Starting phenix.real_space_refine on Tue May 27 05:53:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eh8_48048/05_2025/9eh8_48048.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eh8_48048/05_2025/9eh8_48048.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9eh8_48048/05_2025/9eh8_48048.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eh8_48048/05_2025/9eh8_48048.map" model { file = "/net/cci-nas-00/data/ceres_data/9eh8_48048/05_2025/9eh8_48048.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eh8_48048/05_2025/9eh8_48048.cif" } resolution = 2.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.060 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 150 5.16 5 C 17982 2.51 5 N 4533 2.21 5 O 6453 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 29118 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 8823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1166, 8823 Classifications: {'peptide': 1166} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PCIS': 1, 'PTRANS': 59, 'TRANS': 1105} Chain breaks: 7 Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 304 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 10, 'ASN:plan1': 6, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 18, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 158 Chain: "B" Number of atoms: 8823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1166, 8823 Classifications: {'peptide': 1166} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PCIS': 1, 'PTRANS': 59, 'TRANS': 1105} Chain breaks: 7 Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 304 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 10, 'ASN:plan1': 6, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 18, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 158 Chain: "C" Number of atoms: 8823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1166, 8823 Classifications: {'peptide': 1166} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PCIS': 1, 'PTRANS': 59, 'TRANS': 1105} Chain breaks: 7 Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 304 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 10, 'ASN:plan1': 6, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 18, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 158 Chain: "D" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 97 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 3} 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: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 97 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 3} 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: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "U" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 97 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 3} 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: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "h" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 113 Unusual residues: {'EIC': 1, 'FOL': 1, 'NAG': 5} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'FOL:plan-8': 1, 'FOL:plan-7': 1, 'FOL:plan-6': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 113 Unusual residues: {'EIC': 1, 'FOL': 1, 'NAG': 5} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'FOL:plan-8': 1, 'FOL:plan-7': 1, 'FOL:plan-6': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 113 Unusual residues: {'EIC': 1, 'FOL': 1, 'NAG': 5} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'FOL:plan-8': 1, 'FOL:plan-7': 1, 'FOL:plan-6': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 271 Classifications: {'water': 271} Link IDs: {None: 270} Chain: "B" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 271 Classifications: {'water': 271} Link IDs: {None: 270} Chain: "C" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 271 Classifications: {'water': 271} Link IDs: {None: 270} Time building chain proxies: 17.56, per 1000 atoms: 0.60 Number of scatterers: 29118 At special positions: 0 Unit cell: (147.525, 154.269, 161.856, 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 150 16.00 O 6453 8.00 N 4533 7.00 C 17982 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 34 " - pdb=" SG CYS A 203 " distance=2.05 Simple disulfide: pdb=" SG CYS A 184 " - pdb=" SG CYS A 222 " distance=2.03 Simple disulfide: pdb=" SG CYS A 193 " - pdb=" SG CYS A 246 " distance=2.05 Simple disulfide: pdb=" SG CYS A 348 " - pdb=" SG CYS A 358 " distance=2.04 Simple disulfide: pdb=" SG CYS A 392 " - pdb=" SG CYS A 416 " distance=2.05 Simple disulfide: pdb=" SG CYS A 434 " - pdb=" SG CYS A 487 " distance=2.05 Simple disulfide: pdb=" SG CYS A 446 " - pdb=" SG CYS A 584 " distance=2.04 Simple disulfide: pdb=" SG CYS A 512 " - pdb=" SG CYS A 533 " distance=2.04 Simple disulfide: pdb=" SG CYS A 602 " - pdb=" SG CYS A 653 " distance=2.04 Simple disulfide: pdb=" SG CYS A 619 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 678 " - pdb=" SG CYS A 711 " distance=2.04 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 734 " distance=2.04 Simple disulfide: pdb=" SG CYS A 804 " - pdb=" SG CYS A 826 " distance=2.04 Simple disulfide: pdb=" SG CYS A 809 " - pdb=" SG CYS A 815 " distance=2.05 Simple disulfide: pdb=" SG CYS A 910 " - pdb=" SG CYS A 923 " distance=2.04 Simple disulfide: pdb=" SG CYS A1104 " - pdb=" SG CYS A1115 " distance=2.03 Simple disulfide: pdb=" SG CYS A1154 " - pdb=" SG CYS A1162 " distance=2.04 Simple disulfide: pdb=" SG CYS B 34 " - pdb=" SG CYS B 203 " distance=2.05 Simple disulfide: pdb=" SG CYS B 184 " - pdb=" SG CYS B 222 " distance=2.03 Simple disulfide: pdb=" SG CYS B 193 " - pdb=" SG CYS B 246 " distance=2.05 Simple disulfide: pdb=" SG CYS B 348 " - pdb=" SG CYS B 358 " distance=2.04 Simple disulfide: pdb=" SG CYS B 392 " - pdb=" SG CYS B 416 " distance=2.05 Simple disulfide: pdb=" SG CYS B 434 " - pdb=" SG CYS B 487 " distance=2.05 Simple disulfide: pdb=" SG CYS B 446 " - pdb=" SG CYS B 584 " distance=2.04 Simple disulfide: pdb=" SG CYS B 512 " - pdb=" SG CYS B 533 " distance=2.04 Simple disulfide: pdb=" SG CYS B 602 " - pdb=" SG CYS B 653 " distance=2.04 Simple disulfide: pdb=" SG CYS B 619 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 678 " - pdb=" SG CYS B 711 " distance=2.04 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 734 " distance=2.04 Simple disulfide: pdb=" SG CYS B 804 " - pdb=" SG CYS B 826 " distance=2.04 Simple disulfide: pdb=" SG CYS B 809 " - pdb=" SG CYS B 815 " distance=2.05 Simple disulfide: pdb=" SG CYS B 910 " - pdb=" SG CYS B 923 " distance=2.04 Simple disulfide: pdb=" SG CYS B1104 " - pdb=" SG CYS B1115 " distance=2.03 Simple disulfide: pdb=" SG CYS B1154 " - pdb=" SG CYS B1162 " distance=2.04 Simple disulfide: pdb=" SG CYS C 34 " - pdb=" SG CYS C 203 " distance=2.05 Simple disulfide: pdb=" SG CYS C 184 " - pdb=" SG CYS C 222 " distance=2.03 Simple disulfide: pdb=" SG CYS C 193 " - pdb=" SG CYS C 246 " distance=2.05 Simple disulfide: pdb=" SG CYS C 348 " - pdb=" SG CYS C 358 " distance=2.04 Simple disulfide: pdb=" SG CYS C 392 " - pdb=" SG CYS C 416 " distance=2.04 Simple disulfide: pdb=" SG CYS C 434 " - pdb=" SG CYS C 487 " distance=2.05 Simple disulfide: pdb=" SG CYS C 446 " - pdb=" SG CYS C 584 " distance=2.04 Simple disulfide: pdb=" SG CYS C 512 " - pdb=" SG CYS C 533 " distance=2.04 Simple disulfide: pdb=" SG CYS C 602 " - pdb=" SG CYS C 653 " distance=2.04 Simple disulfide: pdb=" SG CYS C 619 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 678 " - pdb=" SG CYS C 711 " distance=2.04 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 734 " distance=2.04 Simple disulfide: pdb=" SG CYS C 804 " - pdb=" SG CYS C 826 " distance=2.04 Simple disulfide: pdb=" SG CYS C 809 " - pdb=" SG CYS C 815 " distance=2.05 Simple disulfide: pdb=" SG CYS C 910 " - pdb=" SG CYS C 923 " distance=2.04 Simple disulfide: pdb=" SG CYS C1104 " - pdb=" SG CYS C1115 " distance=2.03 Simple disulfide: pdb=" SG CYS C1154 " - pdb=" SG CYS C1162 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN D 5 " - " MAN D 6 " " MAN Q 5 " - " MAN Q 6 " " MAN d 5 " - " MAN d 6 " ALPHA1-3 " BMA D 3 " - " MAN D 7 " " MAN D 4 " - " MAN D 5 " " BMA G 3 " - " MAN G 4 " " BMA Q 3 " - " MAN Q 7 " " MAN Q 4 " - " MAN Q 5 " " BMA T 3 " - " MAN T 4 " " BMA d 3 " - " MAN d 7 " " MAN d 4 " - " MAN d 5 " " BMA g 3 " - " MAN g 4 " ALPHA1-6 " BMA D 3 " - " MAN D 4 " " BMA G 3 " - " MAN G 5 " " BMA H 3 " - " MAN H 4 " " BMA Q 3 " - " MAN Q 4 " " BMA T 3 " - " MAN T 5 " " BMA U 3 " - " MAN U 4 " " BMA d 3 " - " MAN d 4 " " BMA g 3 " - " MAN g 5 " " BMA h 3 " - " MAN h 4 " BETA1-2 " MAN D 7 " - " NAG D 8 " " MAN Q 7 " - " NAG Q 8 " " MAN d 7 " - " NAG d 8 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " 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 P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG 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 c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " 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 p 2 " - " BMA p 3 " NAG-ASN " NAG A1401 " - " ASN A 167 " " NAG A1402 " - " ASN A 73 " " NAG A1403 " - " ASN A1146 " " NAG A1404 " - " ASN A 618 " " NAG A1405 " - " ASN A 591 " " NAG B1401 " - " ASN B 167 " " NAG B1402 " - " ASN B 73 " " NAG B1403 " - " ASN B1146 " " NAG B1404 " - " ASN B 618 " " NAG B1405 " - " ASN B 591 " " NAG C1402 " - " ASN C 167 " " NAG C1403 " - " ASN C 73 " " NAG C1404 " - " ASN C1146 " " NAG C1405 " - " ASN C 618 " " NAG C1406 " - " ASN C 591 " " NAG D 1 " - " ASN A 761 " " NAG E 1 " - " ASN A 111 " " NAG F 1 " - " ASN A 162 " " NAG G 1 " - " ASN A 251 " " NAG H 1 " - " ASN A 419 " " NAG I 1 " - " ASN A 783 " " NAG J 1 " - " ASN A 868 " " NAG K 1 " - " ASN A1173 " " NAG L 1 " - " ASN A1215 " " NAG M 1 " - " ASN A 717 " " NAG N 1 " - " ASN A 174 " " NAG O 1 " - " ASN A 245 " " NAG P 1 " - " ASN A 132 " " NAG Q 1 " - " ASN B 761 " " NAG R 1 " - " ASN B 111 " " NAG S 1 " - " ASN B 162 " " NAG T 1 " - " ASN B 251 " " NAG U 1 " - " ASN B 419 " " NAG V 1 " - " ASN B 783 " " NAG W 1 " - " ASN B 868 " " NAG X 1 " - " ASN B1173 " " NAG Y 1 " - " ASN B1215 " " NAG Z 1 " - " ASN B 717 " " NAG a 1 " - " ASN B 174 " " NAG b 1 " - " ASN B 245 " " NAG c 1 " - " ASN B 132 " " NAG d 1 " - " ASN C 761 " " NAG e 1 " - " ASN C 111 " " NAG f 1 " - " ASN C 162 " " NAG g 1 " - " ASN C 251 " " NAG h 1 " - " ASN C 419 " " NAG i 1 " - " ASN C 783 " " NAG j 1 " - " ASN C 868 " " NAG k 1 " - " ASN C1173 " " NAG l 1 " - " ASN C1215 " " NAG m 1 " - " ASN C 717 " " NAG n 1 " - " ASN C 174 " " NAG o 1 " - " ASN C 245 " " NAG p 1 " - " ASN C 132 " Time building additional restraints: 8.38 Conformation dependent library (CDL) restraints added in 3.5 seconds 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6540 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 63 sheets defined 28.0% alpha, 30.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.88 Creating SS restraints... Processing helix chain 'A' and resid 41 through 44 Processing helix chain 'A' and resid 46 through 50 removed outlier: 3.678A pdb=" N THR A 50 " --> pdb=" O ALA A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 111 through 115 Processing helix chain 'A' and resid 231 through 240 removed outlier: 3.851A pdb=" N TYR A 240 " --> pdb=" O ALA A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 361 Processing helix chain 'A' and resid 394 through 398 Processing helix chain 'A' and resid 404 through 408 Processing helix chain 'A' and resid 419 through 425 Processing helix chain 'A' and resid 438 through 445 Processing helix chain 'A' and resid 458 through 466 removed outlier: 5.220A pdb=" N SER A 463 " --> pdb=" O ASP A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 477 removed outlier: 3.506A pdb=" N GLN A 475 " --> pdb=" O GLY A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 538 Processing helix chain 'A' and resid 587 through 589 No H-bonds generated for 'chain 'A' and resid 587 through 589' Processing helix chain 'A' and resid 624 through 627 Processing helix chain 'A' and resid 677 through 687 removed outlier: 3.648A pdb=" N VAL A 681 " --> pdb=" O ALA A 677 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER A 686 " --> pdb=" O THR A 682 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN A 687 " --> pdb=" O THR A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 810 Processing helix chain 'A' and resid 812 through 820 Processing helix chain 'A' and resid 822 through 849 removed outlier: 3.806A pdb=" N CYS A 826 " --> pdb=" O TYR A 822 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER A 827 " --> pdb=" O GLY A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 854 removed outlier: 3.820A pdb=" N GLN A 854 " --> pdb=" O ILE A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 873 Processing helix chain 'A' and resid 886 through 895 removed outlier: 3.645A pdb=" N LYS A 895 " --> pdb=" O LEU A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 912 Processing helix chain 'A' and resid 924 through 929 Processing helix chain 'A' and resid 938 through 951 Processing helix chain 'A' and resid 969 through 981 removed outlier: 3.592A pdb=" N VAL A 981 " --> pdb=" O ARG A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 991 Processing helix chain 'A' and resid 991 through 1005 removed outlier: 3.502A pdb=" N ALA A1005 " --> pdb=" O GLN A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1010 removed outlier: 4.502A pdb=" N PHE A1010 " --> pdb=" O GLN A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1014 through 1037 removed outlier: 3.637A pdb=" N LEU A1031 " --> pdb=" O ASN A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1040 No H-bonds generated for 'chain 'A' and resid 1038 through 1040' Processing helix chain 'A' and resid 1048 through 1056 Processing helix chain 'A' and resid 1059 through 1105 removed outlier: 3.572A pdb=" N ALA A1063 " --> pdb=" O PRO A1059 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A1068 " --> pdb=" O GLN A1064 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1225 Processing helix chain 'B' and resid 41 through 44 Processing helix chain 'B' and resid 46 through 50 removed outlier: 3.678A pdb=" N THR B 50 " --> pdb=" O ALA B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 111 through 115 Processing helix chain 'B' and resid 231 through 240 removed outlier: 3.851A pdb=" N TYR B 240 " --> pdb=" O ALA B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 361 Processing helix chain 'B' and resid 394 through 398 Processing helix chain 'B' and resid 404 through 408 Processing helix chain 'B' and resid 419 through 425 Processing helix chain 'B' and resid 438 through 445 Processing helix chain 'B' and resid 458 through 466 removed outlier: 5.220A pdb=" N SER B 463 " --> pdb=" O ASP B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 477 removed outlier: 3.506A pdb=" N GLN B 475 " --> pdb=" O GLY B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 538 Processing helix chain 'B' and resid 587 through 589 No H-bonds generated for 'chain 'B' and resid 587 through 589' Processing helix chain 'B' and resid 624 through 627 Processing helix chain 'B' and resid 677 through 687 removed outlier: 3.649A pdb=" N VAL B 681 " --> pdb=" O ALA B 677 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER B 686 " --> pdb=" O THR B 682 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN B 687 " --> pdb=" O THR B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 810 Processing helix chain 'B' and resid 812 through 820 Processing helix chain 'B' and resid 822 through 849 removed outlier: 3.806A pdb=" N CYS B 826 " --> pdb=" O TYR B 822 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER B 827 " --> pdb=" O GLY B 823 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 854 removed outlier: 3.820A pdb=" N GLN B 854 " --> pdb=" O ILE B 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 870 through 873 Processing helix chain 'B' and resid 886 through 895 removed outlier: 3.645A pdb=" N LYS B 895 " --> pdb=" O LEU B 891 " (cutoff:3.500A) Processing helix chain 'B' and resid 905 through 912 Processing helix chain 'B' and resid 924 through 929 Processing helix chain 'B' and resid 938 through 951 Processing helix chain 'B' and resid 969 through 981 removed outlier: 3.592A pdb=" N VAL B 981 " --> pdb=" O ARG B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 984 through 991 Processing helix chain 'B' and resid 991 through 1005 Processing helix chain 'B' and resid 1006 through 1010 removed outlier: 4.502A pdb=" N PHE B1010 " --> pdb=" O GLN B1007 " (cutoff:3.500A) Processing helix chain 'B' and resid 1014 through 1037 removed outlier: 3.637A pdb=" N LEU B1031 " --> pdb=" O ASN B1027 " (cutoff:3.500A) Processing helix chain 'B' and resid 1038 through 1040 No H-bonds generated for 'chain 'B' and resid 1038 through 1040' Processing helix chain 'B' and resid 1048 through 1056 Processing helix chain 'B' and resid 1059 through 1105 removed outlier: 3.572A pdb=" N ALA B1063 " --> pdb=" O PRO B1059 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B1068 " --> pdb=" O GLN B1064 " (cutoff:3.500A) Processing helix chain 'B' and resid 1221 through 1225 Processing helix chain 'C' and resid 41 through 44 Processing helix chain 'C' and resid 46 through 50 removed outlier: 3.679A pdb=" N THR C 50 " --> pdb=" O ALA C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 111 through 115 Processing helix chain 'C' and resid 231 through 240 removed outlier: 3.850A pdb=" N TYR C 240 " --> pdb=" O ALA C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 361 Processing helix chain 'C' and resid 394 through 398 Processing helix chain 'C' and resid 404 through 408 Processing helix chain 'C' and resid 419 through 425 Processing helix chain 'C' and resid 438 through 445 Processing helix chain 'C' and resid 458 through 466 removed outlier: 5.220A pdb=" N SER C 463 " --> pdb=" O ASP C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 477 removed outlier: 3.505A pdb=" N GLN C 475 " --> pdb=" O GLY C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 538 Processing helix chain 'C' and resid 587 through 589 No H-bonds generated for 'chain 'C' and resid 587 through 589' Processing helix chain 'C' and resid 624 through 627 Processing helix chain 'C' and resid 677 through 687 removed outlier: 3.648A pdb=" N VAL C 681 " --> pdb=" O ALA C 677 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER C 686 " --> pdb=" O THR C 682 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN C 687 " --> pdb=" O THR C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 803 through 810 Processing helix chain 'C' and resid 812 through 820 Processing helix chain 'C' and resid 822 through 849 removed outlier: 3.806A pdb=" N CYS C 826 " --> pdb=" O TYR C 822 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER C 827 " --> pdb=" O GLY C 823 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 854 removed outlier: 3.820A pdb=" N GLN C 854 " --> pdb=" O ILE C 851 " (cutoff:3.500A) Processing helix chain 'C' and resid 870 through 873 Processing helix chain 'C' and resid 886 through 895 removed outlier: 3.645A pdb=" N LYS C 895 " --> pdb=" O LEU C 891 " (cutoff:3.500A) Processing helix chain 'C' and resid 905 through 912 Processing helix chain 'C' and resid 924 through 929 Processing helix chain 'C' and resid 938 through 951 Processing helix chain 'C' and resid 969 through 981 removed outlier: 3.592A pdb=" N VAL C 981 " --> pdb=" O ARG C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 984 through 991 Processing helix chain 'C' and resid 991 through 1005 Processing helix chain 'C' and resid 1006 through 1010 removed outlier: 4.502A pdb=" N PHE C1010 " --> pdb=" O GLN C1007 " (cutoff:3.500A) Processing helix chain 'C' and resid 1014 through 1037 removed outlier: 3.637A pdb=" N LEU C1031 " --> pdb=" O ASN C1027 " (cutoff:3.500A) Processing helix chain 'C' and resid 1038 through 1040 No H-bonds generated for 'chain 'C' and resid 1038 through 1040' Processing helix chain 'C' and resid 1048 through 1056 Processing helix chain 'C' and resid 1059 through 1105 removed outlier: 3.572A pdb=" N ALA C1063 " --> pdb=" O PRO C1059 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU C1068 " --> pdb=" O GLN C1064 " (cutoff:3.500A) Processing helix chain 'C' and resid 1221 through 1225 Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 39 Processing sheet with id=AA2, first strand: chain 'A' and resid 70 through 71 removed outlier: 6.547A pdb=" N SER A 70 " --> pdb=" O TYR C 631 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL C 630 " --> pdb=" O VAL C 638 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N VAL C 638 " --> pdb=" O VAL C 650 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N TYR C 647 " --> pdb=" O CYS C 619 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N PHE C 383 " --> pdb=" O SER C 606 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 82 removed outlier: 4.062A pdb=" N LYS A 344 " --> pdb=" O ASN A 335 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 90 through 92 removed outlier: 3.659A pdb=" N ALA A 291 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N SER A 276 " --> pdb=" O HIS A 289 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N HIS A 289 " --> pdb=" O SER A 276 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 95 through 96 removed outlier: 7.103A pdb=" N SER A 95 " --> pdb=" O ILE A 309 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 99 through 100 Processing sheet with id=AA7, first strand: chain 'A' and resid 117 through 118 Processing sheet with id=AA8, first strand: chain 'A' and resid 117 through 118 Processing sheet with id=AA9, first strand: chain 'A' and resid 134 through 137 removed outlier: 5.497A pdb=" N THR A 143 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ALA A 318 " --> pdb=" O PRO A 146 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 160 through 163 removed outlier: 6.186A pdb=" N GLY A 161 " --> pdb=" O GLY A 170 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY A 170 " --> pdb=" O GLY A 161 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE A 168 " --> pdb=" O TYR A 163 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 368 through 372 removed outlier: 4.529A pdb=" N VAL A 658 " --> pdb=" O VAL A 372 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 382 through 385 removed outlier: 6.395A pdb=" N PHE A 383 " --> pdb=" O SER A 606 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N TYR A 647 " --> pdb=" O CYS A 619 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N VAL A 638 " --> pdb=" O VAL A 650 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL A 630 " --> pdb=" O VAL A 638 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 390 through 391 removed outlier: 6.589A pdb=" N GLN A 390 " --> pdb=" O ASN A 417 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N CYS A 416 " --> pdb=" O CYS A 584 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 399 through 400 removed outlier: 3.717A pdb=" N GLY A 400 " --> pdb=" O THR A 499 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 409 through 413 removed outlier: 3.583A pdb=" N SER A 449 " --> pdb=" O GLN A 575 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU A 431 " --> pdb=" O LEU A 490 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N THR A 492 " --> pdb=" O VAL A 429 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N VAL A 429 " --> pdb=" O THR A 492 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 521 through 522 removed outlier: 6.585A pdb=" N THR A 556 " --> pdb=" O THR A 510 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N CYS A 512 " --> pdb=" O THR A 554 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR A 554 " --> pdb=" O CYS A 512 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN A 546 " --> pdb=" O GLY A 557 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 715 through 722 removed outlier: 5.586A pdb=" N THR A 759 " --> pdb=" O THR A 718 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N MET A 720 " --> pdb=" O THR A 759 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N LEU A 733 " --> pdb=" O LEU A 729 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LEU A 727 " --> pdb=" O ALA A 735 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1119 through 1128 removed outlier: 7.112A pdb=" N VAL A1137 " --> pdb=" O ILE A1121 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N SER A1123 " --> pdb=" O PHE A1135 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE A1135 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ALA A1125 " --> pdb=" O TYR A1133 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TYR A1133 " --> pdb=" O ALA A1125 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ASN A1127 " --> pdb=" O GLY A1131 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N GLY A1131 " --> pdb=" O ASN A1127 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N THR A1148 " --> pdb=" O LEU A1172 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N PHE A1170 " --> pdb=" O ALA A1150 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N GLY A1190 " --> pdb=" O HIS A1195 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N HIS A1195 " --> pdb=" O GLY A1190 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1119 through 1128 removed outlier: 7.112A pdb=" N VAL A1137 " --> pdb=" O ILE A1121 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N SER A1123 " --> pdb=" O PHE A1135 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE A1135 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ALA A1125 " --> pdb=" O TYR A1133 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TYR A1133 " --> pdb=" O ALA A1125 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ASN A1127 " --> pdb=" O GLY A1131 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N GLY A1131 " --> pdb=" O ASN A1127 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASN A 783 " --> pdb=" O THR A1142 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N HIS A1144 " --> pdb=" O PRO A 781 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ASN A1146 " --> pdb=" O ALA A 779 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ALA A 779 " --> pdb=" O ASN A1146 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N THR A1148 " --> pdb=" O VAL A 777 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL A 777 " --> pdb=" O THR A1148 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 800 through 802 Processing sheet with id=AC3, first strand: chain 'A' and resid 863 through 864 Processing sheet with id=AC4, first strand: chain 'A' and resid 965 through 966 removed outlier: 6.943A pdb=" N VAL C 777 " --> pdb=" O THR C1148 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N THR C1148 " --> pdb=" O VAL C 777 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ALA C 779 " --> pdb=" O ASN C1146 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ASN C1146 " --> pdb=" O ALA C 779 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N HIS C1144 " --> pdb=" O PRO C 781 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASN C 783 " --> pdb=" O THR C1142 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N GLY C1131 " --> pdb=" O ASN C1127 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ASN C1127 " --> pdb=" O GLY C1131 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TYR C1133 " --> pdb=" O ALA C1125 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ALA C1125 " --> pdb=" O TYR C1133 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE C1135 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N SER C1123 " --> pdb=" O PHE C1135 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N VAL C1137 " --> pdb=" O ILE C1121 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 965 through 966 removed outlier: 6.943A pdb=" N VAL C 777 " --> pdb=" O THR C1148 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N THR C1148 " --> pdb=" O VAL C 777 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ALA C 779 " --> pdb=" O ASN C1146 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ASN C1146 " --> pdb=" O ALA C 779 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N HIS C1144 " --> pdb=" O PRO C 781 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASN C 783 " --> pdb=" O THR C1142 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N THR C1148 " --> pdb=" O LEU C1172 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N PHE C1170 " --> pdb=" O ALA C1150 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N GLY C1190 " --> pdb=" O HIS C1195 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N HIS C1195 " --> pdb=" O GLY C1190 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 1204 through 1207 removed outlier: 4.396A pdb=" N CYS A1162 " --> pdb=" O VAL A1207 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 37 through 39 Processing sheet with id=AC8, first strand: chain 'B' and resid 75 through 82 removed outlier: 4.062A pdb=" N LYS B 344 " --> pdb=" O ASN B 335 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 90 through 92 removed outlier: 3.659A pdb=" N ALA B 291 " --> pdb=" O LEU B 274 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N SER B 276 " --> pdb=" O HIS B 289 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N HIS B 289 " --> pdb=" O SER B 276 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 95 through 96 removed outlier: 7.103A pdb=" N SER B 95 " --> pdb=" O ILE B 309 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 99 through 100 Processing sheet with id=AD3, first strand: chain 'B' and resid 117 through 118 Processing sheet with id=AD4, first strand: chain 'B' and resid 117 through 118 Processing sheet with id=AD5, first strand: chain 'B' and resid 134 through 137 removed outlier: 5.497A pdb=" N THR B 143 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ALA B 318 " --> pdb=" O PRO B 146 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 160 through 163 removed outlier: 6.186A pdb=" N GLY B 161 " --> pdb=" O GLY B 170 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY B 170 " --> pdb=" O GLY B 161 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE B 168 " --> pdb=" O TYR B 163 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 368 through 372 removed outlier: 4.529A pdb=" N VAL B 658 " --> pdb=" O VAL B 372 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 382 through 385 removed outlier: 6.395A pdb=" N PHE B 383 " --> pdb=" O SER B 606 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N TYR B 647 " --> pdb=" O CYS B 619 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N VAL B 638 " --> pdb=" O VAL B 650 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL B 630 " --> pdb=" O VAL B 638 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 390 through 391 removed outlier: 6.589A pdb=" N GLN B 390 " --> pdb=" O ASN B 417 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N CYS B 416 " --> pdb=" O CYS B 584 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'B' and resid 399 through 400 removed outlier: 3.717A pdb=" N GLY B 400 " --> pdb=" O THR B 499 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'B' and resid 409 through 413 removed outlier: 3.583A pdb=" N SER B 449 " --> pdb=" O GLN B 575 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU B 431 " --> pdb=" O LEU B 490 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N THR B 492 " --> pdb=" O VAL B 429 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N VAL B 429 " --> pdb=" O THR B 492 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 521 through 522 removed outlier: 6.584A pdb=" N THR B 556 " --> pdb=" O THR B 510 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N CYS B 512 " --> pdb=" O THR B 554 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR B 554 " --> pdb=" O CYS B 512 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN B 546 " --> pdb=" O GLY B 557 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 715 through 722 removed outlier: 5.584A pdb=" N THR B 759 " --> pdb=" O THR B 718 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N MET B 720 " --> pdb=" O THR B 759 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N LEU B 733 " --> pdb=" O LEU B 729 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LEU B 727 " --> pdb=" O ALA B 735 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 1119 through 1128 removed outlier: 7.113A pdb=" N VAL B1137 " --> pdb=" O ILE B1121 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N SER B1123 " --> pdb=" O PHE B1135 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE B1135 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ALA B1125 " --> pdb=" O TYR B1133 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TYR B1133 " --> pdb=" O ALA B1125 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ASN B1127 " --> pdb=" O GLY B1131 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N GLY B1131 " --> pdb=" O ASN B1127 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N THR B1148 " --> pdb=" O LEU B1172 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N PHE B1170 " --> pdb=" O ALA B1150 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N GLY B1190 " --> pdb=" O HIS B1195 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N HIS B1195 " --> pdb=" O GLY B1190 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 1119 through 1128 removed outlier: 7.113A pdb=" N VAL B1137 " --> pdb=" O ILE B1121 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N SER B1123 " --> pdb=" O PHE B1135 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE B1135 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ALA B1125 " --> pdb=" O TYR B1133 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TYR B1133 " --> pdb=" O ALA B1125 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ASN B1127 " --> pdb=" O GLY B1131 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N GLY B1131 " --> pdb=" O ASN B1127 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASN B 783 " --> pdb=" O THR B1142 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N HIS B1144 " --> pdb=" O PRO B 781 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ASN B1146 " --> pdb=" O ALA B 779 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ALA B 779 " --> pdb=" O ASN B1146 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N THR B1148 " --> pdb=" O VAL B 777 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL B 777 " --> pdb=" O THR B1148 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 800 through 802 Processing sheet with id=AE8, first strand: chain 'B' and resid 863 through 864 Processing sheet with id=AE9, first strand: chain 'B' and resid 1204 through 1207 removed outlier: 4.396A pdb=" N CYS B1162 " --> pdb=" O VAL B1207 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 37 through 39 Processing sheet with id=AF2, first strand: chain 'C' and resid 75 through 82 removed outlier: 4.062A pdb=" N LYS C 344 " --> pdb=" O ASN C 335 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 90 through 92 removed outlier: 3.659A pdb=" N ALA C 291 " --> pdb=" O LEU C 274 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N SER C 276 " --> pdb=" O HIS C 289 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N HIS C 289 " --> pdb=" O SER C 276 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 95 through 96 removed outlier: 7.103A pdb=" N SER C 95 " --> pdb=" O ILE C 309 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'C' and resid 99 through 100 Processing sheet with id=AF6, first strand: chain 'C' and resid 117 through 118 Processing sheet with id=AF7, first strand: chain 'C' and resid 117 through 118 Processing sheet with id=AF8, first strand: chain 'C' and resid 134 through 137 removed outlier: 5.497A pdb=" N THR C 143 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ALA C 318 " --> pdb=" O PRO C 146 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 160 through 163 removed outlier: 6.186A pdb=" N GLY C 161 " --> pdb=" O GLY C 170 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY C 170 " --> pdb=" O GLY C 161 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE C 168 " --> pdb=" O TYR C 163 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 368 through 372 removed outlier: 4.530A pdb=" N VAL C 658 " --> pdb=" O VAL C 372 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 390 through 391 removed outlier: 6.589A pdb=" N GLN C 390 " --> pdb=" O ASN C 417 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N CYS C 416 " --> pdb=" O CYS C 584 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'C' and resid 399 through 400 removed outlier: 3.717A pdb=" N GLY C 400 " --> pdb=" O THR C 499 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'C' and resid 409 through 413 removed outlier: 3.583A pdb=" N SER C 449 " --> pdb=" O GLN C 575 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU C 431 " --> pdb=" O LEU C 490 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N THR C 492 " --> pdb=" O VAL C 429 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N VAL C 429 " --> pdb=" O THR C 492 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 521 through 522 removed outlier: 6.584A pdb=" N THR C 556 " --> pdb=" O THR C 510 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N CYS C 512 " --> pdb=" O THR C 554 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR C 554 " --> pdb=" O CYS C 512 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN C 546 " --> pdb=" O GLY C 557 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'C' and resid 715 through 722 removed outlier: 5.585A pdb=" N THR C 759 " --> pdb=" O THR C 718 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N MET C 720 " --> pdb=" O THR C 759 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N LEU C 733 " --> pdb=" O LEU C 729 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LEU C 727 " --> pdb=" O ALA C 735 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'C' and resid 800 through 802 Processing sheet with id=AG8, first strand: chain 'C' and resid 863 through 864 Processing sheet with id=AG9, first strand: chain 'C' and resid 1204 through 1207 removed outlier: 4.396A pdb=" N CYS C1162 " --> pdb=" O VAL C1207 " (cutoff:3.500A) 1177 hydrogen bonds defined for protein. 3102 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: 18.85 Time building geometry restraints manager: 9.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8658 1.34 - 1.47: 7530 1.47 - 1.59: 12564 1.59 - 1.72: 0 1.72 - 1.84: 198 Bond restraints: 28950 Sorted by residual: bond pdb=" N ILE B 244 " pdb=" CA ILE B 244 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.14e-02 7.69e+03 1.06e+01 bond pdb=" N ILE A 244 " pdb=" CA ILE A 244 " ideal model delta sigma weight residual 1.458 1.494 -0.037 1.14e-02 7.69e+03 1.05e+01 bond pdb=" N ILE C 244 " pdb=" CA ILE C 244 " ideal model delta sigma weight residual 1.458 1.494 -0.037 1.14e-02 7.69e+03 1.04e+01 bond pdb=" N ILE A 194 " pdb=" CA ILE A 194 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.20e-02 6.94e+03 9.04e+00 bond pdb=" N PHE C 248 " pdb=" CA PHE C 248 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.23e-02 6.61e+03 8.96e+00 ... (remaining 28945 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.23: 39032 3.23 - 6.46: 433 6.46 - 9.69: 6 9.69 - 12.92: 3 12.92 - 16.15: 3 Bond angle restraints: 39477 Sorted by residual: angle pdb=" N GLY A1009 " pdb=" CA GLY A1009 " pdb=" C GLY A1009 " ideal model delta sigma weight residual 114.66 130.81 -16.15 1.24e+00 6.50e-01 1.70e+02 angle pdb=" N GLY C1009 " pdb=" CA GLY C1009 " pdb=" C GLY C1009 " ideal model delta sigma weight residual 114.66 130.79 -16.13 1.24e+00 6.50e-01 1.69e+02 angle pdb=" N GLY B1009 " pdb=" CA GLY B1009 " pdb=" C GLY B1009 " ideal model delta sigma weight residual 114.66 130.79 -16.13 1.24e+00 6.50e-01 1.69e+02 angle pdb=" N THR C1008 " pdb=" CA THR C1008 " pdb=" C THR C1008 " ideal model delta sigma weight residual 113.19 124.21 -11.02 1.19e+00 7.06e-01 8.57e+01 angle pdb=" N THR B1008 " pdb=" CA THR B1008 " pdb=" C THR B1008 " ideal model delta sigma weight residual 113.19 124.19 -11.00 1.19e+00 7.06e-01 8.54e+01 ... (remaining 39472 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.41: 18099 27.41 - 54.83: 440 54.83 - 82.24: 172 82.24 - 109.66: 60 109.66 - 137.07: 3 Dihedral angle restraints: 18774 sinusoidal: 8553 harmonic: 10221 Sorted by residual: dihedral pdb=" C THR B1008 " pdb=" N THR B1008 " pdb=" CA THR B1008 " pdb=" CB THR B1008 " ideal model delta harmonic sigma weight residual -122.00 -139.35 17.35 0 2.50e+00 1.60e-01 4.81e+01 dihedral pdb=" C THR C1008 " pdb=" N THR C1008 " pdb=" CA THR C1008 " pdb=" CB THR C1008 " ideal model delta harmonic sigma weight residual -122.00 -139.32 17.32 0 2.50e+00 1.60e-01 4.80e+01 dihedral pdb=" C THR A1008 " pdb=" N THR A1008 " pdb=" CA THR A1008 " pdb=" CB THR A1008 " ideal model delta harmonic sigma weight residual -122.00 -139.31 17.31 0 2.50e+00 1.60e-01 4.79e+01 ... (remaining 18771 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.156: 4758 0.156 - 0.311: 75 0.311 - 0.467: 12 0.467 - 0.622: 3 0.622 - 0.778: 3 Chirality restraints: 4851 Sorted by residual: chirality pdb=" C1 NAG D 8 " pdb=" O2 MAN D 7 " pdb=" C2 NAG D 8 " pdb=" O5 NAG D 8 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-02 2.50e+03 3.87e+02 chirality pdb=" C1 NAG d 8 " pdb=" O2 MAN d 7 " pdb=" C2 NAG d 8 " pdb=" O5 NAG d 8 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-02 2.50e+03 3.86e+02 chirality pdb=" C1 NAG Q 8 " pdb=" O2 MAN Q 7 " pdb=" C2 NAG Q 8 " pdb=" O5 NAG Q 8 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-02 2.50e+03 3.85e+02 ... (remaining 4848 not shown) Planarity restraints: 4962 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 8 " 0.266 2.00e-02 2.50e+03 2.26e-01 6.39e+02 pdb=" C7 NAG D 8 " -0.066 2.00e-02 2.50e+03 pdb=" C8 NAG D 8 " 0.165 2.00e-02 2.50e+03 pdb=" N2 NAG D 8 " -0.391 2.00e-02 2.50e+03 pdb=" O7 NAG D 8 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG Q 8 " -0.265 2.00e-02 2.50e+03 2.26e-01 6.39e+02 pdb=" C7 NAG Q 8 " 0.066 2.00e-02 2.50e+03 pdb=" C8 NAG Q 8 " -0.165 2.00e-02 2.50e+03 pdb=" N2 NAG Q 8 " 0.391 2.00e-02 2.50e+03 pdb=" O7 NAG Q 8 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG d 8 " -0.265 2.00e-02 2.50e+03 2.26e-01 6.38e+02 pdb=" C7 NAG d 8 " 0.066 2.00e-02 2.50e+03 pdb=" C8 NAG d 8 " -0.165 2.00e-02 2.50e+03 pdb=" N2 NAG d 8 " 0.390 2.00e-02 2.50e+03 pdb=" O7 NAG d 8 " -0.026 2.00e-02 2.50e+03 ... (remaining 4959 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2131 2.74 - 3.28: 27973 3.28 - 3.82: 49237 3.82 - 4.36: 62125 4.36 - 4.90: 98706 Nonbonded interactions: 240172 Sorted by model distance: nonbonded pdb=" OG SER B 440 " pdb=" OD2 ASP C1057 " model vdw 2.200 3.040 nonbonded pdb=" OD2 ASP A1057 " pdb=" OG SER C 440 " model vdw 2.200 3.040 nonbonded pdb=" OG SER A 440 " pdb=" OD2 ASP B1057 " model vdw 2.200 3.040 nonbonded pdb=" O HOH B1603 " pdb=" O HOH B1703 " model vdw 2.201 3.040 nonbonded pdb=" O HOH C1603 " pdb=" O HOH C1703 " model vdw 2.201 3.040 ... (remaining 240167 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: 0.10 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 23 through 1227 or resid 1402 through 1405)) selection = (chain 'B' and (resid 23 through 1227 or resid 1402 through 1405)) selection = (chain 'C' and (resid 23 through 1227 or resid 1402 through 1405)) } ncs_group { reference = chain 'D' selection = chain 'Q' selection = chain 'd' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'R' selection = chain 'S' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'e' selection = chain 'f' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' } ncs_group { reference = chain 'G' selection = chain 'T' selection = chain 'g' } ncs_group { reference = chain 'H' selection = chain 'U' selection = chain 'h' } ncs_group { reference = chain 'P' selection = chain 'c' selection = chain 'p' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 19.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 1.080 Check model and map are aligned: 0.220 Set scattering table: 0.240 Process input model: 79.130 Find NCS groups from input model: 2.810 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 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 : 0.007 0.058 29130 Z= 0.373 Angle : 1.066 20.336 39966 Z= 0.543 Chirality : 0.065 0.778 4851 Planarity : 0.009 0.226 4908 Dihedral : 15.395 137.070 12081 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.09 % Favored : 97.83 % Rotamer: Outliers : 0.65 % Allowed : 6.70 % Favored : 92.65 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.13), residues: 3450 helix: 1.41 (0.19), residues: 765 sheet: 0.42 (0.19), residues: 651 loop : -0.13 (0.13), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 51 HIS 0.004 0.001 HIS C1144 PHE 0.029 0.003 PHE C 432 TYR 0.023 0.003 TYR C 506 ARG 0.008 0.001 ARG C1072 Details of bonding type rmsd link_NAG-ASN : bond 0.01087 ( 54) link_NAG-ASN : angle 4.37523 ( 162) link_ALPHA1-6 : bond 0.03598 ( 9) link_ALPHA1-6 : angle 4.53239 ( 27) link_BETA1-2 : bond 0.04199 ( 3) link_BETA1-2 : angle 10.16648 ( 9) link_BETA1-4 : bond 0.04339 ( 51) link_BETA1-4 : angle 6.33453 ( 153) link_ALPHA1-2 : bond 0.04184 ( 3) link_ALPHA1-2 : angle 9.09420 ( 9) link_ALPHA1-3 : bond 0.04460 ( 9) link_ALPHA1-3 : angle 5.66867 ( 27) hydrogen bonds : bond 0.18488 ( 1104) hydrogen bonds : angle 6.94361 ( 3102) SS BOND : bond 0.01237 ( 51) SS BOND : angle 2.39690 ( 102) covalent geometry : bond 0.00650 (28950) covalent geometry : angle 0.90669 (39477) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 216 time to evaluate : 2.954 Fit side-chains REVERT: A 386 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.7974 (pp30) REVERT: A 424 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8535 (mm) REVERT: A 447 TYR cc_start: 0.9328 (OUTLIER) cc_final: 0.7467 (p90) REVERT: B 26 MET cc_start: 0.8417 (mmm) cc_final: 0.7981 (mmm) REVERT: B 386 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8269 (pt0) REVERT: B 841 ASP cc_start: 0.8477 (m-30) cc_final: 0.8260 (m-30) REVERT: B 871 MET cc_start: 0.8117 (mmt) cc_final: 0.7903 (mmm) REVERT: C 106 ARG cc_start: 0.7913 (mtm180) cc_final: 0.7453 (mtm110) REVERT: C 148 LYS cc_start: 0.8161 (mmmm) cc_final: 0.7909 (mmmm) REVERT: C 230 ARG cc_start: 0.7847 (mmm-85) cc_final: 0.7078 (mtp180) REVERT: C 287 MET cc_start: 0.9290 (mtm) cc_final: 0.9084 (mtm) REVERT: C 386 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.8286 (pt0) REVERT: C 447 TYR cc_start: 0.9356 (OUTLIER) cc_final: 0.7478 (p90) REVERT: C 1006 MET cc_start: 0.7576 (mtm) cc_final: 0.7232 (mtm) outliers start: 18 outliers final: 7 residues processed: 226 average time/residue: 1.4524 time to fit residues: 382.7697 Evaluate side-chains 210 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 197 time to evaluate : 2.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 GLN Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 447 TYR Chi-restraints excluded: chain A residue 643 TYR Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain B residue 386 GLN Chi-restraints excluded: chain B residue 447 TYR Chi-restraints excluded: chain B residue 643 TYR Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain C residue 386 GLN Chi-restraints excluded: chain C residue 447 TYR Chi-restraints excluded: chain C residue 643 TYR Chi-restraints excluded: chain C residue 681 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.6924 > 50: distance: 68 - 193: 12.072 distance: 71 - 190: 17.520 distance: 139 - 169: 19.200 distance: 143 - 150: 22.615 distance: 144 - 174: 26.221 distance: 150 - 151: 16.574 distance: 151 - 152: 6.869 distance: 151 - 154: 19.707 distance: 152 - 153: 22.502 distance: 152 - 162: 23.087 distance: 154 - 155: 11.585 distance: 155 - 156: 6.892 distance: 155 - 157: 3.328 distance: 156 - 158: 17.502 distance: 157 - 159: 16.118 distance: 158 - 160: 8.911 distance: 159 - 160: 7.883 distance: 160 - 161: 14.264 distance: 162 - 163: 13.818 distance: 163 - 164: 13.349 distance: 163 - 166: 6.529 distance: 164 - 165: 5.434 distance: 164 - 169: 13.839 distance: 166 - 167: 22.089 distance: 166 - 168: 21.571 distance: 169 - 170: 11.716 distance: 170 - 171: 20.021 distance: 170 - 173: 33.091 distance: 171 - 172: 21.626 distance: 171 - 174: 50.521 distance: 174 - 175: 11.671 distance: 175 - 176: 23.010 distance: 176 - 177: 12.965 distance: 176 - 178: 5.345 distance: 178 - 179: 6.193 distance: 179 - 180: 15.584 distance: 179 - 182: 6.916 distance: 180 - 181: 12.030 distance: 180 - 190: 15.756 distance: 182 - 183: 14.171 distance: 183 - 184: 5.141 distance: 183 - 185: 3.233 distance: 184 - 186: 4.252 distance: 185 - 187: 4.231 distance: 186 - 188: 4.025 distance: 187 - 188: 5.120 distance: 188 - 189: 4.081 distance: 190 - 191: 14.290 distance: 191 - 192: 21.407 distance: 191 - 194: 22.932 distance: 192 - 193: 5.537 distance: 192 - 199: 19.608 distance: 194 - 195: 18.876 distance: 195 - 196: 18.325 distance: 196 - 197: 7.199 distance: 197 - 198: 3.478 distance: 199 - 200: 20.649 distance: 200 - 201: 10.957 distance: 200 - 203: 28.284 distance: 201 - 202: 21.815 distance: 201 - 206: 35.304 distance: 203 - 204: 27.934 distance: 203 - 205: 20.871 distance: 206 - 207: 25.794 distance: 207 - 208: 15.658 distance: 207 - 210: 48.759 distance: 208 - 209: 20.178 distance: 208 - 214: 8.988 distance: 210 - 211: 30.932 distance: 211 - 212: 10.346 distance: 211 - 213: 5.713 distance: 214 - 215: 14.450 distance: 214 - 220: 20.227 distance: 215 - 216: 10.744 distance: 215 - 218: 10.990 distance: 216 - 221: 6.059 distance: 218 - 219: 14.738 distance: 219 - 220: 7.192 distance: 221 - 222: 4.957 distance: 221 - 227: 7.076 distance: 222 - 223: 3.421 distance: 222 - 225: 4.939 distance: 223 - 224: 9.518 distance: 223 - 228: 5.818 distance: 225 - 226: 5.316 distance: 226 - 227: 8.116