Starting phenix.real_space_refine on Fri Mar 6 03:37:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xr8_22292/03_2026/6xr8_22292.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xr8_22292/03_2026/6xr8_22292.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xr8_22292/03_2026/6xr8_22292.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xr8_22292/03_2026/6xr8_22292.map" model { file = "/net/cci-nas-00/data/ceres_data/6xr8_22292/03_2026/6xr8_22292.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xr8_22292/03_2026/6xr8_22292.cif" } resolution = 2.9 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= 0.002 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 120 5.16 5 C 17511 2.51 5 N 4431 2.21 5 O 5565 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 98 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27627 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 8666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1107, 8666 Classifications: {'peptide': 1107} Link IDs: {'PTRANS': 51, 'TRANS': 1055} Chain breaks: 4 Chain: "B" Number of atoms: 8666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1107, 8666 Classifications: {'peptide': 1107} Link IDs: {'PTRANS': 51, 'TRANS': 1055} Chain breaks: 4 Chain: "C" Number of atoms: 8666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1107, 8666 Classifications: {'peptide': 1107} Link IDs: {'PTRANS': 51, 'TRANS': 1055} Chain breaks: 4 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "N" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'MAN': 2, '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: "x" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "0" 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: "2" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "5" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "9" 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: "BA" 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: "DA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "GA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "JA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "MA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "PA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "SA" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'MAN': 2, '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: "cA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "fA" 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: "hA" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "kA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "oA" 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: "qA" 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: "sA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "vA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "yA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "1A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "4A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "7A" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 6.18, per 1000 atoms: 0.22 Number of scatterers: 27627 At special positions: 0 Unit cell: (142.725, 143.55, 197.175, 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 120 16.00 O 5565 8.00 N 4431 7.00 C 17511 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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 ALPHA1-3 " MAN n 3 " - " MAN n 4 " " MAN7A 3 " - " MAN7A 4 " " MANSA 3 " - " MANSA 4 " ALPHA1-4 " NAG 5 2 " - " MAN 5 3 " " NAG I 2 " - " MAN I 3 " " NAG Q 2 " - " MAN Q 3 " " NAG Y 2 " - " MAN Y 3 " " NAG b 2 " - " MAN b 3 " " NAG e 2 " - " MAN e 3 " " NAG h 2 " - " MAN h 3 " " NAG k 2 " - " MAN k 3 " " NAG n 2 " - " MAN n 3 " " NAG x 2 " - " MAN x 3 " " NAG1A 2 " - " MAN1A 3 " " NAG4A 2 " - " MAN4A 3 " " NAG7A 2 " - " MAN7A 3 " " NAGDA 2 " - " MANDA 3 " " NAGGA 2 " - " MANGA 3 " " NAGJA 2 " - " MANJA 3 " " NAGMA 2 " - " MANMA 3 " " NAGPA 2 " - " MANPA 3 " " NAGSA 2 " - " MANSA 3 " " NAGcA 2 " - " MANcA 3 " " NAGkA 2 " - " MANkA 3 " " NAGsA 2 " - " MANsA 3 " " NAGvA 2 " - " MANvA 3 " " NAGyA 2 " - " MANyA 3 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 2 1 " - " NAG 2 2 " " NAG 5 1 " - " NAG 5 2 " " NAG 9 1 " - " NAG 9 2 " " NAG I 1 " - " NAG I 2 " " NAG L 1 " - " NAG L 2 " " NAG N 1 " - " NAG N 2 " " NAG Q 1 " - " NAG Q 2 " " NAG U 1 " - " NAG U 2 " " NAG W 1 " - " NAG W 2 " " NAG Y 1 " - " NAG Y 2 " " NAG b 1 " - " NAG b 2 " " NAG e 1 " - " NAG e 2 " " NAG h 1 " - " NAG h 2 " " NAG k 1 " - " NAG k 2 " " NAG n 1 " - " NAG n 2 " " NAG x 1 " - " NAG x 2 " " NAG1A 1 " - " NAG1A 2 " " NAG4A 1 " - " NAG4A 2 " " NAG7A 1 " - " NAG7A 2 " " NAGBA 1 " - " NAGBA 2 " " NAGDA 1 " - " NAGDA 2 " " NAGGA 1 " - " NAGGA 2 " " NAGJA 1 " - " NAGJA 2 " " NAGMA 1 " - " NAGMA 2 " " NAGPA 1 " - " NAGPA 2 " " NAGSA 1 " - " NAGSA 2 " " NAGcA 1 " - " NAGcA 2 " " NAGfA 1 " - " NAGfA 2 " " NAGhA 1 " - " NAGhA 2 " " NAGkA 1 " - " NAGkA 2 " " NAGoA 1 " - " NAGoA 2 " " NAGqA 1 " - " NAGqA 2 " " NAGsA 1 " - " NAGsA 2 " " NAGvA 1 " - " NAGvA 2 " " NAGyA 1 " - " NAGyA 2 " BETA1-6 " NAG 2 1 " - " FUC 2 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG N 1 " - " FUC N 3 " " NAGhA 1 " - " FUChA 3 " NAG-ASN " NAG 0 1 " - " ASN B 17 " " NAG 2 1 " - " ASN B1074 " " NAG 5 1 " - " ASN B 122 " " NAG 9 1 " - " ASN B 331 " " NAG A1402 " - " ASN A 343 " " NAG A1403 " - " ASN A 603 " " NAG A1404 " - " ASN A 657 " " NAG A1405 " - " ASN A 709 " " NAG A1406 " - " ASN A 149 " " NAG A1407 " - " ASN A1158 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 343 " " NAG B1403 " - " ASN B 603 " " NAG B1404 " - " ASN B 657 " " NAG B1405 " - " ASN B 709 " " NAG B1406 " - " ASN B 149 " " NAG B1407 " - " ASN B1158 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 343 " " NAG C1403 " - " ASN C 603 " " NAG C1404 " - " ASN C 657 " " NAG C1405 " - " ASN C 709 " " NAG C1406 " - " ASN C 149 " " NAG C1407 " - " ASN C1158 " " NAG I 1 " - " ASN A 717 " " NAG L 1 " - " ASN A 17 " " NAG N 1 " - " ASN A1074 " " NAG Q 1 " - " ASN A 122 " " NAG U 1 " - " ASN A 331 " " NAG W 1 " - " ASN A 165 " " NAG Y 1 " - " ASN A 234 " " NAG b 1 " - " ASN A 282 " " NAG e 1 " - " ASN A 616 " " NAG h 1 " - " ASN A 801 " " NAG k 1 " - " ASN A1098 " " NAG n 1 " - " ASN A1134 " " NAG x 1 " - " ASN B 717 " " NAG1A 1 " - " ASN C 801 " " NAG4A 1 " - " ASN C1098 " " NAG7A 1 " - " ASN C1134 " " NAGBA 1 " - " ASN B 165 " " NAGDA 1 " - " ASN B 234 " " NAGGA 1 " - " ASN B 282 " " NAGJA 1 " - " ASN B 616 " " NAGMA 1 " - " ASN B 801 " " NAGPA 1 " - " ASN B1098 " " NAGSA 1 " - " ASN B1134 " " NAGcA 1 " - " ASN C 717 " " NAGfA 1 " - " ASN C 17 " " NAGhA 1 " - " ASN C1074 " " NAGkA 1 " - " ASN C 122 " " NAGoA 1 " - " ASN C 331 " " NAGqA 1 " - " ASN C 165 " " NAGsA 1 " - " ASN C 234 " " NAGvA 1 " - " ASN C 282 " " NAGyA 1 " - " ASN C 616 " Time building additional restraints: 2.99 Conformation dependent library (CDL) restraints added in 1.3 seconds 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6216 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 56 sheets defined 27.2% alpha, 29.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.585A pdb=" N LEU A 368 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.259A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 4.223A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 757 through 783 removed outlier: 4.082A pdb=" N THR A 761 " --> pdb=" O GLY A 757 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.564A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 841 removed outlier: 4.038A pdb=" N LEU A 841 " --> pdb=" O GLY A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 848 removed outlier: 3.692A pdb=" N ALA A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG A 847 " --> pdb=" O ASP A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 856 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.587A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.859A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1161 removed outlier: 3.702A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N PHE A1148 " --> pdb=" O GLU A1144 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER A1161 " --> pdb=" O LYS A1157 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.525A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 369 Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.927A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 removed outlier: 3.871A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA B 411 " --> pdb=" O ARG B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 757 through 783 removed outlier: 4.113A pdb=" N THR B 761 " --> pdb=" O GLY B 757 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 842 through 848 removed outlier: 3.814A pdb=" N ALA B 846 " --> pdb=" O GLY B 842 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG B 847 " --> pdb=" O ASP B 843 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP B 848 " --> pdb=" O ILE B 844 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 842 through 848' Processing helix chain 'B' and resid 848 through 856 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.616A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.682A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.562A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1161 removed outlier: 3.864A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE B1148 " --> pdb=" O GLU B1144 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER B1161 " --> pdb=" O LYS B1157 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 364 through 369 Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.277A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 411 removed outlier: 4.077A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.815A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.361A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.548A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 837 through 841 removed outlier: 4.027A pdb=" N LEU C 841 " --> pdb=" O GLY C 838 " (cutoff:3.500A) Processing helix chain 'C' and resid 842 through 848 removed outlier: 3.709A pdb=" N ALA C 846 " --> pdb=" O GLY C 842 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG C 847 " --> pdb=" O ASP C 843 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 856 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.617A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.597A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.792A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1161 removed outlier: 3.850A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE C1148 " --> pdb=" O GLU C1144 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER C1161 " --> pdb=" O LYS C1157 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.226A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.226A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.591A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 13.083A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 12.254A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 9.798A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.436A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 9.714A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.250A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.426A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N GLY A 142 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N MET A 153 " --> pdb=" O GLY A 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.525A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 315 removed outlier: 4.477A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 3.883A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 324 through 328 removed outlier: 3.883A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.939A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.690A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.903A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.467A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.841A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.304A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 790 removed outlier: 6.270A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 1081 through 1082 Processing sheet with id=AC2, first strand: chain 'A' and resid 1088 through 1090 Processing sheet with id=AC3, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC4, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.991A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.991A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.583A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.012A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.912A pdb=" N CYS B 136 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N SER B 161 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 84 through 85 removed outlier: 12.908A pdb=" N PHE B 238 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 12.564A pdb=" N PHE B 135 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 13.089A pdb=" N THR B 240 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 10.896A pdb=" N ASN B 137 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 10.705A pdb=" N LEU B 242 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.912A pdb=" N CYS B 136 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N SER B 161 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 311 through 315 removed outlier: 4.495A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 324 through 328 removed outlier: 3.856A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.907A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.683A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD5, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD6, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.835A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.614A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AD9, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.884A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.335A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.338A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE4, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.268A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.268A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.663A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.717A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL C 126 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N VAL C 171 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ASN C 165 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N GLN C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ALA C 163 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N CYS C 136 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N SER C 161 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ASP C 138 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL C 159 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N PHE C 140 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N PHE C 157 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 84 through 85 removed outlier: 12.995A pdb=" N PHE C 238 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 12.295A pdb=" N ASN C 137 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 9.896A pdb=" N THR C 240 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N LEU C 242 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL C 126 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N VAL C 171 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ASN C 165 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N GLN C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ALA C 163 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N CYS C 136 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N SER C 161 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ASP C 138 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL C 159 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N PHE C 140 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N PHE C 157 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 311 through 315 removed outlier: 4.510A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 324 through 325 removed outlier: 6.868A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.875A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.745A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF5, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF6, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.881A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AF8, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.893A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.320A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AG2, first strand: chain 'C' and resid 1094 through 1097 1150 hydrogen bonds defined for protein. 3126 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: 7.56 Time building geometry restraints manager: 3.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8575 1.34 - 1.46: 6894 1.46 - 1.58: 12606 1.58 - 1.70: 2 1.70 - 1.82: 150 Bond restraints: 28227 Sorted by residual: bond pdb=" C1 FUChA 3 " pdb=" C2 FUChA 3 " ideal model delta sigma weight residual 1.528 1.590 -0.062 2.00e-02 2.50e+03 9.75e+00 bond pdb=" N VAL A 62 " pdb=" CA VAL A 62 " ideal model delta sigma weight residual 1.459 1.424 0.035 1.19e-02 7.06e+03 8.65e+00 bond pdb=" C1 FUC N 3 " pdb=" C2 FUC N 3 " ideal model delta sigma weight residual 1.528 1.585 -0.057 2.00e-02 2.50e+03 8.15e+00 bond pdb=" C5 MANPA 3 " pdb=" O5 MANPA 3 " ideal model delta sigma weight residual 1.418 1.472 -0.054 2.00e-02 2.50e+03 7.29e+00 bond pdb=" C1 NAG C1401 " pdb=" O5 NAG C1401 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.66e+00 ... (remaining 28222 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 36568 1.46 - 2.92: 1397 2.92 - 4.39: 327 4.39 - 5.85: 57 5.85 - 7.31: 39 Bond angle restraints: 38388 Sorted by residual: angle pdb=" N VAL A 62 " pdb=" CA VAL A 62 " pdb=" C VAL A 62 " ideal model delta sigma weight residual 108.23 101.58 6.65 1.53e+00 4.27e-01 1.89e+01 angle pdb=" N TRP A 258 " pdb=" CA TRP A 258 " pdb=" C TRP A 258 " ideal model delta sigma weight residual 108.19 113.32 -5.13 1.29e+00 6.01e-01 1.58e+01 angle pdb=" N TRP B 258 " pdb=" CA TRP B 258 " pdb=" C TRP B 258 " ideal model delta sigma weight residual 108.19 113.30 -5.11 1.29e+00 6.01e-01 1.57e+01 angle pdb=" N TRP C 258 " pdb=" CA TRP C 258 " pdb=" C TRP C 258 " ideal model delta sigma weight residual 108.19 113.30 -5.11 1.29e+00 6.01e-01 1.57e+01 angle pdb=" N THR A 602 " pdb=" CA THR A 602 " pdb=" C THR A 602 " ideal model delta sigma weight residual 111.28 107.60 3.68 1.09e+00 8.42e-01 1.14e+01 ... (remaining 38383 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.60: 17499 24.60 - 49.19: 625 49.19 - 73.79: 130 73.79 - 98.38: 87 98.38 - 122.98: 40 Dihedral angle restraints: 18381 sinusoidal: 8712 harmonic: 9669 Sorted by residual: dihedral pdb=" CB CYS A 840 " pdb=" SG CYS A 840 " pdb=" SG CYS A 851 " pdb=" CB CYS A 851 " ideal model delta sinusoidal sigma weight residual -86.00 -157.93 71.93 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" CB CYS B 840 " pdb=" SG CYS B 840 " pdb=" SG CYS B 851 " pdb=" CB CYS B 851 " ideal model delta sinusoidal sigma weight residual -86.00 -157.19 71.19 1 1.00e+01 1.00e-02 6.50e+01 dihedral pdb=" CB CYS C 840 " pdb=" SG CYS C 840 " pdb=" SG CYS C 851 " pdb=" CB CYS C 851 " ideal model delta sinusoidal sigma weight residual -86.00 -150.93 64.93 1 1.00e+01 1.00e-02 5.53e+01 ... (remaining 18378 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.338: 4682 0.338 - 0.676: 10 0.676 - 1.013: 0 1.013 - 1.351: 1 1.351 - 1.689: 1 Chirality restraints: 4694 Sorted by residual: chirality pdb=" C1 NAG A1407 " pdb=" ND2 ASN A1158 " pdb=" C2 NAG A1407 " pdb=" O5 NAG A1407 " both_signs ideal model delta sigma weight residual False -2.40 -0.71 -1.69 2.00e-01 2.50e+01 7.13e+01 chirality pdb=" C1 NAG A1404 " pdb=" ND2 ASN A 657 " pdb=" C2 NAG A1404 " pdb=" O5 NAG A1404 " both_signs ideal model delta sigma weight residual False -2.40 -1.32 -1.08 2.00e-01 2.50e+01 2.90e+01 chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -3.00 0.60 2.00e-01 2.50e+01 8.87e+00 ... (remaining 4691 not shown) Planarity restraints: 4844 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " 0.275 2.00e-02 2.50e+03 4.08e-01 2.08e+03 pdb=" CG ASN A 331 " -0.117 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " 0.146 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " -0.733 2.00e-02 2.50e+03 pdb=" C1 NAG U 1 " 0.429 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 657 " 0.270 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" CG ASN A 657 " -0.092 2.00e-02 2.50e+03 pdb=" OD1 ASN A 657 " -0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN A 657 " -0.495 2.00e-02 2.50e+03 pdb=" C1 NAG A1404 " 0.327 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 717 " 0.245 2.00e-02 2.50e+03 2.32e-01 6.72e+02 pdb=" CG ASN A 717 " -0.082 2.00e-02 2.50e+03 pdb=" OD1 ASN A 717 " -0.106 2.00e-02 2.50e+03 pdb=" ND2 ASN A 717 " -0.336 2.00e-02 2.50e+03 pdb=" C1 NAG I 1 " 0.279 2.00e-02 2.50e+03 ... (remaining 4841 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 387 2.65 - 3.21: 25952 3.21 - 3.78: 40993 3.78 - 4.34: 61575 4.34 - 4.90: 99461 Nonbonded interactions: 228368 Sorted by model distance: nonbonded pdb=" OE1 GLU B 406 " pdb=" OH TYR B 495 " model vdw 2.089 3.040 nonbonded pdb=" OE1 GLU C 406 " pdb=" OH TYR C 495 " model vdw 2.101 3.040 nonbonded pdb=" NZ LYS C 97 " pdb=" O GLN C 183 " model vdw 2.112 3.120 nonbonded pdb=" ND2 ASN A 61 " pdb=" C1 NAG A1401 " model vdw 2.149 3.550 nonbonded pdb=" C HIS A 69 " pdb=" N ALA A 260 " model vdw 2.167 3.350 ... (remaining 228363 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: 0.03 Found NCS groups: ncs_group { reference = chain '0' selection = chain '9' selection = chain 'BA' selection = chain 'L' selection = chain 'U' selection = chain 'W' selection = chain 'fA' selection = chain 'oA' selection = chain 'qA' } ncs_group { reference = (chain '1A' and resid 1 through 2) selection = (chain '2' and resid 1 through 2) selection = (chain '4A' and resid 1 through 2) selection = (chain '5' and resid 1 through 2) selection = (chain 'DA' and resid 1 through 2) selection = (chain 'GA' and resid 1 through 2) selection = (chain 'I' and resid 1 through 2) selection = (chain 'JA' and resid 1 through 2) selection = (chain 'MA' and resid 1 through 2) selection = (chain 'N' and resid 1 through 2) selection = (chain 'PA' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) selection = (chain 'Y' and resid 1 through 2) selection = (chain 'b' and resid 1 through 2) selection = (chain 'cA' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) selection = (chain 'h' and resid 1 through 2) selection = (chain 'hA' and resid 1 through 2) selection = (chain 'k' and resid 1 through 2) selection = (chain 'kA' and resid 1 through 2) selection = (chain 'sA' and resid 1 through 2) selection = (chain 'vA' and resid 1 through 2) selection = (chain 'x' and resid 1 through 2) selection = (chain 'yA' and resid 1 through 2) } ncs_group { reference = chain '7A' selection = chain 'SA' selection = chain 'n' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 9.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 0.560 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 29.170 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 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 : 0.008 0.455 28394 Z= 0.419 Angle : 0.893 25.744 38844 Z= 0.403 Chirality : 0.060 1.689 4694 Planarity : 0.003 0.057 4788 Dihedral : 15.807 122.977 12030 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.49 % Favored : 97.45 % Rotamer: Outliers : 0.73 % Allowed : 4.04 % Favored : 95.23 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.13), residues: 3291 helix: -0.83 (0.17), residues: 756 sheet: 0.41 (0.19), residues: 738 loop : -1.39 (0.13), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 509 TYR 0.010 0.001 TYR A 145 PHE 0.012 0.001 PHE A 79 TRP 0.016 0.001 TRP B 258 HIS 0.004 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00509 (28227) covalent geometry : angle 0.71355 (38388) SS BOND : bond 0.00337 ( 45) SS BOND : angle 1.26286 ( 90) hydrogen bonds : bond 0.21353 ( 1118) hydrogen bonds : angle 9.19748 ( 3126) link_ALPHA1-3 : bond 0.00673 ( 3) link_ALPHA1-3 : angle 1.96291 ( 9) link_ALPHA1-4 : bond 0.00900 ( 24) link_ALPHA1-4 : angle 2.54228 ( 72) link_BETA1-4 : bond 0.00852 ( 36) link_BETA1-4 : angle 2.08840 ( 108) link_BETA1-6 : bond 0.01794 ( 3) link_BETA1-6 : angle 2.74600 ( 9) link_NAG-ASN : bond 0.15154 ( 56) link_NAG-ASN : angle 7.80205 ( 168) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 583 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 PHE cc_start: 0.8529 (t80) cc_final: 0.8301 (t80) REVERT: A 567 ARG cc_start: 0.7236 (mtt90) cc_final: 0.6995 (mpt180) REVERT: A 661 GLU cc_start: 0.7726 (tt0) cc_final: 0.7430 (mp0) REVERT: A 872 GLN cc_start: 0.8458 (mt0) cc_final: 0.7980 (mt0) REVERT: B 528 LYS cc_start: 0.7658 (mtpp) cc_final: 0.7350 (mttp) REVERT: B 844 ILE cc_start: 0.4401 (OUTLIER) cc_final: 0.3840 (mm) REVERT: C 265 TYR cc_start: 0.8257 (p90) cc_final: 0.7980 (p90) REVERT: C 462 LYS cc_start: 0.7580 (mtmt) cc_final: 0.7294 (mmtt) REVERT: C 755 GLN cc_start: 0.7162 (mm-40) cc_final: 0.6735 (mt0) REVERT: C 844 ILE cc_start: 0.4195 (OUTLIER) cc_final: 0.3764 (mm) outliers start: 21 outliers final: 10 residues processed: 600 average time/residue: 0.6588 time to fit residues: 457.9109 Evaluate side-chains 295 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 283 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 1146 ASP Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 844 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 0.3980 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 0.0770 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 8.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 409 GLN A 437 ASN A 474 GLN A 606 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 836 GLN B 188 ASN B 317 ASN B 409 GLN B 437 ASN B 474 GLN B 544 ASN B 564 GLN B 606 ASN B 764 ASN B 836 GLN C 115 GLN C 188 ASN C 437 ASN C 474 GLN C 519 HIS C 606 ASN C 779 GLN ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.166035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.133872 restraints weight = 34514.774| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 3.35 r_work: 0.3152 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 28394 Z= 0.158 Angle : 0.749 14.333 38844 Z= 0.355 Chirality : 0.047 0.615 4694 Planarity : 0.004 0.043 4788 Dihedral : 13.461 106.839 6101 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.69 % Allowed : 11.61 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.14), residues: 3291 helix: 0.79 (0.18), residues: 783 sheet: 0.40 (0.18), residues: 810 loop : -1.28 (0.13), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 567 TYR 0.021 0.001 TYR B1067 PHE 0.020 0.002 PHE C 157 TRP 0.018 0.002 TRP C 258 HIS 0.005 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00350 (28227) covalent geometry : angle 0.69164 (38388) SS BOND : bond 0.00335 ( 45) SS BOND : angle 1.38909 ( 90) hydrogen bonds : bond 0.04490 ( 1118) hydrogen bonds : angle 6.28817 ( 3126) link_ALPHA1-3 : bond 0.01124 ( 3) link_ALPHA1-3 : angle 1.53746 ( 9) link_ALPHA1-4 : bond 0.01417 ( 24) link_ALPHA1-4 : angle 2.82175 ( 72) link_BETA1-4 : bond 0.00420 ( 36) link_BETA1-4 : angle 1.25562 ( 108) link_BETA1-6 : bond 0.01452 ( 3) link_BETA1-6 : angle 2.07122 ( 9) link_NAG-ASN : bond 0.00613 ( 56) link_NAG-ASN : angle 3.82372 ( 168) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 315 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6669 (OUTLIER) cc_final: 0.6115 (t-90) REVERT: A 81 ASN cc_start: 0.7898 (p0) cc_final: 0.7467 (p0) REVERT: A 115 GLN cc_start: 0.8016 (mt0) cc_final: 0.7813 (mt0) REVERT: A 319 ARG cc_start: 0.7309 (ptp90) cc_final: 0.6990 (ptm160) REVERT: A 462 LYS cc_start: 0.7839 (mtmt) cc_final: 0.7436 (mmtt) REVERT: A 568 ASP cc_start: 0.7688 (m-30) cc_final: 0.7191 (m-30) REVERT: A 602 THR cc_start: 0.7282 (m) cc_final: 0.6711 (p) REVERT: A 618 THR cc_start: 0.6273 (OUTLIER) cc_final: 0.5953 (p) REVERT: A 661 GLU cc_start: 0.7876 (tt0) cc_final: 0.7484 (mp0) REVERT: A 755 GLN cc_start: 0.7213 (OUTLIER) cc_final: 0.6102 (mp10) REVERT: A 872 GLN cc_start: 0.8555 (mt0) cc_final: 0.8126 (mt0) REVERT: A 900 MET cc_start: 0.8965 (OUTLIER) cc_final: 0.8764 (mtm) REVERT: B 81 ASN cc_start: 0.7960 (p0) cc_final: 0.7641 (p0) REVERT: B 158 ARG cc_start: 0.6243 (mmt90) cc_final: 0.5370 (mmm-85) REVERT: B 462 LYS cc_start: 0.7760 (mtmt) cc_final: 0.7322 (mmtt) REVERT: B 568 ASP cc_start: 0.7693 (m-30) cc_final: 0.7235 (m-30) REVERT: B 755 GLN cc_start: 0.7109 (OUTLIER) cc_final: 0.5745 (mp10) REVERT: B 839 ASP cc_start: 0.6593 (p0) cc_final: 0.6042 (m-30) REVERT: B 900 MET cc_start: 0.9102 (OUTLIER) cc_final: 0.8842 (mtp) REVERT: B 1091 ARG cc_start: 0.8195 (mtt-85) cc_final: 0.7988 (mtt-85) REVERT: C 81 ASN cc_start: 0.7401 (p0) cc_final: 0.7171 (p0) REVERT: C 115 GLN cc_start: 0.7940 (mt0) cc_final: 0.7620 (mt0) REVERT: C 152 TRP cc_start: 0.6423 (m100) cc_final: 0.6164 (m100) REVERT: C 157 PHE cc_start: 0.7999 (t80) cc_final: 0.7608 (t80) REVERT: C 190 ARG cc_start: 0.8146 (mtp85) cc_final: 0.7879 (mtp85) REVERT: C 389 ASP cc_start: 0.6348 (m-30) cc_final: 0.6112 (m-30) REVERT: C 462 LYS cc_start: 0.7793 (mtmt) cc_final: 0.7417 (mmtt) REVERT: C 755 GLN cc_start: 0.6799 (mm-40) cc_final: 0.6374 (mt0) REVERT: C 1091 ARG cc_start: 0.8216 (mtt-85) cc_final: 0.7995 (mtt-85) outliers start: 78 outliers final: 35 residues processed: 372 average time/residue: 0.5737 time to fit residues: 252.7205 Evaluate side-chains 291 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 250 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 839 ASP Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 606 ASN Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 242 optimal weight: 6.9990 chunk 304 optimal weight: 0.8980 chunk 205 optimal weight: 0.9980 chunk 251 optimal weight: 2.9990 chunk 236 optimal weight: 7.9990 chunk 272 optimal weight: 6.9990 chunk 66 optimal weight: 0.6980 chunk 121 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 174 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 606 ASN A 764 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN B 606 ASN B 804 GLN B 919 ASN C 474 GLN C 580 GLN C 919 ASN C 957 GLN C1113 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.164173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.131214 restraints weight = 34492.580| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 3.29 r_work: 0.3128 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 28394 Z= 0.155 Angle : 0.709 14.790 38844 Z= 0.328 Chirality : 0.045 0.411 4694 Planarity : 0.004 0.040 4788 Dihedral : 12.868 107.221 6090 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.63 % Allowed : 13.06 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.14), residues: 3291 helix: 1.27 (0.19), residues: 780 sheet: 0.59 (0.19), residues: 693 loop : -1.08 (0.13), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 577 TYR 0.023 0.001 TYR B 265 PHE 0.015 0.001 PHE C 32 TRP 0.010 0.001 TRP C 258 HIS 0.003 0.001 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00346 (28227) covalent geometry : angle 0.64964 (38388) SS BOND : bond 0.00478 ( 45) SS BOND : angle 1.84055 ( 90) hydrogen bonds : bond 0.04368 ( 1118) hydrogen bonds : angle 5.92989 ( 3126) link_ALPHA1-3 : bond 0.01069 ( 3) link_ALPHA1-3 : angle 1.42152 ( 9) link_ALPHA1-4 : bond 0.01507 ( 24) link_ALPHA1-4 : angle 2.86209 ( 72) link_BETA1-4 : bond 0.00415 ( 36) link_BETA1-4 : angle 1.17060 ( 108) link_BETA1-6 : bond 0.01582 ( 3) link_BETA1-6 : angle 2.24125 ( 9) link_NAG-ASN : bond 0.00458 ( 56) link_NAG-ASN : angle 3.64381 ( 168) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 287 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6709 (OUTLIER) cc_final: 0.6095 (t-90) REVERT: A 81 ASN cc_start: 0.8013 (p0) cc_final: 0.7631 (p0) REVERT: A 319 ARG cc_start: 0.7393 (ptp90) cc_final: 0.7089 (ptm160) REVERT: A 462 LYS cc_start: 0.7827 (mtmt) cc_final: 0.7415 (mmtt) REVERT: A 554 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6873 (mp0) REVERT: A 567 ARG cc_start: 0.7189 (mtt-85) cc_final: 0.6715 (mtt-85) REVERT: A 568 ASP cc_start: 0.7730 (m-30) cc_final: 0.7274 (m-30) REVERT: A 602 THR cc_start: 0.7336 (m) cc_final: 0.6865 (p) REVERT: A 661 GLU cc_start: 0.7946 (tt0) cc_final: 0.7574 (mp0) REVERT: A 790 LYS cc_start: 0.8077 (ptmt) cc_final: 0.7811 (mtmt) REVERT: A 872 GLN cc_start: 0.8576 (mt0) cc_final: 0.8171 (mt0) REVERT: A 878 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8814 (tt) REVERT: B 81 ASN cc_start: 0.8016 (p0) cc_final: 0.7674 (p0) REVERT: B 153 MET cc_start: 0.7218 (tpp) cc_final: 0.6368 (ttt) REVERT: B 462 LYS cc_start: 0.7851 (mtmt) cc_final: 0.7424 (mmtt) REVERT: B 568 ASP cc_start: 0.7594 (m-30) cc_final: 0.7128 (m-30) REVERT: B 755 GLN cc_start: 0.7099 (OUTLIER) cc_final: 0.5706 (mp10) REVERT: B 839 ASP cc_start: 0.6496 (p0) cc_final: 0.5985 (m-30) REVERT: C 81 ASN cc_start: 0.7361 (p0) cc_final: 0.7045 (p0) REVERT: C 115 GLN cc_start: 0.7873 (mt0) cc_final: 0.7606 (mt0) REVERT: C 157 PHE cc_start: 0.7987 (t80) cc_final: 0.7664 (t80) REVERT: C 190 ARG cc_start: 0.8135 (mtp85) cc_final: 0.7917 (mtp85) REVERT: C 462 LYS cc_start: 0.7835 (mtmt) cc_final: 0.7429 (mmtt) REVERT: C 568 ASP cc_start: 0.7623 (m-30) cc_final: 0.7221 (m-30) REVERT: C 586 ASP cc_start: 0.8507 (m-30) cc_final: 0.8233 (m-30) REVERT: C 755 GLN cc_start: 0.6908 (mm-40) cc_final: 0.6446 (mt0) outliers start: 105 outliers final: 44 residues processed: 366 average time/residue: 0.5457 time to fit residues: 238.5825 Evaluate side-chains 298 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 250 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 230 optimal weight: 0.8980 chunk 325 optimal weight: 1.9990 chunk 210 optimal weight: 0.5980 chunk 226 optimal weight: 5.9990 chunk 273 optimal weight: 0.9980 chunk 130 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 321 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 132 optimal weight: 9.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN A 606 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN B 414 GLN B 474 GLN B 804 GLN C 52 GLN C 957 GLN C1113 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.162831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.130118 restraints weight = 34286.461| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 3.26 r_work: 0.3099 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 28394 Z= 0.165 Angle : 0.706 15.151 38844 Z= 0.323 Chirality : 0.045 0.382 4694 Planarity : 0.004 0.043 4788 Dihedral : 12.273 106.367 6087 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.63 % Allowed : 13.99 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.14), residues: 3291 helix: 1.35 (0.19), residues: 780 sheet: 0.50 (0.18), residues: 723 loop : -1.10 (0.13), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 158 TYR 0.023 0.001 TYR B 265 PHE 0.012 0.001 PHE B1121 TRP 0.016 0.001 TRP C 152 HIS 0.003 0.001 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00376 (28227) covalent geometry : angle 0.65015 (38388) SS BOND : bond 0.00398 ( 45) SS BOND : angle 1.85508 ( 90) hydrogen bonds : bond 0.04108 ( 1118) hydrogen bonds : angle 5.77709 ( 3126) link_ALPHA1-3 : bond 0.01042 ( 3) link_ALPHA1-3 : angle 1.30083 ( 9) link_ALPHA1-4 : bond 0.01552 ( 24) link_ALPHA1-4 : angle 2.97476 ( 72) link_BETA1-4 : bond 0.00398 ( 36) link_BETA1-4 : angle 1.11140 ( 108) link_BETA1-6 : bond 0.01743 ( 3) link_BETA1-6 : angle 2.36713 ( 9) link_NAG-ASN : bond 0.00353 ( 56) link_NAG-ASN : angle 3.45887 ( 168) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 277 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6659 (OUTLIER) cc_final: 0.5981 (t-90) REVERT: A 81 ASN cc_start: 0.8192 (p0) cc_final: 0.7821 (p0) REVERT: A 319 ARG cc_start: 0.7408 (ptp90) cc_final: 0.7110 (ptm160) REVERT: A 462 LYS cc_start: 0.7791 (mtmt) cc_final: 0.7402 (mmtt) REVERT: A 471 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7349 (mm-30) REVERT: A 554 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6911 (mp0) REVERT: A 567 ARG cc_start: 0.7282 (mtt-85) cc_final: 0.6982 (mtt-85) REVERT: A 568 ASP cc_start: 0.7783 (m-30) cc_final: 0.7479 (m-30) REVERT: A 602 THR cc_start: 0.7539 (m) cc_final: 0.7049 (p) REVERT: A 618 THR cc_start: 0.6297 (OUTLIER) cc_final: 0.5944 (p) REVERT: A 661 GLU cc_start: 0.7980 (tt0) cc_final: 0.7595 (mp0) REVERT: A 872 GLN cc_start: 0.8622 (mt0) cc_final: 0.8224 (mt0) REVERT: A 878 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8824 (tt) REVERT: A 1113 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.8197 (mm110) REVERT: B 81 ASN cc_start: 0.8077 (p0) cc_final: 0.7711 (p0) REVERT: B 153 MET cc_start: 0.7276 (tpp) cc_final: 0.6444 (ttt) REVERT: B 158 ARG cc_start: 0.6367 (mmt90) cc_final: 0.5405 (mmm-85) REVERT: B 462 LYS cc_start: 0.7869 (mtmt) cc_final: 0.7421 (mmtt) REVERT: B 568 ASP cc_start: 0.7655 (m-30) cc_final: 0.7253 (m-30) REVERT: B 755 GLN cc_start: 0.7071 (OUTLIER) cc_final: 0.5728 (mp10) REVERT: B 839 ASP cc_start: 0.6728 (p0) cc_final: 0.6170 (m-30) REVERT: C 81 ASN cc_start: 0.7292 (p0) cc_final: 0.7048 (p0) REVERT: C 113 LYS cc_start: 0.7334 (mtpt) cc_final: 0.6947 (ttpp) REVERT: C 115 GLN cc_start: 0.7866 (mt0) cc_final: 0.7531 (mt0) REVERT: C 152 TRP cc_start: 0.6341 (m100) cc_final: 0.5973 (m100) REVERT: C 157 PHE cc_start: 0.8060 (t80) cc_final: 0.7718 (t80) REVERT: C 409 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.8072 (mt0) REVERT: C 462 LYS cc_start: 0.7809 (mtmt) cc_final: 0.7391 (mmtt) REVERT: C 568 ASP cc_start: 0.7601 (m-30) cc_final: 0.7331 (m-30) REVERT: C 755 GLN cc_start: 0.6981 (mm-40) cc_final: 0.6462 (mt0) REVERT: C 847 ARG cc_start: 0.4794 (mtm-85) cc_final: 0.4575 (ttp-170) outliers start: 105 outliers final: 48 residues processed: 363 average time/residue: 0.5539 time to fit residues: 239.6219 Evaluate side-chains 305 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 249 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 991 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 254 optimal weight: 2.9990 chunk 162 optimal weight: 6.9990 chunk 14 optimal weight: 8.9990 chunk 220 optimal weight: 9.9990 chunk 118 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 297 optimal weight: 3.9990 chunk 52 optimal weight: 8.9990 chunk 241 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 263 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN A 474 GLN A 519 HIS ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 GLN A 606 ASN A 787 GLN A 919 ASN B 317 ASN B 450 ASN B 474 GLN B 563 GLN B 606 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN C 474 GLN C 606 ASN C 703 ASN C 957 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.157909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.113752 restraints weight = 34364.763| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.08 r_work: 0.3149 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.096 28394 Z= 0.325 Angle : 0.836 16.019 38844 Z= 0.390 Chirality : 0.050 0.422 4694 Planarity : 0.005 0.052 4788 Dihedral : 12.378 108.084 6084 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.70 % Allowed : 13.71 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.14), residues: 3291 helix: 0.81 (0.19), residues: 804 sheet: 0.41 (0.19), residues: 684 loop : -1.18 (0.13), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 158 TYR 0.024 0.002 TYR A 265 PHE 0.018 0.002 PHE C 592 TRP 0.013 0.002 TRP A 104 HIS 0.006 0.002 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00774 (28227) covalent geometry : angle 0.77675 (38388) SS BOND : bond 0.00520 ( 45) SS BOND : angle 2.33501 ( 90) hydrogen bonds : bond 0.05246 ( 1118) hydrogen bonds : angle 6.10678 ( 3126) link_ALPHA1-3 : bond 0.01208 ( 3) link_ALPHA1-3 : angle 1.42894 ( 9) link_ALPHA1-4 : bond 0.01674 ( 24) link_ALPHA1-4 : angle 3.24749 ( 72) link_BETA1-4 : bond 0.00330 ( 36) link_BETA1-4 : angle 1.23122 ( 108) link_BETA1-6 : bond 0.01623 ( 3) link_BETA1-6 : angle 2.38917 ( 9) link_NAG-ASN : bond 0.00456 ( 56) link_NAG-ASN : angle 3.84069 ( 168) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 251 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6742 (OUTLIER) cc_final: 0.5993 (t-90) REVERT: A 81 ASN cc_start: 0.8476 (p0) cc_final: 0.8124 (p0) REVERT: A 113 LYS cc_start: 0.7646 (mtpt) cc_final: 0.7398 (ttpp) REVERT: A 179 LEU cc_start: 0.6548 (OUTLIER) cc_final: 0.6285 (mt) REVERT: A 319 ARG cc_start: 0.7594 (ptp90) cc_final: 0.7249 (ptm160) REVERT: A 462 LYS cc_start: 0.7808 (mtmt) cc_final: 0.7314 (mmtt) REVERT: A 568 ASP cc_start: 0.7897 (m-30) cc_final: 0.7545 (m-30) REVERT: A 618 THR cc_start: 0.6525 (OUTLIER) cc_final: 0.6034 (p) REVERT: A 661 GLU cc_start: 0.8134 (tt0) cc_final: 0.7696 (mp0) REVERT: A 725 GLU cc_start: 0.8812 (tt0) cc_final: 0.8482 (tt0) REVERT: A 847 ARG cc_start: 0.4770 (mtm-85) cc_final: 0.4441 (mtt180) REVERT: A 1113 GLN cc_start: 0.9051 (OUTLIER) cc_final: 0.8310 (mm110) REVERT: B 66 HIS cc_start: 0.6906 (OUTLIER) cc_final: 0.6474 (t-90) REVERT: B 81 ASN cc_start: 0.8322 (p0) cc_final: 0.8006 (p0) REVERT: B 132 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7873 (mt-10) REVERT: B 153 MET cc_start: 0.7260 (OUTLIER) cc_final: 0.6446 (ttt) REVERT: B 158 ARG cc_start: 0.6598 (mtt90) cc_final: 0.5582 (mmm-85) REVERT: B 415 THR cc_start: 0.7826 (OUTLIER) cc_final: 0.7597 (m) REVERT: B 462 LYS cc_start: 0.7939 (mtmt) cc_final: 0.7412 (mmtt) REVERT: B 568 ASP cc_start: 0.7852 (m-30) cc_final: 0.7434 (m-30) REVERT: B 661 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7040 (mp0) REVERT: B 755 GLN cc_start: 0.7205 (OUTLIER) cc_final: 0.5838 (mp10) REVERT: B 839 ASP cc_start: 0.7015 (p0) cc_final: 0.6590 (m-30) REVERT: B 847 ARG cc_start: 0.5327 (mtm-85) cc_final: 0.4941 (mtt-85) REVERT: C 113 LYS cc_start: 0.7715 (mtpt) cc_final: 0.7321 (ttpp) REVERT: C 115 GLN cc_start: 0.7857 (mt0) cc_final: 0.7492 (mt0) REVERT: C 152 TRP cc_start: 0.6479 (m100) cc_final: 0.6165 (m100) REVERT: C 157 PHE cc_start: 0.8094 (t80) cc_final: 0.7880 (t80) REVERT: C 265 TYR cc_start: 0.8359 (p90) cc_final: 0.7895 (p90) REVERT: C 409 GLN cc_start: 0.9036 (OUTLIER) cc_final: 0.8367 (mt0) REVERT: C 462 LYS cc_start: 0.7887 (mtmt) cc_final: 0.7395 (mmtt) REVERT: C 489 TYR cc_start: 0.8150 (m-80) cc_final: 0.7348 (m-80) REVERT: C 725 GLU cc_start: 0.8913 (tt0) cc_final: 0.8601 (tt0) REVERT: C 847 ARG cc_start: 0.5208 (mtm-85) cc_final: 0.4810 (mtt180) REVERT: C 1113 GLN cc_start: 0.9064 (OUTLIER) cc_final: 0.8272 (mm110) outliers start: 136 outliers final: 72 residues processed: 358 average time/residue: 0.5602 time to fit residues: 238.4867 Evaluate side-chains 307 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 223 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 537 LYS Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 250 optimal weight: 0.9990 chunk 196 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 154 optimal weight: 6.9990 chunk 248 optimal weight: 0.7980 chunk 269 optimal weight: 0.1980 chunk 81 optimal weight: 0.6980 chunk 312 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 544 ASN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN B 317 ASN B 409 GLN B 474 GLN B 779 GLN C 52 GLN C 957 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.161921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.118243 restraints weight = 34342.066| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.05 r_work: 0.3217 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 28394 Z= 0.137 Angle : 0.708 16.822 38844 Z= 0.321 Chirality : 0.045 0.456 4694 Planarity : 0.003 0.041 4788 Dihedral : 11.592 104.008 6084 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.18 % Allowed : 15.96 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.14), residues: 3291 helix: 1.11 (0.18), residues: 822 sheet: 0.29 (0.18), residues: 699 loop : -1.06 (0.13), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 567 TYR 0.029 0.001 TYR B 265 PHE 0.012 0.001 PHE A 898 TRP 0.011 0.001 TRP C 436 HIS 0.002 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00299 (28227) covalent geometry : angle 0.64002 (38388) SS BOND : bond 0.00338 ( 45) SS BOND : angle 1.81109 ( 90) hydrogen bonds : bond 0.03924 ( 1118) hydrogen bonds : angle 5.72660 ( 3126) link_ALPHA1-3 : bond 0.01037 ( 3) link_ALPHA1-3 : angle 1.39194 ( 9) link_ALPHA1-4 : bond 0.01628 ( 24) link_ALPHA1-4 : angle 3.20081 ( 72) link_BETA1-4 : bond 0.00647 ( 36) link_BETA1-4 : angle 1.40095 ( 108) link_BETA1-6 : bond 0.01821 ( 3) link_BETA1-6 : angle 2.17753 ( 9) link_NAG-ASN : bond 0.00385 ( 56) link_NAG-ASN : angle 3.79519 ( 168) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 271 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.8483 (p0) cc_final: 0.8109 (p0) REVERT: A 319 ARG cc_start: 0.7406 (ptp90) cc_final: 0.7102 (ptm160) REVERT: A 368 LEU cc_start: 0.8050 (pp) cc_final: 0.7595 (pp) REVERT: A 462 LYS cc_start: 0.7786 (mtmt) cc_final: 0.7349 (mmtt) REVERT: A 470 THR cc_start: 0.8580 (p) cc_final: 0.8347 (t) REVERT: A 554 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6912 (mp0) REVERT: A 568 ASP cc_start: 0.7872 (m-30) cc_final: 0.7601 (m-30) REVERT: A 618 THR cc_start: 0.6488 (OUTLIER) cc_final: 0.5966 (p) REVERT: A 661 GLU cc_start: 0.8090 (tt0) cc_final: 0.7707 (mp0) REVERT: A 847 ARG cc_start: 0.4677 (mtm-85) cc_final: 0.4332 (mtt-85) REVERT: A 872 GLN cc_start: 0.8645 (mt0) cc_final: 0.8229 (mt0) REVERT: B 66 HIS cc_start: 0.6711 (OUTLIER) cc_final: 0.6142 (t-90) REVERT: B 81 ASN cc_start: 0.8185 (p0) cc_final: 0.7885 (p0) REVERT: B 132 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7639 (mt-10) REVERT: B 158 ARG cc_start: 0.6467 (mtt90) cc_final: 0.5540 (mmm-85) REVERT: B 331 ASN cc_start: 0.5297 (OUTLIER) cc_final: 0.4711 (m-40) REVERT: B 462 LYS cc_start: 0.7904 (mtmt) cc_final: 0.7394 (mmtt) REVERT: B 568 ASP cc_start: 0.7748 (m-30) cc_final: 0.7386 (m-30) REVERT: B 839 ASP cc_start: 0.6954 (p0) cc_final: 0.6566 (m-30) REVERT: C 113 LYS cc_start: 0.7576 (mtpt) cc_final: 0.7203 (ttpp) REVERT: C 115 GLN cc_start: 0.7868 (mt0) cc_final: 0.7563 (mt0) REVERT: C 152 TRP cc_start: 0.6504 (m100) cc_final: 0.6150 (m100) REVERT: C 157 PHE cc_start: 0.8089 (t80) cc_final: 0.7835 (t80) REVERT: C 158 ARG cc_start: 0.6923 (mmt90) cc_final: 0.6388 (mmm-85) REVERT: C 265 TYR cc_start: 0.8139 (p90) cc_final: 0.7734 (p90) REVERT: C 462 LYS cc_start: 0.7890 (mtmt) cc_final: 0.7359 (mmtt) REVERT: C 474 GLN cc_start: 0.5888 (tt0) cc_final: 0.5659 (tm-30) REVERT: C 489 TYR cc_start: 0.8148 (m-80) cc_final: 0.7359 (m-80) REVERT: C 567 ARG cc_start: 0.7226 (mtt-85) cc_final: 0.6888 (mmt180) REVERT: C 568 ASP cc_start: 0.7986 (m-30) cc_final: 0.7514 (m-30) REVERT: C 755 GLN cc_start: 0.7288 (OUTLIER) cc_final: 0.6357 (mp10) REVERT: C 847 ARG cc_start: 0.5149 (mtm-85) cc_final: 0.4780 (mtt180) outliers start: 92 outliers final: 44 residues processed: 342 average time/residue: 0.5703 time to fit residues: 232.8705 Evaluate side-chains 294 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 244 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 755 GLN Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 977 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 221 optimal weight: 1.9990 chunk 234 optimal weight: 8.9990 chunk 201 optimal weight: 1.9990 chunk 276 optimal weight: 3.9990 chunk 254 optimal weight: 5.9990 chunk 238 optimal weight: 6.9990 chunk 268 optimal weight: 5.9990 chunk 306 optimal weight: 0.9990 chunk 158 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 606 ASN A 779 GLN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B 450 ASN B 474 GLN B 779 GLN C 52 GLN C 409 GLN C 606 ASN C 804 GLN C 957 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.158354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.115056 restraints weight = 33969.193| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.27 r_work: 0.3120 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 28394 Z= 0.285 Angle : 0.795 16.937 38844 Z= 0.368 Chirality : 0.049 0.407 4694 Planarity : 0.004 0.044 4788 Dihedral : 11.729 106.113 6084 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.73 % Allowed : 16.20 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.14), residues: 3291 helix: 0.97 (0.19), residues: 804 sheet: 0.29 (0.19), residues: 672 loop : -1.11 (0.13), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 567 TYR 0.033 0.002 TYR B 904 PHE 0.017 0.002 PHE C 306 TRP 0.012 0.002 TRP C 436 HIS 0.005 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00678 (28227) covalent geometry : angle 0.73568 (38388) SS BOND : bond 0.00525 ( 45) SS BOND : angle 2.21355 ( 90) hydrogen bonds : bond 0.04840 ( 1118) hydrogen bonds : angle 5.94628 ( 3126) link_ALPHA1-3 : bond 0.01127 ( 3) link_ALPHA1-3 : angle 1.36304 ( 9) link_ALPHA1-4 : bond 0.01716 ( 24) link_ALPHA1-4 : angle 3.35556 ( 72) link_BETA1-4 : bond 0.00403 ( 36) link_BETA1-4 : angle 1.22104 ( 108) link_BETA1-6 : bond 0.01793 ( 3) link_BETA1-6 : angle 2.36460 ( 9) link_NAG-ASN : bond 0.00466 ( 56) link_NAG-ASN : angle 3.68992 ( 168) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 253 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6708 (OUTLIER) cc_final: 0.6002 (t-90) REVERT: A 179 LEU cc_start: 0.6561 (OUTLIER) cc_final: 0.6287 (mt) REVERT: A 319 ARG cc_start: 0.7534 (ptp90) cc_final: 0.7228 (ptm160) REVERT: A 368 LEU cc_start: 0.8079 (pp) cc_final: 0.7604 (pp) REVERT: A 462 LYS cc_start: 0.7897 (mtmt) cc_final: 0.7449 (mmtt) REVERT: A 554 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6909 (mp0) REVERT: A 568 ASP cc_start: 0.7877 (m-30) cc_final: 0.7661 (m-30) REVERT: A 618 THR cc_start: 0.6617 (OUTLIER) cc_final: 0.6095 (p) REVERT: A 661 GLU cc_start: 0.8132 (tt0) cc_final: 0.7751 (mp0) REVERT: A 725 GLU cc_start: 0.8925 (tt0) cc_final: 0.8575 (tt0) REVERT: A 847 ARG cc_start: 0.5076 (mtm-85) cc_final: 0.4705 (mtt-85) REVERT: A 872 GLN cc_start: 0.8704 (mt0) cc_final: 0.8304 (mt0) REVERT: A 878 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8836 (tt) REVERT: A 1113 GLN cc_start: 0.9101 (OUTLIER) cc_final: 0.8379 (mm110) REVERT: B 66 HIS cc_start: 0.6890 (OUTLIER) cc_final: 0.6333 (t-90) REVERT: B 81 ASN cc_start: 0.8391 (p0) cc_final: 0.8075 (p0) REVERT: B 132 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7845 (mt-10) REVERT: B 158 ARG cc_start: 0.6643 (mtt90) cc_final: 0.5710 (mmm-85) REVERT: B 331 ASN cc_start: 0.5362 (OUTLIER) cc_final: 0.4650 (m110) REVERT: B 462 LYS cc_start: 0.7974 (mtmt) cc_final: 0.7449 (mmtt) REVERT: B 568 ASP cc_start: 0.7890 (m-30) cc_final: 0.7517 (m-30) REVERT: B 661 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7006 (mp0) REVERT: B 755 GLN cc_start: 0.7107 (OUTLIER) cc_final: 0.5859 (mp10) REVERT: B 839 ASP cc_start: 0.7021 (p0) cc_final: 0.6699 (m-30) REVERT: B 847 ARG cc_start: 0.5429 (mtm-85) cc_final: 0.5016 (mtt-85) REVERT: B 916 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8522 (tp) REVERT: C 113 LYS cc_start: 0.7830 (mtpt) cc_final: 0.7558 (ttpp) REVERT: C 115 GLN cc_start: 0.7862 (mt0) cc_final: 0.7583 (mt0) REVERT: C 152 TRP cc_start: 0.6621 (m100) cc_final: 0.6324 (m100) REVERT: C 409 GLN cc_start: 0.9067 (OUTLIER) cc_final: 0.8482 (mt0) REVERT: C 462 LYS cc_start: 0.7934 (mtmt) cc_final: 0.7432 (mmtt) REVERT: C 474 GLN cc_start: 0.6081 (tt0) cc_final: 0.5845 (tm-30) REVERT: C 489 TYR cc_start: 0.8269 (m-80) cc_final: 0.7451 (m-80) REVERT: C 546 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7961 (tp) REVERT: C 567 ARG cc_start: 0.7513 (mtt-85) cc_final: 0.7119 (mmt180) REVERT: C 568 ASP cc_start: 0.8067 (m-30) cc_final: 0.7558 (m-30) REVERT: C 725 GLU cc_start: 0.9028 (tt0) cc_final: 0.8737 (tt0) REVERT: C 819 GLU cc_start: 0.8944 (mt-10) cc_final: 0.8615 (mt-10) REVERT: C 847 ARG cc_start: 0.5253 (mtm-85) cc_final: 0.4877 (mtt180) outliers start: 108 outliers final: 59 residues processed: 340 average time/residue: 0.5630 time to fit residues: 226.4275 Evaluate side-chains 312 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 239 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 172 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 216 optimal weight: 0.7980 chunk 203 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN B 314 GLN B 474 GLN B 779 GLN C 52 GLN C 99 ASN C 804 GLN C 957 GLN C1113 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.160886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.117208 restraints weight = 34044.419| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.34 r_work: 0.3152 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 28394 Z= 0.155 Angle : 0.712 15.865 38844 Z= 0.324 Chirality : 0.045 0.377 4694 Planarity : 0.004 0.042 4788 Dihedral : 11.132 103.599 6084 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.28 % Allowed : 17.17 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.14), residues: 3291 helix: 1.15 (0.19), residues: 822 sheet: 0.32 (0.19), residues: 693 loop : -1.10 (0.13), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 567 TYR 0.031 0.001 TYR B 265 PHE 0.013 0.001 PHE A 898 TRP 0.011 0.001 TRP C 436 HIS 0.003 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00350 (28227) covalent geometry : angle 0.65306 (38388) SS BOND : bond 0.00366 ( 45) SS BOND : angle 1.68700 ( 90) hydrogen bonds : bond 0.04006 ( 1118) hydrogen bonds : angle 5.69535 ( 3126) link_ALPHA1-3 : bond 0.00969 ( 3) link_ALPHA1-3 : angle 1.24794 ( 9) link_ALPHA1-4 : bond 0.01740 ( 24) link_ALPHA1-4 : angle 3.31065 ( 72) link_BETA1-4 : bond 0.00424 ( 36) link_BETA1-4 : angle 1.13508 ( 108) link_BETA1-6 : bond 0.01997 ( 3) link_BETA1-6 : angle 2.19494 ( 9) link_NAG-ASN : bond 0.00395 ( 56) link_NAG-ASN : angle 3.52941 ( 168) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 258 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6796 (OUTLIER) cc_final: 0.6053 (t-90) REVERT: A 179 LEU cc_start: 0.6551 (OUTLIER) cc_final: 0.6250 (mt) REVERT: A 319 ARG cc_start: 0.7425 (ptp90) cc_final: 0.7173 (ptm160) REVERT: A 368 LEU cc_start: 0.8108 (pp) cc_final: 0.7648 (pp) REVERT: A 462 LYS cc_start: 0.7860 (mtmt) cc_final: 0.7424 (mmtt) REVERT: A 554 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6918 (mp0) REVERT: A 618 THR cc_start: 0.6602 (OUTLIER) cc_final: 0.6062 (p) REVERT: A 661 GLU cc_start: 0.8166 (tt0) cc_final: 0.7761 (mp0) REVERT: A 847 ARG cc_start: 0.5024 (mtm-85) cc_final: 0.4681 (mtt-85) REVERT: A 872 GLN cc_start: 0.8735 (mt0) cc_final: 0.8332 (mt0) REVERT: A 878 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8836 (tt) REVERT: A 1113 GLN cc_start: 0.9092 (OUTLIER) cc_final: 0.8377 (mm110) REVERT: B 66 HIS cc_start: 0.6781 (OUTLIER) cc_final: 0.6111 (t-90) REVERT: B 81 ASN cc_start: 0.8402 (p0) cc_final: 0.8082 (p0) REVERT: B 132 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7799 (mt-10) REVERT: B 158 ARG cc_start: 0.6588 (mtt90) cc_final: 0.5659 (mmm-85) REVERT: B 331 ASN cc_start: 0.5095 (OUTLIER) cc_final: 0.4433 (m110) REVERT: B 462 LYS cc_start: 0.7993 (mtmt) cc_final: 0.7482 (mmtt) REVERT: B 568 ASP cc_start: 0.7845 (m-30) cc_final: 0.7519 (m-30) REVERT: B 755 GLN cc_start: 0.7061 (OUTLIER) cc_final: 0.5861 (mp10) REVERT: B 839 ASP cc_start: 0.6912 (p0) cc_final: 0.6611 (m-30) REVERT: B 916 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8451 (tp) REVERT: C 113 LYS cc_start: 0.7758 (mtpt) cc_final: 0.7483 (ttpp) REVERT: C 115 GLN cc_start: 0.7893 (mt0) cc_final: 0.7541 (mm-40) REVERT: C 152 TRP cc_start: 0.6654 (m100) cc_final: 0.6386 (m100) REVERT: C 265 TYR cc_start: 0.8310 (p90) cc_final: 0.7919 (p90) REVERT: C 281 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8396 (pm20) REVERT: C 462 LYS cc_start: 0.7926 (mtmt) cc_final: 0.7445 (mmtt) REVERT: C 489 TYR cc_start: 0.8273 (m-80) cc_final: 0.7465 (m-80) REVERT: C 546 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7902 (tp) REVERT: C 568 ASP cc_start: 0.8012 (m-30) cc_final: 0.7593 (m-30) REVERT: C 725 GLU cc_start: 0.8990 (tt0) cc_final: 0.8703 (tt0) REVERT: C 847 ARG cc_start: 0.5298 (mtm-85) cc_final: 0.4930 (mtt180) REVERT: C 904 TYR cc_start: 0.8503 (m-10) cc_final: 0.8229 (m-10) outliers start: 95 outliers final: 52 residues processed: 332 average time/residue: 0.5384 time to fit residues: 212.6037 Evaluate side-chains 298 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 233 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 987 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 10 optimal weight: 5.9990 chunk 297 optimal weight: 0.0010 chunk 282 optimal weight: 0.5980 chunk 97 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 172 optimal weight: 2.9990 chunk 280 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 264 optimal weight: 8.9990 chunk 157 optimal weight: 6.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 519 HIS A 787 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B 450 ASN B 474 GLN C 52 GLN C 474 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.162518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.118475 restraints weight = 34056.332| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.10 r_work: 0.3201 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 28394 Z= 0.135 Angle : 0.701 15.382 38844 Z= 0.318 Chirality : 0.044 0.372 4694 Planarity : 0.003 0.042 4788 Dihedral : 10.510 101.805 6084 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.69 % Allowed : 18.00 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.14), residues: 3291 helix: 1.34 (0.19), residues: 822 sheet: 0.34 (0.19), residues: 687 loop : -1.03 (0.13), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 190 TYR 0.036 0.001 TYR A 265 PHE 0.013 0.001 PHE C 306 TRP 0.010 0.001 TRP C 436 HIS 0.004 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00298 (28227) covalent geometry : angle 0.64134 (38388) SS BOND : bond 0.00349 ( 45) SS BOND : angle 1.83954 ( 90) hydrogen bonds : bond 0.03705 ( 1118) hydrogen bonds : angle 5.52396 ( 3126) link_ALPHA1-3 : bond 0.00986 ( 3) link_ALPHA1-3 : angle 1.31927 ( 9) link_ALPHA1-4 : bond 0.01702 ( 24) link_ALPHA1-4 : angle 3.37764 ( 72) link_BETA1-4 : bond 0.00458 ( 36) link_BETA1-4 : angle 1.16053 ( 108) link_BETA1-6 : bond 0.02179 ( 3) link_BETA1-6 : angle 2.16144 ( 9) link_NAG-ASN : bond 0.00424 ( 56) link_NAG-ASN : angle 3.42365 ( 168) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 261 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 179 LEU cc_start: 0.6542 (OUTLIER) cc_final: 0.6219 (mt) REVERT: A 319 ARG cc_start: 0.7345 (ptp90) cc_final: 0.7112 (ptm160) REVERT: A 462 LYS cc_start: 0.7862 (mtmt) cc_final: 0.7556 (mmtt) REVERT: A 572 THR cc_start: 0.8708 (p) cc_final: 0.8397 (t) REVERT: A 618 THR cc_start: 0.6558 (OUTLIER) cc_final: 0.5992 (p) REVERT: A 661 GLU cc_start: 0.8145 (tt0) cc_final: 0.7761 (mp0) REVERT: A 847 ARG cc_start: 0.5043 (mtm-85) cc_final: 0.4720 (mtt-85) REVERT: A 872 GLN cc_start: 0.8685 (mt0) cc_final: 0.8294 (mt0) REVERT: A 916 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8311 (tp) REVERT: A 1113 GLN cc_start: 0.9033 (OUTLIER) cc_final: 0.8321 (mm110) REVERT: B 81 ASN cc_start: 0.8404 (p0) cc_final: 0.8132 (p0) REVERT: B 158 ARG cc_start: 0.6658 (mtt90) cc_final: 0.5731 (mmm-85) REVERT: B 331 ASN cc_start: 0.4953 (OUTLIER) cc_final: 0.4330 (m110) REVERT: B 458 LYS cc_start: 0.8162 (mtmt) cc_final: 0.7896 (mttp) REVERT: B 462 LYS cc_start: 0.7981 (mtmt) cc_final: 0.7493 (mmtt) REVERT: B 564 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7600 (tt0) REVERT: B 567 ARG cc_start: 0.7553 (mtt-85) cc_final: 0.7165 (mmt180) REVERT: B 568 ASP cc_start: 0.7796 (m-30) cc_final: 0.7504 (m-30) REVERT: B 602 THR cc_start: 0.8098 (m) cc_final: 0.7765 (t) REVERT: B 755 GLN cc_start: 0.7031 (OUTLIER) cc_final: 0.5871 (mp10) REVERT: B 839 ASP cc_start: 0.6825 (p0) cc_final: 0.6553 (m-30) REVERT: B 916 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8511 (tp) REVERT: C 115 GLN cc_start: 0.7925 (mt0) cc_final: 0.7591 (mm-40) REVERT: C 152 TRP cc_start: 0.6732 (m100) cc_final: 0.6517 (m100) REVERT: C 265 TYR cc_start: 0.8262 (p90) cc_final: 0.7919 (p90) REVERT: C 422 ASN cc_start: 0.8114 (p0) cc_final: 0.7889 (p0) REVERT: C 462 LYS cc_start: 0.7897 (mtmt) cc_final: 0.7480 (mmtt) REVERT: C 489 TYR cc_start: 0.8244 (m-80) cc_final: 0.7453 (m-80) REVERT: C 546 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7953 (tp) REVERT: C 568 ASP cc_start: 0.7879 (m-30) cc_final: 0.7553 (m-30) REVERT: C 847 ARG cc_start: 0.5138 (mtm-85) cc_final: 0.4848 (mtt180) REVERT: C 904 TYR cc_start: 0.8463 (m-10) cc_final: 0.8226 (m-10) outliers start: 78 outliers final: 45 residues processed: 324 average time/residue: 0.5263 time to fit residues: 203.8338 Evaluate side-chains 284 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 230 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 233 optimal weight: 9.9990 chunk 47 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 323 optimal weight: 1.9990 chunk 189 optimal weight: 3.9990 chunk 286 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 296 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 150 optimal weight: 5.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 606 ASN A 787 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 314 GLN C 409 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C1125 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.161395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.116961 restraints weight = 33972.482| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.47 r_work: 0.3129 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 28394 Z= 0.183 Angle : 0.730 15.738 38844 Z= 0.332 Chirality : 0.046 0.386 4694 Planarity : 0.004 0.042 4788 Dihedral : 10.315 103.033 6082 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.56 % Allowed : 18.00 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.14), residues: 3291 helix: 1.34 (0.19), residues: 804 sheet: 0.36 (0.19), residues: 687 loop : -1.05 (0.13), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 567 TYR 0.033 0.001 TYR A 265 PHE 0.015 0.001 PHE C 306 TRP 0.010 0.001 TRP C 436 HIS 0.003 0.001 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00425 (28227) covalent geometry : angle 0.67235 (38388) SS BOND : bond 0.00431 ( 45) SS BOND : angle 2.06679 ( 90) hydrogen bonds : bond 0.04065 ( 1118) hydrogen bonds : angle 5.60001 ( 3126) link_ALPHA1-3 : bond 0.01004 ( 3) link_ALPHA1-3 : angle 1.27061 ( 9) link_ALPHA1-4 : bond 0.01768 ( 24) link_ALPHA1-4 : angle 3.43506 ( 72) link_BETA1-4 : bond 0.00386 ( 36) link_BETA1-4 : angle 1.07412 ( 108) link_BETA1-6 : bond 0.02137 ( 3) link_BETA1-6 : angle 2.10397 ( 9) link_NAG-ASN : bond 0.00380 ( 56) link_NAG-ASN : angle 3.40467 ( 168) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 243 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 LEU cc_start: 0.6522 (OUTLIER) cc_final: 0.6196 (mt) REVERT: A 319 ARG cc_start: 0.7427 (ptp90) cc_final: 0.7165 (ptm160) REVERT: A 462 LYS cc_start: 0.7921 (mtmt) cc_final: 0.7448 (mmtt) REVERT: A 572 THR cc_start: 0.8712 (p) cc_final: 0.8463 (t) REVERT: A 661 GLU cc_start: 0.8191 (tt0) cc_final: 0.7751 (mp0) REVERT: A 847 ARG cc_start: 0.5206 (mtm-85) cc_final: 0.4855 (mtt-85) REVERT: A 872 GLN cc_start: 0.8759 (mt0) cc_final: 0.8365 (mt0) REVERT: A 878 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8858 (tt) REVERT: A 916 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8361 (tp) REVERT: A 1113 GLN cc_start: 0.9101 (OUTLIER) cc_final: 0.8382 (mm110) REVERT: B 81 ASN cc_start: 0.8518 (p0) cc_final: 0.8225 (p0) REVERT: B 132 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7815 (mt-10) REVERT: B 158 ARG cc_start: 0.6604 (mtt90) cc_final: 0.5630 (mmm-85) REVERT: B 331 ASN cc_start: 0.4979 (OUTLIER) cc_final: 0.4338 (m110) REVERT: B 458 LYS cc_start: 0.8274 (mtmt) cc_final: 0.7995 (mttp) REVERT: B 462 LYS cc_start: 0.7990 (mtmt) cc_final: 0.7442 (mmtt) REVERT: B 564 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7623 (tt0) REVERT: B 567 ARG cc_start: 0.7598 (mtt-85) cc_final: 0.7184 (mmt180) REVERT: B 568 ASP cc_start: 0.7892 (m-30) cc_final: 0.7567 (m-30) REVERT: B 755 GLN cc_start: 0.7089 (OUTLIER) cc_final: 0.5869 (mp10) REVERT: B 839 ASP cc_start: 0.6888 (p0) cc_final: 0.6600 (m-30) REVERT: B 916 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8528 (tp) REVERT: C 115 GLN cc_start: 0.7873 (mt0) cc_final: 0.7647 (mt0) REVERT: C 152 TRP cc_start: 0.6624 (m100) cc_final: 0.6372 (m100) REVERT: C 409 GLN cc_start: 0.8956 (OUTLIER) cc_final: 0.8376 (mt0) REVERT: C 462 LYS cc_start: 0.7942 (mtmt) cc_final: 0.7466 (mmtt) REVERT: C 489 TYR cc_start: 0.8257 (m-80) cc_final: 0.7394 (m-80) REVERT: C 546 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7920 (tp) REVERT: C 568 ASP cc_start: 0.7931 (m-30) cc_final: 0.7564 (m-30) REVERT: C 606 ASN cc_start: 0.8276 (t0) cc_final: 0.7930 (t160) REVERT: C 725 GLU cc_start: 0.9068 (tt0) cc_final: 0.8760 (tt0) REVERT: C 819 GLU cc_start: 0.8986 (mt-10) cc_final: 0.8726 (mt-10) REVERT: C 847 ARG cc_start: 0.5286 (mtm-85) cc_final: 0.4950 (mtt180) REVERT: C 904 TYR cc_start: 0.8550 (m-10) cc_final: 0.8262 (m-10) outliers start: 74 outliers final: 48 residues processed: 305 average time/residue: 0.5353 time to fit residues: 194.7128 Evaluate side-chains 294 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 235 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 8 optimal weight: 0.8980 chunk 5 optimal weight: 8.9990 chunk 210 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 183 optimal weight: 0.0470 chunk 297 optimal weight: 0.1980 chunk 56 optimal weight: 0.9980 chunk 287 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 158 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 314 GLN A 787 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.160982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.118444 restraints weight = 33887.388| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.32 r_work: 0.3163 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.188 28394 Z= 0.180 Angle : 0.835 59.188 38844 Z= 0.415 Chirality : 0.045 0.491 4694 Planarity : 0.004 0.042 4788 Dihedral : 10.313 102.988 6082 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.45 % Allowed : 18.34 % Favored : 79.21 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.14), residues: 3291 helix: 1.35 (0.19), residues: 804 sheet: 0.36 (0.19), residues: 687 loop : -1.05 (0.13), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 567 TYR 0.030 0.001 TYR A 265 PHE 0.014 0.001 PHE C 306 TRP 0.010 0.001 TRP C 436 HIS 0.003 0.001 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00411 (28227) covalent geometry : angle 0.78622 (38388) SS BOND : bond 0.00399 ( 45) SS BOND : angle 2.00990 ( 90) hydrogen bonds : bond 0.04052 ( 1118) hydrogen bonds : angle 5.59980 ( 3126) link_ALPHA1-3 : bond 0.01025 ( 3) link_ALPHA1-3 : angle 1.26607 ( 9) link_ALPHA1-4 : bond 0.01778 ( 24) link_ALPHA1-4 : angle 3.42983 ( 72) link_BETA1-4 : bond 0.00378 ( 36) link_BETA1-4 : angle 1.06800 ( 108) link_BETA1-6 : bond 0.02148 ( 3) link_BETA1-6 : angle 2.09367 ( 9) link_NAG-ASN : bond 0.00346 ( 56) link_NAG-ASN : angle 3.40719 ( 168) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10467.85 seconds wall clock time: 178 minutes 40.22 seconds (10720.22 seconds total)