Starting phenix.real_space_refine on Mon Jun 23 17:47:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wlu_37632/06_2025/8wlu_37632.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wlu_37632/06_2025/8wlu_37632.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wlu_37632/06_2025/8wlu_37632.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wlu_37632/06_2025/8wlu_37632.map" model { file = "/net/cci-nas-00/data/ceres_data/8wlu_37632/06_2025/8wlu_37632.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wlu_37632/06_2025/8wlu_37632.cif" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 132 5.16 5 C 17355 2.51 5 N 4419 2.21 5 O 5532 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 112 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 27438 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 8604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1106, 8604 Classifications: {'peptide': 1106} Link IDs: {'PTRANS': 58, 'TRANS': 1047} Chain: "C" Number of atoms: 8604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1106, 8604 Classifications: {'peptide': 1106} Link IDs: {'PTRANS': 58, 'TRANS': 1047} Chain: "B" Number of atoms: 8604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1106, 8604 Classifications: {'peptide': 1106} Link IDs: {'PTRANS': 58, 'TRANS': 1047} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "l" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "m" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "o" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "x" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 17.09, per 1000 atoms: 0.62 Number of scatterers: 27438 At special positions: 0 Unit cell: (141.629, 146.021, 169.077, 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 132 16.00 O 5532 8.00 N 4419 7.00 C 17355 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS A 134 " distance=2.03 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 160 " distance=2.03 Simple disulfide: pdb=" SG CYS A 279 " - pdb=" SG CYS A 289 " distance=2.03 Simple disulfide: pdb=" SG CYS A 324 " - pdb=" SG CYS A 349 " distance=2.03 Simple disulfide: pdb=" SG CYS A 367 " - pdb=" SG CYS A 420 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 512 " distance=2.03 Simple disulfide: pdb=" SG CYS A 525 " - pdb=" SG CYS A 577 " distance=2.03 Simple disulfide: pdb=" SG CYS A 604 " - pdb=" SG CYS A 636 " distance=2.03 Simple disulfide: pdb=" SG CYS A 649 " - pdb=" SG CYS A 658 " distance=2.03 Simple disulfide: pdb=" SG CYS A 721 " - pdb=" SG CYS A 743 " distance=2.03 Simple disulfide: pdb=" SG CYS A 726 " - pdb=" SG CYS A 732 " distance=2.02 Simple disulfide: pdb=" SG CYS A 823 " - pdb=" SG CYS A 834 " distance=2.03 Simple disulfide: pdb=" SG CYS A1015 " - pdb=" SG CYS A1026 " distance=2.03 Simple disulfide: pdb=" SG CYS A1065 " - pdb=" SG CYS A1109 " distance=2.03 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS C 134 " distance=2.04 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 160 " distance=2.03 Simple disulfide: pdb=" SG CYS C 279 " - pdb=" SG CYS C 289 " distance=2.03 Simple disulfide: pdb=" SG CYS C 324 " - pdb=" SG CYS C 349 " distance=2.03 Simple disulfide: pdb=" SG CYS C 367 " - pdb=" SG CYS C 420 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 512 " distance=2.03 Simple disulfide: pdb=" SG CYS C 468 " - pdb=" SG CYS C 475 " distance=2.03 Simple disulfide: pdb=" SG CYS C 525 " - pdb=" SG CYS C 577 " distance=2.03 Simple disulfide: pdb=" SG CYS C 604 " - pdb=" SG CYS C 636 " distance=2.03 Simple disulfide: pdb=" SG CYS C 649 " - pdb=" SG CYS C 658 " distance=2.03 Simple disulfide: pdb=" SG CYS C 721 " - pdb=" SG CYS C 743 " distance=2.04 Simple disulfide: pdb=" SG CYS C 726 " - pdb=" SG CYS C 732 " distance=2.02 Simple disulfide: pdb=" SG CYS C 823 " - pdb=" SG CYS C 834 " distance=2.03 Simple disulfide: pdb=" SG CYS C1015 " - pdb=" SG CYS C1026 " distance=2.03 Simple disulfide: pdb=" SG CYS C1065 " - pdb=" SG CYS C1109 " distance=2.03 Simple disulfide: pdb=" SG CYS B 20 " - pdb=" SG CYS B 134 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 160 " distance=2.03 Simple disulfide: pdb=" SG CYS B 279 " - pdb=" SG CYS B 289 " distance=2.03 Simple disulfide: pdb=" SG CYS B 324 " - pdb=" SG CYS B 349 " distance=2.03 Simple disulfide: pdb=" SG CYS B 367 " - pdb=" SG CYS B 420 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 512 " distance=2.03 Simple disulfide: pdb=" SG CYS B 468 " - pdb=" SG CYS B 475 " distance=2.03 Simple disulfide: pdb=" SG CYS B 525 " - pdb=" SG CYS B 577 " distance=2.03 Simple disulfide: pdb=" SG CYS B 604 " - pdb=" SG CYS B 636 " distance=2.03 Simple disulfide: pdb=" SG CYS B 649 " - pdb=" SG CYS B 658 " distance=2.03 Simple disulfide: pdb=" SG CYS B 721 " - pdb=" SG CYS B 743 " distance=2.03 Simple disulfide: pdb=" SG CYS B 726 " - pdb=" SG CYS B 732 " distance=2.02 Simple disulfide: pdb=" SG CYS B 823 " - pdb=" SG CYS B 834 " distance=2.03 Simple disulfide: pdb=" SG CYS B1015 " - pdb=" SG CYS B1026 " distance=2.03 Simple disulfide: pdb=" SG CYS B1065 " - pdb=" SG CYS B1109 " distance=2.02 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " NAG-ASN " NAG A1301 " - " ASN A 145 " " NAG A1302 " - " ASN A 590 " " NAG B1301 " - " ASN B 145 " " NAG B1302 " - " ASN B 590 " " NAG C1301 " - " ASN C 145 " " NAG C1302 " - " ASN C 590 " " NAG D 1 " - " ASN A 66 " " NAG E 1 " - " ASN A 110 " " NAG F 1 " - " ASN A 120 " " NAG G 1 " - " ASN A 159 " " NAG H 1 " - " ASN A 228 " " NAG I 1 " - " ASN A 270 " " NAG J 1 " - " ASN A 331 " " NAG K 1 " - " ASN A 603 " " NAG L 1 " - " ASN A 700 " " NAG M 1 " - " ASN A 784 " " NAG N 1 " - " ASN A1057 " " NAG O 1 " - " ASN A1081 " " NAG P 1 " - " ASN A1117 " " NAG Q 1 " - " ASN A 692 " " NAG R 1 " - " ASN A 319 " " NAG S 1 " - " ASN A 358 " " NAG T 1 " - " ASN C 66 " " NAG U 1 " - " ASN C 110 " " NAG V 1 " - " ASN C 120 " " NAG W 1 " - " ASN C 159 " " NAG X 1 " - " ASN C 228 " " NAG Y 1 " - " ASN C 270 " " NAG Z 1 " - " ASN C 331 " " NAG a 1 " - " ASN C 603 " " NAG b 1 " - " ASN C 700 " " NAG c 1 " - " ASN C 784 " " NAG d 1 " - " ASN C1057 " " NAG e 1 " - " ASN C1081 " " NAG f 1 " - " ASN C1117 " " NAG g 1 " - " ASN C 692 " " NAG h 1 " - " ASN C 319 " " NAG i 1 " - " ASN C 358 " " NAG j 1 " - " ASN B 66 " " NAG k 1 " - " ASN B 110 " " NAG l 1 " - " ASN B 120 " " NAG m 1 " - " ASN B 159 " " NAG n 1 " - " ASN B 228 " " NAG o 1 " - " ASN B 270 " " NAG p 1 " - " ASN B 331 " " NAG q 1 " - " ASN B 603 " " NAG r 1 " - " ASN B 700 " " NAG s 1 " - " ASN B 784 " " NAG t 1 " - " ASN B1057 " " NAG u 1 " - " ASN B1081 " " NAG v 1 " - " ASN B1117 " " NAG w 1 " - " ASN B 692 " " NAG x 1 " - " ASN B 319 " " NAG y 1 " - " ASN B 358 " Time building additional restraints: 8.27 Conformation dependent library (CDL) restraints added in 3.4 seconds 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 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: 75 helices and 48 sheets defined 25.9% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.20 Creating SS restraints... Processing helix chain 'A' and resid 282 through 291 Processing helix chain 'A' and resid 325 through 331 Processing helix chain 'A' and resid 352 through 357 removed outlier: 3.653A pdb=" N VAL A 355 " --> pdb=" O ASP A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 377 removed outlier: 4.693A pdb=" N ASN A 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 398 removed outlier: 4.477A pdb=" N ARG A 396 " --> pdb=" O ASP A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 Processing helix chain 'A' and resid 426 through 431 Processing helix chain 'A' and resid 489 through 492 Processing helix chain 'A' and resid 606 through 611 Processing helix chain 'A' and resid 612 through 616 Processing helix chain 'A' and resid 617 through 625 removed outlier: 3.828A pdb=" N TYR A 623 " --> pdb=" O SER A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 725 Processing helix chain 'A' and resid 729 through 740 removed outlier: 3.504A pdb=" N GLY A 740 " --> pdb=" O LEU A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 766 Processing helix chain 'A' and resid 799 through 809 removed outlier: 3.674A pdb=" N VAL A 809 " --> pdb=" O LEU A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 839 Processing helix chain 'A' and resid 849 through 867 Processing helix chain 'A' and resid 869 through 873 Processing helix chain 'A' and resid 880 through 893 Processing helix chain 'A' and resid 895 through 902 removed outlier: 3.987A pdb=" N LEU A 899 " --> pdb=" O THR A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 923 Processing helix chain 'A' and resid 928 through 948 Processing helix chain 'A' and resid 949 through 951 No H-bonds generated for 'chain 'A' and resid 949 through 951' Processing helix chain 'A' and resid 959 through 967 removed outlier: 3.721A pdb=" N ILE A 963 " --> pdb=" O VAL A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 1016 Processing helix chain 'C' and resid 282 through 291 Processing helix chain 'C' and resid 325 through 331 Processing helix chain 'C' and resid 352 through 357 removed outlier: 3.514A pdb=" N VAL C 355 " --> pdb=" O ASP C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 377 removed outlier: 4.781A pdb=" N ASN C 376 " --> pdb=" O THR C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 398 removed outlier: 4.399A pdb=" N ARG C 396 " --> pdb=" O ASP C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 Processing helix chain 'C' and resid 426 through 431 Processing helix chain 'C' and resid 489 through 492 Processing helix chain 'C' and resid 606 through 611 Processing helix chain 'C' and resid 612 through 616 Processing helix chain 'C' and resid 617 through 625 removed outlier: 3.905A pdb=" N TYR C 623 " --> pdb=" O SER C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 720 through 725 Processing helix chain 'C' and resid 729 through 740 removed outlier: 3.531A pdb=" N GLY C 740 " --> pdb=" O LEU C 736 " (cutoff:3.500A) Processing helix chain 'C' and resid 741 through 766 Processing helix chain 'C' and resid 799 through 809 removed outlier: 3.638A pdb=" N VAL C 809 " --> pdb=" O LEU C 805 " (cutoff:3.500A) Processing helix chain 'C' and resid 831 through 839 Processing helix chain 'C' and resid 849 through 867 Processing helix chain 'C' and resid 869 through 873 Processing helix chain 'C' and resid 880 through 893 Processing helix chain 'C' and resid 895 through 902 removed outlier: 3.982A pdb=" N LEU C 899 " --> pdb=" O THR C 895 " (cutoff:3.500A) Processing helix chain 'C' and resid 902 through 923 Processing helix chain 'C' and resid 928 through 948 Processing helix chain 'C' and resid 949 through 951 No H-bonds generated for 'chain 'C' and resid 949 through 951' Processing helix chain 'C' and resid 959 through 967 removed outlier: 3.667A pdb=" N ILE C 963 " --> pdb=" O VAL C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 968 through 1015 Processing helix chain 'B' and resid 282 through 291 Processing helix chain 'B' and resid 325 through 331 Processing helix chain 'B' and resid 352 through 357 removed outlier: 3.541A pdb=" N VAL B 355 " --> pdb=" O ASP B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 377 removed outlier: 4.689A pdb=" N ASN B 376 " --> pdb=" O THR B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 398 removed outlier: 4.383A pdb=" N ARG B 396 " --> pdb=" O ASP B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 Processing helix chain 'B' and resid 426 through 431 Processing helix chain 'B' and resid 489 through 492 Processing helix chain 'B' and resid 606 through 611 Processing helix chain 'B' and resid 612 through 616 Processing helix chain 'B' and resid 617 through 625 removed outlier: 3.848A pdb=" N TYR B 623 " --> pdb=" O SER B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 725 Processing helix chain 'B' and resid 729 through 740 removed outlier: 3.583A pdb=" N GLY B 740 " --> pdb=" O LEU B 736 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 766 Processing helix chain 'B' and resid 799 through 809 removed outlier: 3.653A pdb=" N VAL B 809 " --> pdb=" O LEU B 805 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 839 Processing helix chain 'B' and resid 849 through 867 Processing helix chain 'B' and resid 869 through 873 Processing helix chain 'B' and resid 880 through 893 Processing helix chain 'B' and resid 895 through 902 removed outlier: 4.000A pdb=" N LEU B 899 " --> pdb=" O THR B 895 " (cutoff:3.500A) Processing helix chain 'B' and resid 902 through 923 Processing helix chain 'B' and resid 928 through 948 Processing helix chain 'B' and resid 949 through 951 No H-bonds generated for 'chain 'B' and resid 949 through 951' Processing helix chain 'B' and resid 959 through 967 removed outlier: 3.650A pdb=" N ILE B 963 " --> pdb=" O VAL B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 968 through 1015 Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 36 removed outlier: 3.746A pdb=" N SER A 65 " --> pdb=" O SER A 36 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ASN A 66 " --> pdb=" O TYR A 257 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N TYR A 257 " --> pdb=" O ASN A 66 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA A 252 " --> pdb=" O THR A 93 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYS A 181 " --> pdb=" O ILE A 204 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N LEU A 195 " --> pdb=" O LYS A 222 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS A 222 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL A 197 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N TYR A 201 " --> pdb=" O ALA A 216 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N ALA A 216 " --> pdb=" O TYR A 201 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N VAL A 41 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 60 removed outlier: 7.874A pdb=" N THR A 262 " --> pdb=" O ASP A 278 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ASP A 278 " --> pdb=" O THR A 262 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N MET A 264 " --> pdb=" O ALA A 276 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ALA A 276 " --> pdb=" O MET A 264 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LYS A 266 " --> pdb=" O THR A 274 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 82 through 83 removed outlier: 6.537A pdb=" N PHE A 139 " --> pdb=" O ALA A 238 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL A 140 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR A 147 " --> pdb=" O LEU A 142 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 82 through 83 removed outlier: 4.416A pdb=" N GLY A 101 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N THR A 237 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE A 99 " --> pdb=" O THR A 237 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ARG A 100 " --> pdb=" O ASN A 119 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASN A 119 " --> pdb=" O ARG A 100 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE A 162 " --> pdb=" O ALA A 128 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ASN A 130 " --> pdb=" O CYS A 160 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N CYS A 160 " --> pdb=" O ASN A 130 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N GLU A 132 " --> pdb=" O PHE A 158 " (cutoff:3.500A) removed outlier: 9.355A pdb=" N PHE A 158 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 299 through 303 removed outlier: 4.439A pdb=" N VAL A 582 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 313 through 316 removed outlier: 5.229A pdb=" N ASP A 561 " --> pdb=" O ILE A 574 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 342 through 346 removed outlier: 3.972A pdb=" N VAL A 383 " --> pdb=" O ILE A 346 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 349 through 350 removed outlier: 6.544A pdb=" N CYS A 349 " --> pdb=" O CYS A 512 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 440 through 442 Processing sheet with id=AB1, first strand: chain 'A' and resid 641 through 642 removed outlier: 6.174A pdb=" N GLU A 641 " --> pdb=" O ALA A 677 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N THR A 679 " --> pdb=" O GLU A 641 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE A 657 " --> pdb=" O ILE A 653 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 684 through 686 removed outlier: 6.777A pdb=" N ALA A 684 " --> pdb=" O MET B 771 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 694 through 711 removed outlier: 6.339A pdb=" N THR A 694 " --> pdb=" O THR A1059 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N THR A1059 " --> pdb=" O THR A 694 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA A 696 " --> pdb=" O ASN A1057 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASN A1057 " --> pdb=" O ALA A 696 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLU A1055 " --> pdb=" O PRO A 698 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLY A1042 " --> pdb=" O ALA A1038 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ALA A1038 " --> pdb=" O GLY A1042 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL A1044 " --> pdb=" O PRO A1036 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU A1046 " --> pdb=" O SER A1034 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N SER A1034 " --> pdb=" O LEU A1046 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL A1048 " --> pdb=" O LEU A1032 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 694 through 711 removed outlier: 6.339A pdb=" N THR A 694 " --> pdb=" O THR A1059 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N THR A1059 " --> pdb=" O THR A 694 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA A 696 " --> pdb=" O ASN A1057 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASN A1057 " --> pdb=" O ALA A 696 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLU A1055 " --> pdb=" O PRO A 698 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N THR A1059 " --> pdb=" O PHE A1080 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA A1061 " --> pdb=" O PHE A1078 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N PHE A1078 " --> pdb=" O ALA A1061 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 716 through 719 removed outlier: 4.382A pdb=" N LYS A 716 " --> pdb=" O LEU A 844 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 770 through 772 removed outlier: 3.584A pdb=" N SER C 686 " --> pdb=" O MET A 771 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 779 through 780 Processing sheet with id=AB8, first strand: chain 'A' and resid 1103 through 1108 removed outlier: 4.295A pdb=" N ALA A1070 " --> pdb=" O SER A1106 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 33 through 36 removed outlier: 3.736A pdb=" N SER C 65 " --> pdb=" O SER C 36 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ASN C 66 " --> pdb=" O TYR C 257 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N TYR C 257 " --> pdb=" O ASN C 66 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA C 252 " --> pdb=" O THR C 93 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYS C 181 " --> pdb=" O ILE C 204 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LEU C 195 " --> pdb=" O LYS C 222 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LYS C 222 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL C 197 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N TYR C 201 " --> pdb=" O ALA C 216 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N ALA C 216 " --> pdb=" O TYR C 201 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N VAL C 41 " --> pdb=" O LEU C 217 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 52 through 60 removed outlier: 7.843A pdb=" N THR C 262 " --> pdb=" O ASP C 278 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ASP C 278 " --> pdb=" O THR C 262 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N MET C 264 " --> pdb=" O ALA C 276 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALA C 276 " --> pdb=" O MET C 264 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LYS C 266 " --> pdb=" O THR C 274 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 82 through 83 removed outlier: 6.405A pdb=" N PHE C 139 " --> pdb=" O ALA C 238 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL C 140 " --> pdb=" O ILE C 149 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR C 147 " --> pdb=" O LEU C 142 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 82 through 83 removed outlier: 4.417A pdb=" N GLY C 101 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N THR C 237 " --> pdb=" O ILE C 99 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE C 99 " --> pdb=" O THR C 237 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ARG C 100 " --> pdb=" O ASN C 119 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASN C 119 " --> pdb=" O ARG C 100 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE C 162 " --> pdb=" O ALA C 128 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N ASN C 130 " --> pdb=" O CYS C 160 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N CYS C 160 " --> pdb=" O ASN C 130 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N GLU C 132 " --> pdb=" O PHE C 158 " (cutoff:3.500A) removed outlier: 9.452A pdb=" N PHE C 158 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 299 through 303 removed outlier: 4.129A pdb=" N VAL C 582 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 313 through 316 removed outlier: 5.252A pdb=" N ASP C 561 " --> pdb=" O ILE C 574 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 342 through 346 removed outlier: 3.967A pdb=" N VAL C 383 " --> pdb=" O ILE C 346 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN C 382 " --> pdb=" O GLU C 503 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 349 through 350 removed outlier: 6.519A pdb=" N CYS C 349 " --> pdb=" O CYS C 512 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 440 through 442 Processing sheet with id=AC9, first strand: chain 'C' and resid 641 through 642 removed outlier: 6.180A pdb=" N GLU C 641 " --> pdb=" O ALA C 677 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N THR C 679 " --> pdb=" O GLU C 641 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE C 657 " --> pdb=" O ILE C 653 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 694 through 711 removed outlier: 6.316A pdb=" N THR C 694 " --> pdb=" O THR C1059 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N THR C1059 " --> pdb=" O THR C 694 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA C 696 " --> pdb=" O ASN C1057 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ASN C1057 " --> pdb=" O ALA C 696 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLU C1055 " --> pdb=" O PRO C 698 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N GLY C1042 " --> pdb=" O ALA C1038 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N ALA C1038 " --> pdb=" O GLY C1042 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL C1044 " --> pdb=" O PRO C1036 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU C1046 " --> pdb=" O SER C1034 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N SER C1034 " --> pdb=" O LEU C1046 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL C1048 " --> pdb=" O LEU C1032 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 694 through 711 removed outlier: 6.316A pdb=" N THR C 694 " --> pdb=" O THR C1059 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N THR C1059 " --> pdb=" O THR C 694 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA C 696 " --> pdb=" O ASN C1057 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ASN C1057 " --> pdb=" O ALA C 696 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLU C1055 " --> pdb=" O PRO C 698 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N THR C1059 " --> pdb=" O PHE C1080 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA C1061 " --> pdb=" O PHE C1078 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N PHE C1078 " --> pdb=" O ALA C1061 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 716 through 719 removed outlier: 4.379A pdb=" N LYS C 716 " --> pdb=" O LEU C 844 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 770 through 772 removed outlier: 3.607A pdb=" N SER B 686 " --> pdb=" O MET C 771 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 779 through 780 Processing sheet with id=AD6, first strand: chain 'C' and resid 1103 through 1108 removed outlier: 4.303A pdb=" N ALA C1070 " --> pdb=" O SER C1106 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 33 through 36 removed outlier: 3.758A pdb=" N SER B 65 " --> pdb=" O SER B 36 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ASN B 66 " --> pdb=" O TYR B 257 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N TYR B 257 " --> pdb=" O ASN B 66 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA B 252 " --> pdb=" O THR B 93 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LYS B 181 " --> pdb=" O ILE B 204 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N LEU B 195 " --> pdb=" O LYS B 222 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS B 222 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL B 197 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N TYR B 201 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ALA B 216 " --> pdb=" O TYR B 201 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N VAL B 41 " --> pdb=" O LEU B 217 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 52 through 60 removed outlier: 7.837A pdb=" N THR B 262 " --> pdb=" O ASP B 278 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N ASP B 278 " --> pdb=" O THR B 262 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N MET B 264 " --> pdb=" O ALA B 276 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ALA B 276 " --> pdb=" O MET B 264 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LYS B 266 " --> pdb=" O THR B 274 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 82 through 83 removed outlier: 6.502A pdb=" N PHE B 139 " --> pdb=" O ALA B 238 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL B 140 " --> pdb=" O ILE B 149 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR B 147 " --> pdb=" O LEU B 142 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 82 through 83 removed outlier: 4.361A pdb=" N GLY B 101 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N THR B 237 " --> pdb=" O ILE B 99 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE B 99 " --> pdb=" O THR B 237 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ARG B 100 " --> pdb=" O ASN B 119 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ASN B 119 " --> pdb=" O ARG B 100 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE B 162 " --> pdb=" O ALA B 128 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ASN B 130 " --> pdb=" O CYS B 160 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N CYS B 160 " --> pdb=" O ASN B 130 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N GLU B 132 " --> pdb=" O PHE B 158 " (cutoff:3.500A) removed outlier: 9.239A pdb=" N PHE B 158 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 299 through 303 removed outlier: 4.436A pdb=" N VAL B 582 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 313 through 316 removed outlier: 5.216A pdb=" N ASP B 561 " --> pdb=" O ILE B 574 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 342 through 346 removed outlier: 3.964A pdb=" N VAL B 383 " --> pdb=" O ILE B 346 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN B 382 " --> pdb=" O GLU B 503 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 349 through 350 removed outlier: 6.547A pdb=" N CYS B 349 " --> pdb=" O CYS B 512 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 440 through 442 Processing sheet with id=AE7, first strand: chain 'B' and resid 641 through 642 removed outlier: 6.151A pdb=" N GLU B 641 " --> pdb=" O ALA B 677 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N THR B 679 " --> pdb=" O GLU B 641 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE B 657 " --> pdb=" O ILE B 653 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 695 through 711 removed outlier: 6.623A pdb=" N ALA B 696 " --> pdb=" O ASN B1057 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ASN B1057 " --> pdb=" O ALA B 696 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLU B1055 " --> pdb=" O PRO B 698 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N GLY B1042 " --> pdb=" O ALA B1038 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ALA B1038 " --> pdb=" O GLY B1042 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL B1044 " --> pdb=" O PRO B1036 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU B1046 " --> pdb=" O SER B1034 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER B1034 " --> pdb=" O LEU B1046 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL B1048 " --> pdb=" O LEU B1032 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 695 through 711 removed outlier: 6.623A pdb=" N ALA B 696 " --> pdb=" O ASN B1057 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ASN B1057 " --> pdb=" O ALA B 696 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLU B1055 " --> pdb=" O PRO B 698 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N THR B1059 " --> pdb=" O PHE B1080 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA B1061 " --> pdb=" O PHE B1078 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N PHE B1078 " --> pdb=" O ALA B1061 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 716 through 719 removed outlier: 4.439A pdb=" N LYS B 716 " --> pdb=" O LEU B 844 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 779 through 780 Processing sheet with id=AF3, first strand: chain 'B' and resid 1103 through 1108 removed outlier: 4.306A pdb=" N ALA B1070 " --> pdb=" O SER B1106 " (cutoff:3.500A) 1105 hydrogen bonds defined for protein. 3006 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: 15.04 Time building geometry restraints manager: 9.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7455 1.33 - 1.45: 5988 1.45 - 1.58: 14439 1.58 - 1.70: 0 1.70 - 1.82: 174 Bond restraints: 28056 Sorted by residual: bond pdb=" C1 NAG T 1 " pdb=" O5 NAG T 1 " ideal model delta sigma weight residual 1.406 1.467 -0.061 2.00e-02 2.50e+03 9.18e+00 bond pdb=" C1 NAG j 1 " pdb=" O5 NAG j 1 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.46e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.35e+00 bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.57e+00 bond pdb=" C ASN C 722 " pdb=" O ASN C 722 " ideal model delta sigma weight residual 1.237 1.212 0.025 1.17e-02 7.31e+03 4.49e+00 ... (remaining 28051 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 36362 1.73 - 3.45: 1533 3.45 - 5.18: 224 5.18 - 6.91: 60 6.91 - 8.63: 20 Bond angle restraints: 38199 Sorted by residual: angle pdb=" N GLY B 727 " pdb=" CA GLY B 727 " pdb=" C GLY B 727 " ideal model delta sigma weight residual 112.73 120.17 -7.44 1.20e+00 6.94e-01 3.85e+01 angle pdb=" N GLY C 727 " pdb=" CA GLY C 727 " pdb=" C GLY C 727 " ideal model delta sigma weight residual 112.73 120.12 -7.39 1.20e+00 6.94e-01 3.79e+01 angle pdb=" N GLY A 740 " pdb=" CA GLY A 740 " pdb=" C GLY A 740 " ideal model delta sigma weight residual 110.63 119.26 -8.63 1.43e+00 4.89e-01 3.64e+01 angle pdb=" N GLY B 740 " pdb=" CA GLY B 740 " pdb=" C GLY B 740 " ideal model delta sigma weight residual 110.63 118.98 -8.35 1.43e+00 4.89e-01 3.41e+01 angle pdb=" N GLY A 727 " pdb=" CA GLY A 727 " pdb=" C GLY A 727 " ideal model delta sigma weight residual 112.73 119.56 -6.83 1.20e+00 6.94e-01 3.23e+01 ... (remaining 38194 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.62: 16617 21.62 - 43.25: 1210 43.25 - 64.87: 253 64.87 - 86.49: 132 86.49 - 108.11: 73 Dihedral angle restraints: 18285 sinusoidal: 8619 harmonic: 9666 Sorted by residual: dihedral pdb=" CB CYS C 726 " pdb=" SG CYS C 726 " pdb=" SG CYS C 732 " pdb=" CB CYS C 732 " ideal model delta sinusoidal sigma weight residual -86.00 -27.99 -58.01 1 1.00e+01 1.00e-02 4.51e+01 dihedral pdb=" CB CYS A 726 " pdb=" SG CYS A 726 " pdb=" SG CYS A 732 " pdb=" CB CYS A 732 " ideal model delta sinusoidal sigma weight residual -86.00 -29.35 -56.65 1 1.00e+01 1.00e-02 4.32e+01 dihedral pdb=" CB CYS B 726 " pdb=" SG CYS B 726 " pdb=" SG CYS B 732 " pdb=" CB CYS B 732 " ideal model delta sinusoidal sigma weight residual -86.00 -32.17 -53.83 1 1.00e+01 1.00e-02 3.93e+01 ... (remaining 18282 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.135: 4539 0.135 - 0.270: 95 0.270 - 0.404: 16 0.404 - 0.539: 0 0.539 - 0.674: 3 Chirality restraints: 4653 Sorted by residual: chirality pdb=" C1 NAG C1301 " pdb=" ND2 ASN C 145 " pdb=" C2 NAG C1301 " pdb=" O5 NAG C1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.73 -0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" C1 NAG B1301 " pdb=" ND2 ASN B 145 " pdb=" C2 NAG B1301 " pdb=" O5 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.73 -0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 145 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.74 -0.66 2.00e-01 2.50e+01 1.10e+01 ... (remaining 4650 not shown) Planarity restraints: 4863 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 590 " -0.009 2.00e-02 2.50e+03 3.75e-02 1.76e+01 pdb=" CG ASN A 590 " 0.060 2.00e-02 2.50e+03 pdb=" OD1 ASN A 590 " -0.045 2.00e-02 2.50e+03 pdb=" ND2 ASN A 590 " 0.023 2.00e-02 2.50e+03 pdb=" C1 NAG A1302 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 590 " 0.015 2.00e-02 2.50e+03 3.09e-02 9.52e+00 pdb=" CG ASN A 590 " -0.053 2.00e-02 2.50e+03 pdb=" OD1 ASN A 590 " 0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN A 590 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 968 " 0.045 5.00e-02 4.00e+02 6.75e-02 7.30e+00 pdb=" N PRO C 969 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO C 969 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 969 " 0.037 5.00e-02 4.00e+02 ... (remaining 4860 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 89 2.51 - 3.11: 19923 3.11 - 3.71: 40017 3.71 - 4.30: 62404 4.30 - 4.90: 101687 Nonbonded interactions: 224120 Sorted by model distance: nonbonded pdb=" O GLY B 581 " pdb=" NE2 GLN B 600 " model vdw 1.919 3.120 nonbonded pdb=" O ASN B 427 " pdb=" OG SER B 431 " model vdw 2.087 3.040 nonbonded pdb=" O ASP C 416 " pdb=" OD1 ASP C 416 " model vdw 2.222 3.040 nonbonded pdb=" NZ LYS A 298 " pdb=" OD1 ASP A 650 " model vdw 2.241 3.120 nonbonded pdb=" O3 NAG u 1 " pdb=" N2 NAG u 2 " model vdw 2.253 3.120 ... (remaining 224115 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'M' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'c' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 's' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 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: 0.020 Extract box with map and model: 1.060 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 69.340 Find NCS groups from input model: 2.090 Set up NCS constraints: 0.350 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:12.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 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 : 0.005 0.063 28220 Z= 0.247 Angle : 0.904 20.964 38647 Z= 0.452 Chirality : 0.058 0.674 4653 Planarity : 0.005 0.068 4809 Dihedral : 18.008 108.114 11937 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.22 % Allowed : 17.19 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.14), residues: 3312 helix: 1.82 (0.19), residues: 699 sheet: 0.25 (0.19), residues: 708 loop : -0.63 (0.13), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 869 HIS 0.006 0.002 HIS B1047 PHE 0.017 0.002 PHE A 881 TYR 0.021 0.002 TYR C 368 ARG 0.014 0.001 ARG A 545 Details of bonding type rmsd link_NAG-ASN : bond 0.00910 ( 54) link_NAG-ASN : angle 4.63624 ( 162) link_BETA1-4 : bond 0.00775 ( 66) link_BETA1-4 : angle 3.51480 ( 198) hydrogen bonds : bond 0.13888 ( 1063) hydrogen bonds : angle 6.93129 ( 3006) SS BOND : bond 0.00466 ( 44) SS BOND : angle 0.84204 ( 88) covalent geometry : bond 0.00477 (28056) covalent geometry : angle 0.81839 (38199) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 179 time to evaluate : 3.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 57 residues processed: 238 average time/residue: 1.2299 time to fit residues: 349.7100 Evaluate side-chains 229 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 172 time to evaluate : 3.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 366 LYS Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 575 SER Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 672 GLN Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 1057 ASN Chi-restraints excluded: chain A residue 1119 THR Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 319 ASN Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 457 SER Chi-restraints excluded: chain C residue 556 VAL Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 575 SER Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 892 ILE Chi-restraints excluded: chain C residue 963 ILE Chi-restraints excluded: chain C residue 1057 ASN Chi-restraints excluded: chain C residue 1098 ILE Chi-restraints excluded: chain C residue 1119 THR Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 685 ASP Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 797 LYS Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 930 LYS Chi-restraints excluded: chain B residue 963 ILE Chi-restraints excluded: chain B residue 1057 ASN Chi-restraints excluded: chain B residue 1079 VAL Chi-restraints excluded: chain B residue 1124 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 278 optimal weight: 2.9990 chunk 250 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 168 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 258 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 157 optimal weight: 5.9990 chunk 192 optimal weight: 0.7980 chunk 299 optimal weight: 7.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 HIS A 302 GLN A 600 GLN A 672 GLN A 948 GLN C 148 GLN C 722 ASN C1089 GLN B 985 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.119308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.089718 restraints weight = 36922.428| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.22 r_work: 0.2878 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.0809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 28220 Z= 0.137 Angle : 0.678 20.061 38647 Z= 0.316 Chirality : 0.049 0.596 4653 Planarity : 0.004 0.064 4809 Dihedral : 11.417 64.969 6151 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.60 % Allowed : 15.94 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.14), residues: 3312 helix: 2.20 (0.19), residues: 699 sheet: 0.12 (0.18), residues: 735 loop : -0.67 (0.13), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 424 HIS 0.003 0.001 HIS A 38 PHE 0.010 0.001 PHE C 90 TYR 0.017 0.001 TYR A1050 ARG 0.007 0.000 ARG A 545 Details of bonding type rmsd link_NAG-ASN : bond 0.00690 ( 54) link_NAG-ASN : angle 3.93242 ( 162) link_BETA1-4 : bond 0.00729 ( 66) link_BETA1-4 : angle 2.52582 ( 198) hydrogen bonds : bond 0.05482 ( 1063) hydrogen bonds : angle 5.52928 ( 3006) SS BOND : bond 0.00422 ( 44) SS BOND : angle 0.75743 ( 88) covalent geometry : bond 0.00295 (28056) covalent geometry : angle 0.60461 (38199) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 184 time to evaluate : 2.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8550 (tt0) REVERT: A 319 ASN cc_start: 0.8363 (OUTLIER) cc_final: 0.8060 (p0) REVERT: A 788 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8390 (mt) REVERT: A 922 THR cc_start: 0.8508 (OUTLIER) cc_final: 0.8162 (m) REVERT: C 313 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8298 (tt0) REVERT: C 319 ASN cc_start: 0.8468 (OUTLIER) cc_final: 0.8145 (p0) REVERT: C 723 MET cc_start: 0.9295 (OUTLIER) cc_final: 0.9075 (ttt) REVERT: B 416 ASP cc_start: 0.8309 (p0) cc_final: 0.7984 (p0) outliers start: 75 outliers final: 32 residues processed: 244 average time/residue: 1.2347 time to fit residues: 358.1961 Evaluate side-chains 214 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 175 time to evaluate : 2.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 468 CYS Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 319 ASN Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 467 SER Chi-restraints excluded: chain C residue 723 MET Chi-restraints excluded: chain C residue 892 ILE Chi-restraints excluded: chain C residue 963 ILE Chi-restraints excluded: chain C residue 1110 ASP Chi-restraints excluded: chain C residue 1124 LEU Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 723 MET Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 1075 GLU Chi-restraints excluded: chain B residue 1079 VAL Chi-restraints excluded: chain B residue 1110 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 293 optimal weight: 1.9990 chunk 204 optimal weight: 5.9990 chunk 199 optimal weight: 4.9990 chunk 210 optimal weight: 0.6980 chunk 257 optimal weight: 2.9990 chunk 165 optimal weight: 0.8980 chunk 269 optimal weight: 1.9990 chunk 275 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 312 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 GLN C 948 GLN C1089 GLN B 938 ASN B 948 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.116986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.087446 restraints weight = 36968.218| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.21 r_work: 0.2837 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 28220 Z= 0.182 Angle : 0.690 19.928 38647 Z= 0.325 Chirality : 0.050 0.517 4653 Planarity : 0.004 0.064 4809 Dihedral : 8.198 58.736 6090 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.85 % Allowed : 15.21 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.14), residues: 3312 helix: 1.98 (0.19), residues: 714 sheet: 0.27 (0.19), residues: 699 loop : -0.78 (0.13), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 869 HIS 0.006 0.002 HIS A 38 PHE 0.013 0.002 PHE A 881 TYR 0.020 0.002 TYR A1050 ARG 0.005 0.001 ARG A 759 Details of bonding type rmsd link_NAG-ASN : bond 0.00665 ( 54) link_NAG-ASN : angle 3.87913 ( 162) link_BETA1-4 : bond 0.00620 ( 66) link_BETA1-4 : angle 2.50386 ( 198) hydrogen bonds : bond 0.05730 ( 1063) hydrogen bonds : angle 5.37786 ( 3006) SS BOND : bond 0.00420 ( 44) SS BOND : angle 0.89440 ( 88) covalent geometry : bond 0.00431 (28056) covalent geometry : angle 0.61890 (38199) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 174 time to evaluate : 2.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8579 (tt0) REVERT: A 319 ASN cc_start: 0.8490 (OUTLIER) cc_final: 0.8161 (p0) REVERT: A 788 ILE cc_start: 0.8834 (OUTLIER) cc_final: 0.8452 (mt) REVERT: C 313 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8315 (tt0) REVERT: C 723 MET cc_start: 0.9353 (mtp) cc_final: 0.9007 (ttt) REVERT: C 933 ASP cc_start: 0.8449 (OUTLIER) cc_final: 0.8155 (m-30) REVERT: C 985 GLN cc_start: 0.8841 (tm-30) cc_final: 0.8548 (tp-100) REVERT: C 1021 LYS cc_start: 0.9235 (OUTLIER) cc_final: 0.8856 (mppt) REVERT: B 172 ASP cc_start: 0.7499 (m-30) cc_final: 0.6255 (p0) REVERT: B 239 PHE cc_start: 0.8473 (m-80) cc_final: 0.8111 (m-80) REVERT: B 416 ASP cc_start: 0.8286 (p0) cc_final: 0.7991 (p0) REVERT: B 817 MET cc_start: 0.6189 (OUTLIER) cc_final: 0.5564 (ptt) REVERT: B 922 THR cc_start: 0.8505 (OUTLIER) cc_final: 0.8296 (m) REVERT: B 1098 ILE cc_start: 0.8793 (OUTLIER) cc_final: 0.8557 (mm) outliers start: 111 outliers final: 55 residues processed: 257 average time/residue: 1.2442 time to fit residues: 387.6845 Evaluate side-chains 231 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 167 time to evaluate : 3.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 468 CYS Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 1055 GLU Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1119 THR Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 319 ASN Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 556 VAL Chi-restraints excluded: chain C residue 892 ILE Chi-restraints excluded: chain C residue 899 LEU Chi-restraints excluded: chain C residue 922 THR Chi-restraints excluded: chain C residue 933 ASP Chi-restraints excluded: chain C residue 963 ILE Chi-restraints excluded: chain C residue 1021 LYS Chi-restraints excluded: chain C residue 1110 ASP Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1119 THR Chi-restraints excluded: chain C residue 1124 LEU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 476 TYR Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 680 MET Chi-restraints excluded: chain B residue 712 VAL Chi-restraints excluded: chain B residue 723 MET Chi-restraints excluded: chain B residue 725 ILE Chi-restraints excluded: chain B residue 817 MET Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 885 MET Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 1079 VAL Chi-restraints excluded: chain B residue 1098 ILE Chi-restraints excluded: chain B residue 1110 ASP Chi-restraints excluded: chain B residue 1124 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 165 optimal weight: 3.9990 chunk 319 optimal weight: 1.9990 chunk 269 optimal weight: 1.9990 chunk 161 optimal weight: 0.7980 chunk 105 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 132 optimal weight: 6.9990 chunk 255 optimal weight: 0.6980 chunk 157 optimal weight: 5.9990 chunk 234 optimal weight: 0.8980 chunk 109 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 GLN A 600 GLN ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 GLN C1089 GLN B 196 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.119355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.089930 restraints weight = 37232.713| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.23 r_work: 0.2881 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28220 Z= 0.119 Angle : 0.611 20.022 38647 Z= 0.285 Chirality : 0.046 0.479 4653 Planarity : 0.004 0.063 4809 Dihedral : 6.705 59.225 6088 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.99 % Allowed : 16.22 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.14), residues: 3312 helix: 2.30 (0.19), residues: 687 sheet: 0.20 (0.19), residues: 735 loop : -0.70 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 424 HIS 0.002 0.001 HIS A 38 PHE 0.012 0.001 PHE A 139 TYR 0.017 0.001 TYR A1050 ARG 0.005 0.000 ARG C 545 Details of bonding type rmsd link_NAG-ASN : bond 0.00593 ( 54) link_NAG-ASN : angle 3.59125 ( 162) link_BETA1-4 : bond 0.00622 ( 66) link_BETA1-4 : angle 2.30523 ( 198) hydrogen bonds : bond 0.04668 ( 1063) hydrogen bonds : angle 5.08696 ( 3006) SS BOND : bond 0.00287 ( 44) SS BOND : angle 0.81418 ( 88) covalent geometry : bond 0.00261 (28056) covalent geometry : angle 0.54162 (38199) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 185 time to evaluate : 2.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 ASP cc_start: 0.5916 (p0) cc_final: 0.5697 (m-30) REVERT: A 313 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8561 (tt0) REVERT: A 319 ASN cc_start: 0.8419 (OUTLIER) cc_final: 0.8072 (p0) REVERT: A 788 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8389 (mt) REVERT: A 922 THR cc_start: 0.8436 (OUTLIER) cc_final: 0.8029 (m) REVERT: A 930 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8368 (mtpp) REVERT: C 313 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.8327 (tt0) REVERT: C 723 MET cc_start: 0.9250 (OUTLIER) cc_final: 0.9000 (ttt) REVERT: C 817 MET cc_start: 0.6158 (tmm) cc_final: 0.5367 (ppp) REVERT: C 904 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8374 (mppt) REVERT: C 985 GLN cc_start: 0.8768 (tm-30) cc_final: 0.8423 (tp-100) REVERT: C 1021 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8969 (mmtp) REVERT: B 239 PHE cc_start: 0.8549 (m-80) cc_final: 0.8194 (m-80) REVERT: B 416 ASP cc_start: 0.8275 (p0) cc_final: 0.7969 (p0) REVERT: B 922 THR cc_start: 0.8678 (OUTLIER) cc_final: 0.8322 (m) REVERT: B 933 ASP cc_start: 0.8398 (OUTLIER) cc_final: 0.8099 (m-30) outliers start: 86 outliers final: 43 residues processed: 247 average time/residue: 1.2917 time to fit residues: 377.0957 Evaluate side-chains 229 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 175 time to evaluate : 2.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 468 CYS Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 930 LYS Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 1055 GLU Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1119 THR Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 319 ASN Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 476 TYR Chi-restraints excluded: chain C residue 723 MET Chi-restraints excluded: chain C residue 879 ILE Chi-restraints excluded: chain C residue 892 ILE Chi-restraints excluded: chain C residue 899 LEU Chi-restraints excluded: chain C residue 904 LYS Chi-restraints excluded: chain C residue 1021 LYS Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1119 THR Chi-restraints excluded: chain C residue 1124 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 476 TYR Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 723 MET Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 885 MET Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 933 ASP Chi-restraints excluded: chain B residue 1059 THR Chi-restraints excluded: chain B residue 1075 GLU Chi-restraints excluded: chain B residue 1079 VAL Chi-restraints excluded: chain B residue 1110 ASP Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain B residue 1124 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 87 optimal weight: 3.9990 chunk 264 optimal weight: 4.9990 chunk 298 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 chunk 234 optimal weight: 0.5980 chunk 195 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 288 optimal weight: 0.9990 chunk 263 optimal weight: 2.9990 chunk 300 optimal weight: 0.0670 overall best weight: 1.1122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 600 GLN ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1089 GLN B 985 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.118417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.088903 restraints weight = 36970.122| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.23 r_work: 0.2865 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 28220 Z= 0.135 Angle : 0.615 19.910 38647 Z= 0.289 Chirality : 0.047 0.471 4653 Planarity : 0.004 0.065 4809 Dihedral : 6.394 58.084 6083 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.33 % Allowed : 16.08 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.14), residues: 3312 helix: 2.32 (0.19), residues: 681 sheet: 0.27 (0.19), residues: 732 loop : -0.73 (0.13), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 424 HIS 0.004 0.001 HIS A 38 PHE 0.010 0.001 PHE C 90 TYR 0.019 0.001 TYR A1050 ARG 0.004 0.000 ARG A 759 Details of bonding type rmsd link_NAG-ASN : bond 0.00569 ( 54) link_NAG-ASN : angle 3.55951 ( 162) link_BETA1-4 : bond 0.00601 ( 66) link_BETA1-4 : angle 2.23918 ( 198) hydrogen bonds : bond 0.04870 ( 1063) hydrogen bonds : angle 5.06899 ( 3006) SS BOND : bond 0.00293 ( 44) SS BOND : angle 0.79653 ( 88) covalent geometry : bond 0.00308 (28056) covalent geometry : angle 0.54911 (38199) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 173 time to evaluate : 2.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8213 (mtpp) REVERT: A 313 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8566 (tt0) REVERT: A 319 ASN cc_start: 0.8459 (OUTLIER) cc_final: 0.8083 (p0) REVERT: A 788 ILE cc_start: 0.8811 (OUTLIER) cc_final: 0.8470 (mt) REVERT: A 930 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8405 (mtpp) REVERT: C 57 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.8003 (tp40) REVERT: C 99 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8259 (mt) REVERT: C 313 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8341 (tt0) REVERT: C 723 MET cc_start: 0.9251 (mtp) cc_final: 0.9034 (ttt) REVERT: C 904 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8376 (mppt) REVERT: C 971 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7338 (pm20) REVERT: C 985 GLN cc_start: 0.8750 (tm-30) cc_final: 0.8444 (tp-100) REVERT: C 1021 LYS cc_start: 0.9241 (OUTLIER) cc_final: 0.8870 (mppt) REVERT: B 239 PHE cc_start: 0.8550 (m-80) cc_final: 0.8206 (m-80) REVERT: B 416 ASP cc_start: 0.8251 (p0) cc_final: 0.7973 (p0) REVERT: B 817 MET cc_start: 0.6101 (OUTLIER) cc_final: 0.5548 (ptt) REVERT: B 922 THR cc_start: 0.8482 (OUTLIER) cc_final: 0.8142 (m) REVERT: B 933 ASP cc_start: 0.8408 (OUTLIER) cc_final: 0.8104 (m-30) REVERT: B 1098 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8522 (mm) outliers start: 96 outliers final: 56 residues processed: 246 average time/residue: 1.3213 time to fit residues: 391.9916 Evaluate side-chains 242 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 171 time to evaluate : 3.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 468 CYS Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 930 LYS Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1119 THR Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 57 GLN Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 319 ASN Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 476 TYR Chi-restraints excluded: chain C residue 619 SER Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 892 ILE Chi-restraints excluded: chain C residue 899 LEU Chi-restraints excluded: chain C residue 904 LYS Chi-restraints excluded: chain C residue 971 GLU Chi-restraints excluded: chain C residue 1021 LYS Chi-restraints excluded: chain C residue 1059 THR Chi-restraints excluded: chain C residue 1110 ASP Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1119 THR Chi-restraints excluded: chain C residue 1124 LEU Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 476 TYR Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 723 MET Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 817 MET Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 879 ILE Chi-restraints excluded: chain B residue 885 MET Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 923 THR Chi-restraints excluded: chain B residue 933 ASP Chi-restraints excluded: chain B residue 1059 THR Chi-restraints excluded: chain B residue 1079 VAL Chi-restraints excluded: chain B residue 1098 ILE Chi-restraints excluded: chain B residue 1110 ASP Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain B residue 1124 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 103 optimal weight: 3.9990 chunk 278 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 237 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 246 optimal weight: 1.9990 chunk 266 optimal weight: 4.9990 chunk 284 optimal weight: 0.9980 chunk 115 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 GLN ** C 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1089 GLN B 474 ASN ** B 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 985 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.115736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.085829 restraints weight = 37055.893| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.24 r_work: 0.2820 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 28220 Z= 0.193 Angle : 0.669 19.821 38647 Z= 0.319 Chirality : 0.049 0.472 4653 Planarity : 0.004 0.066 4809 Dihedral : 6.446 54.705 6083 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.72 % Allowed : 15.90 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.14), residues: 3312 helix: 1.86 (0.19), residues: 717 sheet: 0.27 (0.19), residues: 729 loop : -0.84 (0.13), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 869 HIS 0.006 0.002 HIS A 38 PHE 0.013 0.002 PHE A 528 TYR 0.018 0.002 TYR A1050 ARG 0.006 0.001 ARG A 759 Details of bonding type rmsd link_NAG-ASN : bond 0.00585 ( 54) link_NAG-ASN : angle 3.64264 ( 162) link_BETA1-4 : bond 0.00612 ( 66) link_BETA1-4 : angle 2.28781 ( 198) hydrogen bonds : bond 0.05603 ( 1063) hydrogen bonds : angle 5.27511 ( 3006) SS BOND : bond 0.00348 ( 44) SS BOND : angle 0.92806 ( 88) covalent geometry : bond 0.00465 (28056) covalent geometry : angle 0.60575 (38199) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 167 time to evaluate : 2.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8610 (tt0) REVERT: A 319 ASN cc_start: 0.8592 (OUTLIER) cc_final: 0.8242 (p0) REVERT: A 440 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9073 (mt) REVERT: A 922 THR cc_start: 0.8548 (OUTLIER) cc_final: 0.8177 (m) REVERT: C 57 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.8036 (tp40) REVERT: C 313 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.8405 (tt0) REVERT: C 723 MET cc_start: 0.9302 (mtp) cc_final: 0.8965 (ttt) REVERT: C 962 ASP cc_start: 0.8729 (m-30) cc_final: 0.8519 (m-30) REVERT: C 985 GLN cc_start: 0.8834 (tm-30) cc_final: 0.8560 (tp-100) REVERT: C 1021 LYS cc_start: 0.9219 (OUTLIER) cc_final: 0.8833 (mppt) REVERT: B 239 PHE cc_start: 0.8598 (m-80) cc_final: 0.8376 (m-80) REVERT: B 416 ASP cc_start: 0.8304 (p0) cc_final: 0.8058 (p0) REVERT: B 600 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7103 (mp10) REVERT: B 817 MET cc_start: 0.6137 (OUTLIER) cc_final: 0.5623 (ptt) REVERT: B 922 THR cc_start: 0.8480 (OUTLIER) cc_final: 0.8161 (m) REVERT: B 1098 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8513 (mm) outliers start: 107 outliers final: 68 residues processed: 243 average time/residue: 1.3392 time to fit residues: 386.3458 Evaluate side-chains 247 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 168 time to evaluate : 3.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 468 CYS Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain A residue 827 ILE Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1119 THR Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 57 GLN Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 319 ASN Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 556 VAL Chi-restraints excluded: chain C residue 619 SER Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 899 LEU Chi-restraints excluded: chain C residue 963 ILE Chi-restraints excluded: chain C residue 1021 LYS Chi-restraints excluded: chain C residue 1059 THR Chi-restraints excluded: chain C residue 1110 ASP Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1119 THR Chi-restraints excluded: chain C residue 1124 LEU Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 600 GLN Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 619 SER Chi-restraints excluded: chain B residue 680 MET Chi-restraints excluded: chain B residue 723 MET Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 817 MET Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 879 ILE Chi-restraints excluded: chain B residue 883 MET Chi-restraints excluded: chain B residue 885 MET Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 923 THR Chi-restraints excluded: chain B residue 1059 THR Chi-restraints excluded: chain B residue 1079 VAL Chi-restraints excluded: chain B residue 1090 ARG Chi-restraints excluded: chain B residue 1098 ILE Chi-restraints excluded: chain B residue 1110 ASP Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain B residue 1124 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 34 optimal weight: 0.6980 chunk 191 optimal weight: 0.0980 chunk 194 optimal weight: 5.9990 chunk 290 optimal weight: 0.5980 chunk 326 optimal weight: 1.9990 chunk 300 optimal weight: 0.9990 chunk 211 optimal weight: 0.6980 chunk 318 optimal weight: 3.9990 chunk 243 optimal weight: 0.9980 chunk 316 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1089 GLN B 985 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.119029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.089677 restraints weight = 37003.157| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.22 r_work: 0.2877 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 28220 Z= 0.107 Angle : 0.587 19.919 38647 Z= 0.276 Chirality : 0.045 0.438 4653 Planarity : 0.004 0.063 4809 Dihedral : 5.974 58.178 6081 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.67 % Allowed : 17.01 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.14), residues: 3312 helix: 2.34 (0.20), residues: 669 sheet: 0.27 (0.19), residues: 732 loop : -0.71 (0.13), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 102 HIS 0.002 0.001 HIS C1031 PHE 0.009 0.001 PHE C 910 TYR 0.018 0.001 TYR C1050 ARG 0.004 0.000 ARG B 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00549 ( 54) link_NAG-ASN : angle 3.44549 ( 162) link_BETA1-4 : bond 0.00597 ( 66) link_BETA1-4 : angle 2.11277 ( 198) hydrogen bonds : bond 0.04447 ( 1063) hydrogen bonds : angle 4.96654 ( 3006) SS BOND : bond 0.00260 ( 44) SS BOND : angle 0.70799 ( 88) covalent geometry : bond 0.00226 (28056) covalent geometry : angle 0.52357 (38199) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 184 time to evaluate : 3.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8562 (tt0) REVERT: A 319 ASN cc_start: 0.8530 (OUTLIER) cc_final: 0.8161 (p0) REVERT: A 788 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8350 (mt) REVERT: A 922 THR cc_start: 0.8503 (OUTLIER) cc_final: 0.8090 (m) REVERT: A 930 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8328 (mtpp) REVERT: C 99 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8250 (mt) REVERT: C 723 MET cc_start: 0.9185 (OUTLIER) cc_final: 0.8922 (ttt) REVERT: C 985 GLN cc_start: 0.8758 (tm-30) cc_final: 0.8393 (tp-100) REVERT: C 1021 LYS cc_start: 0.9229 (OUTLIER) cc_final: 0.8852 (mppt) REVERT: B 239 PHE cc_start: 0.8585 (m-80) cc_final: 0.8354 (m-80) REVERT: B 416 ASP cc_start: 0.8278 (p0) cc_final: 0.8058 (p0) REVERT: B 922 THR cc_start: 0.8494 (OUTLIER) cc_final: 0.8124 (m) REVERT: B 1098 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8461 (mm) outliers start: 77 outliers final: 43 residues processed: 237 average time/residue: 1.2532 time to fit residues: 356.9240 Evaluate side-chains 229 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 176 time to evaluate : 2.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 468 CYS Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 930 LYS Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1119 THR Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 319 ASN Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 476 TYR Chi-restraints excluded: chain C residue 723 MET Chi-restraints excluded: chain C residue 899 LEU Chi-restraints excluded: chain C residue 1021 LYS Chi-restraints excluded: chain C residue 1059 THR Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1119 THR Chi-restraints excluded: chain C residue 1124 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 619 SER Chi-restraints excluded: chain B residue 725 ILE Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 885 MET Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 1059 THR Chi-restraints excluded: chain B residue 1075 GLU Chi-restraints excluded: chain B residue 1079 VAL Chi-restraints excluded: chain B residue 1098 ILE Chi-restraints excluded: chain B residue 1110 ASP Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain B residue 1124 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 233 optimal weight: 7.9990 chunk 205 optimal weight: 0.8980 chunk 282 optimal weight: 0.0970 chunk 206 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 129 optimal weight: 0.3980 chunk 53 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 312 optimal weight: 0.9990 chunk 326 optimal weight: 2.9990 chunk 232 optimal weight: 0.8980 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 302 GLN A 600 GLN C 550 GLN C 722 ASN C1089 GLN B 938 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.119277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.089806 restraints weight = 36895.654| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.22 r_work: 0.2880 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 28220 Z= 0.110 Angle : 0.590 19.832 38647 Z= 0.277 Chirality : 0.046 0.429 4653 Planarity : 0.004 0.067 4809 Dihedral : 5.777 56.698 6078 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.64 % Allowed : 17.12 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.14), residues: 3312 helix: 2.40 (0.20), residues: 669 sheet: 0.28 (0.19), residues: 735 loop : -0.69 (0.13), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 102 HIS 0.002 0.001 HIS A 38 PHE 0.012 0.001 PHE C 239 TYR 0.018 0.001 TYR A1050 ARG 0.004 0.000 ARG C 759 Details of bonding type rmsd link_NAG-ASN : bond 0.00545 ( 54) link_NAG-ASN : angle 3.40884 ( 162) link_BETA1-4 : bond 0.00581 ( 66) link_BETA1-4 : angle 2.06254 ( 198) hydrogen bonds : bond 0.04395 ( 1063) hydrogen bonds : angle 4.89254 ( 3006) SS BOND : bond 0.00259 ( 44) SS BOND : angle 0.70827 ( 88) covalent geometry : bond 0.00238 (28056) covalent geometry : angle 0.52855 (38199) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 182 time to evaluate : 2.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8564 (tt0) REVERT: A 319 ASN cc_start: 0.8534 (OUTLIER) cc_final: 0.8146 (p0) REVERT: A 788 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8356 (mt) REVERT: A 922 THR cc_start: 0.8609 (OUTLIER) cc_final: 0.8157 (m) REVERT: C 71 ILE cc_start: 0.8154 (OUTLIER) cc_final: 0.7816 (mt) REVERT: C 99 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8296 (mt) REVERT: C 723 MET cc_start: 0.9205 (OUTLIER) cc_final: 0.8987 (ttt) REVERT: C 985 GLN cc_start: 0.8737 (tm-30) cc_final: 0.8380 (tp-100) REVERT: C 1021 LYS cc_start: 0.9248 (OUTLIER) cc_final: 0.9006 (mmtp) REVERT: B 239 PHE cc_start: 0.8565 (m-80) cc_final: 0.8352 (m-80) REVERT: B 922 THR cc_start: 0.8502 (OUTLIER) cc_final: 0.8118 (m) REVERT: B 1098 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8436 (mm) outliers start: 76 outliers final: 47 residues processed: 237 average time/residue: 1.2762 time to fit residues: 359.2553 Evaluate side-chains 231 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 174 time to evaluate : 3.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 468 CYS Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain A residue 827 ILE Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1119 THR Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 319 ASN Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 556 VAL Chi-restraints excluded: chain C residue 723 MET Chi-restraints excluded: chain C residue 725 ILE Chi-restraints excluded: chain C residue 892 ILE Chi-restraints excluded: chain C residue 899 LEU Chi-restraints excluded: chain C residue 1021 LYS Chi-restraints excluded: chain C residue 1059 THR Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1119 THR Chi-restraints excluded: chain C residue 1124 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 619 SER Chi-restraints excluded: chain B residue 725 ILE Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 885 MET Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 1059 THR Chi-restraints excluded: chain B residue 1079 VAL Chi-restraints excluded: chain B residue 1098 ILE Chi-restraints excluded: chain B residue 1110 ASP Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain B residue 1124 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 305 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 280 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 126 optimal weight: 0.9990 chunk 201 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 94 optimal weight: 0.4980 chunk 186 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1089 GLN B 938 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.117358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.087616 restraints weight = 37156.939| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.24 r_work: 0.2849 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 28220 Z= 0.156 Angle : 0.622 19.822 38647 Z= 0.297 Chirality : 0.047 0.431 4653 Planarity : 0.004 0.065 4809 Dihedral : 5.935 56.399 6078 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.43 % Allowed : 17.43 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.14), residues: 3312 helix: 2.16 (0.20), residues: 681 sheet: 0.25 (0.19), residues: 732 loop : -0.82 (0.13), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 424 HIS 0.004 0.001 HIS A 38 PHE 0.011 0.001 PHE C 239 TYR 0.018 0.001 TYR B1050 ARG 0.005 0.000 ARG A 759 Details of bonding type rmsd link_NAG-ASN : bond 0.00541 ( 54) link_NAG-ASN : angle 3.46123 ( 162) link_BETA1-4 : bond 0.00580 ( 66) link_BETA1-4 : angle 2.09787 ( 198) hydrogen bonds : bond 0.05033 ( 1063) hydrogen bonds : angle 5.06848 ( 3006) SS BOND : bond 0.00299 ( 44) SS BOND : angle 0.84331 ( 88) covalent geometry : bond 0.00365 (28056) covalent geometry : angle 0.56278 (38199) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 176 time to evaluate : 2.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8363 (tt0) REVERT: A 788 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8455 (mt) REVERT: A 922 THR cc_start: 0.8520 (OUTLIER) cc_final: 0.8106 (m) REVERT: C 57 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.7959 (tp40) REVERT: C 99 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.8318 (mt) REVERT: C 723 MET cc_start: 0.9215 (OUTLIER) cc_final: 0.8928 (ttt) REVERT: C 985 GLN cc_start: 0.8745 (tm-30) cc_final: 0.8437 (tp-100) REVERT: C 1021 LYS cc_start: 0.9223 (OUTLIER) cc_final: 0.8820 (mppt) REVERT: B 239 PHE cc_start: 0.8636 (m-80) cc_final: 0.8416 (m-80) REVERT: B 817 MET cc_start: 0.6308 (OUTLIER) cc_final: 0.5807 (ptt) REVERT: B 922 THR cc_start: 0.8416 (OUTLIER) cc_final: 0.8048 (m) REVERT: B 1098 ILE cc_start: 0.8758 (OUTLIER) cc_final: 0.8496 (mm) outliers start: 70 outliers final: 51 residues processed: 222 average time/residue: 1.4526 time to fit residues: 384.2225 Evaluate side-chains 234 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 173 time to evaluate : 2.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 468 CYS Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain A residue 827 ILE Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1119 THR Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 57 GLN Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 319 ASN Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 556 VAL Chi-restraints excluded: chain C residue 619 SER Chi-restraints excluded: chain C residue 723 MET Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 899 LEU Chi-restraints excluded: chain C residue 963 ILE Chi-restraints excluded: chain C residue 1021 LYS Chi-restraints excluded: chain C residue 1059 THR Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1119 THR Chi-restraints excluded: chain C residue 1124 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 619 SER Chi-restraints excluded: chain B residue 725 ILE Chi-restraints excluded: chain B residue 817 MET Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 885 MET Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 1059 THR Chi-restraints excluded: chain B residue 1075 GLU Chi-restraints excluded: chain B residue 1079 VAL Chi-restraints excluded: chain B residue 1098 ILE Chi-restraints excluded: chain B residue 1110 ASP Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain B residue 1124 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 94 optimal weight: 0.0870 chunk 134 optimal weight: 1.9990 chunk 242 optimal weight: 8.9990 chunk 220 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 126 optimal weight: 0.4980 chunk 281 optimal weight: 2.9990 chunk 288 optimal weight: 0.9990 chunk 31 optimal weight: 0.4980 chunk 60 optimal weight: 3.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 GLN C1089 GLN B 938 ASN B 940 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.119322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.090033 restraints weight = 36909.687| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.21 r_work: 0.2884 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 28220 Z= 0.109 Angle : 0.585 19.843 38647 Z= 0.276 Chirality : 0.045 0.413 4653 Planarity : 0.004 0.065 4809 Dihedral : 5.722 58.031 6078 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.12 % Allowed : 17.88 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.14), residues: 3312 helix: 2.41 (0.20), residues: 669 sheet: 0.37 (0.19), residues: 705 loop : -0.71 (0.13), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 102 HIS 0.002 0.001 HIS A 38 PHE 0.013 0.001 PHE C 239 TYR 0.017 0.001 TYR A1050 ARG 0.008 0.000 ARG B1090 Details of bonding type rmsd link_NAG-ASN : bond 0.00539 ( 54) link_NAG-ASN : angle 3.35654 ( 162) link_BETA1-4 : bond 0.00580 ( 66) link_BETA1-4 : angle 1.99702 ( 198) hydrogen bonds : bond 0.04330 ( 1063) hydrogen bonds : angle 4.87118 ( 3006) SS BOND : bond 0.00248 ( 44) SS BOND : angle 0.69874 ( 88) covalent geometry : bond 0.00238 (28056) covalent geometry : angle 0.52606 (38199) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 178 time to evaluate : 3.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8325 (tt0) REVERT: A 788 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8326 (mt) REVERT: A 922 THR cc_start: 0.8600 (OUTLIER) cc_final: 0.8146 (m) REVERT: C 71 ILE cc_start: 0.8117 (OUTLIER) cc_final: 0.7782 (mt) REVERT: C 99 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8303 (mt) REVERT: C 933 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.8030 (m-30) REVERT: C 985 GLN cc_start: 0.8734 (tm-30) cc_final: 0.8369 (tp-100) REVERT: C 1021 LYS cc_start: 0.9248 (OUTLIER) cc_final: 0.8871 (mppt) REVERT: B 239 PHE cc_start: 0.8577 (m-80) cc_final: 0.8357 (m-80) REVERT: B 922 THR cc_start: 0.8468 (OUTLIER) cc_final: 0.8058 (m) REVERT: B 1098 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.8426 (mm) outliers start: 61 outliers final: 48 residues processed: 220 average time/residue: 1.3113 time to fit residues: 343.7833 Evaluate side-chains 229 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 172 time to evaluate : 3.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 468 CYS Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 827 ILE Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1119 THR Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 319 ASN Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 556 VAL Chi-restraints excluded: chain C residue 899 LEU Chi-restraints excluded: chain C residue 933 ASP Chi-restraints excluded: chain C residue 963 ILE Chi-restraints excluded: chain C residue 1021 LYS Chi-restraints excluded: chain C residue 1059 THR Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1119 THR Chi-restraints excluded: chain C residue 1124 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 725 ILE Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 879 ILE Chi-restraints excluded: chain B residue 885 MET Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 1059 THR Chi-restraints excluded: chain B residue 1075 GLU Chi-restraints excluded: chain B residue 1079 VAL Chi-restraints excluded: chain B residue 1098 ILE Chi-restraints excluded: chain B residue 1110 ASP Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain B residue 1124 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 200 optimal weight: 0.3980 chunk 232 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 151 optimal weight: 8.9990 chunk 107 optimal weight: 0.9990 chunk 287 optimal weight: 0.6980 chunk 279 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 149 optimal weight: 0.2980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1089 GLN B 940 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.118735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.089382 restraints weight = 36939.709| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.21 r_work: 0.2873 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 28220 Z= 0.120 Angle : 0.589 19.747 38647 Z= 0.280 Chirality : 0.046 0.411 4653 Planarity : 0.004 0.069 4809 Dihedral : 5.709 57.320 6078 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.33 % Allowed : 17.67 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.14), residues: 3312 helix: 2.41 (0.20), residues: 669 sheet: 0.38 (0.19), residues: 705 loop : -0.72 (0.13), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 424 HIS 0.003 0.001 HIS A 38 PHE 0.014 0.001 PHE C 239 TYR 0.018 0.001 TYR A1050 ARG 0.007 0.000 ARG A 759 Details of bonding type rmsd link_NAG-ASN : bond 0.00529 ( 54) link_NAG-ASN : angle 3.35449 ( 162) link_BETA1-4 : bond 0.00563 ( 66) link_BETA1-4 : angle 1.98190 ( 198) hydrogen bonds : bond 0.04486 ( 1063) hydrogen bonds : angle 4.87785 ( 3006) SS BOND : bond 0.00258 ( 44) SS BOND : angle 0.75679 ( 88) covalent geometry : bond 0.00269 (28056) covalent geometry : angle 0.53077 (38199) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18099.89 seconds wall clock time: 315 minutes 46.70 seconds (18946.70 seconds total)