Starting phenix.real_space_refine on Thu Jun 26 00:14:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k9j_22750/06_2025/7k9j_22750.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k9j_22750/06_2025/7k9j_22750.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7k9j_22750/06_2025/7k9j_22750.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k9j_22750/06_2025/7k9j_22750.map" model { file = "/net/cci-nas-00/data/ceres_data/7k9j_22750/06_2025/7k9j_22750.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k9j_22750/06_2025/7k9j_22750.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.091 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 117 5.16 5 C 18876 2.51 5 N 4779 2.21 5 O 5994 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 93 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 29766 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 7680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 982, 7680 Classifications: {'peptide': 982} Link IDs: {'PTRANS': 48, 'TRANS': 933} Chain breaks: 8 Chain: "B" Number of atoms: 7680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 982, 7680 Classifications: {'peptide': 982} Link IDs: {'PTRANS': 48, 'TRANS': 933} Chain breaks: 8 Chain: "C" Number of atoms: 7680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 982, 7680 Classifications: {'peptide': 982} Link IDs: {'PTRANS': 48, 'TRANS': 933} Chain breaks: 8 Chain: "H" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 947 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "I" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 947 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "J" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 947 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "L" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 806 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "M" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 806 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "N" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 806 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "K" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "O" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: "R" 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: "S" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "T" 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: "U" 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: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" 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: 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: "b" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "c" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "l" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "m" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "q" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: "r" 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: "s" 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: "t" 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: "u" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "v" 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: "w" 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: "x" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 17.47, per 1000 atoms: 0.59 Number of scatterers: 29766 At special positions: 0 Unit cell: (133.1, 147.4, 192.5, 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 117 16.00 O 5994 8.00 N 4779 7.00 C 18876 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " 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=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-6 " BMA S 3 " - " MAN S 4 " " BMA g 3 " - " MAN g 4 " " BMA u 3 " - " MAN u 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " 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 g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " BETA1-6 " NAG K 1 " - " FUC K 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG O 1 " - " FUC O 2 " " NAG b 1 " - " FUC b 4 " " NAG c 1 " - " FUC c 2 " " NAG p 1 " - " FUC p 4 " " NAG q 1 " - " FUC q 2 " NAG-ASN " NAG A1300 " - " ASN A 61 " " NAG B1300 " - " ASN B 61 " " NAG C1300 " - " ASN C 61 " " NAG D 1 " - " ASN A 165 " " NAG E 1 " - " ASN A 234 " " NAG F 1 " - " ASN A 282 " " NAG G 1 " - " ASN A 331 " " NAG K 1 " - " ASN A 343 " " NAG O 1 " - " ASN A 603 " " NAG P 1 " - " ASN A 616 " " NAG Q 1 " - " ASN A 657 " " NAG R 1 " - " ASN A 709 " " NAG S 1 " - " ASN A 717 " " NAG T 1 " - " ASN A 801 " " NAG U 1 " - " ASN A1074 " " NAG V 1 " - " ASN A1098 " " NAG W 1 " - " ASN A1134 " " NAG X 1 " - " ASN B 165 " " NAG Y 1 " - " ASN B 234 " " NAG Z 1 " - " ASN B 282 " " NAG a 1 " - " ASN B 331 " " NAG b 1 " - " ASN B 343 " " NAG c 1 " - " ASN B 603 " " NAG d 1 " - " ASN B 616 " " NAG e 1 " - " ASN B 657 " " NAG f 1 " - " ASN B 709 " " NAG g 1 " - " ASN B 717 " " NAG h 1 " - " ASN B 801 " " NAG i 1 " - " ASN B1074 " " NAG j 1 " - " ASN B1098 " " NAG k 1 " - " ASN B1134 " " NAG l 1 " - " ASN C 165 " " NAG m 1 " - " ASN C 234 " " NAG n 1 " - " ASN C 282 " " NAG o 1 " - " ASN C 331 " " NAG p 1 " - " ASN C 343 " " NAG q 1 " - " ASN C 603 " " NAG r 1 " - " ASN C 616 " " NAG s 1 " - " ASN C 657 " " NAG t 1 " - " ASN C 709 " " NAG u 1 " - " ASN C 717 " " NAG v 1 " - " ASN C 801 " " NAG w 1 " - " ASN C1074 " " NAG x 1 " - " ASN C1098 " " NAG y 1 " - " ASN C1134 " Time building additional restraints: 8.53 Conformation dependent library (CDL) restraints added in 4.0 seconds 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6774 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 66 sheets defined 22.5% alpha, 31.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.55 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.669A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 385 through 389 removed outlier: 3.836A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.442A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.694A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 754 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 759 through 783 removed outlier: 3.888A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.919A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.696A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.555A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.537A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) 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: 4.019A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.769A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.605A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.180A 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 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.669A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 385 through 389 removed outlier: 3.836A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.443A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.694A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 742 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 759 through 783 removed outlier: 3.888A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.920A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.696A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.555A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.536A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER B 940 " --> pdb=" O ASP B 936 " (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: 4.018A 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 982 removed outlier: 3.768A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.605A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.181A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.669A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 385 through 389 removed outlier: 3.836A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.442A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.693A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 754 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 759 through 783 removed outlier: 3.889A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.920A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.695A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.555A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.536A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER C 940 " --> pdb=" O ASP C 936 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.019A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (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 982 removed outlier: 3.768A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.606A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.180A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'I' and resid 62 through 65 Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'J' and resid 62 through 65 Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'M' and resid 79 through 83 Processing helix chain 'N' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.783A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.019A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 52 removed outlier: 7.201A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.686A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 118 through 121 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.204A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 595 " --> pdb=" O SER A 316 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.078A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N THR A 430 " --> pdb=" O PHE A 515 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 3.593A pdb=" N CYS A 525 " --> pdb=" O CYS A 361 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.544A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 702 removed outlier: 7.014A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.553A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.553A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.606A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1123 removed outlier: 3.939A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.783A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.019A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 52 removed outlier: 7.201A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.685A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC4, first strand: chain 'B' and resid 118 through 121 Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.204A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL B 595 " --> pdb=" O SER B 316 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.078A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N THR B 430 " --> pdb=" O PHE B 515 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N ASN B 437 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N PHE B 374 " --> pdb=" O ASN B 437 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 3.593A pdb=" N CYS B 525 " --> pdb=" O CYS B 361 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.544A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.981A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.553A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.553A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.606A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1123 removed outlier: 3.938A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.784A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.019A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 48 through 52 removed outlier: 7.200A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.686A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE2, first strand: chain 'C' and resid 118 through 121 Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.203A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL C 595 " --> pdb=" O SER C 316 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 325 through 328 Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.079A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N THR C 430 " --> pdb=" O PHE C 515 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N ASN C 437 " --> pdb=" O PHE C 374 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N PHE C 374 " --> pdb=" O ASN C 437 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 361 through 362 removed outlier: 3.593A pdb=" N CYS C 525 " --> pdb=" O CYS C 361 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.543A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.553A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.553A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.606A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1123 removed outlier: 3.938A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AF5, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.082A pdb=" N VAL H 12 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE H 34 " --> pdb=" O ASP H 50 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ASP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS H 59 " --> pdb=" O ASP H 50 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.082A pdb=" N VAL H 12 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N TYR H 109 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AF8, first strand: chain 'I' and resid 11 through 12 removed outlier: 4.081A pdb=" N VAL I 12 " --> pdb=" O THR I 117 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE I 34 " --> pdb=" O ASP I 50 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ASP I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS I 59 " --> pdb=" O ASP I 50 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 11 through 12 removed outlier: 4.081A pdb=" N VAL I 12 " --> pdb=" O THR I 117 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N TYR I 109 " --> pdb=" O ARG I 98 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AG2, first strand: chain 'J' and resid 11 through 12 removed outlier: 4.081A pdb=" N VAL J 12 " --> pdb=" O THR J 117 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE J 34 " --> pdb=" O ASP J 50 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ASP J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS J 59 " --> pdb=" O ASP J 50 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 11 through 12 removed outlier: 4.081A pdb=" N VAL J 12 " --> pdb=" O THR J 117 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N TYR J 109 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.961A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER L 63 " --> pdb=" O SER L 74 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.537A pdb=" N LEU L 11 " --> pdb=" O LYS L 103 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'L' and resid 44 through 48 removed outlier: 3.512A pdb=" N ARG L 45 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN L 37 " --> pdb=" O ARG L 45 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR L 36 " --> pdb=" O TYR L 87 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'M' and resid 5 through 6 removed outlier: 3.961A pdb=" N VAL M 19 " --> pdb=" O ILE M 75 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER M 63 " --> pdb=" O SER M 74 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'M' and resid 10 through 12 removed outlier: 3.537A pdb=" N LEU M 11 " --> pdb=" O LYS M 103 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU M 105 " --> pdb=" O LEU M 11 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'M' and resid 44 through 48 removed outlier: 3.511A pdb=" N ARG M 45 " --> pdb=" O GLN M 37 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN M 37 " --> pdb=" O ARG M 45 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR M 36 " --> pdb=" O TYR M 87 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'N' and resid 5 through 6 removed outlier: 3.961A pdb=" N VAL N 19 " --> pdb=" O ILE N 75 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER N 63 " --> pdb=" O SER N 74 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.536A pdb=" N LEU N 11 " --> pdb=" O LYS N 103 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU N 105 " --> pdb=" O LEU N 11 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH2 Processing sheet with id=AH3, first strand: chain 'N' and resid 44 through 48 removed outlier: 3.511A pdb=" N ARG N 45 " --> pdb=" O GLN N 37 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN N 37 " --> pdb=" O ARG N 45 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR N 36 " --> pdb=" O TYR N 87 " (cutoff:3.500A) 1093 hydrogen bonds defined for protein. 2943 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: 14.63 Time building geometry restraints manager: 9.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4774 1.32 - 1.45: 8759 1.45 - 1.57: 16725 1.57 - 1.70: 3 1.70 - 1.82: 147 Bond restraints: 30408 Sorted by residual: bond pdb=" C PHE A 377 " pdb=" O PHE A 377 " ideal model delta sigma weight residual 1.236 1.194 0.042 1.14e-02 7.69e+03 1.37e+01 bond pdb=" C PRO B 384 " pdb=" O PRO B 384 " ideal model delta sigma weight residual 1.238 1.194 0.044 1.33e-02 5.65e+03 1.11e+01 bond pdb=" C1 NAG X 2 " pdb=" O5 NAG X 2 " ideal model delta sigma weight residual 1.406 1.473 -0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.472 -0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" C1 NAG l 2 " pdb=" O5 NAG l 2 " ideal model delta sigma weight residual 1.406 1.472 -0.066 2.00e-02 2.50e+03 1.09e+01 ... (remaining 30403 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 40231 2.26 - 4.52: 943 4.52 - 6.78: 159 6.78 - 9.04: 23 9.04 - 11.30: 5 Bond angle restraints: 41361 Sorted by residual: angle pdb=" CA ALA C 520 " pdb=" C ALA C 520 " pdb=" N PRO C 521 " ideal model delta sigma weight residual 117.96 122.84 -4.88 8.10e-01 1.52e+00 3.63e+01 angle pdb=" CA ALA B 520 " pdb=" C ALA B 520 " pdb=" N PRO B 521 " ideal model delta sigma weight residual 117.96 122.64 -4.68 8.10e-01 1.52e+00 3.34e+01 angle pdb=" N ALA C 520 " pdb=" CA ALA C 520 " pdb=" C ALA C 520 " ideal model delta sigma weight residual 108.22 103.06 5.16 9.00e-01 1.23e+00 3.29e+01 angle pdb=" CA ALA A 520 " pdb=" C ALA A 520 " pdb=" N PRO A 521 " ideal model delta sigma weight residual 117.96 122.47 -4.51 8.10e-01 1.52e+00 3.10e+01 angle pdb=" N ILE C 434 " pdb=" CA ILE C 434 " pdb=" CB ILE C 434 " ideal model delta sigma weight residual 111.90 105.73 6.17 1.26e+00 6.30e-01 2.40e+01 ... (remaining 41356 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.69: 17874 22.69 - 45.39: 960 45.39 - 68.08: 249 68.08 - 90.77: 192 90.77 - 113.46: 186 Dihedral angle restraints: 19461 sinusoidal: 8928 harmonic: 10533 Sorted by residual: dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual -86.00 -176.00 90.00 1 1.00e+01 1.00e-02 9.60e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual -86.00 -175.99 89.99 1 1.00e+01 1.00e-02 9.60e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual -86.00 -175.96 89.96 1 1.00e+01 1.00e-02 9.59e+01 ... (remaining 19458 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 4494 0.090 - 0.180: 467 0.180 - 0.270: 32 0.270 - 0.360: 19 0.360 - 0.451: 10 Chirality restraints: 5022 Sorted by residual: chirality pdb=" C1 NAG A1300 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG A1300 " pdb=" O5 NAG A1300 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.08e+00 chirality pdb=" C1 NAG B1300 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B1300 " pdb=" O5 NAG B1300 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.02e+00 chirality pdb=" C1 NAG C1300 " pdb=" ND2 ASN C 61 " pdb=" C2 NAG C1300 " pdb=" O5 NAG C1300 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 4.99e+00 ... (remaining 5019 not shown) Planarity restraints: 5202 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 81 " -0.055 5.00e-02 4.00e+02 8.40e-02 1.13e+01 pdb=" N PRO C 82 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO C 82 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 82 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 81 " 0.055 5.00e-02 4.00e+02 8.40e-02 1.13e+01 pdb=" N PRO A 82 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 82 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 82 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 81 " -0.055 5.00e-02 4.00e+02 8.38e-02 1.12e+01 pdb=" N PRO B 82 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO B 82 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 82 " -0.046 5.00e-02 4.00e+02 ... (remaining 5199 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 526 2.65 - 3.21: 27487 3.21 - 3.77: 43017 3.77 - 4.34: 61555 4.34 - 4.90: 100880 Nonbonded interactions: 233465 Sorted by model distance: nonbonded pdb=" O ARG J 105 " pdb=" NE2 HIS N 34 " model vdw 2.084 3.120 nonbonded pdb=" OG1 THR A 29 " pdb=" OD2 ASP A 215 " model vdw 2.154 3.040 nonbonded pdb=" OG1 THR B 29 " pdb=" OD2 ASP B 215 " model vdw 2.154 3.040 nonbonded pdb=" OG1 THR C 29 " pdb=" OD2 ASP C 215 " model vdw 2.155 3.040 nonbonded pdb=" OD1 ASP I 90 " pdb=" OH TYR I 94 " model vdw 2.162 3.040 ... (remaining 233460 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'x' selection = chain 'y' } ncs_group { reference = (chain 'F' and resid 1) selection = (chain 'G' and resid 1) selection = (chain 'O' and resid 1) selection = (chain 'P' and resid 1) selection = (chain 'Q' and resid 1) selection = (chain 'R' and resid 1) selection = (chain 'T' and resid 1) selection = (chain 'U' and resid 1) selection = (chain 'Z' and resid 1) selection = (chain 'a' and resid 1) selection = (chain 'c' and resid 1) selection = (chain 'd' and resid 1) selection = (chain 'e' and resid 1) selection = (chain 'f' and resid 1) selection = (chain 'h' and resid 1) selection = (chain 'i' and resid 1) selection = (chain 'n' and resid 1) selection = (chain 'o' and resid 1) selection = (chain 'q' and resid 1) selection = (chain 'r' and resid 1) selection = (chain 's' and resid 1) selection = (chain 't' and resid 1) selection = (chain 'v' and resid 1) selection = (chain 'w' and resid 1) } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = (chain 'K' and resid 1 through 3) selection = (chain 'S' and resid 1 through 3) selection = (chain 'b' and resid 1 through 3) selection = (chain 'g' and resid 1 through 3) selection = (chain 'p' and resid 1 through 3) selection = (chain 'u' and resid 1 through 3) } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.740 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.080 Check model and map are aligned: 0.190 Set scattering table: 0.280 Process input model: 71.710 Find NCS groups from input model: 1.870 Set up NCS constraints: 0.220 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: 0.020 Load rotamer database and sin/cos tables:14.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 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 : 0.005 0.067 30561 Z= 0.259 Angle : 0.877 12.254 41778 Z= 0.451 Chirality : 0.058 0.451 5022 Planarity : 0.005 0.084 5157 Dihedral : 20.825 113.464 12561 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.57 % Allowed : 0.54 % Favored : 98.89 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.13), residues: 3561 helix: -0.06 (0.18), residues: 648 sheet: 0.40 (0.16), residues: 942 loop : -1.29 (0.13), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 353 HIS 0.006 0.001 HIS B1048 PHE 0.029 0.002 PHE C 58 TYR 0.030 0.002 TYR A 904 ARG 0.054 0.002 ARG A 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00533 ( 45) link_NAG-ASN : angle 3.42742 ( 135) link_ALPHA1-6 : bond 0.00218 ( 3) link_ALPHA1-6 : angle 1.73772 ( 9) link_BETA1-4 : bond 0.00774 ( 57) link_BETA1-4 : angle 1.89616 ( 171) hydrogen bonds : bond 0.26096 ( 1063) hydrogen bonds : angle 9.68528 ( 2943) link_BETA1-6 : bond 0.00350 ( 6) link_BETA1-6 : angle 1.64095 ( 18) SS BOND : bond 0.00377 ( 42) SS BOND : angle 2.07292 ( 84) covalent geometry : bond 0.00521 (30408) covalent geometry : angle 0.84449 (41361) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 268 time to evaluate : 3.147 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 GLU cc_start: 0.8309 (mm-30) cc_final: 0.8064 (mm-30) REVERT: A 365 TYR cc_start: 0.8032 (m-80) cc_final: 0.7662 (m-80) REVERT: B 988 GLU cc_start: 0.7362 (mp0) cc_final: 0.6995 (mp0) REVERT: C 306 PHE cc_start: 0.8426 (m-10) cc_final: 0.8062 (m-10) REVERT: C 902 MET cc_start: 0.8180 (mmm) cc_final: 0.7957 (mmt) REVERT: H 10 GLU cc_start: 0.5054 (OUTLIER) cc_final: 0.3902 (tm-30) REVERT: I 50 ASP cc_start: 0.7790 (p0) cc_final: 0.7535 (p0) REVERT: I 81 MET cc_start: 0.5984 (tmm) cc_final: 0.5525 (tmm) REVERT: I 109 TYR cc_start: 0.6535 (m-80) cc_final: 0.6327 (m-80) REVERT: J 50 ASP cc_start: 0.7445 (p0) cc_final: 0.7210 (p0) REVERT: J 81 MET cc_start: 0.5790 (tmm) cc_final: 0.5476 (tmm) REVERT: M 3 VAL cc_start: 0.8740 (t) cc_final: 0.8506 (p) outliers start: 18 outliers final: 6 residues processed: 282 average time/residue: 1.1080 time to fit residues: 384.3880 Evaluate side-chains 207 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 200 time to evaluate : 2.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain J residue 10 GLU Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain M residue 13 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 9.9990 chunk 272 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 184 optimal weight: 0.9990 chunk 145 optimal weight: 2.9990 chunk 282 optimal weight: 1.9990 chunk 109 optimal weight: 9.9990 chunk 171 optimal weight: 2.9990 chunk 210 optimal weight: 0.4980 chunk 326 optimal weight: 4.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 675 GLN A 762 GLN A 804 GLN A 935 GLN B 196 ASN B 804 GLN B 935 GLN L 27 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.204469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.139906 restraints weight = 38518.776| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 3.35 r_work: 0.3637 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 30561 Z= 0.165 Angle : 0.740 10.874 41778 Z= 0.358 Chirality : 0.050 0.425 5022 Planarity : 0.005 0.058 5157 Dihedral : 18.557 94.220 6162 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.79 % Allowed : 6.29 % Favored : 92.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.14), residues: 3561 helix: 1.18 (0.20), residues: 651 sheet: 0.17 (0.16), residues: 987 loop : -1.18 (0.14), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 104 HIS 0.005 0.001 HIS B 207 PHE 0.023 0.002 PHE I 64 TYR 0.022 0.001 TYR B 265 ARG 0.005 0.001 ARG B 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00466 ( 45) link_NAG-ASN : angle 2.88276 ( 135) link_ALPHA1-6 : bond 0.00538 ( 3) link_ALPHA1-6 : angle 1.75107 ( 9) link_BETA1-4 : bond 0.00713 ( 57) link_BETA1-4 : angle 2.48153 ( 171) hydrogen bonds : bond 0.06021 ( 1063) hydrogen bonds : angle 6.86717 ( 2943) link_BETA1-6 : bond 0.00330 ( 6) link_BETA1-6 : angle 1.65202 ( 18) SS BOND : bond 0.00366 ( 42) SS BOND : angle 1.51160 ( 84) covalent geometry : bond 0.00379 (30408) covalent geometry : angle 0.70307 (41361) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 227 time to evaluate : 3.287 Fit side-chains REVERT: A 99 ASN cc_start: 0.7945 (t0) cc_final: 0.7685 (t0) REVERT: A 170 TYR cc_start: 0.7051 (t80) cc_final: 0.6668 (t80) REVERT: A 237 ARG cc_start: 0.7627 (tmt170) cc_final: 0.6989 (tpt-90) REVERT: A 571 ASP cc_start: 0.8197 (t0) cc_final: 0.7846 (t0) REVERT: A 902 MET cc_start: 0.8499 (mmt) cc_final: 0.8261 (tpt) REVERT: A 988 GLU cc_start: 0.8039 (mp0) cc_final: 0.7699 (mp0) REVERT: B 99 ASN cc_start: 0.8067 (t0) cc_final: 0.7830 (t0) REVERT: B 140 PHE cc_start: 0.7978 (p90) cc_final: 0.7683 (p90) REVERT: B 170 TYR cc_start: 0.6837 (t80) cc_final: 0.6433 (t80) REVERT: B 237 ARG cc_start: 0.7595 (tmt170) cc_final: 0.7252 (tmt-80) REVERT: B 571 ASP cc_start: 0.8333 (t0) cc_final: 0.7984 (t0) REVERT: B 646 ARG cc_start: 0.7875 (tmt170) cc_final: 0.7514 (tpt170) REVERT: B 988 GLU cc_start: 0.7948 (mp0) cc_final: 0.7289 (mp0) REVERT: B 1107 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7511 (mmt-90) REVERT: C 99 ASN cc_start: 0.7799 (t0) cc_final: 0.7565 (t0) REVERT: C 237 ARG cc_start: 0.7534 (tmt170) cc_final: 0.7168 (tpt-90) REVERT: C 306 PHE cc_start: 0.8491 (m-10) cc_final: 0.8121 (m-10) REVERT: C 571 ASP cc_start: 0.8255 (t0) cc_final: 0.7866 (t0) REVERT: C 578 ASP cc_start: 0.8246 (t0) cc_final: 0.7884 (t0) REVERT: C 936 ASP cc_start: 0.8530 (t0) cc_final: 0.8185 (t0) REVERT: H 100 ASP cc_start: 0.6168 (t0) cc_final: 0.5942 (p0) REVERT: I 50 ASP cc_start: 0.7997 (p0) cc_final: 0.7737 (p0) REVERT: J 81 MET cc_start: 0.5981 (tmm) cc_final: 0.5590 (tmm) REVERT: J 109 TYR cc_start: 0.6534 (m-80) cc_final: 0.6041 (m-80) REVERT: M 3 VAL cc_start: 0.8445 (t) cc_final: 0.8195 (p) REVERT: N 37 GLN cc_start: 0.6411 (pm20) cc_final: 0.5861 (pm20) REVERT: N 90 GLN cc_start: 0.7498 (pp30) cc_final: 0.6912 (pp30) outliers start: 25 outliers final: 15 residues processed: 243 average time/residue: 1.3974 time to fit residues: 432.0401 Evaluate side-chains 221 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 205 time to evaluate : 3.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 29 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 62 optimal weight: 3.9990 chunk 184 optimal weight: 0.9990 chunk 234 optimal weight: 0.9980 chunk 140 optimal weight: 3.9990 chunk 255 optimal weight: 0.9980 chunk 341 optimal weight: 8.9990 chunk 105 optimal weight: 4.9990 chunk 309 optimal weight: 20.0000 chunk 239 optimal weight: 0.5980 chunk 197 optimal weight: 3.9990 chunk 133 optimal weight: 20.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1002 GLN B 196 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 GLN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.204369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.139228 restraints weight = 38475.191| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 3.13 r_work: 0.3677 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 30561 Z= 0.167 Angle : 0.709 11.047 41778 Z= 0.335 Chirality : 0.049 0.426 5022 Planarity : 0.005 0.058 5157 Dihedral : 14.261 88.542 6153 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.92 % Allowed : 9.14 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.14), residues: 3561 helix: 1.31 (0.20), residues: 672 sheet: 0.08 (0.16), residues: 987 loop : -1.18 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 104 HIS 0.005 0.001 HIS B 207 PHE 0.022 0.002 PHE C 140 TYR 0.023 0.001 TYR B 265 ARG 0.010 0.001 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00457 ( 45) link_NAG-ASN : angle 2.73165 ( 135) link_ALPHA1-6 : bond 0.00630 ( 3) link_ALPHA1-6 : angle 1.79113 ( 9) link_BETA1-4 : bond 0.00787 ( 57) link_BETA1-4 : angle 2.62994 ( 171) hydrogen bonds : bond 0.05279 ( 1063) hydrogen bonds : angle 6.22226 ( 2943) link_BETA1-6 : bond 0.00328 ( 6) link_BETA1-6 : angle 1.60248 ( 18) SS BOND : bond 0.00389 ( 42) SS BOND : angle 1.36370 ( 84) covalent geometry : bond 0.00394 (30408) covalent geometry : angle 0.67038 (41361) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 216 time to evaluate : 3.241 Fit side-chains REVERT: A 99 ASN cc_start: 0.7649 (t0) cc_final: 0.7181 (t0) REVERT: A 170 TYR cc_start: 0.7184 (t80) cc_final: 0.6966 (t80) REVERT: A 201 PHE cc_start: 0.7573 (t80) cc_final: 0.7298 (t80) REVERT: A 237 ARG cc_start: 0.7754 (tmt170) cc_final: 0.7452 (tpt-90) REVERT: A 571 ASP cc_start: 0.8499 (t0) cc_final: 0.8116 (t0) REVERT: A 904 TYR cc_start: 0.7799 (m-80) cc_final: 0.7513 (m-80) REVERT: A 988 GLU cc_start: 0.8290 (mp0) cc_final: 0.7917 (mp0) REVERT: B 99 ASN cc_start: 0.8218 (t0) cc_final: 0.7919 (t0) REVERT: B 140 PHE cc_start: 0.8019 (p90) cc_final: 0.7636 (p90) REVERT: B 196 ASN cc_start: 0.5698 (OUTLIER) cc_final: 0.5404 (m-40) REVERT: B 433 VAL cc_start: 0.8080 (t) cc_final: 0.7878 (m) REVERT: B 571 ASP cc_start: 0.8477 (t0) cc_final: 0.8084 (t0) REVERT: B 988 GLU cc_start: 0.8213 (mp0) cc_final: 0.7619 (mp0) REVERT: B 995 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.8210 (mtp180) REVERT: B 1107 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7614 (mmt-90) REVERT: C 99 ASN cc_start: 0.7992 (t0) cc_final: 0.7726 (t0) REVERT: C 306 PHE cc_start: 0.8530 (m-10) cc_final: 0.8194 (m-10) REVERT: C 571 ASP cc_start: 0.8447 (t0) cc_final: 0.8024 (t0) REVERT: C 574 ASP cc_start: 0.8026 (t0) cc_final: 0.7710 (t0) REVERT: C 578 ASP cc_start: 0.8364 (t0) cc_final: 0.8018 (t0) REVERT: C 740 MET cc_start: 0.8263 (tpt) cc_final: 0.8033 (tpt) REVERT: C 936 ASP cc_start: 0.8607 (t0) cc_final: 0.8286 (t0) REVERT: C 995 ARG cc_start: 0.8453 (mtt-85) cc_final: 0.8175 (mtt180) REVERT: C 1002 GLN cc_start: 0.8381 (tp40) cc_final: 0.7916 (tt0) REVERT: H 100 ASP cc_start: 0.6122 (t0) cc_final: 0.5850 (p0) REVERT: I 100 ASP cc_start: 0.6469 (p0) cc_final: 0.6132 (t70) REVERT: J 50 ASP cc_start: 0.7722 (p0) cc_final: 0.7144 (t0) REVERT: J 81 MET cc_start: 0.5887 (tmm) cc_final: 0.5499 (tmm) REVERT: M 3 VAL cc_start: 0.8601 (t) cc_final: 0.8342 (p) REVERT: N 37 GLN cc_start: 0.6611 (pm20) cc_final: 0.6067 (pm20) REVERT: N 90 GLN cc_start: 0.7807 (pp30) cc_final: 0.7587 (pp30) outliers start: 29 outliers final: 9 residues processed: 233 average time/residue: 0.9802 time to fit residues: 291.6292 Evaluate side-chains 207 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 195 time to evaluate : 3.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 29 ILE Chi-restraints excluded: chain N residue 3 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 62 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 127 optimal weight: 0.4980 chunk 330 optimal weight: 20.0000 chunk 132 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 chunk 68 optimal weight: 0.9980 chunk 301 optimal weight: 0.9990 chunk 40 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 228 optimal weight: 9.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 99 ASN B 49 HIS B 196 ASN C 49 HIS ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN L 6 GLN M 28 ASN N 6 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.214098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.141350 restraints weight = 39699.641| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 3.49 r_work: 0.3613 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 30561 Z= 0.172 Angle : 0.683 11.497 41778 Z= 0.324 Chirality : 0.048 0.413 5022 Planarity : 0.005 0.057 5157 Dihedral : 11.617 82.734 6151 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.33 % Allowed : 10.53 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.14), residues: 3561 helix: 1.44 (0.21), residues: 669 sheet: 0.00 (0.16), residues: 999 loop : -1.16 (0.14), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 99 HIS 0.006 0.001 HIS C 49 PHE 0.023 0.002 PHE A 140 TYR 0.024 0.001 TYR B 265 ARG 0.007 0.001 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00437 ( 45) link_NAG-ASN : angle 2.68145 ( 135) link_ALPHA1-6 : bond 0.00857 ( 3) link_ALPHA1-6 : angle 1.71562 ( 9) link_BETA1-4 : bond 0.00802 ( 57) link_BETA1-4 : angle 2.65036 ( 171) hydrogen bonds : bond 0.04999 ( 1063) hydrogen bonds : angle 5.88376 ( 2943) link_BETA1-6 : bond 0.00307 ( 6) link_BETA1-6 : angle 1.62576 ( 18) SS BOND : bond 0.00324 ( 42) SS BOND : angle 1.44534 ( 84) covalent geometry : bond 0.00412 (30408) covalent geometry : angle 0.64252 (41361) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 205 time to evaluate : 3.371 Fit side-chains REVERT: A 99 ASN cc_start: 0.7525 (t0) cc_final: 0.7096 (t0) REVERT: A 237 ARG cc_start: 0.7619 (tmt170) cc_final: 0.6898 (tmt-80) REVERT: A 512 VAL cc_start: 0.8236 (OUTLIER) cc_final: 0.7962 (m) REVERT: A 571 ASP cc_start: 0.8414 (t0) cc_final: 0.8080 (t0) REVERT: A 574 ASP cc_start: 0.7941 (t0) cc_final: 0.7655 (t0) REVERT: A 988 GLU cc_start: 0.8174 (mp0) cc_final: 0.7854 (mp0) REVERT: B 99 ASN cc_start: 0.7767 (t0) cc_final: 0.7499 (t0) REVERT: B 140 PHE cc_start: 0.8050 (p90) cc_final: 0.7616 (p90) REVERT: B 170 TYR cc_start: 0.7005 (t80) cc_final: 0.6748 (t80) REVERT: B 571 ASP cc_start: 0.8437 (t0) cc_final: 0.8117 (t0) REVERT: B 988 GLU cc_start: 0.8168 (mp0) cc_final: 0.7559 (mp0) REVERT: B 1107 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.7533 (mmt-90) REVERT: C 99 ASN cc_start: 0.8061 (t0) cc_final: 0.7771 (t0) REVERT: C 306 PHE cc_start: 0.8494 (m-80) cc_final: 0.8119 (m-10) REVERT: C 571 ASP cc_start: 0.8383 (t0) cc_final: 0.7894 (t0) REVERT: C 574 ASP cc_start: 0.7900 (t0) cc_final: 0.7580 (t0) REVERT: C 578 ASP cc_start: 0.8315 (t0) cc_final: 0.8014 (t0) REVERT: C 646 ARG cc_start: 0.7715 (tmt170) cc_final: 0.7468 (tmt170) REVERT: C 740 MET cc_start: 0.8056 (tpt) cc_final: 0.7627 (tpt) REVERT: C 995 ARG cc_start: 0.8293 (mtt-85) cc_final: 0.8043 (mtt180) REVERT: C 1002 GLN cc_start: 0.8238 (tp40) cc_final: 0.7807 (tt0) REVERT: H 100 ASP cc_start: 0.6095 (t0) cc_final: 0.5786 (p0) REVERT: I 48 ILE cc_start: 0.7620 (OUTLIER) cc_final: 0.7395 (pp) REVERT: I 100 ASP cc_start: 0.6446 (p0) cc_final: 0.6220 (t0) REVERT: I 108 ASP cc_start: 0.7354 (m-30) cc_final: 0.6705 (p0) REVERT: J 81 MET cc_start: 0.5836 (tmm) cc_final: 0.5383 (tmm) REVERT: J 108 ASP cc_start: 0.7631 (m-30) cc_final: 0.6771 (p0) REVERT: M 3 VAL cc_start: 0.8638 (t) cc_final: 0.8392 (p) REVERT: M 90 GLN cc_start: 0.7727 (pp30) cc_final: 0.7207 (pp30) REVERT: N 37 GLN cc_start: 0.6578 (pm20) cc_final: 0.5927 (pm20) REVERT: N 90 GLN cc_start: 0.7844 (pp30) cc_final: 0.7574 (pp30) outliers start: 42 outliers final: 12 residues processed: 234 average time/residue: 0.9806 time to fit residues: 294.7695 Evaluate side-chains 206 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 191 time to evaluate : 3.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain N residue 3 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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: 69.8822 > 50: distance: 23 - 29: 34.967 distance: 29 - 30: 32.201 distance: 29 - 35: 39.945 distance: 30 - 31: 51.526 distance: 30 - 33: 64.698 distance: 31 - 32: 39.876 distance: 31 - 36: 23.701 distance: 33 - 34: 33.814 distance: 34 - 35: 50.839 distance: 36 - 37: 47.071 distance: 37 - 38: 39.831 distance: 37 - 40: 10.957 distance: 38 - 39: 68.130 distance: 40 - 41: 50.671 distance: 43 - 44: 39.414 distance: 43 - 46: 49.992 distance: 44 - 45: 56.393 distance: 44 - 51: 42.165 distance: 46 - 47: 49.823 distance: 48 - 49: 57.246 distance: 49 - 50: 29.497 distance: 51 - 52: 22.407 distance: 51 - 57: 54.071 distance: 52 - 53: 7.432 distance: 52 - 55: 26.800 distance: 53 - 54: 23.568 distance: 53 - 58: 33.137 distance: 55 - 56: 33.547 distance: 56 - 57: 37.980 distance: 58 - 59: 30.783 distance: 59 - 60: 27.536 distance: 59 - 62: 22.425 distance: 60 - 61: 50.109 distance: 60 - 64: 69.374 distance: 62 - 63: 37.627 distance: 64 - 65: 37.103 distance: 65 - 66: 28.482 distance: 65 - 68: 18.665 distance: 66 - 67: 25.028 distance: 66 - 73: 39.399 distance: 69 - 70: 29.397 distance: 70 - 71: 11.696 distance: 71 - 72: 15.266 distance: 73 - 74: 27.610 distance: 74 - 75: 37.326 distance: 74 - 77: 21.972 distance: 75 - 84: 39.570 distance: 77 - 78: 34.851 distance: 78 - 79: 30.310 distance: 79 - 80: 16.109 distance: 80 - 81: 13.456 distance: 81 - 82: 5.636 distance: 81 - 83: 5.038 distance: 84 - 85: 39.164 distance: 85 - 86: 56.268 distance: 85 - 88: 42.687 distance: 86 - 87: 39.914 distance: 86 - 90: 39.659 distance: 87 - 118: 35.199 distance: 88 - 89: 40.258 distance: 90 - 91: 46.367 distance: 91 - 92: 25.519 distance: 91 - 94: 53.308 distance: 92 - 93: 25.447 distance: 92 - 101: 24.522 distance: 93 - 126: 30.916 distance: 94 - 95: 28.555 distance: 95 - 96: 36.183 distance: 95 - 97: 27.800 distance: 96 - 98: 35.275 distance: 97 - 99: 39.231 distance: 98 - 100: 21.376 distance: 99 - 100: 24.622 distance: 101 - 102: 14.652 distance: 102 - 103: 44.099 distance: 102 - 105: 51.398 distance: 103 - 104: 20.922 distance: 103 - 109: 29.518 distance: 104 - 134: 30.809 distance: 105 - 106: 28.960 distance: 105 - 107: 17.922 distance: 106 - 108: 26.677