Starting phenix.real_space_refine on Sat Mar 7 03:26:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7upy_26678/03_2026/7upy_26678_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7upy_26678/03_2026/7upy_26678.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7upy_26678/03_2026/7upy_26678_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7upy_26678/03_2026/7upy_26678_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7upy_26678/03_2026/7upy_26678.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7upy_26678/03_2026/7upy_26678.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.024 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 153 5.16 5 C 23602 2.51 5 N 6075 2.21 5 O 7482 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 206 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37312 Number of models: 1 Model: "" Number of chains: 46 Chain: "A" Number of atoms: 8665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1109, 8665 Classifications: {'peptide': 1109} Link IDs: {'PTRANS': 52, 'TRANS': 1056} Chain breaks: 4 Chain: "B" Number of atoms: 8534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1090, 8534 Classifications: {'peptide': 1090} Link IDs: {'PTRANS': 52, 'TRANS': 1037} Chain breaks: 5 Chain: "C" Number of atoms: 8678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1109, 8678 Classifications: {'peptide': 1109} Link IDs: {'PTRANS': 53, 'TRANS': 1055} Chain breaks: 4 Chain: "H" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1701 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 213} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1622 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 200} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "D" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1701 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 213} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1622 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 200} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "F" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1701 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 213} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1622 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 200} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 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: {'MAN': 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "S" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "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: {'MAN': 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: 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: 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: "Y" 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: "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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "d" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: {'MAN': 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "o" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "p" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 8.76, per 1000 atoms: 0.23 Number of scatterers: 37312 At special positions: 0 Unit cell: (180.94, 184.26, 247.34, 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 153 16.00 O 7482 8.00 N 6075 7.00 C 23602 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.01 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.05 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.05 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.05 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.00 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.01 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.05 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.00 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.01 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.02 Simple disulfide: pdb=" SG CYS D 140 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 194 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.02 Simple disulfide: pdb=" SG CYS F 140 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 134 " - pdb=" SG CYS G 194 " 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 Atom "HETATM37240 O5 NAG C1402 .*. O " rejected from bonding due to valence issues. Atom "HETATM37044 O5 NAG A1404 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-4 " NAG J 2 " - " MAN J 3 " " NAG Q 2 " - " MAN Q 3 " " NAG R 2 " - " MAN R 3 " " NAG T 2 " - " MAN T 3 " " NAG V 2 " - " MAN V 3 " " NAG b 2 " - " MAN b 3 " " NAG c 2 " - " MAN c 3 " " NAG e 2 " - " MAN e 3 " " NAG g 2 " - " MAN g 3 " " NAG n 2 " - " MAN n 3 " " NAG o 2 " - " MAN o 3 " " NAG q 2 " - " MAN q 3 " BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " BETA1-6 " NAG P 1 " - " FUC P 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG S 1 " - " FUC S 3 " " NAG a 1 " - " FUC a 3 " " NAG d 1 " - " FUC d 3 " " NAG m 1 " - " FUC m 3 " " NAG p 1 " - " FUC p 3 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 149 " " NAG A1403 " - " ASN A 234 " " NAG A1404 " - " ASN A 282 " " NAG A1405 " - " ASN A 603 " " NAG A1406 " - " ASN A 657 " " NAG A1407 " - " ASN A 709 " " NAG A1408 " - " ASN A1158 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 149 " " NAG B1403 " - " ASN B 234 " " NAG B1404 " - " ASN B 331 " " NAG B1405 " - " ASN B 603 " " NAG B1406 " - " ASN B 657 " " NAG B1407 " - " ASN B 709 " " NAG B1408 " - " ASN B1158 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 149 " " NAG C1403 " - " ASN C 331 " " NAG C1404 " - " ASN C 603 " " NAG C1405 " - " ASN C 657 " " NAG C1406 " - " ASN C 709 " " NAG C1407 " - " ASN C1158 " " NAG I 1 " - " ASN A 17 " " NAG J 1 " - " ASN A 122 " " NAG K 1 " - " ASN A 331 " " NAG M 1 " - " ASN A 616 " " NAG N 1 " - " ASN A 717 " " NAG O 1 " - " ASN A 801 " " NAG P 1 " - " ASN A1074 " " NAG Q 1 " - " ASN A1098 " " NAG R 1 " - " ASN A1134 " " NAG S 1 " - " ASN A 343 " " NAG T 1 " - " ASN A 165 " " NAG U 1 " - " ASN B 17 " " NAG V 1 " - " ASN B 122 " " NAG W 1 " - " ASN B 282 " " NAG X 1 " - " ASN B 616 " " NAG Y 1 " - " ASN B 717 " " NAG Z 1 " - " ASN B 801 " " NAG a 1 " - " ASN B1074 " " NAG b 1 " - " ASN B1098 " " NAG c 1 " - " ASN B1134 " " NAG d 1 " - " ASN B 343 " " NAG e 1 " - " ASN B 165 " " NAG f 1 " - " ASN C 17 " " NAG g 1 " - " ASN C 122 " " NAG h 1 " - " ASN C 234 " " NAG i 1 " - " ASN C 282 " " NAG j 1 " - " ASN C 616 " " NAG k 1 " - " ASN C 717 " " NAG l 1 " - " ASN C 801 " " NAG m 1 " - " ASN C1074 " " NAG n 1 " - " ASN C1098 " " NAG o 1 " - " ASN C1134 " " NAG p 1 " - " ASN C 343 " " NAG q 1 " - " ASN C 165 " Time building additional restraints: 3.61 Conformation dependent library (CDL) restraints added in 1.8 seconds 9150 Ramachandran restraints generated. 4575 Oldfield, 0 Emsley, 4575 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8612 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 78 sheets defined 21.6% alpha, 35.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.91 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.273A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 4.988A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 619 through 623 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.629A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.909A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.669A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 848 removed outlier: 3.983A pdb=" N ARG A 847 " --> pdb=" O ASP A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 855 removed outlier: 3.646A pdb=" N ALA A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.777A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.149A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.899A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.049A pdb=" N GLU A 990 " --> pdb=" O LYS A 986 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1161 removed outlier: 4.258A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE A1148 " --> pdb=" O GLU A1144 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER A1161 " --> pdb=" O LYS A1157 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.562A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.538A 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 386 through 389 Processing helix chain 'B' and resid 405 through 411 removed outlier: 4.385A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA B 411 " --> pdb=" O ARG B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 633 through 639 removed outlier: 3.699A pdb=" N THR B 638 " --> pdb=" O VAL B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.623A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.639A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 853 through 856 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.786A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.756A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.908A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1160 removed outlier: 3.897A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N PHE B1148 " --> pdb=" O GLU B1144 " (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 Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.989A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.808A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 411 removed outlier: 4.171A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 618 through 623 removed outlier: 3.721A pdb=" N VAL C 622 " --> pdb=" O THR C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 628 Processing helix chain 'C' and resid 634 through 639 Processing helix chain 'C' and resid 737 through 744 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 758 through 783 removed outlier: 3.878A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.555A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.908A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.510A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.884A 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 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.690A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1161 removed outlier: 4.025A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N PHE C1148 " --> pdb=" O GLU C1144 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER C1161 " --> pdb=" O LYS C1157 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 156 through 158 No H-bonds generated for 'chain 'H' and resid 156 through 158' Processing helix chain 'H' and resid 187 through 191 removed outlier: 3.989A pdb=" N GLY H 190 " --> pdb=" O SER H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 201 through 204 Processing helix chain 'L' and resid 121 through 127 Processing helix chain 'L' and resid 183 through 188 removed outlier: 3.652A pdb=" N GLU L 187 " --> pdb=" O LYS L 183 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS L 188 " --> pdb=" O ALA L 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 183 through 188' Processing helix chain 'D' and resid 61 through 64 Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'D' and resid 156 through 158 No H-bonds generated for 'chain 'D' and resid 156 through 158' Processing helix chain 'D' and resid 187 through 191 removed outlier: 3.990A pdb=" N GLY D 190 " --> pdb=" O SER D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 204 Processing helix chain 'E' and resid 121 through 127 Processing helix chain 'E' and resid 183 through 188 removed outlier: 3.652A pdb=" N GLU E 187 " --> pdb=" O LYS E 183 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS E 188 " --> pdb=" O ALA E 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 183 through 188' Processing helix chain 'F' and resid 61 through 64 Processing helix chain 'F' and resid 73 through 75 No H-bonds generated for 'chain 'F' and resid 73 through 75' Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'F' and resid 156 through 158 No H-bonds generated for 'chain 'F' and resid 156 through 158' Processing helix chain 'F' and resid 187 through 191 removed outlier: 3.990A pdb=" N GLY F 190 " --> pdb=" O SER F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 204 Processing helix chain 'G' and resid 121 through 127 Processing helix chain 'G' and resid 183 through 188 removed outlier: 3.652A pdb=" N GLU G 187 " --> pdb=" O LYS G 183 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS G 188 " --> pdb=" O ALA G 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 183 through 188' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.046A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.046A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.936A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.928A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 9.710A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.191A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.036A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 13.349A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 12.182A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 9.568A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 9.710A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.191A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.036A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 3.858A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.283A 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 removed outlier: 5.195A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.570A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.723A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (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 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.523A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.876A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.870A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.459A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.171A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.507A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.397A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.018A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.520A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.624A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 9.274A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 10.323A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.669A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 12.288A pdb=" N PHE B 238 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 12.176A pdb=" N PHE B 135 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 12.599A pdb=" N THR B 240 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 10.765A pdb=" N ASN B 137 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 10.939A pdb=" N LEU B 242 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 9.274A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 10.323A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.669A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.175A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 324 through 325 removed outlier: 6.817A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.627A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.627A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (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 473 through 474 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.700A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.525A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.779A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.891A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.422A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.482A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.041A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.382A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.215A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.041A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.515A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.587A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.940A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 133 through 135 removed outlier: 6.747A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.043A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 324 through 325 removed outlier: 6.953A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.759A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.759A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.431A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 715 removed outlier: 4.003A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.852A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.399A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.212A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AF8, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.525A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 120 through 124 removed outlier: 5.965A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 120 through 124 removed outlier: 5.965A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 151 through 154 removed outlier: 4.205A pdb=" N TYR H 194 " --> pdb=" O VAL H 211 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 4 through 6 removed outlier: 4.317A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.263A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 114 through 118 removed outlier: 6.411A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 153 through 154 Processing sheet with id=AG7, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AG8, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.525A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'D' and resid 120 through 124 removed outlier: 5.965A pdb=" N TYR D 176 " --> pdb=" O ASP D 144 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'D' and resid 120 through 124 removed outlier: 5.965A pdb=" N TYR D 176 " --> pdb=" O ASP D 144 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'D' and resid 151 through 154 removed outlier: 4.205A pdb=" N TYR D 194 " --> pdb=" O VAL D 211 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'E' and resid 4 through 6 removed outlier: 4.317A pdb=" N ASP E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER E 67 " --> pdb=" O ASP E 70 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.264A pdb=" N GLN E 37 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N LEU E 46 " --> pdb=" O GLN E 37 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'E' and resid 114 through 118 removed outlier: 6.411A pdb=" N TYR E 173 " --> pdb=" O ASN E 138 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'E' and resid 153 through 154 Processing sheet with id=AH7, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AH8, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.524A pdb=" N GLY F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'F' and resid 120 through 124 removed outlier: 5.966A pdb=" N TYR F 176 " --> pdb=" O ASP F 144 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'F' and resid 120 through 124 removed outlier: 5.966A pdb=" N TYR F 176 " --> pdb=" O ASP F 144 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'F' and resid 151 through 154 removed outlier: 4.205A pdb=" N TYR F 194 " --> pdb=" O VAL F 211 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'G' and resid 4 through 6 removed outlier: 4.317A pdb=" N ASP G 70 " --> pdb=" O SER G 67 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER G 67 " --> pdb=" O ASP G 70 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.264A pdb=" N GLN G 37 " --> pdb=" O LEU G 46 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU G 46 " --> pdb=" O GLN G 37 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'G' and resid 114 through 118 removed outlier: 6.411A pdb=" N TYR G 173 " --> pdb=" O ASN G 138 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'G' and resid 153 through 154 1597 hydrogen bonds defined for protein. 4245 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: 10.72 Time building geometry restraints manager: 4.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 6108 1.30 - 1.43: 10210 1.43 - 1.56: 21626 1.56 - 1.69: 5 1.69 - 1.82: 192 Bond restraints: 38141 Sorted by residual: bond pdb=" C TYR F 145 " pdb=" O TYR F 145 " ideal model delta sigma weight residual 1.235 1.174 0.061 1.22e-02 6.72e+03 2.50e+01 bond pdb=" C TYR H 145 " pdb=" O TYR H 145 " ideal model delta sigma weight residual 1.235 1.174 0.061 1.22e-02 6.72e+03 2.49e+01 bond pdb=" C ARG C1014 " pdb=" O ARG C1014 " ideal model delta sigma weight residual 1.237 1.185 0.051 1.19e-02 7.06e+03 1.86e+01 bond pdb=" C1 MAN q 3 " pdb=" O5 MAN q 3 " ideal model delta sigma weight residual 1.399 1.481 -0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" CA ARG C 355 " pdb=" C ARG C 355 " ideal model delta sigma weight residual 1.522 1.568 -0.046 1.14e-02 7.69e+03 1.65e+01 ... (remaining 38136 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.07: 46837 3.07 - 6.15: 4913 6.15 - 9.22: 132 9.22 - 12.29: 15 12.29 - 15.37: 7 Bond angle restraints: 51904 Sorted by residual: angle pdb=" C GLU D 148 " pdb=" N PRO D 149 " pdb=" CA PRO D 149 " ideal model delta sigma weight residual 119.84 133.05 -13.21 1.25e+00 6.40e-01 1.12e+02 angle pdb=" C GLU H 148 " pdb=" N PRO H 149 " pdb=" CA PRO H 149 " ideal model delta sigma weight residual 119.84 133.04 -13.20 1.25e+00 6.40e-01 1.12e+02 angle pdb=" C GLU F 148 " pdb=" N PRO F 149 " pdb=" CA PRO F 149 " ideal model delta sigma weight residual 119.84 132.99 -13.15 1.25e+00 6.40e-01 1.11e+02 angle pdb=" N ASP B 467 " pdb=" CA ASP B 467 " pdb=" C ASP B 467 " ideal model delta sigma weight residual 108.23 123.60 -15.37 1.72e+00 3.38e-01 7.98e+01 angle pdb=" CA ASN C 125 " pdb=" CB ASN C 125 " pdb=" CG ASN C 125 " ideal model delta sigma weight residual 112.60 120.48 -7.88 1.00e+00 1.00e+00 6.21e+01 ... (remaining 51899 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.65: 22875 24.65 - 49.31: 903 49.31 - 73.96: 206 73.96 - 98.61: 71 98.61 - 123.27: 41 Dihedral angle restraints: 24096 sinusoidal: 10682 harmonic: 13414 Sorted by residual: dihedral pdb=" C ASP B 467 " pdb=" N ASP B 467 " pdb=" CA ASP B 467 " pdb=" CB ASP B 467 " ideal model delta harmonic sigma weight residual -122.60 -149.94 27.34 0 2.50e+00 1.60e-01 1.20e+02 dihedral pdb=" N ASP B 467 " pdb=" C ASP B 467 " pdb=" CA ASP B 467 " pdb=" CB ASP B 467 " ideal model delta harmonic sigma weight residual 122.80 149.58 -26.78 0 2.50e+00 1.60e-01 1.15e+02 dihedral pdb=" CB CYS A 840 " pdb=" SG CYS A 840 " pdb=" SG CYS A 851 " pdb=" CB CYS A 851 " ideal model delta sinusoidal sigma weight residual -86.00 -164.68 78.68 1 1.00e+01 1.00e-02 7.71e+01 ... (remaining 24093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.228: 5986 0.228 - 0.456: 181 0.456 - 0.684: 11 0.684 - 0.911: 4 0.911 - 1.139: 5 Chirality restraints: 6187 Sorted by residual: chirality pdb=" C1 FUC m 3 " pdb=" O6 NAG m 1 " pdb=" C2 FUC m 3 " pdb=" O5 FUC m 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.08e+02 chirality pdb=" C1 NAG h 2 " pdb=" O4 NAG h 1 " pdb=" C2 NAG h 2 " pdb=" O5 NAG h 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 8.91e+01 chirality pdb=" C1 NAG l 2 " pdb=" O4 NAG l 1 " pdb=" C2 NAG l 2 " pdb=" O5 NAG l 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.46e+01 ... (remaining 6184 not shown) Planarity restraints: 6608 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 61 " 0.219 2.00e-02 2.50e+03 2.62e-01 8.56e+02 pdb=" CG ASN B 61 " -0.144 2.00e-02 2.50e+03 pdb=" OD1 ASN B 61 " 0.030 2.00e-02 2.50e+03 pdb=" ND2 ASN B 61 " -0.418 2.00e-02 2.50e+03 pdb=" C1 NAG B1401 " 0.313 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 61 " 0.198 2.00e-02 2.50e+03 2.20e-01 6.07e+02 pdb=" CG ASN A 61 " -0.132 2.00e-02 2.50e+03 pdb=" OD1 ASN A 61 " 0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN A 61 " -0.345 2.00e-02 2.50e+03 pdb=" C1 NAG A1401 " 0.258 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 104 " 0.169 2.00e-02 2.50e+03 9.02e-02 2.03e+02 pdb=" CG TRP B 104 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TRP B 104 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP B 104 " -0.089 2.00e-02 2.50e+03 pdb=" NE1 TRP B 104 " -0.058 2.00e-02 2.50e+03 pdb=" CE2 TRP B 104 " -0.016 2.00e-02 2.50e+03 pdb=" CE3 TRP B 104 " -0.132 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 104 " 0.096 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 104 " -0.029 2.00e-02 2.50e+03 pdb=" CH2 TRP B 104 " 0.111 2.00e-02 2.50e+03 ... (remaining 6605 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.33: 23 2.33 - 2.97: 16700 2.97 - 3.61: 50354 3.61 - 4.26: 87105 4.26 - 4.90: 144505 Nonbonded interactions: 298687 Sorted by model distance: nonbonded pdb=" O VAL B 620 " pdb=" NH2 ARG B 634 " model vdw 1.682 3.120 nonbonded pdb=" OE1 GLU A 406 " pdb=" OH TYR A 495 " model vdw 1.693 3.040 nonbonded pdb=" NH2 ARG B 346 " pdb=" OD1 ASP H 95 " model vdw 1.876 3.120 nonbonded pdb=" NH2 ARG B 454 " pdb=" O SER B 469 " model vdw 2.015 3.120 nonbonded pdb=" CD ARG B1107 " pdb=" CE1 TYR C 904 " model vdw 2.090 3.740 ... (remaining 298682 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 68 or resid 77 through 829 or resid 853 through \ 1407)) selection = (chain 'B' and (resid 14 through 623 or resid 636 through 1407)) selection = (chain 'C' and (resid 14 through 68 or resid 77 through 623 or resid 636 through \ 829 or resid 853 through 1407)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'f' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' } ncs_group { reference = (chain 'J' and resid 1 through 2) selection = (chain 'P' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) selection = (chain 'R' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'a' and resid 1 through 2) selection = (chain 'b' and resid 1 through 2) selection = (chain 'c' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) selection = (chain 'g' and resid 1 through 2) selection = (chain 'm' and resid 1 through 2) selection = (chain 'n' and resid 1 through 2) selection = (chain 'o' and resid 1 through 2) selection = (chain 'p' and resid 1 through 2) selection = (chain 'q' and resid 1 through 2) } 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: 10.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.030 Extract box with map and model: 0.780 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 38.320 Find NCS groups from input model: 1.320 Set up NCS constraints: 0.130 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.082 38304 Z= 0.789 Angle : 1.982 54.869 52339 Z= 1.238 Chirality : 0.110 1.139 6187 Planarity : 0.012 0.125 6551 Dihedral : 15.613 123.266 15322 Min Nonbonded Distance : 1.682 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.94 % Allowed : 5.70 % Favored : 93.36 % Rotamer: Outliers : 2.22 % Allowed : 4.94 % Favored : 92.84 % Cbeta Deviations : 0.39 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.11), residues: 4575 helix: -1.64 (0.15), residues: 770 sheet: 0.36 (0.14), residues: 1231 loop : -1.09 (0.11), residues: 2574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 328 TYR 0.119 0.019 TYR B 38 PHE 0.097 0.014 PHE A 718 TRP 0.169 0.020 TRP B 104 HIS 0.020 0.004 HIS B1159 Details of bonding type rmsd covalent geometry : bond 0.01384 (38141) covalent geometry : angle 1.85664 (51904) SS BOND : bond 0.01234 ( 54) SS BOND : angle 2.04346 ( 108) hydrogen bonds : bond 0.16360 ( 1513) hydrogen bonds : angle 8.91670 ( 4245) link_ALPHA1-4 : bond 0.02663 ( 12) link_ALPHA1-4 : angle 4.28354 ( 36) link_BETA1-4 : bond 0.02342 ( 34) link_BETA1-4 : angle 3.98640 ( 102) link_BETA1-6 : bond 0.02578 ( 6) link_BETA1-6 : angle 3.10128 ( 18) link_NAG-ASN : bond 0.01835 ( 57) link_NAG-ASN : angle 11.80505 ( 171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9150 Ramachandran restraints generated. 4575 Oldfield, 0 Emsley, 4575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9150 Ramachandran restraints generated. 4575 Oldfield, 0 Emsley, 4575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 4017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 421 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 568 ASP cc_start: 0.7009 (OUTLIER) cc_final: 0.6780 (m-30) REVERT: B 190 ARG cc_start: 0.6924 (OUTLIER) cc_final: 0.5643 (ttp-110) REVERT: B 571 ASP cc_start: 0.7846 (OUTLIER) cc_final: 0.7633 (t0) REVERT: B 957 GLN cc_start: 0.8027 (tt0) cc_final: 0.7700 (tp40) REVERT: C 53 ASP cc_start: 0.7783 (t0) cc_final: 0.7545 (t0) REVERT: C 78 ARG cc_start: 0.6661 (OUTLIER) cc_final: 0.6378 (tpt90) REVERT: C 144 TYR cc_start: 0.7228 (OUTLIER) cc_final: 0.6614 (t80) REVERT: C 298 GLU cc_start: 0.8183 (tt0) cc_final: 0.7965 (tt0) REVERT: C 420 ASP cc_start: 0.7299 (OUTLIER) cc_final: 0.6914 (m-30) REVERT: C 856 ASN cc_start: 0.7970 (m110) cc_final: 0.7684 (m110) REVERT: C 936 ASP cc_start: 0.7524 (m-30) cc_final: 0.7235 (m-30) REVERT: H 99 TYR cc_start: 0.7663 (m-80) cc_final: 0.7348 (m-80) REVERT: E 183 LYS cc_start: 0.3972 (tptp) cc_final: 0.3725 (pttt) REVERT: E 190 LYS cc_start: 0.7567 (ttmp) cc_final: 0.7162 (ttpt) outliers start: 89 outliers final: 32 residues processed: 495 average time/residue: 0.2384 time to fit residues: 189.6730 Evaluate side-chains 303 residues out of total 4017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 265 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain G residue 14 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 432 optimal weight: 0.4980 chunk 197 optimal weight: 0.7980 chunk 388 optimal weight: 5.9990 chunk 455 optimal weight: 1.9990 chunk 215 optimal weight: 0.4980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 10.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 207 HIS ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN A 926 GLN ** A1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN B 675 GLN B 919 ASN B 926 GLN B 955 ASN B1002 GLN C 121 ASN C 580 GLN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN C 907 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN E 189 HIS G 3 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.225479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.185413 restraints weight = 49785.584| |-----------------------------------------------------------------------------| r_work (start): 0.4047 rms_B_bonded: 5.47 r_work (final): 0.4047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 38304 Z= 0.180 Angle : 0.804 19.567 52339 Z= 0.394 Chirality : 0.051 0.841 6187 Planarity : 0.005 0.087 6551 Dihedral : 12.017 113.851 7274 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.48 % Favored : 96.28 % Rotamer: Outliers : 1.80 % Allowed : 8.11 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.90 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.12), residues: 4575 helix: 0.61 (0.18), residues: 778 sheet: 0.60 (0.14), residues: 1353 loop : -0.86 (0.12), residues: 2444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 567 TYR 0.028 0.002 TYR A 904 PHE 0.034 0.002 PHE D 146 TRP 0.020 0.002 TRP D 103 HIS 0.011 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00395 (38141) covalent geometry : angle 0.75386 (51904) SS BOND : bond 0.00591 ( 54) SS BOND : angle 1.45078 ( 108) hydrogen bonds : bond 0.04653 ( 1513) hydrogen bonds : angle 6.49310 ( 4245) link_ALPHA1-4 : bond 0.01491 ( 12) link_ALPHA1-4 : angle 2.86116 ( 36) link_BETA1-4 : bond 0.00541 ( 34) link_BETA1-4 : angle 2.06860 ( 102) link_BETA1-6 : bond 0.01308 ( 6) link_BETA1-6 : angle 1.60803 ( 18) link_NAG-ASN : bond 0.00894 ( 57) link_NAG-ASN : angle 4.41694 ( 171) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9150 Ramachandran restraints generated. 4575 Oldfield, 0 Emsley, 4575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9150 Ramachandran restraints generated. 4575 Oldfield, 0 Emsley, 4575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 4017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 314 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.6376 (mpp) cc_final: 0.6114 (ptp) REVERT: B 737 ASP cc_start: 0.6622 (t0) cc_final: 0.6347 (t70) REVERT: C 78 ARG cc_start: 0.6831 (OUTLIER) cc_final: 0.6448 (tpt90) REVERT: C 144 TYR cc_start: 0.7287 (OUTLIER) cc_final: 0.6865 (t80) REVERT: C 936 ASP cc_start: 0.7163 (m-30) cc_final: 0.6948 (m-30) REVERT: H 29 PHE cc_start: 0.7532 (t80) cc_final: 0.7253 (t80) REVERT: H 32 THR cc_start: 0.7316 (p) cc_final: 0.6927 (t) REVERT: E 207 LYS cc_start: 0.2243 (tttt) cc_final: 0.1145 (tptt) REVERT: F 80 MET cc_start: 0.2350 (ttp) cc_final: 0.1945 (ttp) REVERT: G 31 ASP cc_start: 0.2147 (p0) cc_final: 0.1749 (t0) outliers start: 72 outliers final: 41 residues processed: 365 average time/residue: 0.2334 time to fit residues: 138.3638 Evaluate side-chains 297 residues out of total 4017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 254 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 214 LYS Chi-restraints excluded: chain F residue 172 SER Chi-restraints excluded: chain F residue 196 CYS Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 136 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 382 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 321 optimal weight: 0.5980 chunk 289 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 chunk 397 optimal weight: 10.0000 chunk 315 optimal weight: 3.9990 chunk 352 optimal weight: 20.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN A1119 ASN B 437 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN C 675 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.225237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.184145 restraints weight = 49853.472| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 5.72 r_work: 0.3374 rms_B_bonded: 5.43 restraints_weight: 2.0000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 38304 Z= 0.151 Angle : 0.711 16.483 52339 Z= 0.344 Chirality : 0.047 0.664 6187 Planarity : 0.004 0.052 6551 Dihedral : 11.084 113.608 7217 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.00 % Favored : 95.83 % Rotamer: Outliers : 2.15 % Allowed : 9.31 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.12), residues: 4575 helix: 1.29 (0.19), residues: 779 sheet: 0.61 (0.14), residues: 1347 loop : -0.79 (0.12), residues: 2449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 237 TYR 0.023 0.002 TYR L 91 PHE 0.030 0.002 PHE C1148 TRP 0.024 0.002 TRP D 103 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00343 (38141) covalent geometry : angle 0.66779 (51904) SS BOND : bond 0.00435 ( 54) SS BOND : angle 1.40425 ( 108) hydrogen bonds : bond 0.04126 ( 1513) hydrogen bonds : angle 5.99722 ( 4245) link_ALPHA1-4 : bond 0.01635 ( 12) link_ALPHA1-4 : angle 3.01500 ( 36) link_BETA1-4 : bond 0.00409 ( 34) link_BETA1-4 : angle 1.73127 ( 102) link_BETA1-6 : bond 0.01416 ( 6) link_BETA1-6 : angle 1.76887 ( 18) link_NAG-ASN : bond 0.00787 ( 57) link_NAG-ASN : angle 3.76558 ( 171) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9150 Ramachandran restraints generated. 4575 Oldfield, 0 Emsley, 4575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9150 Ramachandran restraints generated. 4575 Oldfield, 0 Emsley, 4575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 4017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 272 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1119 ASN cc_start: 0.8525 (m110) cc_final: 0.8220 (m-40) REVERT: B 212 LEU cc_start: 0.5088 (OUTLIER) cc_final: 0.4704 (tt) REVERT: C 78 ARG cc_start: 0.6838 (OUTLIER) cc_final: 0.6499 (tpt90) REVERT: C 109 THR cc_start: 0.8490 (p) cc_final: 0.8276 (t) REVERT: C 144 TYR cc_start: 0.7730 (OUTLIER) cc_final: 0.7226 (t80) REVERT: C 346 ARG cc_start: 0.8027 (mtm-85) cc_final: 0.7595 (mpt180) REVERT: C 936 ASP cc_start: 0.7493 (m-30) cc_final: 0.6966 (m-30) REVERT: H 12 LYS cc_start: 0.4910 (mmtm) cc_final: 0.4710 (tptp) REVERT: H 29 PHE cc_start: 0.8266 (t80) cc_final: 0.7949 (t80) REVERT: H 32 THR cc_start: 0.7590 (p) cc_final: 0.6915 (t) REVERT: H 209 LYS cc_start: 0.3426 (mmmm) cc_final: 0.3115 (mmmm) REVERT: L 188 LYS cc_start: 0.5998 (ptmt) cc_final: 0.5791 (ptmm) REVERT: D 33 TYR cc_start: 0.7486 (m-80) cc_final: 0.7174 (m-10) REVERT: E 207 LYS cc_start: 0.2167 (tttt) cc_final: 0.1166 (tptt) REVERT: F 18 VAL cc_start: 0.0004 (OUTLIER) cc_final: -0.0307 (t) REVERT: F 80 MET cc_start: 0.1767 (ttp) cc_final: 0.1514 (ttp) REVERT: G 4 MET cc_start: 0.3514 (OUTLIER) cc_final: 0.3138 (mtp) REVERT: G 31 ASP cc_start: 0.2795 (p0) cc_final: 0.2260 (t0) REVERT: G 50 ASP cc_start: 0.4261 (m-30) cc_final: 0.4037 (m-30) outliers start: 86 outliers final: 51 residues processed: 339 average time/residue: 0.2274 time to fit residues: 126.3588 Evaluate side-chains 307 residues out of total 4017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 251 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 190 LYS Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 172 SER Chi-restraints excluded: chain F residue 196 CYS Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 136 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 104 optimal weight: 2.9990 chunk 170 optimal weight: 0.0370 chunk 185 optimal weight: 0.6980 chunk 274 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 194 optimal weight: 0.0470 chunk 83 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 449 optimal weight: 9.9990 chunk 322 optimal weight: 0.4980 chunk 222 optimal weight: 0.0070 overall best weight: 0.2574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN B 519 HIS B 856 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 540 ASN C 675 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.226906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.186508 restraints weight = 50011.478| |-----------------------------------------------------------------------------| r_work (start): 0.4054 rms_B_bonded: 5.80 r_work: 0.3382 rms_B_bonded: 5.43 restraints_weight: 2.0000 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 38304 Z= 0.115 Angle : 0.657 15.246 52339 Z= 0.315 Chirality : 0.045 0.602 6187 Planarity : 0.004 0.045 6551 Dihedral : 10.499 110.892 7216 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.23 % Favored : 96.59 % Rotamer: Outliers : 1.82 % Allowed : 10.38 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.12), residues: 4575 helix: 1.61 (0.19), residues: 785 sheet: 0.70 (0.14), residues: 1297 loop : -0.69 (0.12), residues: 2493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 94 TYR 0.021 0.001 TYR D 27 PHE 0.026 0.001 PHE H 146 TRP 0.030 0.001 TRP D 103 HIS 0.006 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00241 (38141) covalent geometry : angle 0.61972 (51904) SS BOND : bond 0.00296 ( 54) SS BOND : angle 1.33935 ( 108) hydrogen bonds : bond 0.03536 ( 1513) hydrogen bonds : angle 5.71070 ( 4245) link_ALPHA1-4 : bond 0.01487 ( 12) link_ALPHA1-4 : angle 2.97908 ( 36) link_BETA1-4 : bond 0.00415 ( 34) link_BETA1-4 : angle 1.55795 ( 102) link_BETA1-6 : bond 0.01517 ( 6) link_BETA1-6 : angle 1.89501 ( 18) link_NAG-ASN : bond 0.00553 ( 57) link_NAG-ASN : angle 3.29605 ( 171) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9150 Ramachandran restraints generated. 4575 Oldfield, 0 Emsley, 4575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9150 Ramachandran restraints generated. 4575 Oldfield, 0 Emsley, 4575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 4017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 269 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 461 LEU cc_start: -0.0144 (OUTLIER) cc_final: -0.0764 (tt) REVERT: A 988 GLU cc_start: 0.8714 (tp30) cc_final: 0.8302 (tp30) REVERT: B 212 LEU cc_start: 0.5193 (OUTLIER) cc_final: 0.4767 (tt) REVERT: B 516 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7148 (tm-30) REVERT: C 144 TYR cc_start: 0.7715 (OUTLIER) cc_final: 0.7173 (t80) REVERT: C 346 ARG cc_start: 0.8006 (mtm-85) cc_final: 0.7560 (mpt180) REVERT: C 560 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7935 (mp) REVERT: C 936 ASP cc_start: 0.7387 (m-30) cc_final: 0.6878 (m-30) REVERT: H 12 LYS cc_start: 0.5071 (mmtm) cc_final: 0.4792 (mptt) REVERT: H 29 PHE cc_start: 0.8270 (t80) cc_final: 0.8005 (t80) REVERT: H 32 THR cc_start: 0.7637 (p) cc_final: 0.6886 (t) REVERT: L 45 LYS cc_start: 0.8261 (ttpp) cc_final: 0.7963 (tttm) REVERT: L 48 ILE cc_start: 0.7747 (mm) cc_final: 0.7508 (mm) REVERT: E 4 MET cc_start: 0.3533 (ptp) cc_final: 0.3202 (ptt) REVERT: E 145 LYS cc_start: 0.2665 (mtmm) cc_final: 0.1842 (ttmm) REVERT: E 207 LYS cc_start: 0.2229 (tttt) cc_final: 0.1243 (tptt) REVERT: F 18 VAL cc_start: 0.0003 (OUTLIER) cc_final: -0.0299 (t) REVERT: F 48 MET cc_start: 0.3479 (tmm) cc_final: 0.2581 (mmt) REVERT: G 31 ASP cc_start: 0.2776 (p0) cc_final: 0.2358 (t0) REVERT: G 50 ASP cc_start: 0.4046 (m-30) cc_final: 0.3765 (m-30) outliers start: 73 outliers final: 50 residues processed: 327 average time/residue: 0.2217 time to fit residues: 119.7937 Evaluate side-chains 298 residues out of total 4017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 242 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 190 LYS Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 196 CYS Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 136 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 437 optimal weight: 40.0000 chunk 433 optimal weight: 0.0020 chunk 239 optimal weight: 1.9990 chunk 387 optimal weight: 9.9990 chunk 115 optimal weight: 8.9990 chunk 97 optimal weight: 1.9990 chunk 349 optimal weight: 10.0000 chunk 440 optimal weight: 20.0000 chunk 129 optimal weight: 9.9990 chunk 242 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 overall best weight: 4.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN A 907 ASN A1005 GLN B 762 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN C 675 GLN C 804 GLN C 935 GLN E 124 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.222772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.193489 restraints weight = 50043.598| |-----------------------------------------------------------------------------| r_work (start): 0.4259 rms_B_bonded: 1.72 r_work: 0.4045 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.4002 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.142 38304 Z= 0.404 Angle : 0.867 14.498 52339 Z= 0.423 Chirality : 0.056 0.540 6187 Planarity : 0.005 0.062 6551 Dihedral : 10.823 122.103 7208 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.57 % Favored : 95.28 % Rotamer: Outliers : 2.79 % Allowed : 11.23 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.12), residues: 4575 helix: 0.90 (0.19), residues: 773 sheet: 0.54 (0.14), residues: 1224 loop : -0.97 (0.12), residues: 2578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 905 TYR 0.030 0.003 TYR L 91 PHE 0.032 0.003 PHE L 73 TRP 0.027 0.003 TRP L 35 HIS 0.015 0.002 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00992 (38141) covalent geometry : angle 0.83154 (51904) SS BOND : bond 0.00608 ( 54) SS BOND : angle 2.04887 ( 108) hydrogen bonds : bond 0.05461 ( 1513) hydrogen bonds : angle 6.23418 ( 4245) link_ALPHA1-4 : bond 0.01788 ( 12) link_ALPHA1-4 : angle 3.06146 ( 36) link_BETA1-4 : bond 0.00392 ( 34) link_BETA1-4 : angle 1.91260 ( 102) link_BETA1-6 : bond 0.01372 ( 6) link_BETA1-6 : angle 1.94370 ( 18) link_NAG-ASN : bond 0.00575 ( 57) link_NAG-ASN : angle 3.61144 ( 171) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9150 Ramachandran restraints generated. 4575 Oldfield, 0 Emsley, 4575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9150 Ramachandran restraints generated. 4575 Oldfield, 0 Emsley, 4575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 4017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 267 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.7086 (OUTLIER) cc_final: 0.6612 (tt) REVERT: A 461 LEU cc_start: 0.0607 (OUTLIER) cc_final: 0.0185 (tt) REVERT: A 988 GLU cc_start: 0.8352 (tp30) cc_final: 0.7951 (tp30) REVERT: A 1149 LYS cc_start: 0.5455 (OUTLIER) cc_final: 0.4851 (mptt) REVERT: B 66 HIS cc_start: 0.5224 (OUTLIER) cc_final: 0.4536 (m90) REVERT: B 212 LEU cc_start: 0.5531 (OUTLIER) cc_final: 0.5178 (tt) REVERT: B 516 GLU cc_start: 0.7045 (OUTLIER) cc_final: 0.6755 (tm-30) REVERT: C 78 ARG cc_start: 0.7068 (OUTLIER) cc_final: 0.6670 (tpt90) REVERT: C 118 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8303 (tp) REVERT: E 145 LYS cc_start: 0.1391 (mtmm) cc_final: 0.0920 (ttmm) REVERT: E 188 LYS cc_start: 0.5531 (mtmt) cc_final: 0.4480 (tmtt) REVERT: E 207 LYS cc_start: 0.2323 (tttt) cc_final: 0.1273 (tptt) REVERT: F 48 MET cc_start: 0.3061 (tmm) cc_final: 0.2637 (mmt) outliers start: 112 outliers final: 67 residues processed: 360 average time/residue: 0.2169 time to fit residues: 128.7427 Evaluate side-chains 314 residues out of total 4017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 239 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1149 LYS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 190 LYS Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 172 SER Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 136 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 406 optimal weight: 30.0000 chunk 281 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 296 optimal weight: 0.5980 chunk 142 optimal weight: 0.9990 chunk 371 optimal weight: 0.0970 chunk 214 optimal weight: 0.9990 chunk 268 optimal weight: 5.9990 chunk 221 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 448 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN C 675 GLN L 189 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.223894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.182209 restraints weight = 49493.968| |-----------------------------------------------------------------------------| r_work (start): 0.3996 rms_B_bonded: 5.87 r_work: 0.3297 rms_B_bonded: 5.18 restraints_weight: 2.0000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 38304 Z= 0.129 Angle : 0.671 14.449 52339 Z= 0.323 Chirality : 0.046 0.508 6187 Planarity : 0.004 0.048 6551 Dihedral : 9.970 113.040 7201 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.26 % Favored : 96.57 % Rotamer: Outliers : 2.10 % Allowed : 12.60 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.12), residues: 4575 helix: 1.50 (0.19), residues: 773 sheet: 0.62 (0.14), residues: 1177 loop : -0.84 (0.12), residues: 2625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 100A TYR 0.041 0.001 TYR E 49 PHE 0.022 0.001 PHE L 73 TRP 0.041 0.002 TRP L 35 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00284 (38141) covalent geometry : angle 0.63517 (51904) SS BOND : bond 0.00340 ( 54) SS BOND : angle 1.68405 ( 108) hydrogen bonds : bond 0.03739 ( 1513) hydrogen bonds : angle 5.76973 ( 4245) link_ALPHA1-4 : bond 0.01610 ( 12) link_ALPHA1-4 : angle 3.14257 ( 36) link_BETA1-4 : bond 0.00429 ( 34) link_BETA1-4 : angle 1.48936 ( 102) link_BETA1-6 : bond 0.01657 ( 6) link_BETA1-6 : angle 1.86075 ( 18) link_NAG-ASN : bond 0.00486 ( 57) link_NAG-ASN : angle 3.13641 ( 171) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9150 Ramachandran restraints generated. 4575 Oldfield, 0 Emsley, 4575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9150 Ramachandran restraints generated. 4575 Oldfield, 0 Emsley, 4575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 4017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 262 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7072 (tt) REVERT: A 461 LEU cc_start: 0.0012 (OUTLIER) cc_final: -0.0614 (tt) REVERT: A 754 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8589 (mp) REVERT: A 988 GLU cc_start: 0.8867 (tp30) cc_final: 0.8482 (tp30) REVERT: B 212 LEU cc_start: 0.5310 (OUTLIER) cc_final: 0.4973 (tt) REVERT: B 516 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7249 (tm-30) REVERT: C 118 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8538 (tp) REVERT: C 567 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7199 (mtm-85) REVERT: C 936 ASP cc_start: 0.7442 (m-30) cc_final: 0.7051 (m-30) REVERT: L 183 LYS cc_start: 0.1712 (mmmt) cc_final: 0.1330 (mmmt) REVERT: E 4 MET cc_start: 0.3733 (ptp) cc_final: 0.3430 (ptt) REVERT: E 145 LYS cc_start: 0.2470 (mtmm) cc_final: 0.1834 (ttmm) REVERT: E 188 LYS cc_start: 0.6946 (mtmt) cc_final: 0.5570 (tmtt) REVERT: E 207 LYS cc_start: 0.2170 (tttt) cc_final: 0.1148 (tptt) REVERT: F 48 MET cc_start: 0.2831 (tmm) cc_final: 0.2590 (mmt) REVERT: G 4 MET cc_start: 0.3733 (OUTLIER) cc_final: 0.3400 (mtp) outliers start: 84 outliers final: 53 residues processed: 326 average time/residue: 0.2128 time to fit residues: 114.8416 Evaluate side-chains 309 residues out of total 4017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 248 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 59 PHE Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 190 LYS Chi-restraints excluded: chain F residue 172 SER Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 136 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 344 optimal weight: 9.9990 chunk 379 optimal weight: 5.9990 chunk 208 optimal weight: 1.9990 chunk 352 optimal weight: 20.0000 chunk 66 optimal weight: 0.3980 chunk 335 optimal weight: 9.9990 chunk 92 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 411 optimal weight: 20.0000 chunk 388 optimal weight: 7.9990 chunk 348 optimal weight: 20.0000 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 762 GLN C 137 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.220073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.191463 restraints weight = 49615.377| |-----------------------------------------------------------------------------| r_work (start): 0.4260 rms_B_bonded: 1.69 r_work: 0.4035 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3979 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 38304 Z= 0.252 Angle : 0.730 13.938 52339 Z= 0.352 Chirality : 0.049 0.492 6187 Planarity : 0.004 0.047 6551 Dihedral : 9.871 117.184 7201 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.42 % Favored : 95.43 % Rotamer: Outliers : 2.20 % Allowed : 13.07 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.12), residues: 4575 helix: 1.28 (0.19), residues: 781 sheet: 0.47 (0.14), residues: 1196 loop : -0.92 (0.12), residues: 2598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 905 TYR 0.023 0.002 TYR L 91 PHE 0.032 0.002 PHE A 541 TRP 0.042 0.002 TRP L 35 HIS 0.009 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00608 (38141) covalent geometry : angle 0.69467 (51904) SS BOND : bond 0.00422 ( 54) SS BOND : angle 1.75039 ( 108) hydrogen bonds : bond 0.04422 ( 1513) hydrogen bonds : angle 5.88109 ( 4245) link_ALPHA1-4 : bond 0.01746 ( 12) link_ALPHA1-4 : angle 3.13733 ( 36) link_BETA1-4 : bond 0.00330 ( 34) link_BETA1-4 : angle 1.61467 ( 102) link_BETA1-6 : bond 0.01557 ( 6) link_BETA1-6 : angle 1.83211 ( 18) link_NAG-ASN : bond 0.00454 ( 57) link_NAG-ASN : angle 3.25056 ( 171) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9150 Ramachandran restraints generated. 4575 Oldfield, 0 Emsley, 4575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9150 Ramachandran restraints generated. 4575 Oldfield, 0 Emsley, 4575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 4017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 247 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 461 LEU cc_start: 0.0683 (OUTLIER) cc_final: 0.0257 (tt) REVERT: A 754 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8331 (mp) REVERT: A 988 GLU cc_start: 0.8291 (tp30) cc_final: 0.7946 (tp30) REVERT: B 212 LEU cc_start: 0.5493 (OUTLIER) cc_final: 0.5178 (tt) REVERT: B 516 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6759 (tm-30) REVERT: C 118 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8344 (tp) REVERT: C 567 ARG cc_start: 0.7683 (OUTLIER) cc_final: 0.7103 (mtm-85) REVERT: C 936 ASP cc_start: 0.7511 (m-30) cc_final: 0.7246 (m-30) REVERT: L 183 LYS cc_start: 0.1844 (mmmt) cc_final: 0.1526 (mmmt) REVERT: E 207 LYS cc_start: 0.2181 (tttt) cc_final: 0.1179 (tptt) REVERT: F 48 MET cc_start: 0.3425 (tmm) cc_final: 0.2873 (mmt) REVERT: F 150 VAL cc_start: 0.0166 (OUTLIER) cc_final: -0.0366 (p) REVERT: G 4 MET cc_start: 0.2775 (OUTLIER) cc_final: 0.2451 (mtp) outliers start: 88 outliers final: 65 residues processed: 318 average time/residue: 0.2213 time to fit residues: 116.3434 Evaluate side-chains 310 residues out of total 4017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 237 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 59 PHE Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 190 LYS Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 172 SER Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 136 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 331 optimal weight: 5.9990 chunk 358 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 320 optimal weight: 0.9980 chunk 311 optimal weight: 0.8980 chunk 258 optimal weight: 0.0980 chunk 239 optimal weight: 0.9990 chunk 273 optimal weight: 6.9990 chunk 404 optimal weight: 20.0000 chunk 297 optimal weight: 0.0050 chunk 401 optimal weight: 20.0000 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.223667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.200110 restraints weight = 49596.329| |-----------------------------------------------------------------------------| r_work (start): 0.4350 rms_B_bonded: 1.21 r_work: 0.4113 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.4052 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.4052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 38304 Z= 0.118 Angle : 0.641 13.994 52339 Z= 0.306 Chirality : 0.045 0.476 6187 Planarity : 0.004 0.045 6551 Dihedral : 9.243 110.756 7201 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.26 % Favored : 96.61 % Rotamer: Outliers : 1.82 % Allowed : 13.80 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.12), residues: 4575 helix: 1.62 (0.19), residues: 785 sheet: 0.59 (0.15), residues: 1191 loop : -0.83 (0.12), residues: 2599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 82B TYR 0.017 0.001 TYR A1067 PHE 0.032 0.001 PHE A 541 TRP 0.041 0.002 TRP L 35 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00254 (38141) covalent geometry : angle 0.60734 (51904) SS BOND : bond 0.00314 ( 54) SS BOND : angle 1.21570 ( 108) hydrogen bonds : bond 0.03495 ( 1513) hydrogen bonds : angle 5.55658 ( 4245) link_ALPHA1-4 : bond 0.01720 ( 12) link_ALPHA1-4 : angle 3.16406 ( 36) link_BETA1-4 : bond 0.00431 ( 34) link_BETA1-4 : angle 1.37863 ( 102) link_BETA1-6 : bond 0.01679 ( 6) link_BETA1-6 : angle 1.94854 ( 18) link_NAG-ASN : bond 0.00472 ( 57) link_NAG-ASN : angle 3.03353 ( 171) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9150 Ramachandran restraints generated. 4575 Oldfield, 0 Emsley, 4575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9150 Ramachandran restraints generated. 4575 Oldfield, 0 Emsley, 4575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 4017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 273 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 461 LEU cc_start: 0.0729 (OUTLIER) cc_final: 0.0273 (tt) REVERT: A 988 GLU cc_start: 0.8222 (tp30) cc_final: 0.7912 (tp30) REVERT: B 212 LEU cc_start: 0.5260 (OUTLIER) cc_final: 0.4965 (tt) REVERT: B 516 GLU cc_start: 0.6914 (OUTLIER) cc_final: 0.6611 (tm-30) REVERT: C 118 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8414 (tp) REVERT: C 567 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.7013 (mtm-85) REVERT: C 934 ILE cc_start: 0.8831 (mm) cc_final: 0.8606 (mm) REVERT: C 936 ASP cc_start: 0.7386 (m-30) cc_final: 0.7008 (m-30) REVERT: L 183 LYS cc_start: 0.1960 (mmmt) cc_final: 0.1683 (mmmt) REVERT: E 207 LYS cc_start: 0.1984 (tttt) cc_final: 0.1129 (tptt) REVERT: F 48 MET cc_start: 0.3234 (tmm) cc_final: 0.2779 (mmt) REVERT: F 150 VAL cc_start: 0.0056 (OUTLIER) cc_final: -0.0461 (p) REVERT: G 4 MET cc_start: 0.2812 (OUTLIER) cc_final: 0.2447 (mtp) outliers start: 73 outliers final: 51 residues processed: 328 average time/residue: 0.2227 time to fit residues: 120.0074 Evaluate side-chains 303 residues out of total 4017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 245 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 59 PHE Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 190 LYS Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 172 SER Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 136 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 102 optimal weight: 0.2980 chunk 270 optimal weight: 4.9990 chunk 59 optimal weight: 0.2980 chunk 247 optimal weight: 0.0870 chunk 111 optimal weight: 0.8980 chunk 311 optimal weight: 0.9990 chunk 154 optimal weight: 7.9990 chunk 401 optimal weight: 9.9990 chunk 445 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.5160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.225609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.178271 restraints weight = 50648.729| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 6.19 r_work: 0.3293 rms_B_bonded: 5.25 restraints_weight: 2.0000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 38304 Z= 0.116 Angle : 0.636 13.522 52339 Z= 0.304 Chirality : 0.045 0.464 6187 Planarity : 0.004 0.042 6551 Dihedral : 8.699 109.805 7201 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.83 % Favored : 96.04 % Rotamer: Outliers : 1.57 % Allowed : 14.00 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.12), residues: 4575 helix: 1.86 (0.19), residues: 780 sheet: 0.63 (0.14), residues: 1196 loop : -0.77 (0.12), residues: 2599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 82B TYR 0.021 0.001 TYR D 27 PHE 0.024 0.001 PHE F 122 TRP 0.040 0.002 TRP L 35 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00251 (38141) covalent geometry : angle 0.60204 (51904) SS BOND : bond 0.00279 ( 54) SS BOND : angle 1.20782 ( 108) hydrogen bonds : bond 0.03403 ( 1513) hydrogen bonds : angle 5.46065 ( 4245) link_ALPHA1-4 : bond 0.01759 ( 12) link_ALPHA1-4 : angle 3.33613 ( 36) link_BETA1-4 : bond 0.00386 ( 34) link_BETA1-4 : angle 1.33383 ( 102) link_BETA1-6 : bond 0.01669 ( 6) link_BETA1-6 : angle 1.97888 ( 18) link_NAG-ASN : bond 0.00433 ( 57) link_NAG-ASN : angle 3.00031 ( 171) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9150 Ramachandran restraints generated. 4575 Oldfield, 0 Emsley, 4575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9150 Ramachandran restraints generated. 4575 Oldfield, 0 Emsley, 4575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 4017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 268 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.7955 (p90) cc_final: 0.7643 (p90) REVERT: A 461 LEU cc_start: 0.0279 (OUTLIER) cc_final: -0.0443 (tt) REVERT: A 988 GLU cc_start: 0.8737 (tp30) cc_final: 0.8368 (tp30) REVERT: B 212 LEU cc_start: 0.5233 (OUTLIER) cc_final: 0.4897 (tt) REVERT: B 516 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.7103 (tm-30) REVERT: C 118 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8541 (tp) REVERT: C 464 PHE cc_start: 0.8440 (m-80) cc_final: 0.8234 (m-80) REVERT: C 567 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7156 (mtm-85) REVERT: C 936 ASP cc_start: 0.7442 (m-30) cc_final: 0.7012 (m-30) REVERT: C 1144 GLU cc_start: 0.7647 (tp30) cc_final: 0.7351 (tm-30) REVERT: L 183 LYS cc_start: 0.1818 (mmmt) cc_final: 0.1440 (mmmt) REVERT: L 190 LYS cc_start: 0.7525 (tptt) cc_final: 0.7126 (tptp) REVERT: D 36 TRP cc_start: 0.6034 (m100) cc_final: 0.5736 (m100) REVERT: D 83 LYS cc_start: 0.6535 (mtmm) cc_final: 0.6317 (mmmm) REVERT: D 201 LYS cc_start: 0.5804 (tptp) cc_final: 0.5589 (mmtm) REVERT: E 207 LYS cc_start: 0.1972 (tttt) cc_final: 0.1064 (tptt) REVERT: F 48 MET cc_start: 0.3143 (tmm) cc_final: 0.2899 (mmt) REVERT: F 150 VAL cc_start: -0.0100 (OUTLIER) cc_final: -0.0525 (p) REVERT: G 4 MET cc_start: 0.3703 (OUTLIER) cc_final: 0.3299 (mtp) outliers start: 63 outliers final: 50 residues processed: 315 average time/residue: 0.2263 time to fit residues: 116.9180 Evaluate side-chains 303 residues out of total 4017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 246 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain H residue 12 LYS Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 59 PHE Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 136 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 102 optimal weight: 0.6980 chunk 444 optimal weight: 5.9990 chunk 126 optimal weight: 0.5980 chunk 414 optimal weight: 10.0000 chunk 374 optimal weight: 20.0000 chunk 431 optimal weight: 6.9990 chunk 220 optimal weight: 2.9990 chunk 172 optimal weight: 5.9990 chunk 93 optimal weight: 0.7980 chunk 373 optimal weight: 8.9990 chunk 439 optimal weight: 4.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.220485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.177823 restraints weight = 49596.027| |-----------------------------------------------------------------------------| r_work (start): 0.3945 rms_B_bonded: 5.62 r_work: 0.3288 rms_B_bonded: 5.17 restraints_weight: 2.0000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 38304 Z= 0.219 Angle : 0.698 13.492 52339 Z= 0.337 Chirality : 0.048 0.454 6187 Planarity : 0.004 0.044 6551 Dihedral : 8.746 112.950 7200 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.26 % Favored : 95.61 % Rotamer: Outliers : 1.60 % Allowed : 14.05 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.12), residues: 4575 helix: 1.64 (0.19), residues: 777 sheet: 0.58 (0.14), residues: 1203 loop : -0.86 (0.12), residues: 2595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 82B TYR 0.022 0.002 TYR L 91 PHE 0.024 0.002 PHE A 133 TRP 0.039 0.002 TRP L 35 HIS 0.007 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00528 (38141) covalent geometry : angle 0.66449 (51904) SS BOND : bond 0.00366 ( 54) SS BOND : angle 1.60362 ( 108) hydrogen bonds : bond 0.04143 ( 1513) hydrogen bonds : angle 5.66561 ( 4245) link_ALPHA1-4 : bond 0.01744 ( 12) link_ALPHA1-4 : angle 3.33321 ( 36) link_BETA1-4 : bond 0.00345 ( 34) link_BETA1-4 : angle 1.47146 ( 102) link_BETA1-6 : bond 0.01606 ( 6) link_BETA1-6 : angle 1.94417 ( 18) link_NAG-ASN : bond 0.00420 ( 57) link_NAG-ASN : angle 3.05533 ( 171) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9150 Ramachandran restraints generated. 4575 Oldfield, 0 Emsley, 4575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9150 Ramachandran restraints generated. 4575 Oldfield, 0 Emsley, 4575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 4017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 249 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 461 LEU cc_start: 0.0277 (OUTLIER) cc_final: -0.0447 (tt) REVERT: A 646 ARG cc_start: 0.8903 (mpp80) cc_final: 0.8350 (ttt-90) REVERT: A 988 GLU cc_start: 0.8884 (tp30) cc_final: 0.8503 (tp30) REVERT: B 212 LEU cc_start: 0.5299 (OUTLIER) cc_final: 0.4930 (tt) REVERT: B 516 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7220 (tm-30) REVERT: C 118 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8508 (tp) REVERT: C 567 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7180 (mtm-85) REVERT: C 936 ASP cc_start: 0.7606 (m-30) cc_final: 0.7204 (m-30) REVERT: C 1144 GLU cc_start: 0.7597 (tp30) cc_final: 0.7336 (tm-30) REVERT: L 183 LYS cc_start: 0.1946 (mmmt) cc_final: 0.1537 (mmmt) REVERT: L 190 LYS cc_start: 0.7373 (tptt) cc_final: 0.7010 (tptp) REVERT: E 145 LYS cc_start: 0.3057 (ttmm) cc_final: 0.2757 (pttt) REVERT: E 207 LYS cc_start: 0.2005 (tttt) cc_final: 0.0986 (tptt) REVERT: F 48 MET cc_start: 0.3031 (tmm) cc_final: 0.2817 (mmt) REVERT: G 4 MET cc_start: 0.3765 (OUTLIER) cc_final: 0.3372 (mtp) outliers start: 64 outliers final: 56 residues processed: 298 average time/residue: 0.2231 time to fit residues: 110.2811 Evaluate side-chains 304 residues out of total 4017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 242 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain H residue 12 LYS Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 59 PHE Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain E residue 190 LYS Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 136 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 345 optimal weight: 20.0000 chunk 46 optimal weight: 30.0000 chunk 63 optimal weight: 0.9990 chunk 406 optimal weight: 20.0000 chunk 79 optimal weight: 9.9990 chunk 108 optimal weight: 3.9990 chunk 453 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 341 optimal weight: 30.0000 chunk 88 optimal weight: 1.9990 chunk 235 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN A 196 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS B 762 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 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 = 0.4567 r_free = 0.4567 target = 0.220276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.175682 restraints weight = 49560.753| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 6.18 r_work: 0.3227 rms_B_bonded: 5.12 restraints_weight: 2.0000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.193 38304 Z= 0.270 Angle : 0.784 59.199 52339 Z= 0.402 Chirality : 0.052 1.388 6187 Planarity : 0.004 0.047 6551 Dihedral : 8.747 112.963 7200 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.28 % Favored : 95.58 % Rotamer: Outliers : 1.67 % Allowed : 14.00 % Favored : 84.33 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.12), residues: 4575 helix: 1.60 (0.19), residues: 777 sheet: 0.58 (0.14), residues: 1203 loop : -0.86 (0.12), residues: 2595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 82B TYR 0.021 0.002 TYR L 91 PHE 0.021 0.002 PHE A 133 TRP 0.039 0.002 TRP L 35 HIS 0.008 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00626 (38141) covalent geometry : angle 0.75163 (51904) SS BOND : bond 0.00974 ( 54) SS BOND : angle 2.31279 ( 108) hydrogen bonds : bond 0.04221 ( 1513) hydrogen bonds : angle 5.66471 ( 4245) link_ALPHA1-4 : bond 0.01762 ( 12) link_ALPHA1-4 : angle 3.33746 ( 36) link_BETA1-4 : bond 0.00366 ( 34) link_BETA1-4 : angle 1.47768 ( 102) link_BETA1-6 : bond 0.01588 ( 6) link_BETA1-6 : angle 1.94349 ( 18) link_NAG-ASN : bond 0.00422 ( 57) link_NAG-ASN : angle 3.05329 ( 171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9877.43 seconds wall clock time: 169 minutes 43.37 seconds (10183.37 seconds total)