Starting phenix.real_space_refine on Mon Aug 25 15:48:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eh8_48048/08_2025/9eh8_48048.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eh8_48048/08_2025/9eh8_48048.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9eh8_48048/08_2025/9eh8_48048.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eh8_48048/08_2025/9eh8_48048.map" model { file = "/net/cci-nas-00/data/ceres_data/9eh8_48048/08_2025/9eh8_48048.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eh8_48048/08_2025/9eh8_48048.cif" } resolution = 2.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.060 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 150 5.16 5 C 17982 2.51 5 N 4533 2.21 5 O 6453 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29118 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 8823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1166, 8823 Classifications: {'peptide': 1166} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PCIS': 1, 'PTRANS': 59, 'TRANS': 1105} Chain breaks: 7 Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 304 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 10, 'ASP:plan': 4, 'GLU:plan': 18, 'PHE:plan': 1, 'ASN:plan1': 6} Unresolved non-hydrogen planarities: 158 Chain: "B" Number of atoms: 8823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1166, 8823 Classifications: {'peptide': 1166} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PCIS': 1, 'PTRANS': 59, 'TRANS': 1105} Chain breaks: 7 Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 304 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 10, 'ASP:plan': 4, 'GLU:plan': 18, 'PHE:plan': 1, 'ASN:plan1': 6} Unresolved non-hydrogen planarities: 158 Chain: "C" Number of atoms: 8823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1166, 8823 Classifications: {'peptide': 1166} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PCIS': 1, 'PTRANS': 59, 'TRANS': 1105} Chain breaks: 7 Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 304 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 10, 'ASP:plan': 4, 'GLU:plan': 18, 'PHE:plan': 1, 'ASN:plan1': 6} Unresolved non-hydrogen planarities: 158 Chain: "D" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 97 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 97 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "U" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 97 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "h" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 113 Unusual residues: {'EIC': 1, 'FOL': 1, 'NAG': 5} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'FOL:plan-6': 1, 'FOL:plan-7': 1, 'FOL:plan-8': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 113 Unusual residues: {'EIC': 1, 'FOL': 1, 'NAG': 5} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'FOL:plan-6': 1, 'FOL:plan-7': 1, 'FOL:plan-8': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 113 Unusual residues: {'EIC': 1, 'FOL': 1, 'NAG': 5} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'FOL:plan-6': 1, 'FOL:plan-7': 1, 'FOL:plan-8': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 271 Classifications: {'water': 271} Link IDs: {None: 270} Chain: "B" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 271 Classifications: {'water': 271} Link IDs: {None: 270} Chain: "C" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 271 Classifications: {'water': 271} Link IDs: {None: 270} Time building chain proxies: 7.61, per 1000 atoms: 0.26 Number of scatterers: 29118 At special positions: 0 Unit cell: (147.525, 154.269, 161.856, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 150 16.00 O 6453 8.00 N 4533 7.00 C 17982 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 34 " - pdb=" SG CYS A 203 " distance=2.05 Simple disulfide: pdb=" SG CYS A 184 " - pdb=" SG CYS A 222 " distance=2.03 Simple disulfide: pdb=" SG CYS A 193 " - pdb=" SG CYS A 246 " distance=2.05 Simple disulfide: pdb=" SG CYS A 348 " - pdb=" SG CYS A 358 " distance=2.04 Simple disulfide: pdb=" SG CYS A 392 " - pdb=" SG CYS A 416 " distance=2.05 Simple disulfide: pdb=" SG CYS A 434 " - pdb=" SG CYS A 487 " distance=2.05 Simple disulfide: pdb=" SG CYS A 446 " - pdb=" SG CYS A 584 " distance=2.04 Simple disulfide: pdb=" SG CYS A 512 " - pdb=" SG CYS A 533 " distance=2.04 Simple disulfide: pdb=" SG CYS A 602 " - pdb=" SG CYS A 653 " distance=2.04 Simple disulfide: pdb=" SG CYS A 619 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 678 " - pdb=" SG CYS A 711 " distance=2.04 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 734 " distance=2.04 Simple disulfide: pdb=" SG CYS A 804 " - pdb=" SG CYS A 826 " distance=2.04 Simple disulfide: pdb=" SG CYS A 809 " - pdb=" SG CYS A 815 " distance=2.05 Simple disulfide: pdb=" SG CYS A 910 " - pdb=" SG CYS A 923 " distance=2.04 Simple disulfide: pdb=" SG CYS A1104 " - pdb=" SG CYS A1115 " distance=2.03 Simple disulfide: pdb=" SG CYS A1154 " - pdb=" SG CYS A1162 " distance=2.04 Simple disulfide: pdb=" SG CYS B 34 " - pdb=" SG CYS B 203 " distance=2.05 Simple disulfide: pdb=" SG CYS B 184 " - pdb=" SG CYS B 222 " distance=2.03 Simple disulfide: pdb=" SG CYS B 193 " - pdb=" SG CYS B 246 " distance=2.05 Simple disulfide: pdb=" SG CYS B 348 " - pdb=" SG CYS B 358 " distance=2.04 Simple disulfide: pdb=" SG CYS B 392 " - pdb=" SG CYS B 416 " distance=2.05 Simple disulfide: pdb=" SG CYS B 434 " - pdb=" SG CYS B 487 " distance=2.05 Simple disulfide: pdb=" SG CYS B 446 " - pdb=" SG CYS B 584 " distance=2.04 Simple disulfide: pdb=" SG CYS B 512 " - pdb=" SG CYS B 533 " distance=2.04 Simple disulfide: pdb=" SG CYS B 602 " - pdb=" SG CYS B 653 " distance=2.04 Simple disulfide: pdb=" SG CYS B 619 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 678 " - pdb=" SG CYS B 711 " distance=2.04 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 734 " distance=2.04 Simple disulfide: pdb=" SG CYS B 804 " - pdb=" SG CYS B 826 " distance=2.04 Simple disulfide: pdb=" SG CYS B 809 " - pdb=" SG CYS B 815 " distance=2.05 Simple disulfide: pdb=" SG CYS B 910 " - pdb=" SG CYS B 923 " distance=2.04 Simple disulfide: pdb=" SG CYS B1104 " - pdb=" SG CYS B1115 " distance=2.03 Simple disulfide: pdb=" SG CYS B1154 " - pdb=" SG CYS B1162 " distance=2.04 Simple disulfide: pdb=" SG CYS C 34 " - pdb=" SG CYS C 203 " distance=2.05 Simple disulfide: pdb=" SG CYS C 184 " - pdb=" SG CYS C 222 " distance=2.03 Simple disulfide: pdb=" SG CYS C 193 " - pdb=" SG CYS C 246 " distance=2.05 Simple disulfide: pdb=" SG CYS C 348 " - pdb=" SG CYS C 358 " distance=2.04 Simple disulfide: pdb=" SG CYS C 392 " - pdb=" SG CYS C 416 " distance=2.04 Simple disulfide: pdb=" SG CYS C 434 " - pdb=" SG CYS C 487 " distance=2.05 Simple disulfide: pdb=" SG CYS C 446 " - pdb=" SG CYS C 584 " distance=2.04 Simple disulfide: pdb=" SG CYS C 512 " - pdb=" SG CYS C 533 " distance=2.04 Simple disulfide: pdb=" SG CYS C 602 " - pdb=" SG CYS C 653 " distance=2.04 Simple disulfide: pdb=" SG CYS C 619 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 678 " - pdb=" SG CYS C 711 " distance=2.04 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 734 " distance=2.04 Simple disulfide: pdb=" SG CYS C 804 " - pdb=" SG CYS C 826 " distance=2.04 Simple disulfide: pdb=" SG CYS C 809 " - pdb=" SG CYS C 815 " distance=2.05 Simple disulfide: pdb=" SG CYS C 910 " - pdb=" SG CYS C 923 " distance=2.04 Simple disulfide: pdb=" SG CYS C1104 " - pdb=" SG CYS C1115 " distance=2.03 Simple disulfide: pdb=" SG CYS C1154 " - pdb=" SG CYS C1162 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN D 5 " - " MAN D 6 " " MAN Q 5 " - " MAN Q 6 " " MAN d 5 " - " MAN d 6 " ALPHA1-3 " BMA D 3 " - " MAN D 7 " " MAN D 4 " - " MAN D 5 " " BMA G 3 " - " MAN G 4 " " BMA Q 3 " - " MAN Q 7 " " MAN Q 4 " - " MAN Q 5 " " BMA T 3 " - " MAN T 4 " " BMA d 3 " - " MAN d 7 " " MAN d 4 " - " MAN d 5 " " BMA g 3 " - " MAN g 4 " ALPHA1-6 " BMA D 3 " - " MAN D 4 " " BMA G 3 " - " MAN G 5 " " BMA H 3 " - " MAN H 4 " " BMA Q 3 " - " MAN Q 4 " " BMA T 3 " - " MAN T 5 " " BMA U 3 " - " MAN U 4 " " BMA d 3 " - " MAN d 4 " " BMA g 3 " - " MAN g 5 " " BMA h 3 " - " MAN h 4 " BETA1-2 " MAN D 7 " - " NAG D 8 " " MAN Q 7 " - " NAG Q 8 " " MAN d 7 " - " NAG d 8 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " NAG-ASN " NAG A1401 " - " ASN A 167 " " NAG A1402 " - " ASN A 73 " " NAG A1403 " - " ASN A1146 " " NAG A1404 " - " ASN A 618 " " NAG A1405 " - " ASN A 591 " " NAG B1401 " - " ASN B 167 " " NAG B1402 " - " ASN B 73 " " NAG B1403 " - " ASN B1146 " " NAG B1404 " - " ASN B 618 " " NAG B1405 " - " ASN B 591 " " NAG C1402 " - " ASN C 167 " " NAG C1403 " - " ASN C 73 " " NAG C1404 " - " ASN C1146 " " NAG C1405 " - " ASN C 618 " " NAG C1406 " - " ASN C 591 " " NAG D 1 " - " ASN A 761 " " NAG E 1 " - " ASN A 111 " " NAG F 1 " - " ASN A 162 " " NAG G 1 " - " ASN A 251 " " NAG H 1 " - " ASN A 419 " " NAG I 1 " - " ASN A 783 " " NAG J 1 " - " ASN A 868 " " NAG K 1 " - " ASN A1173 " " NAG L 1 " - " ASN A1215 " " NAG M 1 " - " ASN A 717 " " NAG N 1 " - " ASN A 174 " " NAG O 1 " - " ASN A 245 " " NAG P 1 " - " ASN A 132 " " NAG Q 1 " - " ASN B 761 " " NAG R 1 " - " ASN B 111 " " NAG S 1 " - " ASN B 162 " " NAG T 1 " - " ASN B 251 " " NAG U 1 " - " ASN B 419 " " NAG V 1 " - " ASN B 783 " " NAG W 1 " - " ASN B 868 " " NAG X 1 " - " ASN B1173 " " NAG Y 1 " - " ASN B1215 " " NAG Z 1 " - " ASN B 717 " " NAG a 1 " - " ASN B 174 " " NAG b 1 " - " ASN B 245 " " NAG c 1 " - " ASN B 132 " " NAG d 1 " - " ASN C 761 " " NAG e 1 " - " ASN C 111 " " NAG f 1 " - " ASN C 162 " " NAG g 1 " - " ASN C 251 " " NAG h 1 " - " ASN C 419 " " NAG i 1 " - " ASN C 783 " " NAG j 1 " - " ASN C 868 " " NAG k 1 " - " ASN C1173 " " NAG l 1 " - " ASN C1215 " " NAG m 1 " - " ASN C 717 " " NAG n 1 " - " ASN C 174 " " NAG o 1 " - " ASN C 245 " " NAG p 1 " - " ASN C 132 " Time building additional restraints: 3.09 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 1.2 microseconds 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6540 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 63 sheets defined 28.0% alpha, 30.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 41 through 44 Processing helix chain 'A' and resid 46 through 50 removed outlier: 3.678A pdb=" N THR A 50 " --> pdb=" O ALA A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 111 through 115 Processing helix chain 'A' and resid 231 through 240 removed outlier: 3.851A pdb=" N TYR A 240 " --> pdb=" O ALA A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 361 Processing helix chain 'A' and resid 394 through 398 Processing helix chain 'A' and resid 404 through 408 Processing helix chain 'A' and resid 419 through 425 Processing helix chain 'A' and resid 438 through 445 Processing helix chain 'A' and resid 458 through 466 removed outlier: 5.220A pdb=" N SER A 463 " --> pdb=" O ASP A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 477 removed outlier: 3.506A pdb=" N GLN A 475 " --> pdb=" O GLY A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 538 Processing helix chain 'A' and resid 587 through 589 No H-bonds generated for 'chain 'A' and resid 587 through 589' Processing helix chain 'A' and resid 624 through 627 Processing helix chain 'A' and resid 677 through 687 removed outlier: 3.648A pdb=" N VAL A 681 " --> pdb=" O ALA A 677 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER A 686 " --> pdb=" O THR A 682 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN A 687 " --> pdb=" O THR A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 810 Processing helix chain 'A' and resid 812 through 820 Processing helix chain 'A' and resid 822 through 849 removed outlier: 3.806A pdb=" N CYS A 826 " --> pdb=" O TYR A 822 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER A 827 " --> pdb=" O GLY A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 854 removed outlier: 3.820A pdb=" N GLN A 854 " --> pdb=" O ILE A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 873 Processing helix chain 'A' and resid 886 through 895 removed outlier: 3.645A pdb=" N LYS A 895 " --> pdb=" O LEU A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 912 Processing helix chain 'A' and resid 924 through 929 Processing helix chain 'A' and resid 938 through 951 Processing helix chain 'A' and resid 969 through 981 removed outlier: 3.592A pdb=" N VAL A 981 " --> pdb=" O ARG A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 991 Processing helix chain 'A' and resid 991 through 1005 removed outlier: 3.502A pdb=" N ALA A1005 " --> pdb=" O GLN A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1010 removed outlier: 4.502A pdb=" N PHE A1010 " --> pdb=" O GLN A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1014 through 1037 removed outlier: 3.637A pdb=" N LEU A1031 " --> pdb=" O ASN A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1040 No H-bonds generated for 'chain 'A' and resid 1038 through 1040' Processing helix chain 'A' and resid 1048 through 1056 Processing helix chain 'A' and resid 1059 through 1105 removed outlier: 3.572A pdb=" N ALA A1063 " --> pdb=" O PRO A1059 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A1068 " --> pdb=" O GLN A1064 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1225 Processing helix chain 'B' and resid 41 through 44 Processing helix chain 'B' and resid 46 through 50 removed outlier: 3.678A pdb=" N THR B 50 " --> pdb=" O ALA B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 111 through 115 Processing helix chain 'B' and resid 231 through 240 removed outlier: 3.851A pdb=" N TYR B 240 " --> pdb=" O ALA B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 361 Processing helix chain 'B' and resid 394 through 398 Processing helix chain 'B' and resid 404 through 408 Processing helix chain 'B' and resid 419 through 425 Processing helix chain 'B' and resid 438 through 445 Processing helix chain 'B' and resid 458 through 466 removed outlier: 5.220A pdb=" N SER B 463 " --> pdb=" O ASP B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 477 removed outlier: 3.506A pdb=" N GLN B 475 " --> pdb=" O GLY B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 538 Processing helix chain 'B' and resid 587 through 589 No H-bonds generated for 'chain 'B' and resid 587 through 589' Processing helix chain 'B' and resid 624 through 627 Processing helix chain 'B' and resid 677 through 687 removed outlier: 3.649A pdb=" N VAL B 681 " --> pdb=" O ALA B 677 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER B 686 " --> pdb=" O THR B 682 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN B 687 " --> pdb=" O THR B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 810 Processing helix chain 'B' and resid 812 through 820 Processing helix chain 'B' and resid 822 through 849 removed outlier: 3.806A pdb=" N CYS B 826 " --> pdb=" O TYR B 822 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER B 827 " --> pdb=" O GLY B 823 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 854 removed outlier: 3.820A pdb=" N GLN B 854 " --> pdb=" O ILE B 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 870 through 873 Processing helix chain 'B' and resid 886 through 895 removed outlier: 3.645A pdb=" N LYS B 895 " --> pdb=" O LEU B 891 " (cutoff:3.500A) Processing helix chain 'B' and resid 905 through 912 Processing helix chain 'B' and resid 924 through 929 Processing helix chain 'B' and resid 938 through 951 Processing helix chain 'B' and resid 969 through 981 removed outlier: 3.592A pdb=" N VAL B 981 " --> pdb=" O ARG B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 984 through 991 Processing helix chain 'B' and resid 991 through 1005 Processing helix chain 'B' and resid 1006 through 1010 removed outlier: 4.502A pdb=" N PHE B1010 " --> pdb=" O GLN B1007 " (cutoff:3.500A) Processing helix chain 'B' and resid 1014 through 1037 removed outlier: 3.637A pdb=" N LEU B1031 " --> pdb=" O ASN B1027 " (cutoff:3.500A) Processing helix chain 'B' and resid 1038 through 1040 No H-bonds generated for 'chain 'B' and resid 1038 through 1040' Processing helix chain 'B' and resid 1048 through 1056 Processing helix chain 'B' and resid 1059 through 1105 removed outlier: 3.572A pdb=" N ALA B1063 " --> pdb=" O PRO B1059 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B1068 " --> pdb=" O GLN B1064 " (cutoff:3.500A) Processing helix chain 'B' and resid 1221 through 1225 Processing helix chain 'C' and resid 41 through 44 Processing helix chain 'C' and resid 46 through 50 removed outlier: 3.679A pdb=" N THR C 50 " --> pdb=" O ALA C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 111 through 115 Processing helix chain 'C' and resid 231 through 240 removed outlier: 3.850A pdb=" N TYR C 240 " --> pdb=" O ALA C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 361 Processing helix chain 'C' and resid 394 through 398 Processing helix chain 'C' and resid 404 through 408 Processing helix chain 'C' and resid 419 through 425 Processing helix chain 'C' and resid 438 through 445 Processing helix chain 'C' and resid 458 through 466 removed outlier: 5.220A pdb=" N SER C 463 " --> pdb=" O ASP C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 477 removed outlier: 3.505A pdb=" N GLN C 475 " --> pdb=" O GLY C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 538 Processing helix chain 'C' and resid 587 through 589 No H-bonds generated for 'chain 'C' and resid 587 through 589' Processing helix chain 'C' and resid 624 through 627 Processing helix chain 'C' and resid 677 through 687 removed outlier: 3.648A pdb=" N VAL C 681 " --> pdb=" O ALA C 677 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER C 686 " --> pdb=" O THR C 682 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN C 687 " --> pdb=" O THR C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 803 through 810 Processing helix chain 'C' and resid 812 through 820 Processing helix chain 'C' and resid 822 through 849 removed outlier: 3.806A pdb=" N CYS C 826 " --> pdb=" O TYR C 822 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER C 827 " --> pdb=" O GLY C 823 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 854 removed outlier: 3.820A pdb=" N GLN C 854 " --> pdb=" O ILE C 851 " (cutoff:3.500A) Processing helix chain 'C' and resid 870 through 873 Processing helix chain 'C' and resid 886 through 895 removed outlier: 3.645A pdb=" N LYS C 895 " --> pdb=" O LEU C 891 " (cutoff:3.500A) Processing helix chain 'C' and resid 905 through 912 Processing helix chain 'C' and resid 924 through 929 Processing helix chain 'C' and resid 938 through 951 Processing helix chain 'C' and resid 969 through 981 removed outlier: 3.592A pdb=" N VAL C 981 " --> pdb=" O ARG C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 984 through 991 Processing helix chain 'C' and resid 991 through 1005 Processing helix chain 'C' and resid 1006 through 1010 removed outlier: 4.502A pdb=" N PHE C1010 " --> pdb=" O GLN C1007 " (cutoff:3.500A) Processing helix chain 'C' and resid 1014 through 1037 removed outlier: 3.637A pdb=" N LEU C1031 " --> pdb=" O ASN C1027 " (cutoff:3.500A) Processing helix chain 'C' and resid 1038 through 1040 No H-bonds generated for 'chain 'C' and resid 1038 through 1040' Processing helix chain 'C' and resid 1048 through 1056 Processing helix chain 'C' and resid 1059 through 1105 removed outlier: 3.572A pdb=" N ALA C1063 " --> pdb=" O PRO C1059 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU C1068 " --> pdb=" O GLN C1064 " (cutoff:3.500A) Processing helix chain 'C' and resid 1221 through 1225 Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 39 Processing sheet with id=AA2, first strand: chain 'A' and resid 70 through 71 removed outlier: 6.547A pdb=" N SER A 70 " --> pdb=" O TYR C 631 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL C 630 " --> pdb=" O VAL C 638 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N VAL C 638 " --> pdb=" O VAL C 650 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N TYR C 647 " --> pdb=" O CYS C 619 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N PHE C 383 " --> pdb=" O SER C 606 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 82 removed outlier: 4.062A pdb=" N LYS A 344 " --> pdb=" O ASN A 335 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 90 through 92 removed outlier: 3.659A pdb=" N ALA A 291 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N SER A 276 " --> pdb=" O HIS A 289 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N HIS A 289 " --> pdb=" O SER A 276 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 95 through 96 removed outlier: 7.103A pdb=" N SER A 95 " --> pdb=" O ILE A 309 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 99 through 100 Processing sheet with id=AA7, first strand: chain 'A' and resid 117 through 118 Processing sheet with id=AA8, first strand: chain 'A' and resid 117 through 118 Processing sheet with id=AA9, first strand: chain 'A' and resid 134 through 137 removed outlier: 5.497A pdb=" N THR A 143 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ALA A 318 " --> pdb=" O PRO A 146 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 160 through 163 removed outlier: 6.186A pdb=" N GLY A 161 " --> pdb=" O GLY A 170 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY A 170 " --> pdb=" O GLY A 161 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE A 168 " --> pdb=" O TYR A 163 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 368 through 372 removed outlier: 4.529A pdb=" N VAL A 658 " --> pdb=" O VAL A 372 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 382 through 385 removed outlier: 6.395A pdb=" N PHE A 383 " --> pdb=" O SER A 606 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N TYR A 647 " --> pdb=" O CYS A 619 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N VAL A 638 " --> pdb=" O VAL A 650 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL A 630 " --> pdb=" O VAL A 638 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 390 through 391 removed outlier: 6.589A pdb=" N GLN A 390 " --> pdb=" O ASN A 417 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N CYS A 416 " --> pdb=" O CYS A 584 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 399 through 400 removed outlier: 3.717A pdb=" N GLY A 400 " --> pdb=" O THR A 499 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 409 through 413 removed outlier: 3.583A pdb=" N SER A 449 " --> pdb=" O GLN A 575 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU A 431 " --> pdb=" O LEU A 490 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N THR A 492 " --> pdb=" O VAL A 429 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N VAL A 429 " --> pdb=" O THR A 492 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 521 through 522 removed outlier: 6.585A pdb=" N THR A 556 " --> pdb=" O THR A 510 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N CYS A 512 " --> pdb=" O THR A 554 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR A 554 " --> pdb=" O CYS A 512 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN A 546 " --> pdb=" O GLY A 557 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 715 through 722 removed outlier: 5.586A pdb=" N THR A 759 " --> pdb=" O THR A 718 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N MET A 720 " --> pdb=" O THR A 759 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N LEU A 733 " --> pdb=" O LEU A 729 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LEU A 727 " --> pdb=" O ALA A 735 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1119 through 1128 removed outlier: 7.112A pdb=" N VAL A1137 " --> pdb=" O ILE A1121 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N SER A1123 " --> pdb=" O PHE A1135 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE A1135 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ALA A1125 " --> pdb=" O TYR A1133 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TYR A1133 " --> pdb=" O ALA A1125 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ASN A1127 " --> pdb=" O GLY A1131 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N GLY A1131 " --> pdb=" O ASN A1127 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N THR A1148 " --> pdb=" O LEU A1172 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N PHE A1170 " --> pdb=" O ALA A1150 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N GLY A1190 " --> pdb=" O HIS A1195 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N HIS A1195 " --> pdb=" O GLY A1190 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1119 through 1128 removed outlier: 7.112A pdb=" N VAL A1137 " --> pdb=" O ILE A1121 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N SER A1123 " --> pdb=" O PHE A1135 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE A1135 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ALA A1125 " --> pdb=" O TYR A1133 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TYR A1133 " --> pdb=" O ALA A1125 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ASN A1127 " --> pdb=" O GLY A1131 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N GLY A1131 " --> pdb=" O ASN A1127 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASN A 783 " --> pdb=" O THR A1142 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N HIS A1144 " --> pdb=" O PRO A 781 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ASN A1146 " --> pdb=" O ALA A 779 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ALA A 779 " --> pdb=" O ASN A1146 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N THR A1148 " --> pdb=" O VAL A 777 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL A 777 " --> pdb=" O THR A1148 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 800 through 802 Processing sheet with id=AC3, first strand: chain 'A' and resid 863 through 864 Processing sheet with id=AC4, first strand: chain 'A' and resid 965 through 966 removed outlier: 6.943A pdb=" N VAL C 777 " --> pdb=" O THR C1148 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N THR C1148 " --> pdb=" O VAL C 777 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ALA C 779 " --> pdb=" O ASN C1146 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ASN C1146 " --> pdb=" O ALA C 779 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N HIS C1144 " --> pdb=" O PRO C 781 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASN C 783 " --> pdb=" O THR C1142 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N GLY C1131 " --> pdb=" O ASN C1127 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ASN C1127 " --> pdb=" O GLY C1131 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TYR C1133 " --> pdb=" O ALA C1125 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ALA C1125 " --> pdb=" O TYR C1133 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE C1135 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N SER C1123 " --> pdb=" O PHE C1135 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N VAL C1137 " --> pdb=" O ILE C1121 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 965 through 966 removed outlier: 6.943A pdb=" N VAL C 777 " --> pdb=" O THR C1148 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N THR C1148 " --> pdb=" O VAL C 777 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ALA C 779 " --> pdb=" O ASN C1146 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ASN C1146 " --> pdb=" O ALA C 779 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N HIS C1144 " --> pdb=" O PRO C 781 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASN C 783 " --> pdb=" O THR C1142 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N THR C1148 " --> pdb=" O LEU C1172 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N PHE C1170 " --> pdb=" O ALA C1150 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N GLY C1190 " --> pdb=" O HIS C1195 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N HIS C1195 " --> pdb=" O GLY C1190 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 1204 through 1207 removed outlier: 4.396A pdb=" N CYS A1162 " --> pdb=" O VAL A1207 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 37 through 39 Processing sheet with id=AC8, first strand: chain 'B' and resid 75 through 82 removed outlier: 4.062A pdb=" N LYS B 344 " --> pdb=" O ASN B 335 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 90 through 92 removed outlier: 3.659A pdb=" N ALA B 291 " --> pdb=" O LEU B 274 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N SER B 276 " --> pdb=" O HIS B 289 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N HIS B 289 " --> pdb=" O SER B 276 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 95 through 96 removed outlier: 7.103A pdb=" N SER B 95 " --> pdb=" O ILE B 309 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 99 through 100 Processing sheet with id=AD3, first strand: chain 'B' and resid 117 through 118 Processing sheet with id=AD4, first strand: chain 'B' and resid 117 through 118 Processing sheet with id=AD5, first strand: chain 'B' and resid 134 through 137 removed outlier: 5.497A pdb=" N THR B 143 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ALA B 318 " --> pdb=" O PRO B 146 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 160 through 163 removed outlier: 6.186A pdb=" N GLY B 161 " --> pdb=" O GLY B 170 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY B 170 " --> pdb=" O GLY B 161 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE B 168 " --> pdb=" O TYR B 163 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 368 through 372 removed outlier: 4.529A pdb=" N VAL B 658 " --> pdb=" O VAL B 372 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 382 through 385 removed outlier: 6.395A pdb=" N PHE B 383 " --> pdb=" O SER B 606 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N TYR B 647 " --> pdb=" O CYS B 619 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N VAL B 638 " --> pdb=" O VAL B 650 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL B 630 " --> pdb=" O VAL B 638 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 390 through 391 removed outlier: 6.589A pdb=" N GLN B 390 " --> pdb=" O ASN B 417 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N CYS B 416 " --> pdb=" O CYS B 584 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'B' and resid 399 through 400 removed outlier: 3.717A pdb=" N GLY B 400 " --> pdb=" O THR B 499 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'B' and resid 409 through 413 removed outlier: 3.583A pdb=" N SER B 449 " --> pdb=" O GLN B 575 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU B 431 " --> pdb=" O LEU B 490 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N THR B 492 " --> pdb=" O VAL B 429 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N VAL B 429 " --> pdb=" O THR B 492 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 521 through 522 removed outlier: 6.584A pdb=" N THR B 556 " --> pdb=" O THR B 510 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N CYS B 512 " --> pdb=" O THR B 554 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR B 554 " --> pdb=" O CYS B 512 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN B 546 " --> pdb=" O GLY B 557 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 715 through 722 removed outlier: 5.584A pdb=" N THR B 759 " --> pdb=" O THR B 718 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N MET B 720 " --> pdb=" O THR B 759 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N LEU B 733 " --> pdb=" O LEU B 729 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LEU B 727 " --> pdb=" O ALA B 735 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 1119 through 1128 removed outlier: 7.113A pdb=" N VAL B1137 " --> pdb=" O ILE B1121 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N SER B1123 " --> pdb=" O PHE B1135 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE B1135 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ALA B1125 " --> pdb=" O TYR B1133 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TYR B1133 " --> pdb=" O ALA B1125 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ASN B1127 " --> pdb=" O GLY B1131 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N GLY B1131 " --> pdb=" O ASN B1127 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N THR B1148 " --> pdb=" O LEU B1172 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N PHE B1170 " --> pdb=" O ALA B1150 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N GLY B1190 " --> pdb=" O HIS B1195 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N HIS B1195 " --> pdb=" O GLY B1190 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 1119 through 1128 removed outlier: 7.113A pdb=" N VAL B1137 " --> pdb=" O ILE B1121 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N SER B1123 " --> pdb=" O PHE B1135 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE B1135 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ALA B1125 " --> pdb=" O TYR B1133 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TYR B1133 " --> pdb=" O ALA B1125 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ASN B1127 " --> pdb=" O GLY B1131 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N GLY B1131 " --> pdb=" O ASN B1127 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASN B 783 " --> pdb=" O THR B1142 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N HIS B1144 " --> pdb=" O PRO B 781 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ASN B1146 " --> pdb=" O ALA B 779 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ALA B 779 " --> pdb=" O ASN B1146 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N THR B1148 " --> pdb=" O VAL B 777 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL B 777 " --> pdb=" O THR B1148 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 800 through 802 Processing sheet with id=AE8, first strand: chain 'B' and resid 863 through 864 Processing sheet with id=AE9, first strand: chain 'B' and resid 1204 through 1207 removed outlier: 4.396A pdb=" N CYS B1162 " --> pdb=" O VAL B1207 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 37 through 39 Processing sheet with id=AF2, first strand: chain 'C' and resid 75 through 82 removed outlier: 4.062A pdb=" N LYS C 344 " --> pdb=" O ASN C 335 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 90 through 92 removed outlier: 3.659A pdb=" N ALA C 291 " --> pdb=" O LEU C 274 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N SER C 276 " --> pdb=" O HIS C 289 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N HIS C 289 " --> pdb=" O SER C 276 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 95 through 96 removed outlier: 7.103A pdb=" N SER C 95 " --> pdb=" O ILE C 309 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'C' and resid 99 through 100 Processing sheet with id=AF6, first strand: chain 'C' and resid 117 through 118 Processing sheet with id=AF7, first strand: chain 'C' and resid 117 through 118 Processing sheet with id=AF8, first strand: chain 'C' and resid 134 through 137 removed outlier: 5.497A pdb=" N THR C 143 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ALA C 318 " --> pdb=" O PRO C 146 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 160 through 163 removed outlier: 6.186A pdb=" N GLY C 161 " --> pdb=" O GLY C 170 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY C 170 " --> pdb=" O GLY C 161 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE C 168 " --> pdb=" O TYR C 163 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 368 through 372 removed outlier: 4.530A pdb=" N VAL C 658 " --> pdb=" O VAL C 372 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 390 through 391 removed outlier: 6.589A pdb=" N GLN C 390 " --> pdb=" O ASN C 417 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N CYS C 416 " --> pdb=" O CYS C 584 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'C' and resid 399 through 400 removed outlier: 3.717A pdb=" N GLY C 400 " --> pdb=" O THR C 499 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'C' and resid 409 through 413 removed outlier: 3.583A pdb=" N SER C 449 " --> pdb=" O GLN C 575 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU C 431 " --> pdb=" O LEU C 490 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N THR C 492 " --> pdb=" O VAL C 429 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N VAL C 429 " --> pdb=" O THR C 492 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 521 through 522 removed outlier: 6.584A pdb=" N THR C 556 " --> pdb=" O THR C 510 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N CYS C 512 " --> pdb=" O THR C 554 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR C 554 " --> pdb=" O CYS C 512 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN C 546 " --> pdb=" O GLY C 557 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'C' and resid 715 through 722 removed outlier: 5.585A pdb=" N THR C 759 " --> pdb=" O THR C 718 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N MET C 720 " --> pdb=" O THR C 759 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N LEU C 733 " --> pdb=" O LEU C 729 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LEU C 727 " --> pdb=" O ALA C 735 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'C' and resid 800 through 802 Processing sheet with id=AG8, first strand: chain 'C' and resid 863 through 864 Processing sheet with id=AG9, first strand: chain 'C' and resid 1204 through 1207 removed outlier: 4.396A pdb=" N CYS C1162 " --> pdb=" O VAL C1207 " (cutoff:3.500A) 1177 hydrogen bonds defined for protein. 3102 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.11 Time building geometry restraints manager: 3.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8658 1.34 - 1.47: 7530 1.47 - 1.59: 12564 1.59 - 1.72: 0 1.72 - 1.84: 198 Bond restraints: 28950 Sorted by residual: bond pdb=" N ILE B 244 " pdb=" CA ILE B 244 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.14e-02 7.69e+03 1.06e+01 bond pdb=" N ILE A 244 " pdb=" CA ILE A 244 " ideal model delta sigma weight residual 1.458 1.494 -0.037 1.14e-02 7.69e+03 1.05e+01 bond pdb=" N ILE C 244 " pdb=" CA ILE C 244 " ideal model delta sigma weight residual 1.458 1.494 -0.037 1.14e-02 7.69e+03 1.04e+01 bond pdb=" N ILE A 194 " pdb=" CA ILE A 194 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.20e-02 6.94e+03 9.04e+00 bond pdb=" N PHE C 248 " pdb=" CA PHE C 248 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.23e-02 6.61e+03 8.96e+00 ... (remaining 28945 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.23: 39032 3.23 - 6.46: 433 6.46 - 9.69: 6 9.69 - 12.92: 3 12.92 - 16.15: 3 Bond angle restraints: 39477 Sorted by residual: angle pdb=" N GLY A1009 " pdb=" CA GLY A1009 " pdb=" C GLY A1009 " ideal model delta sigma weight residual 114.66 130.81 -16.15 1.24e+00 6.50e-01 1.70e+02 angle pdb=" N GLY C1009 " pdb=" CA GLY C1009 " pdb=" C GLY C1009 " ideal model delta sigma weight residual 114.66 130.79 -16.13 1.24e+00 6.50e-01 1.69e+02 angle pdb=" N GLY B1009 " pdb=" CA GLY B1009 " pdb=" C GLY B1009 " ideal model delta sigma weight residual 114.66 130.79 -16.13 1.24e+00 6.50e-01 1.69e+02 angle pdb=" N THR C1008 " pdb=" CA THR C1008 " pdb=" C THR C1008 " ideal model delta sigma weight residual 113.19 124.21 -11.02 1.19e+00 7.06e-01 8.57e+01 angle pdb=" N THR B1008 " pdb=" CA THR B1008 " pdb=" C THR B1008 " ideal model delta sigma weight residual 113.19 124.19 -11.00 1.19e+00 7.06e-01 8.54e+01 ... (remaining 39472 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.41: 18099 27.41 - 54.83: 440 54.83 - 82.24: 172 82.24 - 109.66: 60 109.66 - 137.07: 3 Dihedral angle restraints: 18774 sinusoidal: 8553 harmonic: 10221 Sorted by residual: dihedral pdb=" C THR B1008 " pdb=" N THR B1008 " pdb=" CA THR B1008 " pdb=" CB THR B1008 " ideal model delta harmonic sigma weight residual -122.00 -139.35 17.35 0 2.50e+00 1.60e-01 4.81e+01 dihedral pdb=" C THR C1008 " pdb=" N THR C1008 " pdb=" CA THR C1008 " pdb=" CB THR C1008 " ideal model delta harmonic sigma weight residual -122.00 -139.32 17.32 0 2.50e+00 1.60e-01 4.80e+01 dihedral pdb=" C THR A1008 " pdb=" N THR A1008 " pdb=" CA THR A1008 " pdb=" CB THR A1008 " ideal model delta harmonic sigma weight residual -122.00 -139.31 17.31 0 2.50e+00 1.60e-01 4.79e+01 ... (remaining 18771 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.156: 4758 0.156 - 0.311: 75 0.311 - 0.467: 12 0.467 - 0.622: 3 0.622 - 0.778: 3 Chirality restraints: 4851 Sorted by residual: chirality pdb=" C1 NAG D 8 " pdb=" O2 MAN D 7 " pdb=" C2 NAG D 8 " pdb=" O5 NAG D 8 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-02 2.50e+03 3.87e+02 chirality pdb=" C1 NAG d 8 " pdb=" O2 MAN d 7 " pdb=" C2 NAG d 8 " pdb=" O5 NAG d 8 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-02 2.50e+03 3.86e+02 chirality pdb=" C1 NAG Q 8 " pdb=" O2 MAN Q 7 " pdb=" C2 NAG Q 8 " pdb=" O5 NAG Q 8 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-02 2.50e+03 3.85e+02 ... (remaining 4848 not shown) Planarity restraints: 4962 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 8 " 0.266 2.00e-02 2.50e+03 2.26e-01 6.39e+02 pdb=" C7 NAG D 8 " -0.066 2.00e-02 2.50e+03 pdb=" C8 NAG D 8 " 0.165 2.00e-02 2.50e+03 pdb=" N2 NAG D 8 " -0.391 2.00e-02 2.50e+03 pdb=" O7 NAG D 8 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG Q 8 " -0.265 2.00e-02 2.50e+03 2.26e-01 6.39e+02 pdb=" C7 NAG Q 8 " 0.066 2.00e-02 2.50e+03 pdb=" C8 NAG Q 8 " -0.165 2.00e-02 2.50e+03 pdb=" N2 NAG Q 8 " 0.391 2.00e-02 2.50e+03 pdb=" O7 NAG Q 8 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG d 8 " -0.265 2.00e-02 2.50e+03 2.26e-01 6.38e+02 pdb=" C7 NAG d 8 " 0.066 2.00e-02 2.50e+03 pdb=" C8 NAG d 8 " -0.165 2.00e-02 2.50e+03 pdb=" N2 NAG d 8 " 0.390 2.00e-02 2.50e+03 pdb=" O7 NAG d 8 " -0.026 2.00e-02 2.50e+03 ... (remaining 4959 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2131 2.74 - 3.28: 27973 3.28 - 3.82: 49237 3.82 - 4.36: 62125 4.36 - 4.90: 98706 Nonbonded interactions: 240172 Sorted by model distance: nonbonded pdb=" OG SER B 440 " pdb=" OD2 ASP C1057 " model vdw 2.200 3.040 nonbonded pdb=" OD2 ASP A1057 " pdb=" OG SER C 440 " model vdw 2.200 3.040 nonbonded pdb=" OG SER A 440 " pdb=" OD2 ASP B1057 " model vdw 2.200 3.040 nonbonded pdb=" O HOH B1603 " pdb=" O HOH B1703 " model vdw 2.201 3.040 nonbonded pdb=" O HOH C1603 " pdb=" O HOH C1703 " model vdw 2.201 3.040 ... (remaining 240167 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.07 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 23 through 1227 or resid 1402 through 1405)) selection = (chain 'B' and (resid 23 through 1227 or resid 1402 through 1405)) selection = (chain 'C' and (resid 23 through 1227 or resid 1402 through 1405)) } ncs_group { reference = chain 'D' selection = chain 'Q' selection = chain 'd' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'R' selection = chain 'S' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'e' selection = chain 'f' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' } ncs_group { reference = chain 'G' selection = chain 'T' selection = chain 'g' } ncs_group { reference = chain 'H' selection = chain 'U' selection = chain 'h' } ncs_group { reference = chain 'P' selection = chain 'c' selection = chain 'p' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 21.360 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 32.100 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 29130 Z= 0.373 Angle : 1.066 20.336 39966 Z= 0.543 Chirality : 0.065 0.778 4851 Planarity : 0.009 0.226 4908 Dihedral : 15.395 137.070 12081 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.09 % Favored : 97.83 % Rotamer: Outliers : 0.65 % Allowed : 6.70 % Favored : 92.65 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.13), residues: 3450 helix: 1.41 (0.19), residues: 765 sheet: 0.42 (0.19), residues: 651 loop : -0.13 (0.13), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C1072 TYR 0.023 0.003 TYR C 506 PHE 0.029 0.003 PHE C 432 TRP 0.014 0.002 TRP C 51 HIS 0.004 0.001 HIS C1144 Details of bonding type rmsd covalent geometry : bond 0.00650 (28950) covalent geometry : angle 0.90669 (39477) SS BOND : bond 0.01237 ( 51) SS BOND : angle 2.39690 ( 102) hydrogen bonds : bond 0.18488 ( 1104) hydrogen bonds : angle 6.94361 ( 3102) link_ALPHA1-2 : bond 0.04184 ( 3) link_ALPHA1-2 : angle 9.09420 ( 9) link_ALPHA1-3 : bond 0.04460 ( 9) link_ALPHA1-3 : angle 5.66867 ( 27) link_ALPHA1-6 : bond 0.03598 ( 9) link_ALPHA1-6 : angle 4.53239 ( 27) link_BETA1-2 : bond 0.04199 ( 3) link_BETA1-2 : angle 10.16648 ( 9) link_BETA1-4 : bond 0.04339 ( 51) link_BETA1-4 : angle 6.33453 ( 153) link_NAG-ASN : bond 0.01087 ( 54) link_NAG-ASN : angle 4.37523 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 216 time to evaluate : 1.111 Fit side-chains REVERT: A 386 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.7974 (pp30) REVERT: A 424 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8535 (mm) REVERT: A 447 TYR cc_start: 0.9328 (OUTLIER) cc_final: 0.7467 (p90) REVERT: B 26 MET cc_start: 0.8417 (mmm) cc_final: 0.7981 (mmm) REVERT: B 386 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8269 (pt0) REVERT: B 841 ASP cc_start: 0.8477 (m-30) cc_final: 0.8260 (m-30) REVERT: B 871 MET cc_start: 0.8117 (mmt) cc_final: 0.7903 (mmm) REVERT: C 106 ARG cc_start: 0.7913 (mtm180) cc_final: 0.7453 (mtm110) REVERT: C 148 LYS cc_start: 0.8161 (mmmm) cc_final: 0.7909 (mmmm) REVERT: C 230 ARG cc_start: 0.7847 (mmm-85) cc_final: 0.7078 (mtp180) REVERT: C 287 MET cc_start: 0.9290 (mtm) cc_final: 0.9084 (mtm) REVERT: C 386 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.8286 (pt0) REVERT: C 447 TYR cc_start: 0.9356 (OUTLIER) cc_final: 0.7478 (p90) REVERT: C 1006 MET cc_start: 0.7576 (mtm) cc_final: 0.7232 (mtm) outliers start: 18 outliers final: 7 residues processed: 226 average time/residue: 0.7920 time to fit residues: 206.9611 Evaluate side-chains 210 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 197 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 GLN Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 447 TYR Chi-restraints excluded: chain A residue 643 TYR Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain B residue 386 GLN Chi-restraints excluded: chain B residue 447 TYR Chi-restraints excluded: chain B residue 643 TYR Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain C residue 386 GLN Chi-restraints excluded: chain C residue 447 TYR Chi-restraints excluded: chain C residue 643 TYR Chi-restraints excluded: chain C residue 681 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 9.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN A 189 HIS A 328 HIS A 361 GLN A 417 ASN A 466 GLN A 505 ASN A 575 GLN A1018 ASN B 67 ASN B 189 HIS B 328 HIS B 417 ASN B 505 ASN B 575 GLN B 731 GLN B1018 ASN C 67 ASN C 189 HIS C 328 HIS C 335 ASN C 361 GLN C 417 ASN C 505 ASN C 575 GLN C 641 HIS C 667 ASN C1018 ASN C1140 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.149167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.121341 restraints weight = 22016.324| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.48 r_work: 0.3172 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.0844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29130 Z= 0.153 Angle : 0.672 9.874 39966 Z= 0.345 Chirality : 0.046 0.209 4851 Planarity : 0.004 0.037 4908 Dihedral : 10.463 126.244 6500 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.44 % Allowed : 6.92 % Favored : 91.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.14), residues: 3450 helix: 1.94 (0.19), residues: 762 sheet: 0.50 (0.18), residues: 705 loop : -0.05 (0.13), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1072 TYR 0.013 0.002 TYR A 940 PHE 0.017 0.002 PHE C 290 TRP 0.005 0.001 TRP C 319 HIS 0.003 0.001 HIS A1136 Details of bonding type rmsd covalent geometry : bond 0.00291 (28950) covalent geometry : angle 0.63468 (39477) SS BOND : bond 0.00565 ( 51) SS BOND : angle 1.53279 ( 102) hydrogen bonds : bond 0.07065 ( 1104) hydrogen bonds : angle 5.67453 ( 3102) link_ALPHA1-2 : bond 0.00331 ( 3) link_ALPHA1-2 : angle 2.66766 ( 9) link_ALPHA1-3 : bond 0.00912 ( 9) link_ALPHA1-3 : angle 1.79476 ( 27) link_ALPHA1-6 : bond 0.00258 ( 9) link_ALPHA1-6 : angle 1.78422 ( 27) link_BETA1-2 : bond 0.01902 ( 3) link_BETA1-2 : angle 5.71041 ( 9) link_BETA1-4 : bond 0.00458 ( 51) link_BETA1-4 : angle 2.36906 ( 153) link_NAG-ASN : bond 0.00348 ( 54) link_NAG-ASN : angle 1.79067 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 207 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 386 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.8053 (pp30) REVERT: A 424 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8430 (mm) REVERT: A 447 TYR cc_start: 0.9280 (OUTLIER) cc_final: 0.7435 (p90) REVERT: B 26 MET cc_start: 0.8354 (mmm) cc_final: 0.7954 (mmm) REVERT: B 309 ILE cc_start: 0.8570 (mm) cc_final: 0.8229 (mp) REVERT: B 390 GLN cc_start: 0.7740 (mm110) cc_final: 0.7509 (mm-40) REVERT: C 148 LYS cc_start: 0.8260 (mmmm) cc_final: 0.8017 (mmmm) REVERT: C 230 ARG cc_start: 0.7876 (mmm-85) cc_final: 0.7105 (mtp180) REVERT: C 447 TYR cc_start: 0.9308 (OUTLIER) cc_final: 0.7382 (p90) REVERT: C 1006 MET cc_start: 0.7470 (mtm) cc_final: 0.7191 (mtm) outliers start: 40 outliers final: 17 residues processed: 234 average time/residue: 0.7533 time to fit residues: 205.4445 Evaluate side-chains 222 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 201 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 386 GLN Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 447 TYR Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 643 TYR Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 447 TYR Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 643 TYR Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 946 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 447 TYR Chi-restraints excluded: chain C residue 594 SER Chi-restraints excluded: chain C residue 643 TYR Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 946 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 260 optimal weight: 8.9990 chunk 213 optimal weight: 0.0870 chunk 232 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 329 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 294 optimal weight: 4.9990 chunk 347 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 261 optimal weight: 0.0870 chunk 186 optimal weight: 1.9990 overall best weight: 0.5936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 ASN A 756 GLN A1140 GLN B 335 ASN C 667 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.151073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.123611 restraints weight = 22171.029| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.46 r_work: 0.3208 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 29130 Z= 0.125 Angle : 0.590 7.167 39966 Z= 0.303 Chirality : 0.044 0.195 4851 Planarity : 0.004 0.035 4908 Dihedral : 8.263 105.656 6494 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.15 % Allowed : 7.21 % Favored : 91.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.14), residues: 3450 helix: 2.24 (0.20), residues: 762 sheet: 0.64 (0.18), residues: 702 loop : 0.04 (0.13), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 230 TYR 0.011 0.001 TYR C 454 PHE 0.013 0.001 PHE C 290 TRP 0.005 0.001 TRP B 319 HIS 0.003 0.001 HIS C 189 Details of bonding type rmsd covalent geometry : bond 0.00228 (28950) covalent geometry : angle 0.56034 (39477) SS BOND : bond 0.00676 ( 51) SS BOND : angle 1.36812 ( 102) hydrogen bonds : bond 0.06044 ( 1104) hydrogen bonds : angle 5.31839 ( 3102) link_ALPHA1-2 : bond 0.00061 ( 3) link_ALPHA1-2 : angle 2.10926 ( 9) link_ALPHA1-3 : bond 0.00981 ( 9) link_ALPHA1-3 : angle 1.56356 ( 27) link_ALPHA1-6 : bond 0.00552 ( 9) link_ALPHA1-6 : angle 1.65748 ( 27) link_BETA1-2 : bond 0.01794 ( 3) link_BETA1-2 : angle 4.10013 ( 9) link_BETA1-4 : bond 0.00486 ( 51) link_BETA1-4 : angle 1.95943 ( 153) link_NAG-ASN : bond 0.00290 ( 54) link_NAG-ASN : angle 1.55958 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 205 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 386 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.7917 (pp30) REVERT: A 424 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8446 (mm) REVERT: A 447 TYR cc_start: 0.9241 (OUTLIER) cc_final: 0.7416 (p90) REVERT: A 720 MET cc_start: 0.7821 (ttm) cc_final: 0.7372 (ttm) REVERT: B 26 MET cc_start: 0.8292 (mmm) cc_final: 0.7872 (mmm) REVERT: B 309 ILE cc_start: 0.8566 (mm) cc_final: 0.8236 (mp) REVERT: B 390 GLN cc_start: 0.7734 (mm110) cc_final: 0.7496 (mm-40) REVERT: B 600 ASP cc_start: 0.8280 (m-30) cc_final: 0.8007 (m-30) REVERT: B 905 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.8254 (mt0) REVERT: C 40 GLN cc_start: 0.8013 (tp40) cc_final: 0.7784 (mm-40) REVERT: C 148 LYS cc_start: 0.8281 (mmmm) cc_final: 0.7960 (mmmm) REVERT: C 386 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.8226 (pm20) REVERT: C 447 TYR cc_start: 0.9282 (OUTLIER) cc_final: 0.7443 (p90) REVERT: C 592 ASP cc_start: 0.7939 (m-30) cc_final: 0.7714 (m-30) REVERT: C 774 THR cc_start: 0.8237 (p) cc_final: 0.7997 (p) REVERT: C 1006 MET cc_start: 0.7402 (mtm) cc_final: 0.7178 (mtm) outliers start: 32 outliers final: 14 residues processed: 230 average time/residue: 0.7704 time to fit residues: 205.5604 Evaluate side-chains 215 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 195 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 GLN Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 447 TYR Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 643 TYR Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 447 TYR Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 643 TYR Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 905 GLN Chi-restraints excluded: chain B residue 946 THR Chi-restraints excluded: chain C residue 386 GLN Chi-restraints excluded: chain C residue 447 TYR Chi-restraints excluded: chain C residue 594 SER Chi-restraints excluded: chain C residue 643 TYR Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 946 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 57 optimal weight: 0.2980 chunk 59 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 218 optimal weight: 6.9990 chunk 206 optimal weight: 6.9990 chunk 153 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 chunk 336 optimal weight: 3.9990 chunk 110 optimal weight: 0.0980 chunk 173 optimal weight: 4.9990 chunk 175 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1140 GLN B 857 GLN B1082 GLN B1112 ASN C 667 ASN C 756 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.147397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.119428 restraints weight = 21761.503| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.46 r_work: 0.3146 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 29130 Z= 0.208 Angle : 0.743 8.113 39966 Z= 0.388 Chirality : 0.049 0.239 4851 Planarity : 0.005 0.045 4908 Dihedral : 8.091 114.703 6494 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.62 % Allowed : 6.92 % Favored : 91.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.14), residues: 3450 helix: 1.79 (0.19), residues: 780 sheet: 0.51 (0.18), residues: 687 loop : -0.04 (0.13), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B1072 TYR 0.017 0.002 TYR B 172 PHE 0.027 0.002 PHE A 432 TRP 0.007 0.002 TRP C1186 HIS 0.005 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00411 (28950) covalent geometry : angle 0.71063 (39477) SS BOND : bond 0.01071 ( 51) SS BOND : angle 1.96203 ( 102) hydrogen bonds : bond 0.08016 ( 1104) hydrogen bonds : angle 5.69837 ( 3102) link_ALPHA1-2 : bond 0.00514 ( 3) link_ALPHA1-2 : angle 2.67186 ( 9) link_ALPHA1-3 : bond 0.00990 ( 9) link_ALPHA1-3 : angle 1.75122 ( 27) link_ALPHA1-6 : bond 0.00506 ( 9) link_ALPHA1-6 : angle 1.85974 ( 27) link_BETA1-2 : bond 0.01728 ( 3) link_BETA1-2 : angle 4.68475 ( 9) link_BETA1-4 : bond 0.00476 ( 51) link_BETA1-4 : angle 2.20567 ( 153) link_NAG-ASN : bond 0.00368 ( 54) link_NAG-ASN : angle 1.88071 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 201 time to evaluate : 1.027 Fit side-chains revert: symmetry clash REVERT: A 148 LYS cc_start: 0.8244 (mmmm) cc_final: 0.7936 (mmmm) REVERT: A 386 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.7992 (pp30) REVERT: A 424 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8497 (mm) REVERT: A 447 TYR cc_start: 0.9306 (OUTLIER) cc_final: 0.7464 (p90) REVERT: B 148 LYS cc_start: 0.8213 (mmmm) cc_final: 0.7818 (mmtm) REVERT: B 230 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7130 (mtm-85) REVERT: B 390 GLN cc_start: 0.7803 (mm110) cc_final: 0.7578 (mm-40) REVERT: C 148 LYS cc_start: 0.8325 (mmmm) cc_final: 0.8020 (mmmm) REVERT: C 230 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7172 (mtp180) REVERT: C 386 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8031 (pm20) REVERT: C 447 TYR cc_start: 0.9332 (OUTLIER) cc_final: 0.7403 (p90) REVERT: C 1006 MET cc_start: 0.7513 (mtm) cc_final: 0.7270 (mtm) outliers start: 45 outliers final: 22 residues processed: 234 average time/residue: 0.6992 time to fit residues: 190.9893 Evaluate side-chains 228 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 199 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 386 GLN Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 447 TYR Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 643 TYR Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain B residue 447 TYR Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 643 TYR Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 757 ILE Chi-restraints excluded: chain B residue 946 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 230 ARG Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 386 GLN Chi-restraints excluded: chain C residue 447 TYR Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 594 SER Chi-restraints excluded: chain C residue 643 TYR Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain C residue 946 THR Chi-restraints excluded: chain C residue 994 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 170 optimal weight: 1.9990 chunk 221 optimal weight: 1.9990 chunk 175 optimal weight: 4.9990 chunk 315 optimal weight: 4.9990 chunk 273 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 244 optimal weight: 3.9990 chunk 323 optimal weight: 0.0770 chunk 250 optimal weight: 0.9990 chunk 203 optimal weight: 6.9990 chunk 86 optimal weight: 0.5980 overall best weight: 1.1344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 HIS A1140 GLN B 857 GLN C 667 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.148674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.120967 restraints weight = 21980.554| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.50 r_work: 0.3164 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 29130 Z= 0.161 Angle : 0.665 7.419 39966 Z= 0.346 Chirality : 0.046 0.233 4851 Planarity : 0.004 0.039 4908 Dihedral : 7.676 106.314 6494 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.30 % Allowed : 7.06 % Favored : 91.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.14), residues: 3450 helix: 2.07 (0.19), residues: 762 sheet: 0.52 (0.18), residues: 681 loop : -0.06 (0.13), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1072 TYR 0.013 0.002 TYR C 940 PHE 0.019 0.002 PHE A 432 TRP 0.006 0.001 TRP A 215 HIS 0.004 0.001 HIS B 189 Details of bonding type rmsd covalent geometry : bond 0.00310 (28950) covalent geometry : angle 0.63215 (39477) SS BOND : bond 0.00800 ( 51) SS BOND : angle 2.00666 ( 102) hydrogen bonds : bond 0.07003 ( 1104) hydrogen bonds : angle 5.52394 ( 3102) link_ALPHA1-2 : bond 0.00314 ( 3) link_ALPHA1-2 : angle 2.34304 ( 9) link_ALPHA1-3 : bond 0.01007 ( 9) link_ALPHA1-3 : angle 1.64003 ( 27) link_ALPHA1-6 : bond 0.00619 ( 9) link_ALPHA1-6 : angle 1.72235 ( 27) link_BETA1-2 : bond 0.01664 ( 3) link_BETA1-2 : angle 4.18415 ( 9) link_BETA1-4 : bond 0.00475 ( 51) link_BETA1-4 : angle 1.96732 ( 153) link_NAG-ASN : bond 0.00296 ( 54) link_NAG-ASN : angle 1.77541 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 200 time to evaluate : 1.040 Fit side-chains revert: symmetry clash REVERT: A 148 LYS cc_start: 0.8250 (mmmm) cc_final: 0.7947 (mmmm) REVERT: A 386 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.7895 (pp30) REVERT: A 424 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8468 (mm) REVERT: A 447 TYR cc_start: 0.9291 (OUTLIER) cc_final: 0.7448 (p90) REVERT: B 148 LYS cc_start: 0.8213 (mmmm) cc_final: 0.7813 (mmtm) REVERT: B 390 GLN cc_start: 0.7783 (mm110) cc_final: 0.7546 (mm-40) REVERT: B 726 GLN cc_start: 0.7579 (OUTLIER) cc_final: 0.7332 (tt0) REVERT: B 905 GLN cc_start: 0.8543 (pt0) cc_final: 0.8323 (mt0) REVERT: C 148 LYS cc_start: 0.8311 (mmmm) cc_final: 0.8006 (mmmm) REVERT: C 230 ARG cc_start: 0.7847 (mmm-85) cc_final: 0.7104 (mtp180) REVERT: C 364 ASP cc_start: 0.7711 (OUTLIER) cc_final: 0.7485 (p0) REVERT: C 386 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.7917 (pm20) REVERT: C 447 TYR cc_start: 0.9315 (OUTLIER) cc_final: 0.7424 (p90) REVERT: C 592 ASP cc_start: 0.7933 (m-30) cc_final: 0.7455 (m-30) REVERT: C 1006 MET cc_start: 0.7414 (mtm) cc_final: 0.7187 (mtm) outliers start: 36 outliers final: 19 residues processed: 228 average time/residue: 0.7071 time to fit residues: 186.7086 Evaluate side-chains 224 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 198 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 386 GLN Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 447 TYR Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 643 TYR Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain B residue 447 TYR Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 643 TYR Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 726 GLN Chi-restraints excluded: chain B residue 757 ILE Chi-restraints excluded: chain B residue 946 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 386 GLN Chi-restraints excluded: chain C residue 447 TYR Chi-restraints excluded: chain C residue 594 SER Chi-restraints excluded: chain C residue 643 TYR Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 946 THR Chi-restraints excluded: chain C residue 994 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 233 optimal weight: 0.0980 chunk 191 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 152 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 147 optimal weight: 3.9990 chunk 204 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 318 optimal weight: 3.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 HIS A 641 HIS A1140 GLN B 641 HIS B 857 GLN C 667 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.147024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.118981 restraints weight = 21820.615| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.47 r_work: 0.3140 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 29130 Z= 0.217 Angle : 0.767 8.102 39966 Z= 0.401 Chirality : 0.049 0.249 4851 Planarity : 0.005 0.046 4908 Dihedral : 8.038 111.668 6494 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.62 % Allowed : 6.88 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.13), residues: 3450 helix: 1.70 (0.19), residues: 780 sheet: 0.38 (0.18), residues: 666 loop : -0.12 (0.13), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B1072 TYR 0.018 0.002 TYR B 172 PHE 0.026 0.002 PHE A 432 TRP 0.008 0.002 TRP C1186 HIS 0.006 0.001 HIS A 175 Details of bonding type rmsd covalent geometry : bond 0.00431 (28950) covalent geometry : angle 0.73161 (39477) SS BOND : bond 0.01160 ( 51) SS BOND : angle 2.47689 ( 102) hydrogen bonds : bond 0.08148 ( 1104) hydrogen bonds : angle 5.73724 ( 3102) link_ALPHA1-2 : bond 0.00561 ( 3) link_ALPHA1-2 : angle 2.67354 ( 9) link_ALPHA1-3 : bond 0.00906 ( 9) link_ALPHA1-3 : angle 1.85137 ( 27) link_ALPHA1-6 : bond 0.00573 ( 9) link_ALPHA1-6 : angle 1.66080 ( 27) link_BETA1-2 : bond 0.01741 ( 3) link_BETA1-2 : angle 4.61456 ( 9) link_BETA1-4 : bond 0.00505 ( 51) link_BETA1-4 : angle 2.16724 ( 153) link_NAG-ASN : bond 0.00387 ( 54) link_NAG-ASN : angle 1.93237 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 195 time to evaluate : 1.075 Fit side-chains revert: symmetry clash REVERT: A 148 LYS cc_start: 0.8254 (mmmm) cc_final: 0.7955 (mmmm) REVERT: A 184 CYS cc_start: 0.7171 (m) cc_final: 0.6851 (m) REVERT: A 386 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.7948 (pp30) REVERT: A 424 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8523 (mm) REVERT: A 447 TYR cc_start: 0.9310 (OUTLIER) cc_final: 0.7463 (p90) REVERT: B 148 LYS cc_start: 0.8226 (mmmm) cc_final: 0.7820 (mmtm) REVERT: B 230 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7193 (mtm-85) REVERT: B 386 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.7950 (pm20) REVERT: B 604 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8382 (mt-10) REVERT: C 148 LYS cc_start: 0.8308 (mmmm) cc_final: 0.7963 (mmmm) REVERT: C 230 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7249 (mtp180) REVERT: C 364 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.7478 (p0) REVERT: C 386 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.7839 (pm20) REVERT: C 447 TYR cc_start: 0.9333 (OUTLIER) cc_final: 0.7391 (p90) REVERT: C 497 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.6987 (tt) REVERT: C 592 ASP cc_start: 0.7930 (m-30) cc_final: 0.7393 (m-30) REVERT: C 604 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8316 (mm-30) outliers start: 45 outliers final: 22 residues processed: 229 average time/residue: 0.7482 time to fit residues: 198.6914 Evaluate side-chains 228 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 194 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 386 GLN Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 447 TYR Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 643 TYR Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain B residue 386 GLN Chi-restraints excluded: chain B residue 447 TYR Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 604 GLU Chi-restraints excluded: chain B residue 643 TYR Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 757 ILE Chi-restraints excluded: chain B residue 946 THR Chi-restraints excluded: chain C residue 230 ARG Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 386 GLN Chi-restraints excluded: chain C residue 447 TYR Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 594 SER Chi-restraints excluded: chain C residue 604 GLU Chi-restraints excluded: chain C residue 643 TYR Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain C residue 946 THR Chi-restraints excluded: chain C residue 994 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 342 optimal weight: 5.9990 chunk 236 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 190 optimal weight: 4.9990 chunk 248 optimal weight: 5.9990 chunk 324 optimal weight: 3.9990 chunk 298 optimal weight: 9.9990 chunk 164 optimal weight: 4.9990 chunk 235 optimal weight: 0.6980 chunk 119 optimal weight: 5.9990 chunk 246 optimal weight: 4.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 HIS A1140 GLN B 857 GLN C 175 HIS C 667 ASN C1140 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.146061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.118125 restraints weight = 21791.326| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.51 r_work: 0.3122 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 29130 Z= 0.267 Angle : 0.858 11.989 39966 Z= 0.450 Chirality : 0.053 0.331 4851 Planarity : 0.006 0.056 4908 Dihedral : 8.553 122.078 6494 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.41 % Allowed : 7.03 % Favored : 91.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.13), residues: 3450 helix: 1.62 (0.19), residues: 762 sheet: 0.32 (0.18), residues: 666 loop : -0.23 (0.13), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B1072 TYR 0.022 0.003 TYR B 172 PHE 0.027 0.003 PHE A 432 TRP 0.010 0.002 TRP B1186 HIS 0.005 0.002 HIS B 189 Details of bonding type rmsd covalent geometry : bond 0.00545 (28950) covalent geometry : angle 0.81784 (39477) SS BOND : bond 0.01450 ( 51) SS BOND : angle 3.05987 ( 102) hydrogen bonds : bond 0.08776 ( 1104) hydrogen bonds : angle 5.92451 ( 3102) link_ALPHA1-2 : bond 0.00774 ( 3) link_ALPHA1-2 : angle 2.68605 ( 9) link_ALPHA1-3 : bond 0.00786 ( 9) link_ALPHA1-3 : angle 1.99089 ( 27) link_ALPHA1-6 : bond 0.00531 ( 9) link_ALPHA1-6 : angle 1.61683 ( 27) link_BETA1-2 : bond 0.01843 ( 3) link_BETA1-2 : angle 5.00236 ( 9) link_BETA1-4 : bond 0.00519 ( 51) link_BETA1-4 : angle 2.36434 ( 153) link_NAG-ASN : bond 0.00434 ( 54) link_NAG-ASN : angle 2.11223 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 199 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 184 CYS cc_start: 0.7219 (m) cc_final: 0.6878 (m) REVERT: A 332 TYR cc_start: 0.9079 (OUTLIER) cc_final: 0.8822 (m-80) REVERT: A 386 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.7941 (pp30) REVERT: A 424 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8552 (mm) REVERT: A 447 TYR cc_start: 0.9317 (OUTLIER) cc_final: 0.7467 (p90) REVERT: B 148 LYS cc_start: 0.8248 (mmmm) cc_final: 0.7835 (mmtm) REVERT: B 230 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7191 (mtm-85) REVERT: B 361 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.8415 (mm110) REVERT: B 386 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8113 (pm20) REVERT: B 604 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8426 (mt-10) REVERT: C 148 LYS cc_start: 0.8318 (mmmm) cc_final: 0.7977 (mmmm) REVERT: C 230 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7254 (mtp180) REVERT: C 364 ASP cc_start: 0.7682 (OUTLIER) cc_final: 0.7438 (p0) REVERT: C 386 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.7902 (pm20) REVERT: C 447 TYR cc_start: 0.9346 (OUTLIER) cc_final: 0.7439 (p90) REVERT: C 604 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8330 (mm-30) outliers start: 39 outliers final: 22 residues processed: 229 average time/residue: 0.6817 time to fit residues: 181.9705 Evaluate side-chains 225 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 190 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 386 GLN Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 447 TYR Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 643 TYR Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 386 GLN Chi-restraints excluded: chain B residue 447 TYR Chi-restraints excluded: chain B residue 542 SER Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 604 GLU Chi-restraints excluded: chain B residue 643 TYR Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 757 ILE Chi-restraints excluded: chain C residue 230 ARG Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 386 GLN Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain C residue 447 TYR Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 594 SER Chi-restraints excluded: chain C residue 604 GLU Chi-restraints excluded: chain C residue 643 TYR Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain C residue 946 THR Chi-restraints excluded: chain C residue 994 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 306 optimal weight: 4.9990 chunk 336 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 288 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 258 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 173 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1140 GLN B 756 GLN C 175 HIS C 667 ASN C1140 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.147369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.119935 restraints weight = 21877.305| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.39 r_work: 0.3135 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 29130 Z= 0.194 Angle : 0.743 13.650 39966 Z= 0.388 Chirality : 0.048 0.299 4851 Planarity : 0.005 0.043 4908 Dihedral : 8.216 116.753 6494 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.48 % Allowed : 7.17 % Favored : 91.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.13), residues: 3450 helix: 1.86 (0.19), residues: 762 sheet: 0.45 (0.18), residues: 678 loop : -0.17 (0.13), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1072 TYR 0.016 0.002 TYR A 192 PHE 0.022 0.002 PHE A 432 TRP 0.008 0.001 TRP B1186 HIS 0.004 0.001 HIS B 189 Details of bonding type rmsd covalent geometry : bond 0.00378 (28950) covalent geometry : angle 0.70319 (39477) SS BOND : bond 0.01083 ( 51) SS BOND : angle 2.90381 ( 102) hydrogen bonds : bond 0.07660 ( 1104) hydrogen bonds : angle 5.69479 ( 3102) link_ALPHA1-2 : bond 0.00467 ( 3) link_ALPHA1-2 : angle 2.50572 ( 9) link_ALPHA1-3 : bond 0.00893 ( 9) link_ALPHA1-3 : angle 1.81071 ( 27) link_ALPHA1-6 : bond 0.00608 ( 9) link_ALPHA1-6 : angle 1.60810 ( 27) link_BETA1-2 : bond 0.01725 ( 3) link_BETA1-2 : angle 4.43076 ( 9) link_BETA1-4 : bond 0.00485 ( 51) link_BETA1-4 : angle 2.11417 ( 153) link_NAG-ASN : bond 0.00345 ( 54) link_NAG-ASN : angle 1.94650 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 197 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 184 CYS cc_start: 0.7139 (m) cc_final: 0.6787 (m) REVERT: A 386 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.7844 (pp30) REVERT: A 424 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8491 (mm) REVERT: A 447 TYR cc_start: 0.9298 (OUTLIER) cc_final: 0.7456 (p90) REVERT: B 148 LYS cc_start: 0.8248 (mmmm) cc_final: 0.7844 (mmtm) REVERT: B 386 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.7827 (pm20) REVERT: B 604 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8382 (mt-10) REVERT: B 860 GLN cc_start: 0.8020 (mt0) cc_final: 0.7722 (mt0) REVERT: C 139 ILE cc_start: 0.8125 (OUTLIER) cc_final: 0.7900 (tt) REVERT: C 148 LYS cc_start: 0.8293 (mmmm) cc_final: 0.7957 (mmmm) REVERT: C 230 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7133 (mtp180) REVERT: C 364 ASP cc_start: 0.7714 (OUTLIER) cc_final: 0.7481 (p0) REVERT: C 386 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.7906 (pm20) REVERT: C 447 TYR cc_start: 0.9328 (OUTLIER) cc_final: 0.7429 (p90) REVERT: C 604 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8291 (mm-30) REVERT: C 726 GLN cc_start: 0.7765 (OUTLIER) cc_final: 0.7375 (tt0) outliers start: 41 outliers final: 20 residues processed: 228 average time/residue: 0.7800 time to fit residues: 205.8637 Evaluate side-chains 226 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 194 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 386 GLN Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 447 TYR Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 643 TYR Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain B residue 386 GLN Chi-restraints excluded: chain B residue 447 TYR Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 542 SER Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 604 GLU Chi-restraints excluded: chain B residue 643 TYR Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 757 ILE Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 230 ARG Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 386 GLN Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain C residue 447 TYR Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 594 SER Chi-restraints excluded: chain C residue 604 GLU Chi-restraints excluded: chain C residue 643 TYR Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 726 GLN Chi-restraints excluded: chain C residue 946 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 248 optimal weight: 5.9990 chunk 107 optimal weight: 0.5980 chunk 89 optimal weight: 4.9990 chunk 142 optimal weight: 0.9980 chunk 286 optimal weight: 1.9990 chunk 210 optimal weight: 3.9990 chunk 105 optimal weight: 0.0980 chunk 345 optimal weight: 3.9990 chunk 332 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 129 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1140 GLN C 667 ASN C1140 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.148323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.120736 restraints weight = 21942.999| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.49 r_work: 0.3162 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29130 Z= 0.162 Angle : 0.689 14.083 39966 Z= 0.359 Chirality : 0.046 0.274 4851 Planarity : 0.004 0.040 4908 Dihedral : 7.787 105.152 6494 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.23 % Allowed : 7.71 % Favored : 91.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.14), residues: 3450 helix: 2.05 (0.19), residues: 762 sheet: 0.53 (0.18), residues: 681 loop : -0.10 (0.13), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1072 TYR 0.013 0.002 TYR C 940 PHE 0.018 0.002 PHE C 290 TRP 0.006 0.001 TRP A 215 HIS 0.004 0.001 HIS B 189 Details of bonding type rmsd covalent geometry : bond 0.00309 (28950) covalent geometry : angle 0.65084 (39477) SS BOND : bond 0.00868 ( 51) SS BOND : angle 2.80184 ( 102) hydrogen bonds : bond 0.06979 ( 1104) hydrogen bonds : angle 5.52866 ( 3102) link_ALPHA1-2 : bond 0.00274 ( 3) link_ALPHA1-2 : angle 2.22978 ( 9) link_ALPHA1-3 : bond 0.00915 ( 9) link_ALPHA1-3 : angle 1.73912 ( 27) link_ALPHA1-6 : bond 0.00684 ( 9) link_ALPHA1-6 : angle 1.59835 ( 27) link_BETA1-2 : bond 0.01613 ( 3) link_BETA1-2 : angle 4.00289 ( 9) link_BETA1-4 : bond 0.00476 ( 51) link_BETA1-4 : angle 1.92892 ( 153) link_NAG-ASN : bond 0.00315 ( 54) link_NAG-ASN : angle 1.87016 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 196 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 332 TYR cc_start: 0.9035 (OUTLIER) cc_final: 0.8813 (m-80) REVERT: A 386 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.7856 (pp30) REVERT: A 424 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8450 (mm) REVERT: A 447 TYR cc_start: 0.9292 (OUTLIER) cc_final: 0.7449 (p90) REVERT: B 148 LYS cc_start: 0.8223 (mmmm) cc_final: 0.7815 (mmtm) REVERT: B 361 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.8308 (mm110) REVERT: B 604 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8381 (mt-10) REVERT: B 720 MET cc_start: 0.7867 (ttm) cc_final: 0.7488 (mtp) REVERT: B 860 GLN cc_start: 0.8025 (mt0) cc_final: 0.7716 (mt0) REVERT: B 905 GLN cc_start: 0.8517 (pt0) cc_final: 0.8312 (mt0) REVERT: C 139 ILE cc_start: 0.8143 (OUTLIER) cc_final: 0.7888 (tt) REVERT: C 148 LYS cc_start: 0.8290 (mmmm) cc_final: 0.7949 (mmmm) REVERT: C 230 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7041 (mtp180) REVERT: C 364 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.7477 (p0) REVERT: C 386 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.7854 (pm20) REVERT: C 447 TYR cc_start: 0.9315 (OUTLIER) cc_final: 0.7425 (p90) REVERT: C 592 ASP cc_start: 0.7946 (m-30) cc_final: 0.7420 (m-30) REVERT: C 604 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8291 (mm-30) REVERT: C 726 GLN cc_start: 0.7696 (OUTLIER) cc_final: 0.7320 (tt0) REVERT: C 774 THR cc_start: 0.8226 (p) cc_final: 0.7999 (p) outliers start: 34 outliers final: 17 residues processed: 225 average time/residue: 0.6920 time to fit residues: 180.5627 Evaluate side-chains 226 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 196 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 386 GLN Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 447 TYR Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 643 TYR Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 447 TYR Chi-restraints excluded: chain B residue 542 SER Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 604 GLU Chi-restraints excluded: chain B residue 643 TYR Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 230 ARG Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 386 GLN Chi-restraints excluded: chain C residue 447 TYR Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 594 SER Chi-restraints excluded: chain C residue 604 GLU Chi-restraints excluded: chain C residue 643 TYR Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 726 GLN Chi-restraints excluded: chain C residue 946 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 277 optimal weight: 0.5980 chunk 343 optimal weight: 3.9990 chunk 206 optimal weight: 6.9990 chunk 138 optimal weight: 0.8980 chunk 175 optimal weight: 1.9990 chunk 225 optimal weight: 5.9990 chunk 193 optimal weight: 0.6980 chunk 318 optimal weight: 3.9990 chunk 233 optimal weight: 0.5980 chunk 48 optimal weight: 4.9990 chunk 312 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1140 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.149107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.121521 restraints weight = 21948.046| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.49 r_work: 0.3171 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29130 Z= 0.151 Angle : 0.668 14.315 39966 Z= 0.347 Chirality : 0.045 0.264 4851 Planarity : 0.004 0.043 4908 Dihedral : 7.410 92.297 6494 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.19 % Allowed : 7.71 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.14), residues: 3450 helix: 2.16 (0.19), residues: 762 sheet: 0.53 (0.18), residues: 711 loop : -0.07 (0.13), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1072 TYR 0.013 0.001 TYR C 454 PHE 0.017 0.002 PHE C 290 TRP 0.006 0.001 TRP A 215 HIS 0.004 0.001 HIS B 189 Details of bonding type rmsd covalent geometry : bond 0.00285 (28950) covalent geometry : angle 0.63083 (39477) SS BOND : bond 0.00785 ( 51) SS BOND : angle 2.80497 ( 102) hydrogen bonds : bond 0.06696 ( 1104) hydrogen bonds : angle 5.44577 ( 3102) link_ALPHA1-2 : bond 0.00195 ( 3) link_ALPHA1-2 : angle 2.09640 ( 9) link_ALPHA1-3 : bond 0.00934 ( 9) link_ALPHA1-3 : angle 1.70310 ( 27) link_ALPHA1-6 : bond 0.00748 ( 9) link_ALPHA1-6 : angle 1.59851 ( 27) link_BETA1-2 : bond 0.01516 ( 3) link_BETA1-2 : angle 3.66812 ( 9) link_BETA1-4 : bond 0.00465 ( 51) link_BETA1-4 : angle 1.81056 ( 153) link_NAG-ASN : bond 0.00318 ( 54) link_NAG-ASN : angle 1.78815 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 198 time to evaluate : 1.065 Fit side-chains revert: symmetry clash REVERT: A 386 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.7854 (pp30) REVERT: A 424 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8440 (mm) REVERT: A 447 TYR cc_start: 0.9284 (OUTLIER) cc_final: 0.7448 (p90) REVERT: B 148 LYS cc_start: 0.8227 (mmmm) cc_final: 0.7838 (mmtm) REVERT: B 309 ILE cc_start: 0.8604 (mm) cc_final: 0.8287 (mp) REVERT: B 332 TYR cc_start: 0.9031 (OUTLIER) cc_final: 0.8752 (m-80) REVERT: B 600 ASP cc_start: 0.8297 (m-30) cc_final: 0.8005 (m-30) REVERT: B 604 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8377 (mt-10) REVERT: C 139 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7925 (tt) REVERT: C 148 LYS cc_start: 0.8301 (mmmm) cc_final: 0.8019 (mmmm) REVERT: C 364 ASP cc_start: 0.7696 (OUTLIER) cc_final: 0.7473 (p0) REVERT: C 386 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.7866 (pm20) REVERT: C 447 TYR cc_start: 0.9310 (OUTLIER) cc_final: 0.7383 (p90) REVERT: C 592 ASP cc_start: 0.7956 (m-30) cc_final: 0.7440 (m-30) REVERT: C 604 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8308 (mm-30) REVERT: C 726 GLN cc_start: 0.7677 (OUTLIER) cc_final: 0.7344 (tt0) REVERT: C 774 THR cc_start: 0.8246 (p) cc_final: 0.8023 (p) outliers start: 33 outliers final: 17 residues processed: 224 average time/residue: 0.6988 time to fit residues: 181.8731 Evaluate side-chains 221 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 193 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 386 GLN Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 447 TYR Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 643 TYR Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain B residue 332 TYR Chi-restraints excluded: chain B residue 447 TYR Chi-restraints excluded: chain B residue 542 SER Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 604 GLU Chi-restraints excluded: chain B residue 643 TYR Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 386 GLN Chi-restraints excluded: chain C residue 447 TYR Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 594 SER Chi-restraints excluded: chain C residue 604 GLU Chi-restraints excluded: chain C residue 643 TYR Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 726 GLN Chi-restraints excluded: chain C residue 946 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 225 optimal weight: 3.9990 chunk 171 optimal weight: 0.7980 chunk 106 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 346 optimal weight: 4.9990 chunk 332 optimal weight: 3.9990 chunk 342 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 218 optimal weight: 5.9990 chunk 146 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1140 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.147762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.120395 restraints weight = 21935.053| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.35 r_work: 0.3143 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 29130 Z= 0.187 Angle : 0.752 27.417 39966 Z= 0.391 Chirality : 0.048 0.453 4851 Planarity : 0.005 0.043 4908 Dihedral : 7.616 95.302 6494 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.15 % Allowed : 7.60 % Favored : 91.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.14), residues: 3450 helix: 1.86 (0.19), residues: 780 sheet: 0.47 (0.18), residues: 687 loop : -0.05 (0.13), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1072 TYR 0.015 0.002 TYR B 172 PHE 0.023 0.002 PHE A 432 TRP 0.007 0.001 TRP B1186 HIS 0.005 0.001 HIS B 189 Details of bonding type rmsd covalent geometry : bond 0.00364 (28950) covalent geometry : angle 0.71405 (39477) SS BOND : bond 0.01011 ( 51) SS BOND : angle 3.14761 ( 102) hydrogen bonds : bond 0.07527 ( 1104) hydrogen bonds : angle 5.63341 ( 3102) link_ALPHA1-2 : bond 0.00361 ( 3) link_ALPHA1-2 : angle 2.27159 ( 9) link_ALPHA1-3 : bond 0.00854 ( 9) link_ALPHA1-3 : angle 1.81785 ( 27) link_ALPHA1-6 : bond 0.00722 ( 9) link_ALPHA1-6 : angle 1.56194 ( 27) link_BETA1-2 : bond 0.01528 ( 3) link_BETA1-2 : angle 3.90718 ( 9) link_BETA1-4 : bond 0.00458 ( 51) link_BETA1-4 : angle 1.93278 ( 153) link_NAG-ASN : bond 0.00344 ( 54) link_NAG-ASN : angle 1.86400 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14628.62 seconds wall clock time: 249 minutes 2.00 seconds (14942.00 seconds total)