Starting phenix.real_space_refine on Wed May 28 00:00:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ea0_47823/05_2025/9ea0_47823.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ea0_47823/05_2025/9ea0_47823.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/9ea0_47823/05_2025/9ea0_47823.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ea0_47823/05_2025/9ea0_47823.map" model { file = "/net/cci-nas-00/data/ceres_data/9ea0_47823/05_2025/9ea0_47823.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ea0_47823/05_2025/9ea0_47823.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= 0.056 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 6 6.06 5 S 159 5.16 5 C 18297 2.51 5 N 4614 2.21 5 O 6926 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 30002 Number of models: 1 Model: "" Number of chains: 51 Chain: "A" Number of atoms: 8972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1185, 8972 Classifications: {'peptide': 1185} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 61, 'TRANS': 1123} Chain breaks: 3 Unresolved non-hydrogen bonds: 239 Unresolved non-hydrogen angles: 311 Unresolved non-hydrogen dihedrals: 170 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 1, 'ASN:plan1': 9, 'ASP:plan': 6, 'GLU:plan': 13, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 147 Chain: "B" Number of atoms: 8972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1185, 8972 Classifications: {'peptide': 1185} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 61, 'TRANS': 1123} Chain breaks: 3 Unresolved non-hydrogen bonds: 239 Unresolved non-hydrogen angles: 311 Unresolved non-hydrogen dihedrals: 170 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 1, 'ASN:plan1': 9, 'ASP:plan': 6, 'GLU:plan': 13, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 147 Chain: "C" Number of atoms: 8972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1185, 8972 Classifications: {'peptide': 1185} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 61, 'TRANS': 1123} Chain breaks: 3 Unresolved non-hydrogen bonds: 239 Unresolved non-hydrogen angles: 311 Unresolved non-hydrogen dihedrals: 170 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 1, 'ASN:plan1': 9, 'ASP:plan': 6, 'GLU:plan': 13, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 147 Chain: "D" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 108 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 3} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 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: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "R" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 108 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 3} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 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: 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: 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: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 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: 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: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "f" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 108 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 3} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 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: "l" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 87 Unusual residues: {' ZN': 2, 'EIC': 1, 'FOL': 1, 'NAG': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 4 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: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 87 Unusual residues: {' ZN': 2, 'EIC': 1, 'FOL': 1, 'NAG': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 4 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: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 87 Unusual residues: {' ZN': 2, 'EIC': 1, 'FOL': 1, 'NAG': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 4 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: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 405 Classifications: {'water': 405} Link IDs: {None: 404} Chain: "B" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 405 Classifications: {'water': 405} Link IDs: {None: 404} Chain: "C" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 404 Classifications: {'water': 404} Link IDs: {None: 403} Time building chain proxies: 18.66, per 1000 atoms: 0.62 Number of scatterers: 30002 At special positions: 0 Unit cell: (147.525, 154.269, 161.013, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 6 29.99 S 159 16.00 O 6926 8.00 N 4614 7.00 C 18297 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 348 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 392 " - pdb=" SG CYS A 416 " distance=2.03 Simple disulfide: pdb=" SG CYS A 434 " - pdb=" SG CYS A 487 " distance=2.03 Simple disulfide: pdb=" SG CYS A 446 " - pdb=" SG CYS A 584 " distance=2.03 Simple disulfide: pdb=" SG CYS A 512 " - pdb=" SG CYS A 533 " distance=2.03 Simple disulfide: pdb=" SG CYS A 602 " - pdb=" SG CYS A 653 " distance=2.03 Simple disulfide: pdb=" SG CYS A 619 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 678 " - pdb=" SG CYS A 711 " distance=2.03 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 734 " distance=2.03 Simple disulfide: pdb=" SG CYS A 804 " - pdb=" SG CYS A 826 " distance=2.03 Simple disulfide: pdb=" SG CYS A 809 " - pdb=" SG CYS A 815 " distance=2.03 Simple disulfide: pdb=" SG CYS A 910 " - pdb=" SG CYS A 923 " distance=2.03 Simple disulfide: pdb=" SG CYS A1104 " - pdb=" SG CYS A1115 " distance=2.03 Simple disulfide: pdb=" SG CYS A1154 " - pdb=" SG CYS A1162 " distance=2.03 Simple disulfide: pdb=" SG CYS B 34 " - pdb=" SG CYS B 203 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 348 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 392 " - pdb=" SG CYS B 416 " distance=2.03 Simple disulfide: pdb=" SG CYS B 434 " - pdb=" SG CYS B 487 " distance=2.03 Simple disulfide: pdb=" SG CYS B 446 " - pdb=" SG CYS B 584 " distance=2.03 Simple disulfide: pdb=" SG CYS B 512 " - pdb=" SG CYS B 533 " distance=2.03 Simple disulfide: pdb=" SG CYS B 602 " - pdb=" SG CYS B 653 " distance=2.03 Simple disulfide: pdb=" SG CYS B 619 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 678 " - pdb=" SG CYS B 711 " distance=2.03 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 734 " distance=2.03 Simple disulfide: pdb=" SG CYS B 804 " - pdb=" SG CYS B 826 " distance=2.03 Simple disulfide: pdb=" SG CYS B 809 " - pdb=" SG CYS B 815 " distance=2.03 Simple disulfide: pdb=" SG CYS B 910 " - pdb=" SG CYS B 923 " distance=2.03 Simple disulfide: pdb=" SG CYS B1104 " - pdb=" SG CYS B1115 " distance=2.04 Simple disulfide: pdb=" SG CYS B1154 " - pdb=" SG CYS B1162 " distance=2.03 Simple disulfide: pdb=" SG CYS C 34 " - pdb=" SG CYS C 203 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 348 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 392 " - pdb=" SG CYS C 416 " distance=2.03 Simple disulfide: pdb=" SG CYS C 434 " - pdb=" SG CYS C 487 " distance=2.03 Simple disulfide: pdb=" SG CYS C 446 " - pdb=" SG CYS C 584 " distance=2.03 Simple disulfide: pdb=" SG CYS C 512 " - pdb=" SG CYS C 533 " distance=2.03 Simple disulfide: pdb=" SG CYS C 602 " - pdb=" SG CYS C 653 " distance=2.03 Simple disulfide: pdb=" SG CYS C 619 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 678 " - pdb=" SG CYS C 711 " distance=2.03 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 734 " distance=2.03 Simple disulfide: pdb=" SG CYS C 804 " - pdb=" SG CYS C 826 " distance=2.03 Simple disulfide: pdb=" SG CYS C 809 " - pdb=" SG CYS C 815 " distance=2.03 Simple disulfide: pdb=" SG CYS C 910 " - pdb=" SG CYS C 923 " distance=2.03 Simple disulfide: pdb=" SG CYS C1104 " - pdb=" SG CYS C1115 " distance=2.04 Simple disulfide: pdb=" SG CYS C1154 " - pdb=" SG CYS C1162 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN D 5 " - " MAN D 6 " " MAN R 5 " - " MAN R 6 " " MAN f 5 " - " MAN f 6 " ALPHA1-3 " BMA D 3 " - " MAN D 8 " " MAN D 4 " - " MAN D 5 " " BMA I 3 " - " MAN I 4 " " BMA R 3 " - " MAN R 8 " " MAN R 4 " - " MAN R 5 " " BMA W 3 " - " MAN W 4 " " BMA f 3 " - " MAN f 8 " " MAN f 4 " - " MAN f 5 " " BMA k 3 " - " MAN k 4 " ALPHA1-6 " BMA D 3 " - " MAN D 4 " " MAN D 4 " - " MAN D 7 " " BMA I 3 " - " MAN I 5 " " BMA R 3 " - " MAN R 4 " " MAN R 4 " - " MAN R 7 " " BMA W 3 " - " MAN W 5 " " BMA f 3 " - " MAN f 4 " " MAN f 4 " - " MAN f 7 " " BMA k 3 " - " MAN k 5 " BETA1-2 " MAN D 8 " - " NAG D 9 " " MAN R 8 " - " NAG R 9 " " MAN f 8 " - " NAG f 9 " 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 H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " 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 W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " 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 e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " 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 k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " 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 s 2 " - " BMA s 3 " BETA1-6 " NAG Q 1 " - " FUC Q 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG e 1 " - " FUC e 4 " " NAG s 1 " - " FUC s 4 " NAG-ASN " NAG A1401 " - " ASN A 73 " " NAG A1402 " - " ASN A 167 " " NAG A1403 " - " ASN A1146 " " NAG B1401 " - " ASN B 73 " " NAG B1402 " - " ASN B 167 " " NAG B1403 " - " ASN B1146 " " NAG C1402 " - " ASN C 73 " " NAG C1403 " - " ASN C 167 " " NAG C1404 " - " ASN C1146 " " NAG D 1 " - " ASN A 761 " " NAG E 1 " - " ASN A 111 " " NAG F 1 " - " ASN A 162 " " NAG G 1 " - " ASN A 174 " " NAG H 1 " - " ASN A 245 " " NAG I 1 " - " ASN A 251 " " NAG J 1 " - " ASN A 419 " " NAG K 1 " - " ASN A 591 " " NAG L 1 " - " ASN A 717 " " NAG M 1 " - " ASN A 783 " " NAG N 1 " - " ASN A 868 " " NAG O 1 " - " ASN A1173 " " NAG P 1 " - " ASN A1215 " " NAG Q 1 " - " ASN A 132 " " NAG R 1 " - " ASN B 761 " " NAG S 1 " - " ASN B 111 " " NAG T 1 " - " ASN B 162 " " NAG U 1 " - " ASN B 174 " " NAG V 1 " - " ASN B 245 " " NAG W 1 " - " ASN B 251 " " NAG X 1 " - " ASN B 419 " " NAG Y 1 " - " ASN B 591 " " NAG Z 1 " - " ASN B 717 " " NAG a 1 " - " ASN B 783 " " NAG b 1 " - " ASN B 868 " " NAG c 1 " - " ASN B1173 " " NAG d 1 " - " ASN B1215 " " NAG e 1 " - " ASN B 132 " " NAG f 1 " - " ASN C 761 " " NAG g 1 " - " ASN C 111 " " NAG h 1 " - " ASN C 162 " " NAG i 1 " - " ASN C 174 " " NAG j 1 " - " ASN C 245 " " NAG k 1 " - " ASN C 251 " " NAG l 1 " - " ASN C 419 " " NAG m 1 " - " ASN C 591 " " NAG n 1 " - " ASN C 717 " " NAG o 1 " - " ASN C 783 " " NAG p 1 " - " ASN C 868 " " NAG q 1 " - " ASN C1173 " " NAG r 1 " - " ASN C1215 " " NAG s 1 " - " ASN C 132 " Time building additional restraints: 9.34 Conformation dependent library (CDL) restraints added in 3.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1404 " pdb="ZN ZN A1404 " - pdb=" ND1 HIS A 617 " pdb="ZN ZN A1404 " - pdb=" NE2 HIS A 680 " pdb=" ZN A1405 " pdb="ZN ZN A1405 " - pdb=" ND1 HIS A 273 " pdb="ZN ZN A1405 " - pdb=" NE2 HIS A 289 " pdb=" ZN B1404 " pdb="ZN ZN B1404 " - pdb=" ND1 HIS B 617 " pdb="ZN ZN B1404 " - pdb=" NE2 HIS B 680 " pdb=" ZN B1405 " pdb="ZN ZN B1405 " - pdb=" ND1 HIS B 273 " pdb="ZN ZN B1405 " - pdb=" NE2 HIS B 289 " pdb=" ZN C1405 " pdb="ZN ZN C1405 " - pdb=" ND1 HIS C 617 " pdb="ZN ZN C1405 " - pdb=" NE2 HIS C 680 " pdb=" ZN C1406 " pdb="ZN ZN C1406 " - pdb=" ND1 HIS C 273 " pdb="ZN ZN C1406 " - pdb=" NE2 HIS C 289 " 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6654 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 63 sheets defined 27.6% alpha, 29.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.15 Creating SS restraints... Processing helix chain 'A' and resid 41 through 44 Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 231 through 240 removed outlier: 3.509A pdb=" N LEU A 239 " --> pdb=" O ASN A 235 " (cutoff:3.500A) removed outlier: 4.063A 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 399 Processing helix chain 'A' and resid 404 through 408 Processing helix chain 'A' and resid 419 through 426 removed outlier: 3.628A pdb=" N LEU A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 444 Processing helix chain 'A' and resid 458 through 466 removed outlier: 4.995A pdb=" N SER A 463 " --> pdb=" O ASP A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 477 removed outlier: 3.590A 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 677 through 684 removed outlier: 3.768A pdb=" N THR A 683 " --> pdb=" O SER A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 699 removed outlier: 3.577A pdb=" N ARG A 699 " --> pdb=" O ASN A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 810 Processing helix chain 'A' and resid 812 through 820 removed outlier: 3.592A pdb=" N THR A 820 " --> pdb=" O GLU A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 823 No H-bonds generated for 'chain 'A' and resid 821 through 823' Processing helix chain 'A' and resid 824 through 849 Processing helix chain 'A' and resid 850 through 854 removed outlier: 3.744A pdb=" N GLN A 854 " --> pdb=" O ILE A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 895 removed outlier: 3.639A pdb=" N LYS A 895 " --> pdb=" O LEU A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 914 removed outlier: 3.783A pdb=" N MET A 911 " --> pdb=" O TYR A 907 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY A 914 " --> pdb=" O CYS A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 918 No H-bonds generated for 'chain 'A' and resid 916 through 918' Processing helix chain 'A' and resid 919 through 924 Processing helix chain 'A' and resid 924 through 929 Processing helix chain 'A' and resid 938 through 951 removed outlier: 3.565A pdb=" N GLU A 942 " --> pdb=" O ASP A 938 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 980 Processing helix chain 'A' and resid 984 through 991 Processing helix chain 'A' and resid 991 through 1006 removed outlier: 3.946A pdb=" N MET A1006 " --> pdb=" O ALA A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1009 No H-bonds generated for 'chain 'A' and resid 1007 through 1009' Processing helix chain 'A' and resid 1014 through 1037 removed outlier: 3.767A pdb=" N VAL A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN A1021 " --> pdb=" O PHE A1017 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU A1031 " --> pdb=" O ASN A1027 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU A1037 " --> pdb=" O LYS A1033 " (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 1057 through 1105 removed outlier: 3.920A pdb=" N GLU A1062 " --> pdb=" O PRO A1058 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N ALA A1063 " --> pdb=" O PRO A1059 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLN A1064 " --> pdb=" O GLU A1060 " (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 56 through 60 Processing helix chain 'B' and resid 231 through 240 removed outlier: 3.509A pdb=" N LEU B 239 " --> pdb=" O ASN B 235 " (cutoff:3.500A) removed outlier: 4.063A 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 399 Processing helix chain 'B' and resid 404 through 408 Processing helix chain 'B' and resid 419 through 426 removed outlier: 3.628A pdb=" N LEU B 426 " --> pdb=" O LYS B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 444 Processing helix chain 'B' and resid 458 through 466 removed outlier: 4.995A pdb=" N SER B 463 " --> pdb=" O ASP B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 477 removed outlier: 3.590A 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 677 through 684 removed outlier: 3.768A pdb=" N THR B 683 " --> pdb=" O SER B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 699 removed outlier: 3.577A pdb=" N ARG B 699 " --> pdb=" O ASN B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 810 Processing helix chain 'B' and resid 812 through 820 removed outlier: 3.592A pdb=" N THR B 820 " --> pdb=" O GLU B 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 823 No H-bonds generated for 'chain 'B' and resid 821 through 823' Processing helix chain 'B' and resid 824 through 849 Processing helix chain 'B' and resid 850 through 854 removed outlier: 3.744A pdb=" N GLN B 854 " --> pdb=" O ILE B 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 895 removed outlier: 3.639A pdb=" N LYS B 895 " --> pdb=" O LEU B 891 " (cutoff:3.500A) Processing helix chain 'B' and resid 905 through 914 removed outlier: 3.784A pdb=" N MET B 911 " --> pdb=" O TYR B 907 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY B 914 " --> pdb=" O CYS B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 918 No H-bonds generated for 'chain 'B' and resid 916 through 918' Processing helix chain 'B' and resid 919 through 924 Processing helix chain 'B' and resid 924 through 929 Processing helix chain 'B' and resid 938 through 951 removed outlier: 3.566A pdb=" N GLU B 942 " --> pdb=" O ASP B 938 " (cutoff:3.500A) Processing helix chain 'B' and resid 969 through 980 Processing helix chain 'B' and resid 984 through 991 Processing helix chain 'B' and resid 991 through 1006 removed outlier: 3.946A pdb=" N MET B1006 " --> pdb=" O ALA B1002 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1009 No H-bonds generated for 'chain 'B' and resid 1007 through 1009' Processing helix chain 'B' and resid 1014 through 1037 removed outlier: 3.767A pdb=" N VAL B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN B1021 " --> pdb=" O PHE B1017 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU B1031 " --> pdb=" O ASN B1027 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU B1037 " --> pdb=" O LYS B1033 " (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 1057 through 1105 removed outlier: 3.919A pdb=" N GLU B1062 " --> pdb=" O PRO B1058 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N ALA B1063 " --> pdb=" O PRO B1059 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLN B1064 " --> pdb=" O GLU B1060 " (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 56 through 60 Processing helix chain 'C' and resid 231 through 240 removed outlier: 3.510A pdb=" N LEU C 239 " --> pdb=" O ASN C 235 " (cutoff:3.500A) removed outlier: 4.063A 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 399 Processing helix chain 'C' and resid 404 through 408 Processing helix chain 'C' and resid 419 through 426 removed outlier: 3.628A pdb=" N LEU C 426 " --> pdb=" O LYS C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 444 Processing helix chain 'C' and resid 458 through 466 removed outlier: 4.995A pdb=" N SER C 463 " --> pdb=" O ASP C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 477 removed outlier: 3.590A 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 677 through 684 removed outlier: 3.768A pdb=" N THR C 683 " --> pdb=" O SER C 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 689 through 699 removed outlier: 3.577A pdb=" N ARG C 699 " --> pdb=" O ASN C 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 803 through 810 Processing helix chain 'C' and resid 812 through 820 removed outlier: 3.591A pdb=" N THR C 820 " --> pdb=" O GLU C 816 " (cutoff:3.500A) Processing helix chain 'C' and resid 821 through 823 No H-bonds generated for 'chain 'C' and resid 821 through 823' Processing helix chain 'C' and resid 824 through 849 Processing helix chain 'C' and resid 850 through 854 removed outlier: 3.744A pdb=" N GLN C 854 " --> pdb=" O ILE C 851 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 895 removed outlier: 3.639A pdb=" N LYS C 895 " --> pdb=" O LEU C 891 " (cutoff:3.500A) Processing helix chain 'C' and resid 905 through 914 removed outlier: 3.783A pdb=" N MET C 911 " --> pdb=" O TYR C 907 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY C 914 " --> pdb=" O CYS C 910 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 918 No H-bonds generated for 'chain 'C' and resid 916 through 918' Processing helix chain 'C' and resid 919 through 924 Processing helix chain 'C' and resid 924 through 929 Processing helix chain 'C' and resid 938 through 951 removed outlier: 3.565A pdb=" N GLU C 942 " --> pdb=" O ASP C 938 " (cutoff:3.500A) Processing helix chain 'C' and resid 969 through 980 Processing helix chain 'C' and resid 984 through 991 Processing helix chain 'C' and resid 991 through 1006 removed outlier: 3.946A pdb=" N MET C1006 " --> pdb=" O ALA C1002 " (cutoff:3.500A) Processing helix chain 'C' and resid 1007 through 1009 No H-bonds generated for 'chain 'C' and resid 1007 through 1009' Processing helix chain 'C' and resid 1014 through 1037 removed outlier: 3.767A pdb=" N VAL C1020 " --> pdb=" O ALA C1016 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN C1021 " --> pdb=" O PHE C1017 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU C1031 " --> pdb=" O ASN C1027 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU C1037 " --> pdb=" O LYS C1033 " (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 1057 through 1105 removed outlier: 3.919A pdb=" N GLU C1062 " --> pdb=" O PRO C1058 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N ALA C1063 " --> pdb=" O PRO C1059 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLN C1064 " --> pdb=" O GLU C1060 " (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 removed outlier: 5.698A pdb=" N GLN A 38 " --> pdb=" O VAL A 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 74 through 82 removed outlier: 3.588A pdb=" N ILE A 74 " --> pdb=" O PHE A 336 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LYS A 344 " --> pdb=" O ASN A 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 removed outlier: 3.821A pdb=" N ALA A 291 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N SER A 276 " --> pdb=" O HIS A 289 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N HIS A 289 " --> pdb=" O SER A 276 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 95 through 96 removed outlier: 7.450A pdb=" N SER A 95 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N VAL A 214 " --> pdb=" O SER A 308 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 99 through 100 Processing sheet with id=AA6, first strand: chain 'A' and resid 117 through 118 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 134 through 136 removed outlier: 3.815A pdb=" N ALA A 318 " --> pdb=" O PRO A 146 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 159 through 163 removed outlier: 7.293A pdb=" N SER A 159 " --> pdb=" O TYR A 172 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N TYR A 172 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N GLY A 161 " --> pdb=" O GLY A 170 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE A 168 " --> pdb=" O TYR A 163 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 368 through 371 removed outlier: 3.568A pdb=" N GLY A 710 " --> pdb=" O THR A 707 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 381 through 385 removed outlier: 6.443A pdb=" N GLY A 381 " --> pdb=" O GLU A 604 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N SER A 606 " --> pdb=" O GLY A 381 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N PHE A 383 " --> pdb=" O SER A 606 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TYR A 647 " --> pdb=" O CYS A 619 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL A 638 " --> pdb=" O VAL A 650 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 390 through 391 removed outlier: 6.511A pdb=" N GLN A 390 " --> pdb=" O ASN A 417 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS A 584 " --> pdb=" O CYS A 416 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 409 through 413 removed outlier: 3.778A pdb=" N SER A 449 " --> pdb=" O GLN A 575 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU A 431 " --> pdb=" O LEU A 490 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N THR A 492 " --> pdb=" O VAL A 429 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N VAL A 429 " --> pdb=" O THR A 492 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 520 through 522 removed outlier: 6.661A pdb=" N THR A 556 " --> pdb=" O THR A 510 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N CYS A 512 " --> pdb=" O THR A 554 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR A 554 " --> pdb=" O CYS A 512 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN A 546 " --> pdb=" O GLY A 557 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 715 through 722 removed outlier: 6.792A pdb=" N PHE A 755 " --> pdb=" O ILE A 716 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N THR A 718 " --> pdb=" O PHE A 755 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ILE A 757 " --> pdb=" O THR A 718 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N MET A 720 " --> pdb=" O ILE A 757 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1119 through 1128 removed outlier: 3.625A pdb=" N THR A1119 " --> pdb=" O TYR A1139 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N VAL A1137 " --> pdb=" O ILE A1121 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N SER A1123 " --> pdb=" O PHE A1135 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N PHE A1135 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA A1125 " --> pdb=" O TYR A1133 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TYR A1133 " --> pdb=" O ALA A1125 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N ASN A1127 " --> pdb=" O GLY A1131 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N GLY A1131 " --> pdb=" O ASN A1127 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N THR A1148 " --> pdb=" O LEU A1172 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N PHE A1170 " --> pdb=" O ALA A1150 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N GLY A1190 " --> pdb=" O HIS A1195 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N HIS A1195 " --> pdb=" O GLY A1190 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1119 through 1128 removed outlier: 3.625A pdb=" N THR A1119 " --> pdb=" O TYR A1139 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N VAL A1137 " --> pdb=" O ILE A1121 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N SER A1123 " --> pdb=" O PHE A1135 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N PHE A1135 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA A1125 " --> pdb=" O TYR A1133 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TYR A1133 " --> pdb=" O ALA A1125 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N ASN A1127 " --> pdb=" O GLY A1131 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N GLY A1131 " --> pdb=" O ASN A1127 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ASN A 783 " --> pdb=" O THR A1142 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N HIS A1144 " --> pdb=" O PRO A 781 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ASN A1146 " --> pdb=" O ALA A 779 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ALA A 779 " --> pdb=" O ASN A1146 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N THR A1148 " --> pdb=" O VAL A 777 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL A 777 " --> pdb=" O THR A1148 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 800 through 802 Processing sheet with id=AC1, first strand: chain 'A' and resid 863 through 864 removed outlier: 3.622A pdb=" N PHE A 867 " --> pdb=" O ASN A 864 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 965 through 966 removed outlier: 6.887A pdb=" N VAL C 777 " --> pdb=" O THR C1148 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N THR C1148 " --> pdb=" O VAL C 777 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ALA C 779 " --> pdb=" O ASN C1146 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ASN C1146 " --> pdb=" O ALA C 779 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N HIS C1144 " --> pdb=" O PRO C 781 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ASN C 783 " --> pdb=" O THR C1142 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N GLY C1131 " --> pdb=" O ASN C1127 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ASN C1127 " --> pdb=" O GLY C1131 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TYR C1133 " --> pdb=" O ALA C1125 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA C1125 " --> pdb=" O TYR C1133 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N PHE C1135 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N SER C1123 " --> pdb=" O PHE C1135 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N VAL C1137 " --> pdb=" O ILE C1121 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR C1119 " --> pdb=" O TYR C1139 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 965 through 966 removed outlier: 6.887A pdb=" N VAL C 777 " --> pdb=" O THR C1148 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N THR C1148 " --> pdb=" O VAL C 777 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ALA C 779 " --> pdb=" O ASN C1146 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ASN C1146 " --> pdb=" O ALA C 779 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N HIS C1144 " --> pdb=" O PRO C 781 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ASN C 783 " --> pdb=" O THR C1142 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N THR C1148 " --> pdb=" O LEU C1172 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N PHE C1170 " --> pdb=" O ALA C1150 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N GLY C1190 " --> pdb=" O HIS C1195 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N HIS C1195 " --> pdb=" O GLY C1190 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1153 through 1154 Processing sheet with id=AC5, first strand: chain 'A' and resid 1162 through 1165 removed outlier: 3.924A pdb=" N CYS A1162 " --> pdb=" O VAL A1207 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 37 through 39 removed outlier: 5.698A pdb=" N GLN B 38 " --> pdb=" O VAL B 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 74 through 82 removed outlier: 3.588A pdb=" N ILE B 74 " --> pdb=" O PHE B 336 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS B 344 " --> pdb=" O ASN B 335 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 90 through 92 removed outlier: 3.821A pdb=" N ALA B 291 " --> pdb=" O LEU B 274 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N SER B 276 " --> pdb=" O HIS B 289 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N HIS B 289 " --> pdb=" O SER B 276 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 95 through 96 removed outlier: 7.450A pdb=" N SER B 95 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N VAL B 214 " --> pdb=" O SER B 308 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 99 through 100 Processing sheet with id=AD2, first strand: chain 'B' and resid 117 through 118 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 134 through 136 removed outlier: 3.816A pdb=" N ALA B 318 " --> pdb=" O PRO B 146 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 159 through 163 removed outlier: 7.293A pdb=" N SER B 159 " --> pdb=" O TYR B 172 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N TYR B 172 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLY B 161 " --> pdb=" O GLY B 170 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE B 168 " --> pdb=" O TYR B 163 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 368 through 371 removed outlier: 3.570A pdb=" N GLY B 710 " --> pdb=" O THR B 707 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 381 through 385 removed outlier: 6.443A pdb=" N GLY B 381 " --> pdb=" O GLU B 604 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N SER B 606 " --> pdb=" O GLY B 381 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N PHE B 383 " --> pdb=" O SER B 606 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TYR B 647 " --> pdb=" O CYS B 619 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL B 638 " --> pdb=" O VAL B 650 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 390 through 391 removed outlier: 6.511A pdb=" N GLN B 390 " --> pdb=" O ASN B 417 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS B 584 " --> pdb=" O CYS B 416 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 409 through 413 removed outlier: 3.779A pdb=" N SER B 449 " --> pdb=" O GLN B 575 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU B 431 " --> pdb=" O LEU B 490 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N THR B 492 " --> pdb=" O VAL B 429 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N VAL B 429 " --> pdb=" O THR B 492 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 520 through 522 removed outlier: 6.661A pdb=" N THR B 556 " --> pdb=" O THR B 510 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N CYS B 512 " --> pdb=" O THR B 554 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR B 554 " --> pdb=" O CYS B 512 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN B 546 " --> pdb=" O GLY B 557 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 715 through 722 removed outlier: 6.792A pdb=" N PHE B 755 " --> pdb=" O ILE B 716 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N THR B 718 " --> pdb=" O PHE B 755 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ILE B 757 " --> pdb=" O THR B 718 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N MET B 720 " --> pdb=" O ILE B 757 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 1119 through 1128 removed outlier: 3.625A pdb=" N THR B1119 " --> pdb=" O TYR B1139 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N VAL B1137 " --> pdb=" O ILE B1121 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N SER B1123 " --> pdb=" O PHE B1135 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N PHE B1135 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA B1125 " --> pdb=" O TYR B1133 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TYR B1133 " --> pdb=" O ALA B1125 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ASN B1127 " --> pdb=" O GLY B1131 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N GLY B1131 " --> pdb=" O ASN B1127 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N THR B1148 " --> pdb=" O LEU B1172 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N PHE B1170 " --> pdb=" O ALA B1150 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N GLY B1190 " --> pdb=" O HIS B1195 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N HIS B1195 " --> pdb=" O GLY B1190 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 1119 through 1128 removed outlier: 3.625A pdb=" N THR B1119 " --> pdb=" O TYR B1139 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N VAL B1137 " --> pdb=" O ILE B1121 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N SER B1123 " --> pdb=" O PHE B1135 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N PHE B1135 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA B1125 " --> pdb=" O TYR B1133 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TYR B1133 " --> pdb=" O ALA B1125 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ASN B1127 " --> pdb=" O GLY B1131 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N GLY B1131 " --> pdb=" O ASN B1127 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ASN B 783 " --> pdb=" O THR B1142 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N HIS B1144 " --> pdb=" O PRO B 781 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ASN B1146 " --> pdb=" O ALA B 779 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ALA B 779 " --> pdb=" O ASN B1146 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N THR B1148 " --> pdb=" O VAL B 777 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL B 777 " --> pdb=" O THR B1148 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 800 through 802 Processing sheet with id=AE6, first strand: chain 'B' and resid 863 through 864 removed outlier: 3.621A pdb=" N PHE B 867 " --> pdb=" O ASN B 864 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 1153 through 1154 Processing sheet with id=AE8, first strand: chain 'B' and resid 1162 through 1165 removed outlier: 3.925A pdb=" N CYS B1162 " --> pdb=" O VAL B1207 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 37 through 39 removed outlier: 5.697A pdb=" N GLN C 38 " --> pdb=" O VAL C 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'C' and resid 74 through 82 removed outlier: 3.588A pdb=" N ILE C 74 " --> pdb=" O PHE C 336 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LYS C 344 " --> pdb=" O ASN C 335 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 90 through 92 removed outlier: 3.821A pdb=" N ALA C 291 " --> pdb=" O LEU C 274 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N SER C 276 " --> pdb=" O HIS C 289 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N HIS C 289 " --> pdb=" O SER C 276 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 95 through 96 removed outlier: 7.451A pdb=" N SER C 95 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N VAL C 214 " --> pdb=" O SER C 308 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'C' and resid 99 through 100 Processing sheet with id=AF5, first strand: chain 'C' and resid 117 through 118 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 134 through 136 removed outlier: 3.816A pdb=" N ALA C 318 " --> pdb=" O PRO C 146 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 159 through 163 removed outlier: 7.293A pdb=" N SER C 159 " --> pdb=" O TYR C 172 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N TYR C 172 " --> pdb=" O SER C 159 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N GLY C 161 " --> pdb=" O GLY C 170 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE C 168 " --> pdb=" O TYR C 163 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 368 through 371 removed outlier: 3.569A pdb=" N GLY C 710 " --> pdb=" O THR C 707 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 381 through 385 removed outlier: 6.443A pdb=" N GLY C 381 " --> pdb=" O GLU C 604 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N SER C 606 " --> pdb=" O GLY C 381 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N PHE C 383 " --> pdb=" O SER C 606 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TYR C 647 " --> pdb=" O CYS C 619 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL C 638 " --> pdb=" O VAL C 650 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 390 through 391 removed outlier: 6.511A pdb=" N GLN C 390 " --> pdb=" O ASN C 417 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS C 584 " --> pdb=" O CYS C 416 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 409 through 413 removed outlier: 3.779A pdb=" N SER C 449 " --> pdb=" O GLN C 575 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU C 431 " --> pdb=" O LEU C 490 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N THR C 492 " --> pdb=" O VAL C 429 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N VAL C 429 " --> pdb=" O THR C 492 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 520 through 522 removed outlier: 6.661A pdb=" N THR C 556 " --> pdb=" O THR C 510 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N CYS C 512 " --> pdb=" O THR C 554 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR C 554 " --> pdb=" O CYS C 512 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN C 546 " --> pdb=" O GLY C 557 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 715 through 722 removed outlier: 6.793A pdb=" N PHE C 755 " --> pdb=" O ILE C 716 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N THR C 718 " --> pdb=" O PHE C 755 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ILE C 757 " --> pdb=" O THR C 718 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N MET C 720 " --> pdb=" O ILE C 757 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'C' and resid 800 through 802 Processing sheet with id=AG7, first strand: chain 'C' and resid 863 through 864 removed outlier: 3.621A pdb=" N PHE C 867 " --> pdb=" O ASN C 864 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 1153 through 1154 Processing sheet with id=AG9, first strand: chain 'C' and resid 1162 through 1165 removed outlier: 3.924A pdb=" N CYS C1162 " --> pdb=" O VAL C1207 " (cutoff:3.500A) 1127 hydrogen bonds defined for protein. 3027 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: 16.87 Time building geometry restraints manager: 10.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8786 1.34 - 1.46: 6876 1.46 - 1.58: 13570 1.58 - 1.70: 0 1.70 - 1.82: 216 Bond restraints: 29448 Sorted by residual: bond pdb=" N LEU B 173 " pdb=" CA LEU B 173 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.19e-02 7.06e+03 8.78e+00 bond pdb=" N ASP A 87 " pdb=" CA ASP A 87 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.22e-02 6.72e+03 8.74e+00 bond pdb=" N ASP B 87 " pdb=" CA ASP B 87 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.22e-02 6.72e+03 8.73e+00 bond pdb=" N ASP C 87 " pdb=" CA ASP C 87 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.22e-02 6.72e+03 8.68e+00 bond pdb=" N LEU C 173 " pdb=" CA LEU C 173 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.19e-02 7.06e+03 8.54e+00 ... (remaining 29443 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 38915 1.30 - 2.59: 929 2.59 - 3.89: 228 3.89 - 5.18: 67 5.18 - 6.48: 7 Bond angle restraints: 40146 Sorted by residual: angle pdb=" C TYR C 172 " pdb=" CA TYR C 172 " pdb=" CB TYR C 172 " ideal model delta sigma weight residual 109.80 116.28 -6.48 1.64e+00 3.72e-01 1.56e+01 angle pdb=" C TYR A 172 " pdb=" CA TYR A 172 " pdb=" CB TYR A 172 " ideal model delta sigma weight residual 109.80 116.26 -6.46 1.64e+00 3.72e-01 1.55e+01 angle pdb=" C TYR B 172 " pdb=" CA TYR B 172 " pdb=" CB TYR B 172 " ideal model delta sigma weight residual 109.80 116.25 -6.45 1.64e+00 3.72e-01 1.55e+01 angle pdb=" CA GLY A 89 " pdb=" C GLY A 89 " pdb=" O GLY A 89 " ideal model delta sigma weight residual 121.83 117.68 4.15 1.26e+00 6.30e-01 1.08e+01 angle pdb=" CA GLY C 89 " pdb=" C GLY C 89 " pdb=" O GLY C 89 " ideal model delta sigma weight residual 121.83 117.72 4.11 1.26e+00 6.30e-01 1.06e+01 ... (remaining 40141 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.92: 18744 34.92 - 69.84: 279 69.84 - 104.75: 114 104.75 - 139.67: 6 139.67 - 174.59: 3 Dihedral angle restraints: 19146 sinusoidal: 8742 harmonic: 10404 Sorted by residual: dihedral pdb=" N FOL C1407 " pdb=" C FOL C1407 " pdb=" C11 FOL C1407 " pdb=" C16 FOL C1407 " ideal model delta sinusoidal sigma weight residual -0.09 174.50 -174.59 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" N FOL A1406 " pdb=" C FOL A1406 " pdb=" C11 FOL A1406 " pdb=" C16 FOL A1406 " ideal model delta sinusoidal sigma weight residual -0.09 174.47 -174.56 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" N FOL B1406 " pdb=" C FOL B1406 " pdb=" C11 FOL B1406 " pdb=" C16 FOL B1406 " ideal model delta sinusoidal sigma weight residual -0.09 174.43 -174.52 1 2.00e+01 2.50e-03 4.79e+01 ... (remaining 19143 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 4770 0.111 - 0.222: 126 0.222 - 0.333: 6 0.333 - 0.443: 0 0.443 - 0.554: 6 Chirality restraints: 4908 Sorted by residual: chirality pdb=" C1 MAN f 6 " pdb=" O2 MAN f 5 " pdb=" C2 MAN f 6 " pdb=" O5 MAN f 6 " both_signs ideal model delta sigma weight residual False 2.40 1.85 0.55 2.00e-02 2.50e+03 7.68e+02 chirality pdb=" C1 MAN R 6 " pdb=" O2 MAN R 5 " pdb=" C2 MAN R 6 " pdb=" O5 MAN R 6 " both_signs ideal model delta sigma weight residual False 2.40 1.85 0.55 2.00e-02 2.50e+03 7.67e+02 chirality pdb=" C1 MAN D 6 " pdb=" O2 MAN D 5 " pdb=" C2 MAN D 6 " pdb=" O5 MAN D 6 " both_signs ideal model delta sigma weight residual False 2.40 1.85 0.55 2.00e-02 2.50e+03 7.65e+02 ... (remaining 4905 not shown) Planarity restraints: 5055 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 85 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.76e+00 pdb=" C ALA B 85 " -0.029 2.00e-02 2.50e+03 pdb=" O ALA B 85 " 0.011 2.00e-02 2.50e+03 pdb=" N ASN B 86 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 171 " -0.149 9.50e-02 1.11e+02 6.67e-02 2.75e+00 pdb=" NE ARG A 171 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG A 171 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 171 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 171 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 85 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" C ALA A 85 " -0.029 2.00e-02 2.50e+03 pdb=" O ALA A 85 " 0.011 2.00e-02 2.50e+03 pdb=" N ASN A 86 " 0.010 2.00e-02 2.50e+03 ... (remaining 5052 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 6313 2.78 - 3.31: 27114 3.31 - 3.84: 52508 3.84 - 4.37: 62742 4.37 - 4.90: 103629 Nonbonded interactions: 252306 Sorted by model distance: nonbonded pdb=" OD1 ASP B 268 " pdb=" NE2 HIS B 273 " model vdw 2.253 3.120 nonbonded pdb=" OD1 ASP A 268 " pdb=" NE2 HIS A 273 " model vdw 2.254 3.120 nonbonded pdb=" OD1 ASP C 268 " pdb=" NE2 HIS C 273 " model vdw 2.254 3.120 nonbonded pdb=" OG1 THR B 292 " pdb="ZN ZN B1405 " model vdw 2.273 2.230 nonbonded pdb=" OG1 THR A 292 " pdb="ZN ZN A1405 " model vdw 2.273 2.230 ... (remaining 252301 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: 0.09 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 23 through 1227 or resid 1402 through 1403 or resid 1405)) \ selection = (chain 'B' and (resid 23 through 1227 or resid 1402 through 1403 or resid 1405)) \ selection = (chain 'C' and (resid 23 through 1227 or resid 1402 through 1403 or resid 1405)) \ } ncs_group { reference = chain 'D' selection = chain 'R' selection = chain 'f' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' } ncs_group { reference = chain 'I' selection = chain 'W' selection = chain 'k' } ncs_group { reference = chain 'J' selection = chain 'X' selection = chain 'l' } ncs_group { reference = chain 'Q' selection = chain 'e' selection = chain 's' } 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: 23.790 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: 0.070 Extract box with map and model: 1.240 Check model and map are aligned: 0.220 Set scattering table: 0.280 Process input model: 83.360 Find NCS groups from input model: 2.550 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:11.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 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 : 0.004 0.173 29643 Z= 0.193 Angle : 0.601 14.074 40644 Z= 0.298 Chirality : 0.047 0.554 4908 Planarity : 0.004 0.067 5004 Dihedral : 13.937 174.589 12339 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.86 % Allowed : 4.07 % Favored : 95.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.14), residues: 3531 helix: 1.63 (0.19), residues: 789 sheet: 0.87 (0.18), residues: 807 loop : -0.63 (0.13), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 319 HIS 0.005 0.001 HIS A1120 PHE 0.007 0.001 PHE A 432 TYR 0.013 0.001 TYR A 192 ARG 0.004 0.000 ARG A1086 Details of bonding type rmsd link_NAG-ASN : bond 0.00346 ( 51) link_NAG-ASN : angle 1.56332 ( 153) link_ALPHA1-6 : bond 0.03132 ( 9) link_ALPHA1-6 : angle 2.83289 ( 27) link_BETA1-2 : bond 0.01670 ( 3) link_BETA1-2 : angle 3.26331 ( 9) link_BETA1-4 : bond 0.01046 ( 54) link_BETA1-4 : angle 1.86598 ( 162) link_ALPHA1-2 : bond 0.04431 ( 3) link_ALPHA1-2 : angle 9.64790 ( 9) link_ALPHA1-3 : bond 0.03656 ( 9) link_ALPHA1-3 : angle 6.17637 ( 27) hydrogen bonds : bond 0.19948 ( 1056) hydrogen bonds : angle 7.48123 ( 3027) link_BETA1-6 : bond 0.00595 ( 3) link_BETA1-6 : angle 1.77843 ( 9) metal coordination : bond 0.10399 ( 12) SS BOND : bond 0.00197 ( 51) SS BOND : angle 0.54525 ( 102) covalent geometry : bond 0.00280 (29448) covalent geometry : angle 0.53550 (40146) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 278 time to evaluate : 3.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 720 MET cc_start: 0.7824 (mtm) cc_final: 0.7373 (ttm) REVERT: A 814 LYS cc_start: 0.8233 (tptt) cc_final: 0.7770 (mppt) REVERT: A 911 MET cc_start: 0.8244 (mtm) cc_final: 0.7944 (mtt) REVERT: A 919 ARG cc_start: 0.7355 (mmm160) cc_final: 0.7109 (mtp180) REVERT: A 986 GLN cc_start: 0.8072 (tt0) cc_final: 0.7700 (mm-40) REVERT: A 994 ILE cc_start: 0.8596 (mp) cc_final: 0.8072 (tp) REVERT: A 1019 LYS cc_start: 0.8542 (mttt) cc_final: 0.8260 (mtpm) REVERT: B 287 MET cc_start: 0.9189 (mtm) cc_final: 0.8787 (mtm) REVERT: B 384 ILE cc_start: 0.8457 (mt) cc_final: 0.8250 (mm) REVERT: B 423 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8653 (tm) REVERT: B 720 MET cc_start: 0.7708 (mtm) cc_final: 0.7233 (ttm) REVERT: B 905 GLN cc_start: 0.7914 (mt0) cc_final: 0.7712 (mt0) REVERT: B 909 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7936 (mt-10) REVERT: B 911 MET cc_start: 0.8326 (mtm) cc_final: 0.8009 (mtt) REVERT: C 397 MET cc_start: 0.8824 (ttp) cc_final: 0.8370 (ttp) REVERT: C 685 MET cc_start: 0.7319 (mtm) cc_final: 0.7028 (mtm) REVERT: C 713 MET cc_start: 0.8425 (mtp) cc_final: 0.8196 (mtp) REVERT: C 720 MET cc_start: 0.7779 (mtm) cc_final: 0.7430 (ttm) REVERT: C 911 MET cc_start: 0.8281 (mtm) cc_final: 0.7975 (mtt) REVERT: C 1019 LYS cc_start: 0.8500 (mttt) cc_final: 0.8254 (mtpm) REVERT: C 1082 GLN cc_start: 0.8641 (pp30) cc_final: 0.8297 (mp10) outliers start: 24 outliers final: 5 residues processed: 293 average time/residue: 1.4019 time to fit residues: 485.0947 Evaluate side-chains 222 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 216 time to evaluate : 2.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 TYR Chi-restraints excluded: chain B residue 332 TYR Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 447 TYR Chi-restraints excluded: chain C residue 332 TYR Chi-restraints excluded: chain C residue 447 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 298 optimal weight: 1.9990 chunk 268 optimal weight: 0.8980 chunk 148 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 180 optimal weight: 0.5980 chunk 143 optimal weight: 0.7980 chunk 277 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 206 optimal weight: 6.9990 chunk 321 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN A 297 GLN A 646 ASN A 834 HIS A 854 GLN A1098 GLN A1174 GLN B 144 ASN B 297 GLN B 646 ASN B 834 HIS B 854 GLN B1098 GLN B1174 GLN B1185 GLN C 297 GLN C 646 ASN C 834 HIS C 854 GLN C 986 GLN C1098 GLN C1174 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.156145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.126554 restraints weight = 23438.962| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.27 r_work: 0.3330 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29643 Z= 0.136 Angle : 0.614 6.767 40644 Z= 0.312 Chirality : 0.044 0.201 4908 Planarity : 0.004 0.059 5004 Dihedral : 10.068 166.344 6609 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.54 % Allowed : 5.64 % Favored : 92.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.14), residues: 3531 helix: 1.73 (0.20), residues: 816 sheet: 0.78 (0.17), residues: 795 loop : -0.47 (0.13), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 319 HIS 0.005 0.001 HIS B1136 PHE 0.015 0.002 PHE A 154 TYR 0.014 0.002 TYR A 360 ARG 0.005 0.001 ARG B 410 Details of bonding type rmsd link_NAG-ASN : bond 0.00372 ( 51) link_NAG-ASN : angle 1.76959 ( 153) link_ALPHA1-6 : bond 0.00348 ( 9) link_ALPHA1-6 : angle 1.62171 ( 27) link_BETA1-2 : bond 0.02380 ( 3) link_BETA1-2 : angle 3.82399 ( 9) link_BETA1-4 : bond 0.00459 ( 54) link_BETA1-4 : angle 2.09722 ( 162) link_ALPHA1-2 : bond 0.00694 ( 3) link_ALPHA1-2 : angle 1.94544 ( 9) link_ALPHA1-3 : bond 0.00526 ( 9) link_ALPHA1-3 : angle 1.61358 ( 27) hydrogen bonds : bond 0.06469 ( 1056) hydrogen bonds : angle 5.58738 ( 3027) link_BETA1-6 : bond 0.00271 ( 3) link_BETA1-6 : angle 2.09048 ( 9) metal coordination : bond 0.01275 ( 12) SS BOND : bond 0.00508 ( 51) SS BOND : angle 1.23718 ( 102) covalent geometry : bond 0.00264 (29448) covalent geometry : angle 0.58313 (40146) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 247 time to evaluate : 3.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.6605 (mt-10) REVERT: A 720 MET cc_start: 0.7622 (mtm) cc_final: 0.7098 (ttm) REVERT: A 814 LYS cc_start: 0.8408 (tptt) cc_final: 0.8152 (mppt) REVERT: A 911 MET cc_start: 0.8308 (mtm) cc_final: 0.8065 (mtt) REVERT: A 986 GLN cc_start: 0.8301 (tt0) cc_final: 0.7878 (mm-40) REVERT: A 994 ILE cc_start: 0.8644 (mp) cc_final: 0.8155 (tp) REVERT: B 423 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8489 (tm) REVERT: B 447 TYR cc_start: 0.8617 (OUTLIER) cc_final: 0.8297 (m-80) REVERT: B 680 HIS cc_start: 0.7754 (t-170) cc_final: 0.7532 (t-170) REVERT: B 720 MET cc_start: 0.7591 (mtm) cc_final: 0.7284 (mtp) REVERT: B 814 LYS cc_start: 0.8473 (tptt) cc_final: 0.8167 (mppt) REVERT: B 863 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8102 (mp) REVERT: B 911 MET cc_start: 0.8378 (mtm) cc_final: 0.8108 (mtt) REVERT: C 145 ARG cc_start: 0.6820 (mtp85) cc_final: 0.6591 (mmt-90) REVERT: C 148 LYS cc_start: 0.7315 (OUTLIER) cc_final: 0.7085 (mptt) REVERT: C 397 MET cc_start: 0.8966 (ttp) cc_final: 0.8487 (ttp) REVERT: C 685 MET cc_start: 0.7479 (mtm) cc_final: 0.7230 (mtm) REVERT: C 720 MET cc_start: 0.7607 (mtm) cc_final: 0.7214 (ttm) REVERT: C 814 LYS cc_start: 0.8430 (tptt) cc_final: 0.8133 (mppt) REVERT: C 863 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8082 (mp) REVERT: C 911 MET cc_start: 0.8350 (mtm) cc_final: 0.8062 (mtt) REVERT: C 941 MET cc_start: 0.8637 (tpp) cc_final: 0.8402 (tpp) REVERT: C 1019 LYS cc_start: 0.8545 (mttt) cc_final: 0.8312 (mtpm) outliers start: 43 outliers final: 16 residues processed: 270 average time/residue: 1.3916 time to fit residues: 447.0025 Evaluate side-chains 250 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 228 time to evaluate : 3.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 447 TYR Chi-restraints excluded: chain A residue 953 ILE Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 447 TYR Chi-restraints excluded: chain B residue 863 LEU Chi-restraints excluded: chain B residue 953 ILE Chi-restraints excluded: chain B residue 994 ILE Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 447 TYR Chi-restraints excluded: chain C residue 863 LEU Chi-restraints excluded: chain C residue 953 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 220 optimal weight: 0.9980 chunk 236 optimal weight: 6.9990 chunk 280 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 167 optimal weight: 6.9990 chunk 192 optimal weight: 0.0370 chunk 45 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 180 optimal weight: 20.0000 chunk 15 optimal weight: 0.9980 chunk 225 optimal weight: 0.9980 overall best weight: 0.7658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN B 144 ASN C 986 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.155555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.125019 restraints weight = 23331.191| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.37 r_work: 0.3304 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29643 Z= 0.131 Angle : 0.601 6.562 40644 Z= 0.305 Chirality : 0.044 0.197 4908 Planarity : 0.004 0.052 5004 Dihedral : 7.842 153.096 6605 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.39 % Allowed : 6.54 % Favored : 92.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.14), residues: 3531 helix: 1.72 (0.19), residues: 819 sheet: 0.61 (0.18), residues: 765 loop : -0.48 (0.13), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 319 HIS 0.004 0.001 HIS C 617 PHE 0.012 0.001 PHE C 248 TYR 0.012 0.001 TYR A 360 ARG 0.005 0.001 ARG A 145 Details of bonding type rmsd link_NAG-ASN : bond 0.00346 ( 51) link_NAG-ASN : angle 1.82251 ( 153) link_ALPHA1-6 : bond 0.00488 ( 9) link_ALPHA1-6 : angle 1.82339 ( 27) link_BETA1-2 : bond 0.01823 ( 3) link_BETA1-2 : angle 3.78461 ( 9) link_BETA1-4 : bond 0.00481 ( 54) link_BETA1-4 : angle 1.94907 ( 162) link_ALPHA1-2 : bond 0.00112 ( 3) link_ALPHA1-2 : angle 1.67423 ( 9) link_ALPHA1-3 : bond 0.00870 ( 9) link_ALPHA1-3 : angle 1.63641 ( 27) hydrogen bonds : bond 0.06162 ( 1056) hydrogen bonds : angle 5.39417 ( 3027) link_BETA1-6 : bond 0.00279 ( 3) link_BETA1-6 : angle 1.84517 ( 9) metal coordination : bond 0.00768 ( 12) SS BOND : bond 0.00648 ( 51) SS BOND : angle 1.21995 ( 102) covalent geometry : bond 0.00254 (29448) covalent geometry : angle 0.57042 (40146) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 246 time to evaluate : 2.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 LYS cc_start: 0.7374 (mmmm) cc_final: 0.7050 (mtmt) REVERT: A 720 MET cc_start: 0.7614 (mtm) cc_final: 0.7279 (mtm) REVERT: A 814 LYS cc_start: 0.8402 (tptt) cc_final: 0.8036 (mppt) REVERT: A 911 MET cc_start: 0.8307 (mtm) cc_final: 0.8084 (mtt) REVERT: A 912 GLN cc_start: 0.7287 (mm-40) cc_final: 0.7080 (mm-40) REVERT: A 986 GLN cc_start: 0.8352 (tt0) cc_final: 0.7897 (mm-40) REVERT: A 994 ILE cc_start: 0.8641 (mp) cc_final: 0.8133 (tp) REVERT: B 447 TYR cc_start: 0.8621 (OUTLIER) cc_final: 0.8230 (m-80) REVERT: B 720 MET cc_start: 0.7584 (mtm) cc_final: 0.7255 (mtm) REVERT: B 814 LYS cc_start: 0.8519 (tptt) cc_final: 0.8135 (mppt) REVERT: B 863 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8162 (mp) REVERT: B 911 MET cc_start: 0.8310 (mtm) cc_final: 0.8073 (mtt) REVERT: B 912 GLN cc_start: 0.7162 (mp10) cc_final: 0.6819 (mp-120) REVERT: B 985 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.8103 (tm-30) REVERT: C 148 LYS cc_start: 0.7374 (OUTLIER) cc_final: 0.7116 (mptt) REVERT: C 397 MET cc_start: 0.8999 (ttp) cc_final: 0.8620 (ttp) REVERT: C 685 MET cc_start: 0.7473 (mtm) cc_final: 0.7230 (mtm) REVERT: C 814 LYS cc_start: 0.8407 (tptt) cc_final: 0.8090 (mppt) REVERT: C 863 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8099 (mp) REVERT: C 905 GLN cc_start: 0.8140 (mt0) cc_final: 0.7927 (pt0) REVERT: C 911 MET cc_start: 0.8397 (mtm) cc_final: 0.8184 (mtt) REVERT: C 941 MET cc_start: 0.8687 (tpp) cc_final: 0.8449 (tpp) REVERT: C 1019 LYS cc_start: 0.8578 (mttt) cc_final: 0.8303 (mtpm) outliers start: 39 outliers final: 13 residues processed: 268 average time/residue: 1.3412 time to fit residues: 428.0002 Evaluate side-chains 247 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 229 time to evaluate : 3.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 447 TYR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 447 TYR Chi-restraints excluded: chain B residue 863 LEU Chi-restraints excluded: chain B residue 985 GLN Chi-restraints excluded: chain B residue 994 ILE Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 447 TYR Chi-restraints excluded: chain C residue 863 LEU Chi-restraints excluded: chain C residue 953 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 114 optimal weight: 1.9990 chunk 337 optimal weight: 1.9990 chunk 89 optimal weight: 0.0980 chunk 336 optimal weight: 1.9990 chunk 290 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 309 optimal weight: 6.9990 chunk 349 optimal weight: 0.9990 chunk 239 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN A1185 GLN B 144 ASN C 144 ASN C 986 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.154429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.124006 restraints weight = 23163.881| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.35 r_work: 0.3285 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29643 Z= 0.158 Angle : 0.655 7.297 40644 Z= 0.334 Chirality : 0.045 0.206 4908 Planarity : 0.004 0.074 5004 Dihedral : 7.424 140.512 6603 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.39 % Allowed : 6.93 % Favored : 91.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.14), residues: 3531 helix: 1.66 (0.19), residues: 816 sheet: 0.57 (0.18), residues: 732 loop : -0.49 (0.13), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 319 HIS 0.004 0.001 HIS B 189 PHE 0.013 0.002 PHE B 154 TYR 0.015 0.002 TYR A 360 ARG 0.005 0.001 ARG A1072 Details of bonding type rmsd link_NAG-ASN : bond 0.00687 ( 51) link_NAG-ASN : angle 2.05705 ( 153) link_ALPHA1-6 : bond 0.00483 ( 9) link_ALPHA1-6 : angle 1.81676 ( 27) link_BETA1-2 : bond 0.01923 ( 3) link_BETA1-2 : angle 3.86753 ( 9) link_BETA1-4 : bond 0.00455 ( 54) link_BETA1-4 : angle 1.97871 ( 162) link_ALPHA1-2 : bond 0.00045 ( 3) link_ALPHA1-2 : angle 1.81419 ( 9) link_ALPHA1-3 : bond 0.00894 ( 9) link_ALPHA1-3 : angle 1.65102 ( 27) hydrogen bonds : bond 0.06693 ( 1056) hydrogen bonds : angle 5.52687 ( 3027) link_BETA1-6 : bond 0.00234 ( 3) link_BETA1-6 : angle 1.95282 ( 9) metal coordination : bond 0.01020 ( 12) SS BOND : bond 0.00907 ( 51) SS BOND : angle 1.47249 ( 102) covalent geometry : bond 0.00312 (29448) covalent geometry : angle 0.62286 (40146) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 235 time to evaluate : 2.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 LYS cc_start: 0.7391 (OUTLIER) cc_final: 0.7075 (mtmt) REVERT: A 604 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8136 (mp0) REVERT: A 720 MET cc_start: 0.7616 (mtm) cc_final: 0.7316 (mtm) REVERT: A 814 LYS cc_start: 0.8410 (tptt) cc_final: 0.8029 (mppt) REVERT: A 911 MET cc_start: 0.8346 (mtm) cc_final: 0.8141 (mtt) REVERT: A 986 GLN cc_start: 0.8349 (tt0) cc_final: 0.7909 (mm-40) REVERT: A 994 ILE cc_start: 0.8632 (mp) cc_final: 0.8120 (tp) REVERT: B 423 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8500 (tm) REVERT: B 447 TYR cc_start: 0.8635 (OUTLIER) cc_final: 0.8234 (m-80) REVERT: B 680 HIS cc_start: 0.7869 (t-170) cc_final: 0.7619 (t-170) REVERT: B 720 MET cc_start: 0.7569 (mtm) cc_final: 0.7277 (mtm) REVERT: B 814 LYS cc_start: 0.8509 (tptt) cc_final: 0.8140 (mppt) REVERT: B 863 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8099 (mp) REVERT: B 911 MET cc_start: 0.8235 (mtm) cc_final: 0.7992 (mtt) REVERT: C 148 LYS cc_start: 0.7394 (OUTLIER) cc_final: 0.7126 (mptt) REVERT: C 397 MET cc_start: 0.9006 (ttp) cc_final: 0.8696 (ttp) REVERT: C 685 MET cc_start: 0.7479 (mtm) cc_final: 0.7240 (mtm) REVERT: C 814 LYS cc_start: 0.8466 (tptt) cc_final: 0.8154 (mppt) REVERT: C 863 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8080 (mp) REVERT: C 911 MET cc_start: 0.8419 (mtm) cc_final: 0.8204 (mtt) REVERT: C 941 MET cc_start: 0.8723 (tpp) cc_final: 0.8430 (tpp) REVERT: C 1019 LYS cc_start: 0.8624 (mttt) cc_final: 0.8336 (mtpm) outliers start: 39 outliers final: 16 residues processed: 260 average time/residue: 1.4136 time to fit residues: 437.7126 Evaluate side-chains 245 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 223 time to evaluate : 3.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 447 TYR Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 953 ILE Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 447 TYR Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 863 LEU Chi-restraints excluded: chain B residue 994 ILE Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 447 TYR Chi-restraints excluded: chain C residue 863 LEU Chi-restraints excluded: chain C residue 953 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 257 optimal weight: 5.9990 chunk 199 optimal weight: 5.9990 chunk 238 optimal weight: 0.9990 chunk 340 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 274 optimal weight: 0.7980 chunk 267 optimal weight: 0.6980 chunk 193 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN A 175 HIS B 144 ASN C 144 ASN C 617 HIS C 986 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.153890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.123365 restraints weight = 22862.331| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.36 r_work: 0.3272 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 2.159 29643 Z= 0.450 Angle : 0.675 8.362 40644 Z= 0.345 Chirality : 0.046 0.237 4908 Planarity : 0.004 0.077 5004 Dihedral : 7.320 127.667 6603 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.36 % Allowed : 7.11 % Favored : 91.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.14), residues: 3531 helix: 1.63 (0.19), residues: 813 sheet: 0.51 (0.18), residues: 723 loop : -0.48 (0.13), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 319 HIS 0.004 0.001 HIS B 189 PHE 0.013 0.002 PHE C 241 TYR 0.014 0.002 TYR A 360 ARG 0.005 0.001 ARG A1072 Details of bonding type rmsd link_NAG-ASN : bond 0.00467 ( 51) link_NAG-ASN : angle 2.10565 ( 153) link_ALPHA1-6 : bond 0.00537 ( 9) link_ALPHA1-6 : angle 1.74188 ( 27) link_BETA1-2 : bond 0.01985 ( 3) link_BETA1-2 : angle 3.95202 ( 9) link_BETA1-4 : bond 0.00462 ( 54) link_BETA1-4 : angle 1.95824 ( 162) link_ALPHA1-2 : bond 0.00058 ( 3) link_ALPHA1-2 : angle 1.81246 ( 9) link_ALPHA1-3 : bond 0.00867 ( 9) link_ALPHA1-3 : angle 1.68249 ( 27) hydrogen bonds : bond 0.06833 ( 1056) hydrogen bonds : angle 5.58683 ( 3027) link_BETA1-6 : bond 0.00197 ( 3) link_BETA1-6 : angle 1.96590 ( 9) metal coordination : bond 0.62337 ( 12) SS BOND : bond 0.00916 ( 51) SS BOND : angle 1.66247 ( 102) covalent geometry : bond 0.00333 (29448) covalent geometry : angle 0.64211 (40146) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 236 time to evaluate : 3.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 LYS cc_start: 0.7439 (OUTLIER) cc_final: 0.7128 (mtmt) REVERT: A 604 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8161 (mp0) REVERT: A 720 MET cc_start: 0.7654 (mtm) cc_final: 0.7376 (mtm) REVERT: A 814 LYS cc_start: 0.8395 (tptt) cc_final: 0.8086 (mppt) REVERT: A 985 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.8121 (tm-30) REVERT: A 986 GLN cc_start: 0.8380 (tt0) cc_final: 0.7950 (mm-40) REVERT: A 994 ILE cc_start: 0.8668 (mp) cc_final: 0.8169 (tp) REVERT: B 216 ASP cc_start: 0.7267 (p0) cc_final: 0.6987 (p0) REVERT: B 423 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8524 (tm) REVERT: B 447 TYR cc_start: 0.8623 (OUTLIER) cc_final: 0.8266 (m-80) REVERT: B 680 HIS cc_start: 0.7914 (t-170) cc_final: 0.7641 (t-170) REVERT: B 720 MET cc_start: 0.7583 (mtm) cc_final: 0.7305 (mtm) REVERT: B 814 LYS cc_start: 0.8569 (tptt) cc_final: 0.8195 (mppt) REVERT: B 863 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8032 (mp) REVERT: C 148 LYS cc_start: 0.7422 (OUTLIER) cc_final: 0.7067 (mtmt) REVERT: C 397 MET cc_start: 0.8993 (ttp) cc_final: 0.8668 (ttp) REVERT: C 685 MET cc_start: 0.7493 (mtm) cc_final: 0.7266 (mtm) REVERT: C 726 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.8038 (mt0) REVERT: C 814 LYS cc_start: 0.8495 (tptt) cc_final: 0.8191 (mppt) REVERT: C 863 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8073 (mp) REVERT: C 911 MET cc_start: 0.8418 (mtm) cc_final: 0.8215 (mtt) REVERT: C 941 MET cc_start: 0.8745 (tpp) cc_final: 0.8452 (tpp) REVERT: C 985 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.7796 (tm-30) REVERT: C 1019 LYS cc_start: 0.8639 (mttt) cc_final: 0.8355 (mtpm) outliers start: 38 outliers final: 15 residues processed: 257 average time/residue: 1.4225 time to fit residues: 434.2618 Evaluate side-chains 247 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 223 time to evaluate : 3.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 447 TYR Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 953 ILE Chi-restraints excluded: chain A residue 985 GLN Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 447 TYR Chi-restraints excluded: chain B residue 676 VAL Chi-restraints excluded: chain B residue 863 LEU Chi-restraints excluded: chain B residue 994 ILE Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 447 TYR Chi-restraints excluded: chain C residue 726 GLN Chi-restraints excluded: chain C residue 863 LEU Chi-restraints excluded: chain C residue 953 ILE Chi-restraints excluded: chain C residue 985 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 207 optimal weight: 3.9990 chunk 318 optimal weight: 10.0000 chunk 118 optimal weight: 5.9990 chunk 348 optimal weight: 6.9990 chunk 166 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 213 optimal weight: 8.9990 chunk 257 optimal weight: 4.9990 chunk 297 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN A 175 HIS B 144 ASN B 986 GLN C 144 ASN C 986 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.150389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.120688 restraints weight = 22637.423| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.23 r_work: 0.3249 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.084 29643 Z= 0.357 Angle : 0.983 12.426 40644 Z= 0.507 Chirality : 0.059 0.405 4908 Planarity : 0.007 0.146 5004 Dihedral : 8.656 126.903 6603 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.07 % Allowed : 6.54 % Favored : 91.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.13), residues: 3531 helix: 0.96 (0.19), residues: 813 sheet: 0.46 (0.18), residues: 651 loop : -0.71 (0.12), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 319 HIS 0.009 0.003 HIS C 189 PHE 0.026 0.003 PHE C 975 TYR 0.028 0.004 TYR B 360 ARG 0.014 0.002 ARG A1072 Details of bonding type rmsd link_NAG-ASN : bond 0.00954 ( 51) link_NAG-ASN : angle 2.79386 ( 153) link_ALPHA1-6 : bond 0.00524 ( 9) link_ALPHA1-6 : angle 2.07618 ( 27) link_BETA1-2 : bond 0.02523 ( 3) link_BETA1-2 : angle 5.08957 ( 9) link_BETA1-4 : bond 0.00647 ( 54) link_BETA1-4 : angle 2.63899 ( 162) link_ALPHA1-2 : bond 0.00481 ( 3) link_ALPHA1-2 : angle 2.57705 ( 9) link_ALPHA1-3 : bond 0.00695 ( 9) link_ALPHA1-3 : angle 2.00848 ( 27) hydrogen bonds : bond 0.09284 ( 1056) hydrogen bonds : angle 6.15446 ( 3027) link_BETA1-6 : bond 0.00121 ( 3) link_BETA1-6 : angle 2.62683 ( 9) metal coordination : bond 0.03204 ( 12) SS BOND : bond 0.01812 ( 51) SS BOND : angle 2.42840 ( 102) covalent geometry : bond 0.00763 (29448) covalent geometry : angle 0.94425 (40146) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 228 time to evaluate : 2.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 604 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8122 (mp0) REVERT: A 720 MET cc_start: 0.7798 (mtm) cc_final: 0.7577 (mtm) REVERT: A 814 LYS cc_start: 0.8473 (tptt) cc_final: 0.8168 (mppt) REVERT: A 985 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.8213 (tm-30) REVERT: A 986 GLN cc_start: 0.8359 (tt0) cc_final: 0.7998 (mm-40) REVERT: A 994 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8232 (tp) REVERT: B 216 ASP cc_start: 0.7297 (p0) cc_final: 0.7014 (p0) REVERT: B 423 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8633 (tm) REVERT: B 447 TYR cc_start: 0.8655 (OUTLIER) cc_final: 0.8176 (m-80) REVERT: B 720 MET cc_start: 0.7667 (mtm) cc_final: 0.7435 (mtm) REVERT: B 863 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.7922 (mp) REVERT: B 882 ARG cc_start: 0.7135 (OUTLIER) cc_final: 0.6657 (ptt-90) REVERT: C 604 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8218 (mp0) REVERT: C 814 LYS cc_start: 0.8549 (tptt) cc_final: 0.8221 (mppt) REVERT: C 863 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8084 (mp) REVERT: C 941 MET cc_start: 0.8790 (tpp) cc_final: 0.8403 (tpp) REVERT: C 1019 LYS cc_start: 0.8780 (mttt) cc_final: 0.8542 (mtpm) outliers start: 58 outliers final: 27 residues processed: 266 average time/residue: 1.3266 time to fit residues: 422.1140 Evaluate side-chains 255 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 220 time to evaluate : 3.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 985 GLN Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1058 PRO Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 332 TYR Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 447 TYR Chi-restraints excluded: chain B residue 676 VAL Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 863 LEU Chi-restraints excluded: chain B residue 882 ARG Chi-restraints excluded: chain B residue 953 ILE Chi-restraints excluded: chain B residue 985 GLN Chi-restraints excluded: chain B residue 994 ILE Chi-restraints excluded: chain B residue 1003 LEU Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 604 GLU Chi-restraints excluded: chain C residue 676 VAL Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 863 LEU Chi-restraints excluded: chain C residue 985 GLN Chi-restraints excluded: chain C residue 994 ILE Chi-restraints excluded: chain C residue 1058 PRO Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 132 optimal weight: 5.9990 chunk 105 optimal weight: 0.8980 chunk 261 optimal weight: 0.8980 chunk 117 optimal weight: 5.9990 chunk 319 optimal weight: 0.4980 chunk 334 optimal weight: 1.9990 chunk 228 optimal weight: 0.5980 chunk 54 optimal weight: 0.6980 chunk 309 optimal weight: 1.9990 chunk 238 optimal weight: 0.5980 chunk 163 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN A 175 HIS B 144 ASN B 175 HIS C 144 ASN C 986 GLN C1140 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.154934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.124807 restraints weight = 22890.902| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.36 r_work: 0.3302 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29643 Z= 0.133 Angle : 0.638 9.375 40644 Z= 0.322 Chirality : 0.044 0.240 4908 Planarity : 0.004 0.064 5004 Dihedral : 7.564 110.639 6599 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.14 % Allowed : 7.61 % Favored : 91.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.14), residues: 3531 helix: 1.58 (0.19), residues: 813 sheet: 0.53 (0.18), residues: 753 loop : -0.59 (0.13), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 319 HIS 0.005 0.001 HIS B 680 PHE 0.014 0.001 PHE C 119 TYR 0.015 0.001 TYR A 447 ARG 0.005 0.000 ARG C 230 Details of bonding type rmsd link_NAG-ASN : bond 0.00452 ( 51) link_NAG-ASN : angle 2.05588 ( 153) link_ALPHA1-6 : bond 0.00572 ( 9) link_ALPHA1-6 : angle 1.67789 ( 27) link_BETA1-2 : bond 0.01989 ( 3) link_BETA1-2 : angle 4.11838 ( 9) link_BETA1-4 : bond 0.00480 ( 54) link_BETA1-4 : angle 1.90065 ( 162) link_ALPHA1-2 : bond 0.00140 ( 3) link_ALPHA1-2 : angle 1.71102 ( 9) link_ALPHA1-3 : bond 0.00921 ( 9) link_ALPHA1-3 : angle 1.57619 ( 27) hydrogen bonds : bond 0.06015 ( 1056) hydrogen bonds : angle 5.46554 ( 3027) link_BETA1-6 : bond 0.00172 ( 3) link_BETA1-6 : angle 1.71321 ( 9) metal coordination : bond 0.01073 ( 12) SS BOND : bond 0.00596 ( 51) SS BOND : angle 1.61010 ( 102) covalent geometry : bond 0.00261 (29448) covalent geometry : angle 0.60492 (40146) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 222 time to evaluate : 3.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 LYS cc_start: 0.7409 (mmmm) cc_final: 0.7081 (mtmt) REVERT: A 604 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8145 (mp0) REVERT: A 720 MET cc_start: 0.7618 (mtm) cc_final: 0.7348 (mtm) REVERT: A 814 LYS cc_start: 0.8394 (tptt) cc_final: 0.8078 (mppt) REVERT: A 986 GLN cc_start: 0.8357 (tt0) cc_final: 0.7945 (mm-40) REVERT: A 994 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8068 (tp) REVERT: B 26 MET cc_start: 0.7627 (mmm) cc_final: 0.7351 (mmp) REVERT: B 216 ASP cc_start: 0.7279 (p0) cc_final: 0.6974 (p0) REVERT: B 423 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8491 (tm) REVERT: B 720 MET cc_start: 0.7614 (mtm) cc_final: 0.7354 (mtm) REVERT: B 814 LYS cc_start: 0.8499 (tptt) cc_final: 0.8133 (mppt) REVERT: B 863 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.7869 (mp) REVERT: B 882 ARG cc_start: 0.7106 (OUTLIER) cc_final: 0.6682 (ptt-90) REVERT: C 814 LYS cc_start: 0.8429 (tptt) cc_final: 0.8127 (mppt) REVERT: C 863 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.7916 (mp) REVERT: C 911 MET cc_start: 0.8395 (mtm) cc_final: 0.8103 (mtt) REVERT: C 941 MET cc_start: 0.8682 (tpp) cc_final: 0.8410 (tpp) REVERT: C 985 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.7796 (tm-30) outliers start: 32 outliers final: 11 residues processed: 245 average time/residue: 1.3644 time to fit residues: 398.4800 Evaluate side-chains 230 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 213 time to evaluate : 2.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 447 TYR Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 447 TYR Chi-restraints excluded: chain B residue 863 LEU Chi-restraints excluded: chain B residue 882 ARG Chi-restraints excluded: chain B residue 994 ILE Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 863 LEU Chi-restraints excluded: chain C residue 985 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 285 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 352 optimal weight: 0.9990 chunk 150 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 246 optimal weight: 0.5980 chunk 216 optimal weight: 6.9990 chunk 222 optimal weight: 0.9980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN B 144 ASN B 617 HIS B 986 GLN C 144 ASN C 986 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.153018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.123207 restraints weight = 22856.735| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.26 r_work: 0.3275 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 2.198 29643 Z= 0.464 Angle : 0.731 14.793 40644 Z= 0.373 Chirality : 0.047 0.278 4908 Planarity : 0.005 0.095 5004 Dihedral : 7.527 100.424 6599 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.96 % Allowed : 7.90 % Favored : 91.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.14), residues: 3531 helix: 1.51 (0.19), residues: 813 sheet: 0.51 (0.18), residues: 711 loop : -0.56 (0.13), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 319 HIS 0.005 0.001 HIS B 189 PHE 0.014 0.002 PHE A 154 TYR 0.017 0.002 TYR A 447 ARG 0.006 0.001 ARG A1072 Details of bonding type rmsd link_NAG-ASN : bond 0.00446 ( 51) link_NAG-ASN : angle 2.31256 ( 153) link_ALPHA1-6 : bond 0.00589 ( 9) link_ALPHA1-6 : angle 1.76907 ( 27) link_BETA1-2 : bond 0.02012 ( 3) link_BETA1-2 : angle 4.08393 ( 9) link_BETA1-4 : bond 0.00487 ( 54) link_BETA1-4 : angle 2.03992 ( 162) link_ALPHA1-2 : bond 0.00047 ( 3) link_ALPHA1-2 : angle 1.84487 ( 9) link_ALPHA1-3 : bond 0.00808 ( 9) link_ALPHA1-3 : angle 1.68612 ( 27) hydrogen bonds : bond 0.07113 ( 1056) hydrogen bonds : angle 5.68140 ( 3027) link_BETA1-6 : bond 0.00131 ( 3) link_BETA1-6 : angle 2.03369 ( 9) metal coordination : bond 0.63475 ( 12) SS BOND : bond 0.01115 ( 51) SS BOND : angle 2.37865 ( 102) covalent geometry : bond 0.00375 (29448) covalent geometry : angle 0.69280 (40146) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 216 time to evaluate : 3.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 LYS cc_start: 0.7410 (mmmm) cc_final: 0.7154 (mtmt) REVERT: A 604 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8146 (mp0) REVERT: A 720 MET cc_start: 0.7675 (mtm) cc_final: 0.7426 (mtm) REVERT: A 814 LYS cc_start: 0.8427 (tptt) cc_final: 0.8131 (mppt) REVERT: A 985 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.8123 (tm-30) REVERT: A 986 GLN cc_start: 0.8346 (tt0) cc_final: 0.7951 (mm-40) REVERT: A 994 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.8161 (tp) REVERT: B 26 MET cc_start: 0.7637 (mmm) cc_final: 0.7403 (mmp) REVERT: B 216 ASP cc_start: 0.7288 (p0) cc_final: 0.7009 (p0) REVERT: B 423 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8518 (tm) REVERT: B 447 TYR cc_start: 0.8590 (OUTLIER) cc_final: 0.8218 (m-80) REVERT: B 720 MET cc_start: 0.7664 (mtm) cc_final: 0.7407 (mtm) REVERT: B 814 LYS cc_start: 0.8535 (tptt) cc_final: 0.8188 (mppt) REVERT: B 863 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.7906 (mp) REVERT: B 882 ARG cc_start: 0.7118 (OUTLIER) cc_final: 0.6689 (ptt-90) REVERT: C 814 LYS cc_start: 0.8506 (tptt) cc_final: 0.8201 (mppt) REVERT: C 863 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.7912 (mp) REVERT: C 911 MET cc_start: 0.8404 (mtm) cc_final: 0.8135 (mtt) REVERT: C 941 MET cc_start: 0.8763 (tpp) cc_final: 0.8481 (tpp) REVERT: C 985 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.7842 (tm-30) outliers start: 27 outliers final: 14 residues processed: 236 average time/residue: 1.3933 time to fit residues: 391.5928 Evaluate side-chains 231 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 209 time to evaluate : 3.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 985 GLN Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 447 TYR Chi-restraints excluded: chain B residue 863 LEU Chi-restraints excluded: chain B residue 882 ARG Chi-restraints excluded: chain B residue 953 ILE Chi-restraints excluded: chain B residue 985 GLN Chi-restraints excluded: chain B residue 994 ILE Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 676 VAL Chi-restraints excluded: chain C residue 863 LEU Chi-restraints excluded: chain C residue 985 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 147 optimal weight: 2.9990 chunk 233 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 232 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 188 optimal weight: 0.8980 chunk 195 optimal weight: 0.9990 chunk 306 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 179 optimal weight: 10.0000 chunk 22 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN B 144 ASN B 617 HIS B 986 GLN C 144 ASN C 986 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.154639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.123990 restraints weight = 22671.283| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.38 r_work: 0.3292 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 2.056 29643 Z= 0.423 Angle : 0.669 15.665 40644 Z= 0.338 Chirality : 0.045 0.273 4908 Planarity : 0.004 0.059 5004 Dihedral : 7.146 83.652 6599 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.04 % Allowed : 8.07 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.29 (0.14), residues: 3531 helix: 1.67 (0.19), residues: 813 sheet: 0.48 (0.18), residues: 753 loop : -0.55 (0.13), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 319 HIS 0.004 0.001 HIS C1144 PHE 0.013 0.002 PHE A 241 TYR 0.016 0.001 TYR A 447 ARG 0.004 0.000 ARG C 230 Details of bonding type rmsd link_NAG-ASN : bond 0.00421 ( 51) link_NAG-ASN : angle 2.08665 ( 153) link_ALPHA1-6 : bond 0.00627 ( 9) link_ALPHA1-6 : angle 1.68685 ( 27) link_BETA1-2 : bond 0.01925 ( 3) link_BETA1-2 : angle 3.81880 ( 9) link_BETA1-4 : bond 0.00465 ( 54) link_BETA1-4 : angle 1.86969 ( 162) link_ALPHA1-2 : bond 0.00098 ( 3) link_ALPHA1-2 : angle 1.68876 ( 9) link_ALPHA1-3 : bond 0.00860 ( 9) link_ALPHA1-3 : angle 1.60649 ( 27) hydrogen bonds : bond 0.06243 ( 1056) hydrogen bonds : angle 5.47296 ( 3027) link_BETA1-6 : bond 0.00158 ( 3) link_BETA1-6 : angle 1.79723 ( 9) metal coordination : bond 0.59368 ( 12) SS BOND : bond 0.00806 ( 51) SS BOND : angle 2.61257 ( 102) covalent geometry : bond 0.00283 (29448) covalent geometry : angle 0.62955 (40146) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 218 time to evaluate : 3.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 LYS cc_start: 0.7414 (mmmm) cc_final: 0.7097 (mtmt) REVERT: A 604 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8146 (mp0) REVERT: A 720 MET cc_start: 0.7639 (mtm) cc_final: 0.7374 (mtm) REVERT: A 814 LYS cc_start: 0.8410 (tptt) cc_final: 0.8102 (mppt) REVERT: A 986 GLN cc_start: 0.8342 (tt0) cc_final: 0.7935 (mm-40) REVERT: A 994 ILE cc_start: 0.8626 (OUTLIER) cc_final: 0.8124 (tp) REVERT: B 216 ASP cc_start: 0.7315 (p0) cc_final: 0.7026 (p0) REVERT: B 423 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8518 (tm) REVERT: B 617 HIS cc_start: 0.7939 (m90) cc_final: 0.7725 (m-70) REVERT: B 720 MET cc_start: 0.7637 (mtm) cc_final: 0.7373 (mtm) REVERT: B 814 LYS cc_start: 0.8517 (tptt) cc_final: 0.8141 (mppt) REVERT: B 863 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.7922 (mp) REVERT: B 882 ARG cc_start: 0.7119 (OUTLIER) cc_final: 0.6698 (ptt-90) REVERT: C 814 LYS cc_start: 0.8485 (tptt) cc_final: 0.8166 (mppt) REVERT: C 863 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.7868 (mp) REVERT: C 911 MET cc_start: 0.8391 (mtm) cc_final: 0.8135 (mtt) REVERT: C 941 MET cc_start: 0.8729 (tpp) cc_final: 0.8447 (tpp) REVERT: C 985 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.7822 (tm-30) outliers start: 29 outliers final: 13 residues processed: 239 average time/residue: 1.3908 time to fit residues: 397.3004 Evaluate side-chains 233 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 214 time to evaluate : 3.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1208 SER Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 447 TYR Chi-restraints excluded: chain B residue 863 LEU Chi-restraints excluded: chain B residue 882 ARG Chi-restraints excluded: chain B residue 953 ILE Chi-restraints excluded: chain B residue 994 ILE Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 863 LEU Chi-restraints excluded: chain C residue 985 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 278 optimal weight: 0.2980 chunk 332 optimal weight: 1.9990 chunk 168 optimal weight: 0.8980 chunk 309 optimal weight: 3.9990 chunk 326 optimal weight: 4.9990 chunk 298 optimal weight: 0.7980 chunk 176 optimal weight: 4.9990 chunk 317 optimal weight: 3.9990 chunk 260 optimal weight: 0.9980 chunk 262 optimal weight: 4.9990 chunk 259 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN B 144 ASN B 986 GLN C 144 ASN C 233 ASN C 986 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.154441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.123894 restraints weight = 22802.858| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.42 r_work: 0.3287 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29643 Z= 0.152 Angle : 0.694 18.215 40644 Z= 0.351 Chirality : 0.045 0.277 4908 Planarity : 0.004 0.068 5004 Dihedral : 6.997 68.362 6599 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.79 % Allowed : 8.22 % Favored : 91.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.27 (0.14), residues: 3531 helix: 1.66 (0.19), residues: 813 sheet: 0.48 (0.18), residues: 723 loop : -0.55 (0.13), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 319 HIS 0.018 0.001 HIS B 617 PHE 0.013 0.002 PHE C 290 TYR 0.020 0.002 TYR B 332 ARG 0.004 0.000 ARG A1072 Details of bonding type rmsd link_NAG-ASN : bond 0.00447 ( 51) link_NAG-ASN : angle 2.10249 ( 153) link_ALPHA1-6 : bond 0.00659 ( 9) link_ALPHA1-6 : angle 1.69917 ( 27) link_BETA1-2 : bond 0.01905 ( 3) link_BETA1-2 : angle 3.72959 ( 9) link_BETA1-4 : bond 0.00470 ( 54) link_BETA1-4 : angle 1.86666 ( 162) link_ALPHA1-2 : bond 0.00112 ( 3) link_ALPHA1-2 : angle 1.70807 ( 9) link_ALPHA1-3 : bond 0.00819 ( 9) link_ALPHA1-3 : angle 1.63307 ( 27) hydrogen bonds : bond 0.06424 ( 1056) hydrogen bonds : angle 5.49840 ( 3027) link_BETA1-6 : bond 0.00167 ( 3) link_BETA1-6 : angle 1.83285 ( 9) metal coordination : bond 0.01244 ( 12) SS BOND : bond 0.00866 ( 51) SS BOND : angle 2.89297 ( 102) covalent geometry : bond 0.00303 (29448) covalent geometry : angle 0.65383 (40146) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 219 time to evaluate : 2.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 LYS cc_start: 0.7394 (mmmm) cc_final: 0.7080 (mtmt) REVERT: A 604 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8119 (mp0) REVERT: A 720 MET cc_start: 0.7643 (mtm) cc_final: 0.7377 (mtm) REVERT: A 814 LYS cc_start: 0.8375 (tptt) cc_final: 0.8058 (mppt) REVERT: A 986 GLN cc_start: 0.8322 (tt0) cc_final: 0.7908 (mm-40) REVERT: A 994 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8099 (tp) REVERT: B 216 ASP cc_start: 0.7288 (p0) cc_final: 0.7004 (p0) REVERT: B 423 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8502 (tm) REVERT: B 720 MET cc_start: 0.7652 (mtm) cc_final: 0.7389 (mtm) REVERT: B 814 LYS cc_start: 0.8501 (tptt) cc_final: 0.8114 (mppt) REVERT: B 863 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.7894 (mp) REVERT: B 882 ARG cc_start: 0.7100 (OUTLIER) cc_final: 0.6677 (ptt-90) REVERT: B 1209 MET cc_start: 0.8094 (tpt) cc_final: 0.7739 (tpt) REVERT: C 814 LYS cc_start: 0.8464 (tptt) cc_final: 0.8139 (mppt) REVERT: C 863 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.7894 (mp) REVERT: C 911 MET cc_start: 0.8382 (mtm) cc_final: 0.8040 (mtt) REVERT: C 941 MET cc_start: 0.8738 (tpp) cc_final: 0.8457 (tpp) REVERT: C 985 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.7793 (tm-30) outliers start: 22 outliers final: 15 residues processed: 235 average time/residue: 1.3537 time to fit residues: 377.7730 Evaluate side-chains 234 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 213 time to evaluate : 2.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1208 SER Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 447 TYR Chi-restraints excluded: chain B residue 863 LEU Chi-restraints excluded: chain B residue 882 ARG Chi-restraints excluded: chain B residue 953 ILE Chi-restraints excluded: chain B residue 985 GLN Chi-restraints excluded: chain B residue 994 ILE Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 863 LEU Chi-restraints excluded: chain C residue 985 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 140 optimal weight: 0.9980 chunk 178 optimal weight: 8.9990 chunk 28 optimal weight: 0.6980 chunk 240 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 252 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 340 optimal weight: 0.8980 chunk 292 optimal weight: 3.9990 chunk 210 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN B 144 ASN B 680 HIS B 986 GLN C 144 ASN C 986 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.155228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.124514 restraints weight = 22558.298| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.35 r_work: 0.3289 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 29643 Z= 0.140 Angle : 0.662 18.104 40644 Z= 0.335 Chirality : 0.044 0.266 4908 Planarity : 0.004 0.058 5004 Dihedral : 6.705 64.638 6599 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.86 % Allowed : 8.29 % Favored : 90.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.32 (0.14), residues: 3531 helix: 1.72 (0.19), residues: 813 sheet: 0.49 (0.18), residues: 753 loop : -0.53 (0.13), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 319 HIS 0.005 0.001 HIS B 680 PHE 0.013 0.001 PHE C 322 TYR 0.016 0.001 TYR C 447 ARG 0.004 0.000 ARG C 230 Details of bonding type rmsd link_NAG-ASN : bond 0.00376 ( 51) link_NAG-ASN : angle 1.97106 ( 153) link_ALPHA1-6 : bond 0.00695 ( 9) link_ALPHA1-6 : angle 1.64635 ( 27) link_BETA1-2 : bond 0.01854 ( 3) link_BETA1-2 : angle 3.50512 ( 9) link_BETA1-4 : bond 0.00455 ( 54) link_BETA1-4 : angle 1.77795 ( 162) link_ALPHA1-2 : bond 0.00152 ( 3) link_ALPHA1-2 : angle 1.67567 ( 9) link_ALPHA1-3 : bond 0.00823 ( 9) link_ALPHA1-3 : angle 1.59948 ( 27) hydrogen bonds : bond 0.06059 ( 1056) hydrogen bonds : angle 5.39673 ( 3027) link_BETA1-6 : bond 0.00190 ( 3) link_BETA1-6 : angle 1.71612 ( 9) metal coordination : bond 0.02937 ( 12) SS BOND : bond 0.00784 ( 51) SS BOND : angle 2.81825 ( 102) covalent geometry : bond 0.00275 (29448) covalent geometry : angle 0.62320 (40146) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 30154.75 seconds wall clock time: 521 minutes 49.44 seconds (31309.44 seconds total)