 (m90) cc_final: 0.6441 (p90) REVERT: B 122 ASN cc_start: 0.2390 (OUTLIER) cc_final: 0.2030 (p0) REVERT: B 1029 MET cc_start: 0.9119 (tpp) cc_final: 0.8609 (ttm) REVERT: C 165 ASN cc_start: 0.8016 (OUTLIER) cc_final: 0.6865 (p0) REVERT: C 456 PHE cc_start: 0.8404 (m-80) cc_final: 0.8170 (m-80) REVERT: C 902 MET cc_start: 0.9403 (tpp) cc_final: 0.8770 (tpt) outliers start: 28 outliers final: 13 residues processed: 62 average time/residue: 0.3367 time to fit residues: 37.3187 Evaluate side-chains 51 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 34 time to evaluate : 2.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 229 optimal weight: 7.9990 chunk 206 optimal weight: 0.4980 chunk 4 optimal weight: 3.9990 chunk 155 optimal weight: 8.9990 chunk 299 optimal weight: 1.9990 chunk 281 optimal weight: 3.9990 chunk 209 optimal weight: 2.9990 chunk 41 optimal weight: 0.0870 chunk 180 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 172 optimal weight: 1.9990 overall best weight: 1.1164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 625 HIS A1088 HIS ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN B 493 GLN C 955 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.054767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.038753 restraints weight = 142723.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.040286 restraints weight = 77822.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.040511 restraints weight = 40952.678| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.096 25121 Z= 0.150 Angle : 0.526 9.863 34174 Z= 0.275 Chirality : 0.043 0.258 4073 Planarity : 0.004 0.152 4340 Dihedral : 5.775 69.017 4544 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.94 % Favored : 95.89 % Rotamer: Outliers : 0.94 % Allowed : 6.70 % Favored : 92.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.69 % 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: 0.24 (0.15), residues: 2994 helix: 1.71 (0.20), residues: 687 sheet: 0.33 (0.19), residues: 705 loop : -0.59 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 436 HIS 0.009 0.001 HIS A 625 PHE 0.018 0.001 PHE C 392 TYR 0.015 0.001 TYR B1067 ARG 0.002 0.000 ARG C 457 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 34 time to evaluate : 3.021 Fit side-chains revert: symmetry clash REVERT: A 408 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.8425 (ptt-90) REVERT: A 468 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7845 (mm) REVERT: A 519 HIS cc_start: 0.6592 (m90) cc_final: 0.6286 (p90) REVERT: B 1029 MET cc_start: 0.9106 (tpp) cc_final: 0.8648 (ttm) REVERT: C 165 ASN cc_start: 0.7686 (OUTLIER) cc_final: 0.6722 (p0) REVERT: C 869 MET cc_start: 0.8587 (mtm) cc_final: 0.8350 (mtm) outliers start: 25 outliers final: 13 residues processed: 55 average time/residue: 0.3672 time to fit residues: 35.9077 Evaluate side-chains 50 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 34 time to evaluate : 3.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 188 optimal weight: 5.9990 chunk 265 optimal weight: 7.9990 chunk 138 optimal weight: 20.0000 chunk 253 optimal weight: 7.9990 chunk 73 optimal weight: 0.0670 chunk 51 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 173 optimal weight: 10.0000 chunk 209 optimal weight: 9.9990 chunk 10 optimal weight: 0.7980 chunk 158 optimal weight: 8.9990 overall best weight: 4.5724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 901 GLN B 955 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.053921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.037844 restraints weight = 144988.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.039247 restraints weight = 81163.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.039450 restraints weight = 45413.701| |-----------------------------------------------------------------------------| r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 25121 Z= 0.354 Angle : 0.606 10.701 34174 Z= 0.311 Chirality : 0.045 0.259 4073 Planarity : 0.004 0.154 4340 Dihedral : 5.908 67.314 4542 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.74 % Favored : 95.06 % Rotamer: Outliers : 1.36 % Allowed : 6.89 % Favored : 91.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.69 % 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: 0.03 (0.15), residues: 2994 helix: 1.46 (0.20), residues: 701 sheet: 0.17 (0.18), residues: 721 loop : -0.70 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.007 0.001 HIS A1064 PHE 0.014 0.002 PHE A 275 TYR 0.020 0.001 TYR A1067 ARG 0.004 0.000 ARG A 634 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 34 time to evaluate : 2.924 Fit side-chains REVERT: A 408 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.8535 (ptt-90) REVERT: A 468 ILE cc_start: 0.8158 (OUTLIER) cc_final: 0.7819 (mm) REVERT: A 519 HIS cc_start: 0.6808 (m90) cc_final: 0.6373 (p90) REVERT: B 122 ASN cc_start: 0.2471 (OUTLIER) cc_final: 0.2142 (p0) REVERT: B 985 ASP cc_start: 0.8430 (OUTLIER) cc_final: 0.8124 (m-30) REVERT: B 1029 MET cc_start: 0.9137 (tpp) cc_final: 0.8656 (ttm) REVERT: C 165 ASN cc_start: 0.7817 (OUTLIER) cc_final: 0.6958 (p0) outliers start: 36 outliers final: 22 residues processed: 66 average time/residue: 0.3518 time to fit residues: 41.9629 Evaluate side-chains 61 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 34 time to evaluate : 3.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 166 optimal weight: 6.9990 chunk 125 optimal weight: 8.9990 chunk 243 optimal weight: 20.0000 chunk 39 optimal weight: 30.0000 chunk 87 optimal weight: 3.9990 chunk 135 optimal weight: 8.9990 chunk 80 optimal weight: 4.9990 chunk 14 optimal weight: 20.0000 chunk 145 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 108 optimal weight: 30.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN C 955 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.053262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.036930 restraints weight = 146260.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.037977 restraints weight = 77919.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.038641 restraints weight = 53095.965| |-----------------------------------------------------------------------------| r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.077 25121 Z= 0.495 Angle : 0.683 11.017 34174 Z= 0.351 Chirality : 0.047 0.247 4073 Planarity : 0.005 0.154 4340 Dihedral : 6.354 67.086 4542 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.64 % Favored : 94.15 % Rotamer: Outliers : 1.43 % Allowed : 7.31 % Favored : 91.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.69 % 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: -0.26 (0.15), residues: 2994 helix: 1.17 (0.20), residues: 697 sheet: 0.05 (0.18), residues: 699 loop : -0.87 (0.15), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 886 HIS 0.008 0.002 HIS B 655 PHE 0.023 0.002 PHE A 486 TYR 0.022 0.002 TYR A1067 ARG 0.004 0.000 ARG A 634 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 35 time to evaluate : 2.660 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 ILE cc_start: 0.8147 (OUTLIER) cc_final: 0.7785 (mm) REVERT: B 122 ASN cc_start: 0.2510 (OUTLIER) cc_final: 0.2177 (p0) REVERT: B 985 ASP cc_start: 0.8510 (OUTLIER) cc_final: 0.8192 (m-30) REVERT: B 1029 MET cc_start: 0.9100 (tpp) cc_final: 0.8655 (ttm) outliers start: 38 outliers final: 28 residues processed: 68 average time/residue: 0.3509 time to fit residues: 41.9994 Evaluate side-chains 66 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 35 time to evaluate : 2.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1135 ASN Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 249 optimal weight: 0.0870 chunk 94 optimal weight: 1.9990 chunk 193 optimal weight: 0.9990 chunk 143 optimal weight: 0.0370 chunk 191 optimal weight: 2.9990 chunk 119 optimal weight: 40.0000 chunk 126 optimal weight: 6.9990 chunk 261 optimal weight: 7.9990 chunk 265 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 overall best weight: 0.8242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN C 955 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.054651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.038640 restraints weight = 143469.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.040064 restraints weight = 78935.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.040290 restraints weight = 43963.461| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.091 25121 Z= 0.154 Angle : 0.523 9.786 34174 Z= 0.273 Chirality : 0.043 0.244 4073 Planarity : 0.004 0.150 4340 Dihedral : 5.652 70.712 4542 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.18 % Favored : 95.69 % Rotamer: Outliers : 1.17 % Allowed : 7.68 % Favored : 91.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.69 % 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: 0.10 (0.15), residues: 2994 helix: 1.66 (0.20), residues: 702 sheet: 0.16 (0.18), residues: 713 loop : -0.69 (0.16), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 353 HIS 0.003 0.000 HIS B1048 PHE 0.013 0.001 PHE B 65 TYR 0.017 0.001 TYR B 421 ARG 0.002 0.000 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 35 time to evaluate : 2.727 Fit side-chains revert: symmetry clash REVERT: A 468 ILE cc_start: 0.8097 (OUTLIER) cc_final: 0.7705 (mm) REVERT: A 519 HIS cc_start: 0.6862 (m90) cc_final: 0.6361 (p90) REVERT: B 122 ASN cc_start: 0.2647 (OUTLIER) cc_final: 0.2303 (p0) REVERT: B 985 ASP cc_start: 0.8324 (OUTLIER) cc_final: 0.8030 (m-30) REVERT: B 1029 MET cc_start: 0.9080 (tpp) cc_final: 0.8667 (ttm) REVERT: C 165 ASN cc_start: 0.7862 (OUTLIER) cc_final: 0.6791 (p0) outliers start: 31 outliers final: 17 residues processed: 62 average time/residue: 0.3334 time to fit residues: 37.1197 Evaluate side-chains 55 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 34 time to evaluate : 2.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.339 > 50: distance: 23 - 123: 29.634 distance: 42 - 47: 34.034 distance: 47 - 48: 14.940 distance: 48 - 49: 47.151 distance: 48 - 51: 14.909 distance: 49 - 50: 41.189 distance: 49 - 53: 60.201 distance: 53 - 54: 22.012 distance: 54 - 55: 39.530 distance: 54 - 57: 40.877 distance: 62 - 63: 39.438 distance: 62 - 65: 46.393 distance: 65 - 66: 23.954 distance: 69 - 70: 57.366 distance: 70 - 71: 50.577 distance: 70 - 73: 41.018 distance: 71 - 72: 28.727 distance: 71 - 76: 50.376 distance: 73 - 74: 39.840 distance: 76 - 77: 40.787 distance: 77 - 78: 12.117 distance: 78 - 79: 11.097 distance: 78 - 87: 11.053 distance: 81 - 83: 40.776 distance: 83 - 85: 39.189 distance: 84 - 86: 5.834 distance: 85 - 86: 48.656 distance: 87 - 88: 40.206 distance: 88 - 89: 56.452 distance: 88 - 91: 39.813 distance: 89 - 90: 39.168 distance: 91 - 92: 56.885 distance: 92 - 94: 56.466 distance: 95 - 96: 38.787 distance: 96 - 97: 40.665 distance: 96 - 99: 8.848 distance: 97 - 98: 39.846 distance: 97 - 103: 40.397 distance: 99 - 100: 38.695 distance: 100 - 101: 40.712 distance: 100 - 102: 40.677 distance: 104 - 107: 39.326 distance: 105 - 106: 39.866 distance: 107 - 109: 56.918 distance: 110 - 111: 40.020 distance: 111 - 112: 49.535 distance: 111 - 114: 39.880 distance: 112 - 113: 40.995 distance: 112 - 118: 32.660 distance: 114 - 115: 50.302 distance: 115 - 116: 50.405 distance: 115 - 117: 41.077 distance: 117 - 169: 27.969 distance: 118 - 119: 9.730 distance: 119 - 120: 29.372 distance: 120 - 121: 10.228 distance: 120 - 124: 28.759 distance: 122 - 123: 49.891