Starting phenix.real_space_refine on Sat Mar 7 06:40:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y21_33578/03_2026/7y21_33578.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y21_33578/03_2026/7y21_33578.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7y21_33578/03_2026/7y21_33578.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y21_33578/03_2026/7y21_33578.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7y21_33578/03_2026/7y21_33578.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y21_33578/03_2026/7y21_33578.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.095 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 195 5.16 5 C 25204 2.51 5 N 6429 2.21 5 O 7719 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39547 Number of models: 1 Model: "" Number of chains: 50 Chain: "A" Number of atoms: 7825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7825 Classifications: {'peptide': 998} Link IDs: {'PTRANS': 54, 'TRANS': 943} Chain breaks: 9 Chain: "B" Number of atoms: 7831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 999, 7831 Classifications: {'peptide': 999} Link IDs: {'PTRANS': 54, 'TRANS': 944} Chain breaks: 9 Chain: "C" Number of atoms: 7825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7825 Classifications: {'peptide': 998} Link IDs: {'PTRANS': 54, 'TRANS': 943} Chain breaks: 9 Chain: "D" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 27, 'TRANS': 569} Chain: "F" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 27, 'TRANS': 569} Chain: "H" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 27, 'TRANS': 569} 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: "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: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 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: 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: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 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: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.72, per 1000 atoms: 0.22 Number of scatterers: 39547 At special positions: 0 Unit cell: (178.268, 198.921, 247.836, 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 195 16.00 O 7719 8.00 N 6429 7.00 C 25204 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.09 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.07 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.14 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=1.87 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.06 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.05 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.08 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.04 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.20 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.09 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=1.89 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.14 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=1.86 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.06 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.05 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.12 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.18 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.07 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.14 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.09 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.22 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.14 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.06 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.05 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.26 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=1.97 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.17 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.10 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.04 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS F 133 " - pdb=" SG CYS F 141 " distance=2.03 Simple disulfide: pdb=" SG CYS F 344 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 530 " - pdb=" SG CYS F 542 " distance=2.03 Simple disulfide: pdb=" SG CYS H 133 " - pdb=" SG CYS H 141 " distance=2.03 Simple disulfide: pdb=" SG CYS H 344 " - pdb=" SG CYS H 361 " distance=2.03 Simple disulfide: pdb=" SG CYS H 530 " - pdb=" SG CYS H 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG 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 V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG 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 l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 165 " " NAG A1404 " - " ASN A 234 " " NAG A1405 " - " ASN A 282 " " NAG A1406 " - " ASN A 603 " " NAG A1407 " - " ASN A 616 " " NAG A1408 " - " ASN A 657 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 122 " " NAG B1403 " - " ASN B 165 " " NAG B1404 " - " ASN B 234 " " NAG B1405 " - " ASN B 282 " " NAG B1406 " - " ASN B 603 " " NAG B1407 " - " ASN B 616 " " NAG B1408 " - " ASN B 657 " " NAG B1409 " - " ASN B 709 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 122 " " NAG C1403 " - " ASN C 165 " " NAG C1404 " - " ASN C 234 " " NAG C1405 " - " ASN C 282 " " NAG C1406 " - " ASN C 603 " " NAG C1407 " - " ASN C 616 " " NAG C1408 " - " ASN C 657 " " NAG D 701 " - " ASN D 322 " " NAG E 1 " - " ASN A 331 " " NAG F 701 " - " ASN F 322 " " NAG G 1 " - " ASN A 343 " " NAG H 701 " - " ASN H 322 " " NAG I 1 " - " ASN A 709 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN A 801 " " NAG L 1 " - " ASN A1074 " " NAG M 1 " - " ASN A1098 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN B 331 " " NAG P 1 " - " ASN B 343 " " NAG Q 1 " - " ASN B 717 " " NAG R 1 " - " ASN B 801 " " NAG S 1 " - " ASN B1074 " " NAG T 1 " - " ASN B1098 " " NAG U 1 " - " ASN B1134 " " NAG V 1 " - " ASN C 331 " " NAG W 1 " - " ASN C 343 " " NAG X 1 " - " ASN C 709 " " NAG Y 1 " - " ASN C 717 " " NAG Z 1 " - " ASN C 801 " " NAG a 1 " - " ASN C1074 " " NAG b 1 " - " ASN C1098 " " NAG c 1 " - " ASN C1134 " " NAG d 1 " - " ASN D 53 " " NAG e 1 " - " ASN D 90 " " NAG f 1 " - " ASN D 103 " " NAG g 1 " - " ASN D 432 " " NAG h 1 " - " ASN D 546 " " NAG i 1 " - " ASN F 53 " " NAG j 1 " - " ASN F 90 " " NAG k 1 " - " ASN F 103 " " NAG l 1 " - " ASN F 432 " " NAG m 1 " - " ASN F 546 " " NAG n 1 " - " ASN H 53 " " NAG o 1 " - " ASN H 90 " " NAG p 1 " - " ASN H 103 " " NAG q 1 " - " ASN H 432 " " NAG r 1 " - " ASN H 546 " Time building additional restraints: 3.28 Conformation dependent library (CDL) restraints added in 1.6 seconds 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9008 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 54 sheets defined 37.8% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.823A pdb=" N ASN A 343 " --> pdb=" O ASP A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.884A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 385 through 389 removed outlier: 4.276A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 385 through 389' Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 753 Processing helix chain 'A' and resid 754 through 756 No H-bonds generated for 'chain 'A' and resid 754 through 756' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.612A pdb=" N ILE A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.655A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 933 Processing helix chain 'A' and resid 933 through 939 Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.322A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 981 removed outlier: 3.810A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.931A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 Processing helix chain 'B' and resid 294 through 304 removed outlier: 4.311A pdb=" N GLU B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N THR B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.823A pdb=" N ASN B 343 " --> pdb=" O ASP B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.884A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 385 through 389 removed outlier: 4.276A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 385 through 389' Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.530A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.791A pdb=" N LYS B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN B 774 " --> pdb=" O ILE B 770 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 815 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.700A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.252A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 932 Processing helix chain 'B' and resid 933 through 940 Processing helix chain 'B' and resid 945 through 964 removed outlier: 3.761A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 968 removed outlier: 3.702A pdb=" N SER B 968 " --> pdb=" O GLN B 965 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 965 through 968' Processing helix chain 'B' and resid 976 through 981 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.758A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.982A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.823A pdb=" N ASN C 343 " --> pdb=" O ASP C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.884A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 385 through 389 removed outlier: 4.276A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 385 through 389' Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 747 through 754 removed outlier: 4.087A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.985A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 823 removed outlier: 3.590A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.515A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.577A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.650A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.592A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 removed outlier: 4.077A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.757A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 983 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.323A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 Processing helix chain 'D' and resid 20 through 52 removed outlier: 3.566A pdb=" N GLN D 24 " --> pdb=" O THR D 20 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS D 26 " --> pdb=" O GLU D 22 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR D 27 " --> pdb=" O GLU D 23 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS D 31 " --> pdb=" O THR D 27 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N HIS D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU D 37 " --> pdb=" O ASN D 33 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR D 41 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN D 42 " --> pdb=" O ASP D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 81 removed outlier: 3.642A pdb=" N ASN D 63 " --> pdb=" O VAL D 59 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA D 65 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE D 72 " --> pdb=" O LYS D 68 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR D 78 " --> pdb=" O LYS D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 98 Processing helix chain 'D' and resid 109 through 129 removed outlier: 3.835A pdb=" N SER D 124 " --> pdb=" O LEU D 120 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N THR D 125 " --> pdb=" O ASN D 121 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE D 126 " --> pdb=" O THR D 122 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR D 127 " --> pdb=" O MET D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 155 removed outlier: 3.904A pdb=" N ALA D 153 " --> pdb=" O ASN D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 172 removed outlier: 3.900A pdb=" N TRP D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 194 removed outlier: 4.152A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA D 193 " --> pdb=" O GLU D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 220 through 230 removed outlier: 4.141A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 249 removed outlier: 3.941A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 279 removed outlier: 3.531A pdb=" N TYR D 279 " --> pdb=" O THR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 300 removed outlier: 3.527A pdb=" N VAL D 298 " --> pdb=" O THR D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 319 removed outlier: 4.083A pdb=" N PHE D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE D 314 " --> pdb=" O GLU D 310 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE D 315 " --> pdb=" O ALA D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.801A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR D 381 " --> pdb=" O GLY D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 removed outlier: 3.776A pdb=" N ARG D 393 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 399 No H-bonds generated for 'chain 'D' and resid 397 through 399' Processing helix chain 'D' and resid 400 through 412 removed outlier: 3.722A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE D 407 " --> pdb=" O ALA D 403 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 447 removed outlier: 4.135A pdb=" N ASN D 437 " --> pdb=" O GLU D 433 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 465 Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 499 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 533 removed outlier: 4.011A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA D 532 " --> pdb=" O ALA D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.559A pdb=" N LYS D 541 " --> pdb=" O PRO D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.922A pdb=" N GLY D 551 " --> pdb=" O SER D 547 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS D 553 " --> pdb=" O GLU D 549 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN D 556 " --> pdb=" O GLN D 552 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 575 removed outlier: 3.791A pdb=" N GLU D 571 " --> pdb=" O THR D 567 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL D 573 " --> pdb=" O ALA D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 588 removed outlier: 3.765A pdb=" N PHE D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 597 removed outlier: 3.622A pdb=" N ASP D 597 " --> pdb=" O THR D 593 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 52 removed outlier: 3.566A pdb=" N GLN F 24 " --> pdb=" O THR F 20 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS F 26 " --> pdb=" O GLU F 22 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR F 27 " --> pdb=" O GLU F 23 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS F 31 " --> pdb=" O THR F 27 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N HIS F 34 " --> pdb=" O ASP F 30 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU F 37 " --> pdb=" O ASN F 33 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR F 41 " --> pdb=" O GLU F 37 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN F 42 " --> pdb=" O ASP F 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 81 removed outlier: 3.643A pdb=" N ASN F 63 " --> pdb=" O VAL F 59 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA F 65 " --> pdb=" O ASN F 61 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE F 72 " --> pdb=" O LYS F 68 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR F 78 " --> pdb=" O LYS F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 98 Processing helix chain 'F' and resid 109 through 129 removed outlier: 3.835A pdb=" N SER F 124 " --> pdb=" O LEU F 120 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N THR F 125 " --> pdb=" O ASN F 121 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE F 126 " --> pdb=" O THR F 122 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR F 127 " --> pdb=" O MET F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 155 removed outlier: 3.904A pdb=" N ALA F 153 " --> pdb=" O ASN F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 172 removed outlier: 3.900A pdb=" N TRP F 168 " --> pdb=" O ALA F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 194 removed outlier: 4.152A pdb=" N GLU F 182 " --> pdb=" O PRO F 178 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL F 185 " --> pdb=" O GLU F 181 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA F 193 " --> pdb=" O GLU F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 205 Processing helix chain 'F' and resid 220 through 230 removed outlier: 4.141A pdb=" N GLU F 224 " --> pdb=" O GLY F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 249 removed outlier: 3.940A pdb=" N HIS F 239 " --> pdb=" O PRO F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 279 removed outlier: 3.531A pdb=" N TYR F 279 " --> pdb=" O THR F 276 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 300 removed outlier: 3.528A pdb=" N VAL F 298 " --> pdb=" O THR F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 319 removed outlier: 4.083A pdb=" N PHE F 308 " --> pdb=" O ALA F 304 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE F 314 " --> pdb=" O GLU F 310 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE F 315 " --> pdb=" O ALA F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 385 removed outlier: 3.801A pdb=" N HIS F 373 " --> pdb=" O PHE F 369 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS F 378 " --> pdb=" O HIS F 374 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR F 381 " --> pdb=" O GLY F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 393 removed outlier: 3.776A pdb=" N ARG F 393 " --> pdb=" O PHE F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 399 No H-bonds generated for 'chain 'F' and resid 397 through 399' Processing helix chain 'F' and resid 400 through 412 removed outlier: 3.722A pdb=" N GLY F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE F 407 " --> pdb=" O ALA F 403 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER F 409 " --> pdb=" O GLY F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 447 removed outlier: 4.135A pdb=" N ASN F 437 " --> pdb=" O GLU F 433 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR F 445 " --> pdb=" O LYS F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 465 Processing helix chain 'F' and resid 472 through 484 Processing helix chain 'F' and resid 499 through 502 Processing helix chain 'F' and resid 503 through 508 Processing helix chain 'F' and resid 513 through 533 removed outlier: 4.011A pdb=" N THR F 519 " --> pdb=" O TYR F 515 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU F 520 " --> pdb=" O TYR F 516 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE F 523 " --> pdb=" O THR F 519 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA F 532 " --> pdb=" O ALA F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 542 removed outlier: 3.559A pdb=" N LYS F 541 " --> pdb=" O PRO F 538 " (cutoff:3.500A) Processing helix chain 'F' and resid 547 through 559 removed outlier: 3.922A pdb=" N GLY F 551 " --> pdb=" O SER F 547 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS F 553 " --> pdb=" O GLU F 549 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN F 556 " --> pdb=" O GLN F 552 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N MET F 557 " --> pdb=" O LYS F 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 575 removed outlier: 3.790A pdb=" N GLU F 571 " --> pdb=" O THR F 567 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL F 573 " --> pdb=" O ALA F 569 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 588 removed outlier: 3.764A pdb=" N PHE F 588 " --> pdb=" O LEU F 584 " (cutoff:3.500A) Processing helix chain 'F' and resid 588 through 597 removed outlier: 3.622A pdb=" N ASP F 597 " --> pdb=" O THR F 593 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 52 removed outlier: 3.565A pdb=" N GLN H 24 " --> pdb=" O THR H 20 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS H 26 " --> pdb=" O GLU H 22 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR H 27 " --> pdb=" O GLU H 23 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS H 31 " --> pdb=" O THR H 27 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N HIS H 34 " --> pdb=" O ASP H 30 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU H 37 " --> pdb=" O ASN H 33 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR H 41 " --> pdb=" O GLU H 37 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN H 42 " --> pdb=" O ASP H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 81 removed outlier: 3.643A pdb=" N ASN H 63 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA H 65 " --> pdb=" O ASN H 61 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE H 72 " --> pdb=" O LYS H 68 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR H 78 " --> pdb=" O LYS H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 98 Processing helix chain 'H' and resid 109 through 129 removed outlier: 3.835A pdb=" N SER H 124 " --> pdb=" O LEU H 120 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N THR H 125 " --> pdb=" O ASN H 121 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE H 126 " --> pdb=" O THR H 122 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR H 127 " --> pdb=" O MET H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 147 through 155 removed outlier: 3.904A pdb=" N ALA H 153 " --> pdb=" O ASN H 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 157 through 172 removed outlier: 3.900A pdb=" N TRP H 168 " --> pdb=" O ALA H 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 194 removed outlier: 4.151A pdb=" N GLU H 182 " --> pdb=" O PRO H 178 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL H 185 " --> pdb=" O GLU H 181 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA H 193 " --> pdb=" O GLU H 189 " (cutoff:3.500A) Processing helix chain 'H' and resid 198 through 205 Processing helix chain 'H' and resid 220 through 230 removed outlier: 4.140A pdb=" N GLU H 224 " --> pdb=" O GLY H 220 " (cutoff:3.500A) Processing helix chain 'H' and resid 233 through 249 removed outlier: 3.941A pdb=" N HIS H 239 " --> pdb=" O PRO H 235 " (cutoff:3.500A) Processing helix chain 'H' and resid 275 through 279 removed outlier: 3.530A pdb=" N TYR H 279 " --> pdb=" O THR H 276 " (cutoff:3.500A) Processing helix chain 'H' and resid 294 through 300 removed outlier: 3.528A pdb=" N VAL H 298 " --> pdb=" O THR H 294 " (cutoff:3.500A) Processing helix chain 'H' and resid 303 through 319 removed outlier: 4.084A pdb=" N PHE H 308 " --> pdb=" O ALA H 304 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE H 314 " --> pdb=" O GLU H 310 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE H 315 " --> pdb=" O ALA H 311 " (cutoff:3.500A) Processing helix chain 'H' and resid 365 through 385 removed outlier: 3.801A pdb=" N HIS H 373 " --> pdb=" O PHE H 369 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS H 378 " --> pdb=" O HIS H 374 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR H 381 " --> pdb=" O GLY H 377 " (cutoff:3.500A) Processing helix chain 'H' and resid 389 through 393 removed outlier: 3.775A pdb=" N ARG H 393 " --> pdb=" O PHE H 390 " (cutoff:3.500A) Processing helix chain 'H' and resid 397 through 399 No H-bonds generated for 'chain 'H' and resid 397 through 399' Processing helix chain 'H' and resid 400 through 412 removed outlier: 3.723A pdb=" N GLY H 405 " --> pdb=" O HIS H 401 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE H 407 " --> pdb=" O ALA H 403 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N MET H 408 " --> pdb=" O VAL H 404 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER H 409 " --> pdb=" O GLY H 405 " (cutoff:3.500A) Processing helix chain 'H' and resid 431 through 447 removed outlier: 4.136A pdb=" N ASN H 437 " --> pdb=" O GLU H 433 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR H 445 " --> pdb=" O LYS H 441 " (cutoff:3.500A) Processing helix chain 'H' and resid 449 through 465 Processing helix chain 'H' and resid 472 through 484 Processing helix chain 'H' and resid 499 through 502 Processing helix chain 'H' and resid 503 through 508 Processing helix chain 'H' and resid 513 through 533 removed outlier: 4.011A pdb=" N THR H 519 " --> pdb=" O TYR H 515 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU H 520 " --> pdb=" O TYR H 516 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N PHE H 523 " --> pdb=" O THR H 519 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA H 532 " --> pdb=" O ALA H 528 " (cutoff:3.500A) Processing helix chain 'H' and resid 538 through 542 removed outlier: 3.559A pdb=" N LYS H 541 " --> pdb=" O PRO H 538 " (cutoff:3.500A) Processing helix chain 'H' and resid 547 through 559 removed outlier: 3.922A pdb=" N GLY H 551 " --> pdb=" O SER H 547 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS H 553 " --> pdb=" O GLU H 549 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN H 556 " --> pdb=" O GLN H 552 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N MET H 557 " --> pdb=" O LYS H 553 " (cutoff:3.500A) Processing helix chain 'H' and resid 565 through 575 removed outlier: 3.791A pdb=" N GLU H 571 " --> pdb=" O THR H 567 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL H 573 " --> pdb=" O ALA H 569 " (cutoff:3.500A) Processing helix chain 'H' and resid 581 through 588 removed outlier: 3.765A pdb=" N PHE H 588 " --> pdb=" O LEU H 584 " (cutoff:3.500A) Processing helix chain 'H' and resid 588 through 597 removed outlier: 3.622A pdb=" N ASP H 597 " --> pdb=" O THR H 593 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.685A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 55 removed outlier: 7.498A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.924A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU A 117 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N GLU A 132 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ASN A 165 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N GLN A 134 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ALA A 163 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 90 through 92 removed outlier: 3.739A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.249A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 323 through 328 removed outlier: 5.846A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.523A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL A 512 " --> pdb=" O ASP A 398 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.523A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.969A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.892A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.892A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 735 removed outlier: 4.302A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.639A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.685A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 49 through 55 removed outlier: 7.497A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.924A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N GLU B 132 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 90 through 92 removed outlier: 3.739A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.170A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.613A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.523A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL B 512 " --> pdb=" O ASP B 398 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 513 " --> pdb=" O CYS B 432 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.040A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE B 693 " --> pdb=" O SER B 673 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER B 673 " --> pdb=" O ILE B 693 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.752A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.752A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.485A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.851A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.686A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 49 through 55 removed outlier: 7.498A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.924A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU C 117 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N GLU C 132 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ASN C 165 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N GLN C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ALA C 163 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 90 through 92 removed outlier: 3.740A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.164A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 323 through 327 removed outlier: 6.231A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASN C 540 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.522A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL C 512 " --> pdb=" O ASP C 398 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU C 513 " --> pdb=" O CYS C 432 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'C' and resid 659 through 660 removed outlier: 3.743A pdb=" N TYR C 660 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE C 693 " --> pdb=" O SER C 673 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 7.152A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 7.152A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.498A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.943A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 132 through 133 Processing sheet with id=AF2, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.911A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.300A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 132 through 133 Processing sheet with id=AF5, first strand: chain 'F' and resid 262 through 263 removed outlier: 5.912A pdb=" N LEU F 262 " --> pdb=" O VAL F 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'F' and resid 347 through 352 removed outlier: 6.299A pdb=" N ASP F 355 " --> pdb=" O LEU F 351 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 132 through 133 Processing sheet with id=AF8, first strand: chain 'H' and resid 262 through 263 removed outlier: 5.912A pdb=" N LEU H 262 " --> pdb=" O VAL H 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'H' and resid 347 through 352 removed outlier: 6.299A pdb=" N ASP H 355 " --> pdb=" O LEU H 351 " (cutoff:3.500A) 1511 hydrogen bonds defined for protein. 4263 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.05 Time building geometry restraints manager: 4.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 7880 1.33 - 1.46: 13210 1.46 - 1.59: 19129 1.59 - 1.72: 0 1.72 - 1.85: 285 Bond restraints: 40504 Sorted by residual: bond pdb=" CA SER B 698 " pdb=" C SER B 698 " ideal model delta sigma weight residual 1.522 1.443 0.079 1.20e-02 6.94e+03 4.38e+01 bond pdb=" C LEU C 293 " pdb=" N ASP C 294 " ideal model delta sigma weight residual 1.331 1.455 -0.124 2.07e-02 2.33e+03 3.61e+01 bond pdb=" C THR C 208 " pdb=" N PRO C 209 " ideal model delta sigma weight residual 1.329 1.388 -0.059 1.20e-02 6.94e+03 2.41e+01 bond pdb=" C THR A 208 " pdb=" N PRO A 209 " ideal model delta sigma weight residual 1.329 1.387 -0.058 1.20e-02 6.94e+03 2.35e+01 bond pdb=" C THR B 208 " pdb=" N PRO B 209 " ideal model delta sigma weight residual 1.329 1.387 -0.058 1.20e-02 6.94e+03 2.34e+01 ... (remaining 40499 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 53786 2.56 - 5.11: 1170 5.11 - 7.67: 81 7.67 - 10.23: 19 10.23 - 12.79: 7 Bond angle restraints: 55063 Sorted by residual: angle pdb=" N VAL H 107 " pdb=" CA VAL H 107 " pdb=" C VAL H 107 " ideal model delta sigma weight residual 113.53 105.71 7.82 9.80e-01 1.04e+00 6.37e+01 angle pdb=" N VAL D 107 " pdb=" CA VAL D 107 " pdb=" C VAL D 107 " ideal model delta sigma weight residual 113.53 105.75 7.78 9.80e-01 1.04e+00 6.30e+01 angle pdb=" N VAL F 107 " pdb=" CA VAL F 107 " pdb=" C VAL F 107 " ideal model delta sigma weight residual 113.53 105.82 7.71 9.80e-01 1.04e+00 6.20e+01 angle pdb=" N ILE B 794 " pdb=" CA ILE B 794 " pdb=" C ILE B 794 " ideal model delta sigma weight residual 110.05 103.18 6.87 1.09e+00 8.42e-01 3.97e+01 angle pdb=" C THR C 208 " pdb=" N PRO C 209 " pdb=" CA PRO C 209 " ideal model delta sigma weight residual 120.31 114.34 5.97 9.80e-01 1.04e+00 3.71e+01 ... (remaining 55058 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 23204 17.92 - 35.84: 1545 35.84 - 53.76: 498 53.76 - 71.68: 114 71.68 - 89.60: 56 Dihedral angle restraints: 25417 sinusoidal: 11434 harmonic: 13983 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -16.73 -69.27 1 1.00e+01 1.00e-02 6.20e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -23.71 -62.29 1 1.00e+01 1.00e-02 5.14e+01 dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -138.57 52.57 1 1.00e+01 1.00e-02 3.77e+01 ... (remaining 25414 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.330: 6337 0.330 - 0.661: 6 0.661 - 0.991: 2 0.991 - 1.322: 1 1.322 - 1.652: 1 Chirality restraints: 6347 Sorted by residual: chirality pdb=" C1 NAG a 2 " pdb=" O4 NAG a 1 " pdb=" C2 NAG a 2 " pdb=" O5 NAG a 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.72 0.32 2.00e-02 2.50e+03 2.57e+02 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-02 2.50e+03 1.95e+02 chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN A1134 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.75 -1.65 2.00e-01 2.50e+01 6.83e+01 ... (remaining 6344 not shown) Planarity restraints: 7047 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 709 " 0.117 2.00e-02 2.50e+03 2.32e-01 6.73e+02 pdb=" CG ASN B 709 " -0.066 2.00e-02 2.50e+03 pdb=" OD1 ASN B 709 " 0.103 2.00e-02 2.50e+03 pdb=" ND2 ASN B 709 " -0.415 2.00e-02 2.50e+03 pdb=" C1 NAG B1409 " 0.261 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " 0.050 2.00e-02 2.50e+03 1.85e-01 4.26e+02 pdb=" CG ASN A 331 " -0.049 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " 0.126 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " -0.330 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " 0.202 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 61 " -0.166 2.00e-02 2.50e+03 1.73e-01 3.73e+02 pdb=" CG ASN B 61 " 0.063 2.00e-02 2.50e+03 pdb=" OD1 ASN B 61 " 0.060 2.00e-02 2.50e+03 pdb=" ND2 ASN B 61 " 0.260 2.00e-02 2.50e+03 pdb=" C1 NAG B1401 " -0.216 2.00e-02 2.50e+03 ... (remaining 7044 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 120 2.46 - 3.07: 25826 3.07 - 3.68: 54181 3.68 - 4.29: 85449 4.29 - 4.90: 141975 Nonbonded interactions: 307551 Sorted by model distance: nonbonded pdb=" O ASN A 334 " pdb=" CG LEU A 335 " model vdw 1.848 3.470 nonbonded pdb=" O ARG A 328 " pdb=" CD1 PHE A 329 " model vdw 2.114 3.340 nonbonded pdb=" OG SER A 591 " pdb=" OE2 GLU A 619 " model vdw 2.204 3.040 nonbonded pdb=" OD1 ASP B 442 " pdb=" OH TYR B 451 " model vdw 2.220 3.040 nonbonded pdb=" OD1 ASP C 442 " pdb=" OH TYR C 451 " model vdw 2.221 3.040 ... (remaining 307546 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 27 through 939 or resid 944 through 1408)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' } 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: 1.520 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: 0.700 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 36.340 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.210 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:7.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4843 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.232 40656 Z= 0.456 Angle : 1.062 48.948 55471 Z= 0.597 Chirality : 0.065 1.652 6347 Planarity : 0.005 0.131 6981 Dihedral : 13.988 89.602 16265 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 1.21 % Allowed : 6.36 % Favored : 92.44 % Rotamer: Outliers : 3.40 % Allowed : 9.12 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.48 (0.10), residues: 4720 helix: -2.02 (0.10), residues: 1715 sheet: -1.41 (0.18), residues: 694 loop : -2.84 (0.11), residues: 2311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 204 TYR 0.018 0.001 TYR H 183 PHE 0.018 0.001 PHE B 592 TRP 0.013 0.001 TRP D 165 HIS 0.004 0.001 HIS F 241 Details of bonding type rmsd covalent geometry : bond 0.00760 (40504) covalent geometry : angle 0.90777 (55063) SS BOND : bond 0.08128 ( 48) SS BOND : angle 6.89204 ( 96) hydrogen bonds : bond 0.21869 ( 1482) hydrogen bonds : angle 7.73527 ( 4263) link_BETA1-4 : bond 0.01306 ( 38) link_BETA1-4 : angle 3.36953 ( 114) link_NAG-ASN : bond 0.03133 ( 66) link_NAG-ASN : angle 7.56626 ( 198) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 673 time to evaluate : 1.336 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 revert: symmetry clash revert: symmetry clash REVERT: B 1028 LYS cc_start: 0.7708 (mttt) cc_final: 0.7437 (mttp) REVERT: C 801 ASN cc_start: 0.6863 (t0) cc_final: 0.6222 (m110) REVERT: D 480 MET cc_start: 0.1882 (mtp) cc_final: 0.1405 (ptt) REVERT: F 44 SER cc_start: 0.1766 (OUTLIER) cc_final: 0.1183 (p) REVERT: F 474 MET cc_start: -0.0305 (mmp) cc_final: -0.0984 (mmm) REVERT: H 428 PHE cc_start: 0.0311 (t80) cc_final: -0.0195 (t80) REVERT: H 480 MET cc_start: -0.0029 (mtp) cc_final: -0.0477 (ptm) outliers start: 143 outliers final: 27 residues processed: 807 average time/residue: 0.6445 time to fit residues: 641.9584 Evaluate side-chains 304 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 276 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 314 PHE Chi-restraints excluded: chain F residue 333 LEU Chi-restraints excluded: chain F residue 598 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 432 optimal weight: 40.0000 chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 50.0000 chunk 455 optimal weight: 20.0000 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 10.0000 chunk 470 optimal weight: 0.0170 overall best weight: 1.7822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 422 ASN A 804 GLN A 901 GLN A 949 GLN A 957 GLN A 992 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN B 690 GLN B 774 GLN B 779 GLN B 913 GLN B 957 GLN B1010 GLN B1101 HIS C 354 ASN C 422 ASN C 755 GLN C 762 GLN C 784 GLN C 954 HIS C1083 HIS D 42 GLN D 58 ASN D 210 ASN D 239 HIS D 277 ASN D 330 ASN D 340 GLN D 472 GLN D 522 GLN ** D 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 601 ASN F 42 GLN F 58 ASN F 76 GLN F 330 ASN F 340 GLN F 472 GLN F 522 GLN ** F 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 580 ASN F 599 ASN F 601 ASN H 42 GLN H 58 ASN H 117 ASN H 139 GLN H 175 GLN H 210 ASN H 239 HIS H 340 GLN H 378 HIS H 472 GLN H 493 HIS H 522 GLN H 524 GLN H 599 ASN H 601 ASN Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5114 r_free = 0.5114 target = 0.284617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4752 r_free = 0.4752 target = 0.233822 restraints weight = 55151.190| |-----------------------------------------------------------------------------| r_work (start): 0.4698 rms_B_bonded: 3.33 r_work: 0.4062 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 40656 Z= 0.185 Angle : 0.798 16.708 55471 Z= 0.390 Chirality : 0.050 0.842 6347 Planarity : 0.005 0.066 6981 Dihedral : 7.145 59.656 7359 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.93 % Favored : 93.81 % Rotamer: Outliers : 3.97 % Allowed : 15.08 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.34 (0.11), residues: 4720 helix: -0.89 (0.12), residues: 1734 sheet: -0.98 (0.18), residues: 688 loop : -2.27 (0.12), residues: 2298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 482 TYR 0.029 0.002 TYR A1067 PHE 0.022 0.002 PHE A 192 TRP 0.022 0.002 TRP A1102 HIS 0.013 0.001 HIS F 401 Details of bonding type rmsd covalent geometry : bond 0.00419 (40504) covalent geometry : angle 0.74836 (55063) SS BOND : bond 0.01064 ( 48) SS BOND : angle 3.52307 ( 96) hydrogen bonds : bond 0.05573 ( 1482) hydrogen bonds : angle 5.60878 ( 4263) link_BETA1-4 : bond 0.00923 ( 38) link_BETA1-4 : angle 2.03271 ( 114) link_NAG-ASN : bond 0.00834 ( 66) link_NAG-ASN : angle 3.79599 ( 198) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 337 time to evaluate : 1.367 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: A 285 ILE cc_start: 0.5152 (OUTLIER) cc_final: 0.4822 (pt) REVERT: A 309 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7544 (mm-30) REVERT: A 358 ILE cc_start: 0.1315 (OUTLIER) cc_final: 0.0698 (tp) REVERT: A 580 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.7446 (mm110) REVERT: B 44 ARG cc_start: 0.7686 (OUTLIER) cc_final: 0.7388 (mtt-85) REVERT: B 52 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.6194 (tp40) REVERT: B 237 ARG cc_start: 0.7520 (mtm180) cc_final: 0.6905 (mmm-85) REVERT: B 298 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7570 (tt0) REVERT: B 528 LYS cc_start: 0.4593 (OUTLIER) cc_final: 0.3521 (pptt) REVERT: B 814 LYS cc_start: 0.7319 (mttt) cc_final: 0.7017 (mmpt) REVERT: B 904 TYR cc_start: 0.7860 (m-10) cc_final: 0.7482 (m-10) REVERT: B 1014 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7039 (ptm160) REVERT: C 224 GLU cc_start: 0.6654 (OUTLIER) cc_final: 0.5956 (pp20) REVERT: C 314 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7655 (tt0) REVERT: C 607 GLN cc_start: 0.7791 (mt0) cc_final: 0.7472 (mt0) REVERT: C 983 ARG cc_start: 0.7308 (OUTLIER) cc_final: 0.6840 (mtt-85) REVERT: D 169 ARG cc_start: -0.0878 (OUTLIER) cc_final: -0.2035 (tpt170) REVERT: D 358 ILE cc_start: 0.1911 (OUTLIER) cc_final: 0.1688 (tp) REVERT: D 360 MET cc_start: 0.0821 (mtp) cc_final: 0.0362 (mtm) REVERT: D 455 MET cc_start: 0.2880 (OUTLIER) cc_final: 0.2665 (ptm) REVERT: D 462 MET cc_start: 0.2490 (ptm) cc_final: 0.1658 (mmt) REVERT: D 480 MET cc_start: 0.1493 (mtp) cc_final: 0.1202 (ptt) REVERT: F 44 SER cc_start: -0.0122 (OUTLIER) cc_final: -0.0667 (p) REVERT: F 67 ASP cc_start: 0.4723 (p0) cc_final: 0.4490 (m-30) REVERT: F 165 TRP cc_start: -0.1169 (OUTLIER) cc_final: -0.1444 (t60) REVERT: F 287 GLN cc_start: 0.2543 (pm20) cc_final: 0.2327 (pm20) REVERT: F 288 LYS cc_start: 0.1243 (mmpt) cc_final: 0.0869 (mptp) REVERT: F 332 MET cc_start: 0.2308 (ttm) cc_final: 0.0590 (mpt) REVERT: F 363 LYS cc_start: 0.2168 (OUTLIER) cc_final: 0.1153 (mtmt) REVERT: F 416 LYS cc_start: -0.0140 (OUTLIER) cc_final: -0.0878 (mttt) REVERT: F 474 MET cc_start: -0.0291 (mmp) cc_final: -0.0680 (mmm) REVERT: F 480 MET cc_start: -0.0570 (mtm) cc_final: -0.0850 (mtt) REVERT: H 82 MET cc_start: 0.4323 (mtt) cc_final: 0.3874 (mtt) REVERT: H 123 MET cc_start: -0.0005 (ptp) cc_final: -0.0417 (tpt) REVERT: H 297 MET cc_start: -0.3551 (OUTLIER) cc_final: -0.4231 (mtp) REVERT: H 332 MET cc_start: 0.0336 (mtt) cc_final: -0.0712 (tpp) REVERT: H 360 MET cc_start: -0.0914 (tpt) cc_final: -0.1182 (tpt) REVERT: H 383 MET cc_start: 0.2663 (mtp) cc_final: 0.1714 (pp-130) REVERT: H 428 PHE cc_start: 0.1149 (t80) cc_final: -0.0101 (t80) REVERT: H 455 MET cc_start: 0.3381 (tmt) cc_final: 0.2748 (ptm) outliers start: 167 outliers final: 53 residues processed: 477 average time/residue: 0.6509 time to fit residues: 386.4494 Evaluate side-chains 323 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 250 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1014 ARG Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 983 ARG Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 169 ARG Chi-restraints excluded: chain D residue 261 CYS Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 421 ILE Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 165 TRP Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 333 LEU Chi-restraints excluded: chain F residue 363 LYS Chi-restraints excluded: chain F residue 416 LYS Chi-restraints excluded: chain F residue 584 LEU Chi-restraints excluded: chain H residue 228 HIS Chi-restraints excluded: chain H residue 297 MET Chi-restraints excluded: chain H residue 362 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 152 optimal weight: 7.9990 chunk 311 optimal weight: 50.0000 chunk 68 optimal weight: 1.9990 chunk 463 optimal weight: 0.3980 chunk 43 optimal weight: 40.0000 chunk 393 optimal weight: 30.0000 chunk 468 optimal weight: 7.9990 chunk 97 optimal weight: 0.0870 chunk 162 optimal weight: 6.9990 chunk 326 optimal weight: 30.0000 chunk 155 optimal weight: 1.9990 overall best weight: 2.2964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN A 493 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 965 GLN C 239 GLN C 762 GLN C 784 GLN C 920 GLN C 954 HIS C1106 GLN D 139 GLN D 340 GLN D 524 GLN D 552 GLN D 599 ASN F 139 GLN F 524 GLN F 598 GLN H 117 ASN H 277 ASN H 374 HIS ** H 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 505 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5085 r_free = 0.5085 target = 0.280960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.228884 restraints weight = 53892.560| |-----------------------------------------------------------------------------| r_work (start): 0.4655 rms_B_bonded: 3.57 r_work: 0.3968 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 40656 Z= 0.182 Angle : 0.761 19.816 55471 Z= 0.369 Chirality : 0.049 0.681 6347 Planarity : 0.005 0.069 6981 Dihedral : 6.818 59.367 7337 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.06 % Favored : 93.73 % Rotamer: Outliers : 4.11 % Allowed : 16.01 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.11), residues: 4720 helix: -0.58 (0.12), residues: 1749 sheet: -0.78 (0.18), residues: 667 loop : -2.12 (0.12), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 319 TYR 0.028 0.001 TYR A 741 PHE 0.021 0.002 PHE C 275 TRP 0.047 0.001 TRP D 461 HIS 0.008 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00422 (40504) covalent geometry : angle 0.71088 (55063) SS BOND : bond 0.00552 ( 48) SS BOND : angle 2.87863 ( 96) hydrogen bonds : bond 0.05386 ( 1482) hydrogen bonds : angle 5.28348 ( 4263) link_BETA1-4 : bond 0.00690 ( 38) link_BETA1-4 : angle 2.01532 ( 114) link_NAG-ASN : bond 0.00823 ( 66) link_NAG-ASN : angle 3.91357 ( 198) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 278 time to evaluate : 1.705 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 REVERT: A 321 GLN cc_start: 0.7201 (OUTLIER) cc_final: 0.6084 (mp-120) REVERT: A 358 ILE cc_start: 0.0634 (OUTLIER) cc_final: 0.0080 (tp) REVERT: A 580 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7700 (mp-120) REVERT: B 44 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7686 (mtt-85) REVERT: B 46 SER cc_start: 0.8357 (OUTLIER) cc_final: 0.8001 (p) REVERT: B 52 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.6364 (tp40) REVERT: B 319 ARG cc_start: 0.7539 (OUTLIER) cc_final: 0.6859 (ttp80) REVERT: B 528 LYS cc_start: 0.4437 (OUTLIER) cc_final: 0.3487 (pptt) REVERT: B 556 ASN cc_start: 0.6809 (m-40) cc_final: 0.6305 (t0) REVERT: B 613 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.8083 (mt0) REVERT: B 814 LYS cc_start: 0.7519 (mttt) cc_final: 0.7204 (mmpt) REVERT: B 904 TYR cc_start: 0.8181 (m-10) cc_final: 0.7811 (m-10) REVERT: B 1014 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.7643 (ptm160) REVERT: C 122 ASN cc_start: 0.5525 (OUTLIER) cc_final: 0.4964 (p0) REVERT: C 226 LEU cc_start: 0.7048 (OUTLIER) cc_final: 0.6552 (mp) REVERT: C 239 GLN cc_start: 0.7763 (tt0) cc_final: 0.7242 (tm-30) REVERT: C 314 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7817 (tt0) REVERT: C 517 LEU cc_start: 0.2934 (OUTLIER) cc_final: 0.2377 (tt) REVERT: C 983 ARG cc_start: 0.7252 (OUTLIER) cc_final: 0.6687 (mtt-85) REVERT: D 358 ILE cc_start: 0.1819 (OUTLIER) cc_final: 0.1605 (tp) REVERT: D 360 MET cc_start: 0.1014 (mtp) cc_final: 0.0673 (mtm) REVERT: D 455 MET cc_start: 0.3009 (ptm) cc_final: 0.2773 (ptm) REVERT: D 462 MET cc_start: 0.3054 (ptm) cc_final: 0.1961 (mmp) REVERT: D 480 MET cc_start: 0.1647 (mtp) cc_final: 0.1137 (ptt) REVERT: D 524 GLN cc_start: 0.2063 (mt0) cc_final: 0.1799 (mt0) REVERT: F 62 MET cc_start: 0.1828 (ttt) cc_final: 0.0297 (tmt) REVERT: F 287 GLN cc_start: 0.2315 (pm20) cc_final: 0.2053 (pm20) REVERT: F 288 LYS cc_start: 0.1272 (mmpt) cc_final: 0.0894 (mptp) REVERT: F 332 MET cc_start: 0.2969 (ttm) cc_final: 0.1151 (mpt) REVERT: F 376 MET cc_start: 0.2431 (OUTLIER) cc_final: 0.2053 (ttm) REVERT: F 408 MET cc_start: 0.2292 (tpp) cc_final: 0.1318 (mtt) REVERT: F 416 LYS cc_start: -0.0056 (OUTLIER) cc_final: -0.0856 (mttt) REVERT: F 474 MET cc_start: -0.0128 (mmp) cc_final: -0.0727 (mmm) REVERT: H 82 MET cc_start: 0.4098 (mtt) cc_final: 0.3653 (mtt) REVERT: H 85 LEU cc_start: 0.0166 (OUTLIER) cc_final: -0.0245 (tt) REVERT: H 123 MET cc_start: -0.0115 (ptp) cc_final: -0.0515 (tpt) REVERT: H 291 ILE cc_start: -0.0529 (OUTLIER) cc_final: -0.0940 (pt) REVERT: H 297 MET cc_start: -0.3400 (OUTLIER) cc_final: -0.4124 (mtp) REVERT: H 332 MET cc_start: 0.0306 (OUTLIER) cc_final: -0.0445 (tpp) REVERT: H 360 MET cc_start: -0.0960 (tpt) cc_final: -0.1221 (tpt) REVERT: H 428 PHE cc_start: 0.1333 (t80) cc_final: 0.0055 (t80) REVERT: H 480 MET cc_start: 0.0376 (ttm) cc_final: -0.0434 (ptm) REVERT: H 504 PHE cc_start: 0.4594 (OUTLIER) cc_final: 0.3982 (t80) REVERT: H 534 LYS cc_start: 0.4403 (mtmm) cc_final: 0.3732 (pttm) outliers start: 173 outliers final: 72 residues processed: 416 average time/residue: 0.6534 time to fit residues: 339.4944 Evaluate side-chains 320 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 225 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1014 ARG Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 983 ARG Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 169 ARG Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 421 ILE Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 530 CYS Chi-restraints excluded: chain F residue 333 LEU Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 376 MET Chi-restraints excluded: chain F residue 416 LYS Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 584 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain H residue 291 ILE Chi-restraints excluded: chain H residue 297 MET Chi-restraints excluded: chain H residue 332 MET Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 504 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 351 optimal weight: 50.0000 chunk 414 optimal weight: 50.0000 chunk 33 optimal weight: 50.0000 chunk 11 optimal weight: 5.9990 chunk 132 optimal weight: 50.0000 chunk 62 optimal weight: 2.9990 chunk 228 optimal weight: 6.9990 chunk 157 optimal weight: 0.0370 chunk 7 optimal weight: 20.0000 chunk 358 optimal weight: 50.0000 chunk 123 optimal weight: 10.0000 overall best weight: 5.2068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN A 370 ASN A 493 GLN A 913 GLN A 935 GLN A 965 GLN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN B 564 GLN B 613 GLN C 784 GLN C1083 HIS D 505 HIS D 552 GLN F 287 GLN H 117 ASN H 340 GLN ** H 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5048 r_free = 0.5048 target = 0.275698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.225794 restraints weight = 53528.041| |-----------------------------------------------------------------------------| r_work (start): 0.4629 rms_B_bonded: 3.51 r_work: 0.3891 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.4759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.133 40656 Z= 0.310 Angle : 0.893 21.496 55471 Z= 0.436 Chirality : 0.055 0.778 6347 Planarity : 0.006 0.110 6981 Dihedral : 7.167 58.551 7333 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.65 % Favored : 93.16 % Rotamer: Outliers : 4.94 % Allowed : 16.94 % Favored : 78.12 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.19 (0.11), residues: 4720 helix: -0.72 (0.12), residues: 1737 sheet: -0.77 (0.19), residues: 688 loop : -2.26 (0.12), residues: 2295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 482 TYR 0.033 0.002 TYR B 38 PHE 0.033 0.003 PHE B 86 TRP 0.032 0.002 TRP D 165 HIS 0.023 0.002 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00755 (40504) covalent geometry : angle 0.84219 (55063) SS BOND : bond 0.00985 ( 48) SS BOND : angle 2.64663 ( 96) hydrogen bonds : bond 0.06652 ( 1482) hydrogen bonds : angle 5.64527 ( 4263) link_BETA1-4 : bond 0.00845 ( 38) link_BETA1-4 : angle 1.99117 ( 114) link_NAG-ASN : bond 0.00941 ( 66) link_NAG-ASN : angle 4.52993 ( 198) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 208 poor density : 261 time to evaluate : 1.367 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7424 (OUTLIER) cc_final: 0.6265 (tt0) REVERT: A 53 ASP cc_start: 0.6478 (t0) cc_final: 0.6181 (t70) REVERT: A 326 ILE cc_start: 0.6149 (mt) cc_final: 0.5869 (pt) REVERT: A 358 ILE cc_start: 0.0910 (OUTLIER) cc_final: 0.0299 (tp) REVERT: A 580 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7640 (mp-120) REVERT: B 44 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.7626 (mtt-85) REVERT: B 52 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.6354 (tp40) REVERT: B 206 LYS cc_start: 0.7273 (OUTLIER) cc_final: 0.6914 (ttmt) REVERT: B 319 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.7093 (ttp80) REVERT: B 646 ARG cc_start: 0.7745 (mpt90) cc_final: 0.7124 (mpp-170) REVERT: B 904 TYR cc_start: 0.8450 (m-10) cc_final: 0.8181 (m-10) REVERT: C 61 ASN cc_start: 0.6838 (p0) cc_final: 0.6625 (p0) REVERT: C 122 ASN cc_start: 0.5795 (OUTLIER) cc_final: 0.5241 (p0) REVERT: C 273 ARG cc_start: 0.7407 (OUTLIER) cc_final: 0.6750 (mmt180) REVERT: C 312 ILE cc_start: 0.8598 (OUTLIER) cc_final: 0.8171 (tt) REVERT: C 314 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7845 (tt0) REVERT: C 517 LEU cc_start: 0.2997 (OUTLIER) cc_final: 0.2298 (tt) REVERT: D 293 VAL cc_start: -0.0591 (OUTLIER) cc_final: -0.0887 (m) REVERT: D 360 MET cc_start: 0.1632 (mtp) cc_final: 0.1030 (mtp) REVERT: D 366 MET cc_start: 0.2299 (ttt) cc_final: 0.0873 (tmt) REVERT: D 462 MET cc_start: 0.3092 (OUTLIER) cc_final: 0.2022 (mmp) REVERT: D 524 GLN cc_start: 0.2452 (mt0) cc_final: 0.1936 (mt0) REVERT: D 529 LEU cc_start: 0.1850 (pp) cc_final: 0.0607 (tp) REVERT: F 212 VAL cc_start: 0.2828 (OUTLIER) cc_final: 0.2580 (t) REVERT: F 288 LYS cc_start: 0.1516 (OUTLIER) cc_final: 0.0968 (mptp) REVERT: F 332 MET cc_start: 0.3385 (ttm) cc_final: 0.1433 (mpt) REVERT: F 376 MET cc_start: 0.2411 (OUTLIER) cc_final: 0.1840 (ttm) REVERT: F 416 LYS cc_start: -0.0362 (OUTLIER) cc_final: -0.1294 (mttt) REVERT: F 474 MET cc_start: -0.0343 (mmp) cc_final: -0.0876 (mmm) REVERT: H 161 ARG cc_start: -0.2688 (OUTLIER) cc_final: -0.3901 (tmt170) REVERT: H 291 ILE cc_start: -0.0475 (OUTLIER) cc_final: -0.0945 (pt) REVERT: H 295 ASP cc_start: 0.3183 (m-30) cc_final: 0.2973 (p0) REVERT: H 297 MET cc_start: -0.3029 (OUTLIER) cc_final: -0.3773 (mtp) REVERT: H 332 MET cc_start: 0.0353 (OUTLIER) cc_final: -0.0463 (tpp) REVERT: H 428 PHE cc_start: 0.1334 (t80) cc_final: 0.0102 (t80) REVERT: H 534 LYS cc_start: 0.4306 (mtmm) cc_final: 0.3581 (pttm) outliers start: 208 outliers final: 106 residues processed: 434 average time/residue: 0.6323 time to fit residues: 343.5949 Evaluate side-chains 354 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 226 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 969 LYS Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1014 ARG Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 273 ARG Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 169 ARG Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 421 ILE Chi-restraints excluded: chain D residue 432 ASN Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 530 CYS Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 288 LYS Chi-restraints excluded: chain F residue 333 LEU Chi-restraints excluded: chain F residue 376 MET Chi-restraints excluded: chain F residue 416 LYS Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 584 LEU Chi-restraints excluded: chain H residue 161 ARG Chi-restraints excluded: chain H residue 261 CYS Chi-restraints excluded: chain H residue 291 ILE Chi-restraints excluded: chain H residue 297 MET Chi-restraints excluded: chain H residue 332 MET Chi-restraints excluded: chain H residue 334 THR Chi-restraints excluded: chain H residue 343 VAL Chi-restraints excluded: chain H residue 357 ARG Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 504 PHE Chi-restraints excluded: chain H residue 548 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 178 optimal weight: 2.9990 chunk 185 optimal weight: 0.7980 chunk 32 optimal weight: 0.0060 chunk 443 optimal weight: 9.9990 chunk 42 optimal weight: 50.0000 chunk 400 optimal weight: 50.0000 chunk 227 optimal weight: 9.9990 chunk 154 optimal weight: 0.8980 chunk 465 optimal weight: 30.0000 chunk 390 optimal weight: 20.0000 chunk 78 optimal weight: 0.7980 overall best weight: 1.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 913 GLN A 949 GLN A 965 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B1106 GLN C 762 GLN D 34 HIS F 505 HIS H 378 HIS H 522 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5068 r_free = 0.5068 target = 0.278104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.224341 restraints weight = 53658.746| |-----------------------------------------------------------------------------| r_work (start): 0.4619 rms_B_bonded: 3.50 r_work: 0.3934 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.4906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 40656 Z= 0.128 Angle : 0.685 19.833 55471 Z= 0.330 Chirality : 0.046 0.640 6347 Planarity : 0.004 0.062 6981 Dihedral : 6.576 59.633 7333 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.83 % Favored : 94.00 % Rotamer: Outliers : 3.33 % Allowed : 19.50 % Favored : 77.17 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.12), residues: 4720 helix: -0.16 (0.12), residues: 1744 sheet: -0.51 (0.19), residues: 666 loop : -1.97 (0.12), residues: 2310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 482 TYR 0.019 0.001 TYR A1067 PHE 0.031 0.001 PHE B 855 TRP 0.026 0.001 TRP D 478 HIS 0.005 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00283 (40504) covalent geometry : angle 0.64014 (55063) SS BOND : bond 0.00383 ( 48) SS BOND : angle 1.98498 ( 96) hydrogen bonds : bond 0.04513 ( 1482) hydrogen bonds : angle 5.10674 ( 4263) link_BETA1-4 : bond 0.00658 ( 38) link_BETA1-4 : angle 1.81179 ( 114) link_NAG-ASN : bond 0.00612 ( 66) link_NAG-ASN : angle 3.68612 ( 198) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 252 time to evaluate : 1.417 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: A 194 PHE cc_start: 0.6400 (m-80) cc_final: 0.5713 (m-10) REVERT: A 358 ILE cc_start: 0.0545 (OUTLIER) cc_final: -0.0000 (tp) REVERT: A 361 CYS cc_start: 0.2683 (OUTLIER) cc_final: 0.2307 (m) REVERT: A 580 GLN cc_start: 0.7742 (OUTLIER) cc_final: 0.7458 (mp-120) REVERT: B 52 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.6573 (tp40) REVERT: B 237 ARG cc_start: 0.7757 (mtm180) cc_final: 0.7235 (mmm-85) REVERT: B 319 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.7004 (ttp80) REVERT: B 613 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8505 (mt0) REVERT: B 904 TYR cc_start: 0.8252 (m-10) cc_final: 0.7943 (m-10) REVERT: B 969 LYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7418 (mmtm) REVERT: C 122 ASN cc_start: 0.5748 (OUTLIER) cc_final: 0.5183 (p0) REVERT: C 226 LEU cc_start: 0.6793 (OUTLIER) cc_final: 0.6310 (mp) REVERT: C 273 ARG cc_start: 0.7228 (OUTLIER) cc_final: 0.5284 (mtt-85) REVERT: C 517 LEU cc_start: 0.2692 (OUTLIER) cc_final: 0.2082 (tt) REVERT: C 549 THR cc_start: 0.8280 (m) cc_final: 0.7910 (t) REVERT: C 784 GLN cc_start: 0.7035 (mt0) cc_final: 0.6582 (mt0) REVERT: D 360 MET cc_start: 0.1509 (mtp) cc_final: 0.1164 (mtm) REVERT: D 366 MET cc_start: 0.1745 (ttt) cc_final: 0.0645 (tmt) REVERT: D 455 MET cc_start: 0.2951 (ptm) cc_final: 0.1703 (ttt) REVERT: D 462 MET cc_start: 0.2869 (ptm) cc_final: 0.2072 (mmp) REVERT: D 480 MET cc_start: 0.1105 (mtp) cc_final: 0.0709 (mtm) REVERT: D 524 GLN cc_start: 0.2429 (mt0) cc_final: 0.1890 (mt0) REVERT: D 529 LEU cc_start: 0.1715 (pp) cc_final: 0.0814 (tp) REVERT: D 557 MET cc_start: 0.2477 (tmm) cc_final: 0.2228 (tmm) REVERT: F 62 MET cc_start: 0.1731 (ttp) cc_final: 0.0176 (tmt) REVERT: F 332 MET cc_start: 0.3246 (ttm) cc_final: 0.1398 (mpt) REVERT: F 376 MET cc_start: 0.2366 (OUTLIER) cc_final: 0.1905 (ttm) REVERT: F 408 MET cc_start: 0.2354 (tpp) cc_final: 0.1417 (mtt) REVERT: F 416 LYS cc_start: -0.0373 (OUTLIER) cc_final: -0.1133 (mttt) REVERT: F 474 MET cc_start: -0.0247 (mmp) cc_final: -0.0695 (mmm) REVERT: H 82 MET cc_start: 0.4079 (mtt) cc_final: 0.3794 (mtt) REVERT: H 161 ARG cc_start: -0.3111 (OUTLIER) cc_final: -0.4112 (tmt170) REVERT: H 291 ILE cc_start: -0.0635 (OUTLIER) cc_final: -0.0965 (pt) REVERT: H 295 ASP cc_start: 0.3479 (m-30) cc_final: 0.3075 (p0) REVERT: H 297 MET cc_start: -0.3177 (OUTLIER) cc_final: -0.3681 (mtp) REVERT: H 332 MET cc_start: 0.0164 (mtt) cc_final: -0.0421 (tpp) REVERT: H 428 PHE cc_start: 0.1419 (t80) cc_final: 0.0101 (t80) REVERT: H 455 MET cc_start: 0.2738 (tmt) cc_final: 0.2317 (tmm) REVERT: H 534 LYS cc_start: 0.4431 (mtmm) cc_final: 0.3735 (pttm) outliers start: 140 outliers final: 64 residues processed: 366 average time/residue: 0.6125 time to fit residues: 280.7026 Evaluate side-chains 298 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 218 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 969 LYS Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 273 ARG Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 169 ARG Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 421 ILE Chi-restraints excluded: chain D residue 530 CYS Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 333 LEU Chi-restraints excluded: chain F residue 376 MET Chi-restraints excluded: chain F residue 416 LYS Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 584 LEU Chi-restraints excluded: chain H residue 161 ARG Chi-restraints excluded: chain H residue 291 ILE Chi-restraints excluded: chain H residue 297 MET Chi-restraints excluded: chain H residue 343 VAL Chi-restraints excluded: chain H residue 357 ARG Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 504 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 105 optimal weight: 10.0000 chunk 405 optimal weight: 30.0000 chunk 109 optimal weight: 4.9990 chunk 470 optimal weight: 50.0000 chunk 216 optimal weight: 2.9990 chunk 291 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 352 optimal weight: 40.0000 chunk 422 optimal weight: 7.9990 chunk 136 optimal weight: 30.0000 chunk 48 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 913 GLN A 949 GLN A 965 GLN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN C 87 ASN C 321 GLN C 784 GLN D 42 GLN D 442 GLN H 175 GLN ** H 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5048 r_free = 0.5048 target = 0.275665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.223219 restraints weight = 53735.583| |-----------------------------------------------------------------------------| r_work (start): 0.4611 rms_B_bonded: 3.60 r_work: 0.3880 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.5227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 40656 Z= 0.207 Angle : 0.758 22.128 55471 Z= 0.365 Chirality : 0.050 0.893 6347 Planarity : 0.005 0.075 6981 Dihedral : 6.693 59.318 7329 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.55 % Favored : 93.28 % Rotamer: Outliers : 3.75 % Allowed : 19.60 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.12), residues: 4720 helix: -0.19 (0.12), residues: 1744 sheet: -0.65 (0.19), residues: 683 loop : -2.03 (0.12), residues: 2293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 482 TYR 0.025 0.002 TYR A1067 PHE 0.029 0.002 PHE B 86 TRP 0.028 0.001 TRP D 478 HIS 0.012 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00491 (40504) covalent geometry : angle 0.71107 (55063) SS BOND : bond 0.00497 ( 48) SS BOND : angle 2.04749 ( 96) hydrogen bonds : bond 0.05489 ( 1482) hydrogen bonds : angle 5.25395 ( 4263) link_BETA1-4 : bond 0.00636 ( 38) link_BETA1-4 : angle 1.81047 ( 114) link_NAG-ASN : bond 0.00582 ( 66) link_NAG-ASN : angle 4.07111 ( 198) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 240 time to evaluate : 1.517 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 314 GLN cc_start: 0.8116 (pt0) cc_final: 0.7726 (tm-30) REVERT: A 358 ILE cc_start: 0.0712 (OUTLIER) cc_final: 0.0123 (tp) REVERT: A 361 CYS cc_start: 0.3107 (OUTLIER) cc_final: 0.2631 (m) REVERT: A 580 GLN cc_start: 0.7876 (OUTLIER) cc_final: 0.7492 (mp-120) REVERT: B 52 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.6576 (tp40) REVERT: B 237 ARG cc_start: 0.7865 (mtm180) cc_final: 0.7294 (mmm-85) REVERT: B 319 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7129 (ttp80) REVERT: B 646 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7085 (mpp-170) REVERT: B 969 LYS cc_start: 0.7824 (OUTLIER) cc_final: 0.7409 (mmmm) REVERT: C 122 ASN cc_start: 0.5880 (OUTLIER) cc_final: 0.5320 (p0) REVERT: C 224 GLU cc_start: 0.6864 (OUTLIER) cc_final: 0.6476 (pp20) REVERT: C 226 LEU cc_start: 0.6969 (OUTLIER) cc_final: 0.6554 (mp) REVERT: C 273 ARG cc_start: 0.7363 (OUTLIER) cc_final: 0.5138 (mtt-85) REVERT: C 517 LEU cc_start: 0.2862 (OUTLIER) cc_final: 0.2151 (tt) REVERT: C 549 THR cc_start: 0.8350 (m) cc_final: 0.8098 (t) REVERT: D 360 MET cc_start: 0.1654 (mtp) cc_final: 0.1208 (mtm) REVERT: D 366 MET cc_start: 0.1961 (ttt) cc_final: 0.0620 (tmt) REVERT: D 455 MET cc_start: 0.2546 (OUTLIER) cc_final: 0.1573 (ttt) REVERT: D 462 MET cc_start: 0.2654 (ptm) cc_final: 0.1592 (mmm) REVERT: D 478 TRP cc_start: 0.1025 (m100) cc_final: -0.0971 (m-90) REVERT: D 480 MET cc_start: 0.0844 (mtp) cc_final: 0.0458 (mtm) REVERT: D 524 GLN cc_start: 0.2518 (mt0) cc_final: 0.1925 (mt0) REVERT: D 529 LEU cc_start: 0.1618 (pp) cc_final: 0.0700 (tp) REVERT: D 557 MET cc_start: 0.2525 (tmm) cc_final: 0.2321 (tmm) REVERT: F 62 MET cc_start: 0.1989 (ttp) cc_final: 0.0168 (tmt) REVERT: F 212 VAL cc_start: 0.2995 (OUTLIER) cc_final: 0.2733 (t) REVERT: F 332 MET cc_start: 0.3272 (ttm) cc_final: 0.1431 (mpt) REVERT: F 376 MET cc_start: 0.2388 (OUTLIER) cc_final: 0.1810 (mtm) REVERT: F 416 LYS cc_start: -0.0547 (OUTLIER) cc_final: -0.1296 (mttt) REVERT: F 470 LYS cc_start: -0.0460 (mmtt) cc_final: -0.1461 (mmmt) REVERT: F 474 MET cc_start: -0.0355 (mmp) cc_final: -0.0784 (mmm) REVERT: H 82 MET cc_start: 0.4130 (mtt) cc_final: 0.3776 (mtt) REVERT: H 85 LEU cc_start: 0.0673 (OUTLIER) cc_final: 0.0233 (tt) REVERT: H 123 MET cc_start: 0.2118 (tpp) cc_final: 0.1901 (mtt) REVERT: H 291 ILE cc_start: -0.0472 (OUTLIER) cc_final: -0.0824 (tt) REVERT: H 295 ASP cc_start: 0.3798 (m-30) cc_final: 0.3246 (p0) REVERT: H 297 MET cc_start: -0.3223 (OUTLIER) cc_final: -0.3774 (mtp) REVERT: H 332 MET cc_start: 0.0173 (mtt) cc_final: -0.0406 (tpp) REVERT: H 428 PHE cc_start: 0.1321 (t80) cc_final: -0.0000 (t80) REVERT: H 534 LYS cc_start: 0.4357 (mtmm) cc_final: 0.3635 (pttm) outliers start: 158 outliers final: 87 residues processed: 368 average time/residue: 0.5933 time to fit residues: 277.3017 Evaluate side-chains 329 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 223 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 969 LYS Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 273 ARG Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 530 CYS Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 333 LEU Chi-restraints excluded: chain F residue 376 MET Chi-restraints excluded: chain F residue 416 LYS Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 584 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 291 ILE Chi-restraints excluded: chain H residue 297 MET Chi-restraints excluded: chain H residue 334 THR Chi-restraints excluded: chain H residue 343 VAL Chi-restraints excluded: chain H residue 357 ARG Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 366 MET Chi-restraints excluded: chain H residue 504 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 63 optimal weight: 4.9990 chunk 317 optimal weight: 30.0000 chunk 12 optimal weight: 5.9990 chunk 233 optimal weight: 6.9990 chunk 387 optimal weight: 0.0670 chunk 111 optimal weight: 4.9990 chunk 134 optimal weight: 0.9990 chunk 424 optimal weight: 50.0000 chunk 247 optimal weight: 4.9990 chunk 283 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 overall best weight: 2.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 GLN A 949 GLN A 965 GLN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 784 GLN D 552 GLN F 305 GLN ** H 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5060 r_free = 0.5060 target = 0.277535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.225865 restraints weight = 53436.636| |-----------------------------------------------------------------------------| r_work (start): 0.4622 rms_B_bonded: 3.40 r_work: 0.3924 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.5421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 40656 Z= 0.158 Angle : 0.706 19.814 55471 Z= 0.337 Chirality : 0.048 0.850 6347 Planarity : 0.004 0.061 6981 Dihedral : 6.506 58.333 7329 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.95 % Favored : 93.88 % Rotamer: Outliers : 3.61 % Allowed : 19.71 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.12), residues: 4720 helix: -0.01 (0.12), residues: 1752 sheet: -0.62 (0.19), residues: 689 loop : -1.95 (0.12), residues: 2279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 482 TYR 0.024 0.001 TYR A1067 PHE 0.027 0.002 PHE B 86 TRP 0.024 0.001 TRP D 168 HIS 0.008 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00372 (40504) covalent geometry : angle 0.65854 (55063) SS BOND : bond 0.00443 ( 48) SS BOND : angle 1.95963 ( 96) hydrogen bonds : bond 0.04809 ( 1482) hydrogen bonds : angle 5.09530 ( 4263) link_BETA1-4 : bond 0.00601 ( 38) link_BETA1-4 : angle 1.75970 ( 114) link_NAG-ASN : bond 0.00588 ( 66) link_NAG-ASN : angle 3.92806 ( 198) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 233 time to evaluate : 1.280 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 314 GLN cc_start: 0.8004 (pt0) cc_final: 0.7687 (tm-30) REVERT: A 321 GLN cc_start: 0.7252 (OUTLIER) cc_final: 0.6517 (mp10) REVERT: A 358 ILE cc_start: 0.0893 (OUTLIER) cc_final: 0.0300 (tp) REVERT: A 361 CYS cc_start: 0.3049 (OUTLIER) cc_final: 0.2634 (m) REVERT: A 580 GLN cc_start: 0.7764 (OUTLIER) cc_final: 0.7447 (mp-120) REVERT: A 933 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8411 (mtpm) REVERT: B 104 TRP cc_start: 0.7738 (m-90) cc_final: 0.7305 (m-90) REVERT: B 118 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7756 (pp) REVERT: B 237 ARG cc_start: 0.7879 (mtm180) cc_final: 0.7312 (mmm-85) REVERT: B 319 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.7049 (ttp80) REVERT: B 524 VAL cc_start: 0.4730 (OUTLIER) cc_final: 0.4430 (m) REVERT: B 646 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7121 (mpp-170) REVERT: B 752 LEU cc_start: 0.8329 (mt) cc_final: 0.8100 (tt) REVERT: C 122 ASN cc_start: 0.5765 (OUTLIER) cc_final: 0.5198 (p0) REVERT: C 226 LEU cc_start: 0.6857 (OUTLIER) cc_final: 0.6497 (mp) REVERT: C 273 ARG cc_start: 0.7347 (OUTLIER) cc_final: 0.5252 (mtt-85) REVERT: C 324 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6909 (tt0) REVERT: C 517 LEU cc_start: 0.2758 (OUTLIER) cc_final: 0.1992 (tt) REVERT: C 549 THR cc_start: 0.8353 (m) cc_final: 0.8025 (t) REVERT: C 565 PHE cc_start: 0.7332 (p90) cc_final: 0.7120 (p90) REVERT: D 297 MET cc_start: -0.0834 (mtp) cc_final: -0.1058 (ttp) REVERT: D 360 MET cc_start: 0.1778 (mtp) cc_final: 0.1282 (mtp) REVERT: D 366 MET cc_start: 0.1974 (ttt) cc_final: 0.0605 (tmt) REVERT: D 462 MET cc_start: 0.2603 (ptm) cc_final: 0.1408 (mmm) REVERT: D 480 MET cc_start: 0.0785 (mtp) cc_final: 0.0505 (mtm) REVERT: D 524 GLN cc_start: 0.2677 (mt0) cc_final: 0.2076 (mt0) REVERT: D 529 LEU cc_start: 0.1586 (pp) cc_final: 0.0755 (tp) REVERT: F 62 MET cc_start: 0.2118 (ttp) cc_final: 0.0210 (tmt) REVERT: F 108 LEU cc_start: -0.1036 (OUTLIER) cc_final: -0.1345 (pp) REVERT: F 183 TYR cc_start: -0.1438 (OUTLIER) cc_final: -0.1932 (t80) REVERT: F 332 MET cc_start: 0.3189 (ttm) cc_final: 0.2407 (ptm) REVERT: F 376 MET cc_start: 0.2372 (OUTLIER) cc_final: 0.1806 (mtm) REVERT: F 408 MET cc_start: 0.2397 (tpp) cc_final: 0.1467 (mtt) REVERT: F 416 LYS cc_start: -0.0353 (OUTLIER) cc_final: -0.1095 (mttt) REVERT: F 470 LYS cc_start: -0.0210 (mmtt) cc_final: -0.1223 (mmmt) REVERT: F 474 MET cc_start: -0.0530 (mmp) cc_final: -0.0960 (mmm) REVERT: H 82 MET cc_start: 0.4123 (mtt) cc_final: 0.3831 (mtt) REVERT: H 85 LEU cc_start: 0.0712 (OUTLIER) cc_final: 0.0250 (tt) REVERT: H 291 ILE cc_start: -0.0617 (OUTLIER) cc_final: -0.0937 (tt) REVERT: H 295 ASP cc_start: 0.3910 (m-30) cc_final: 0.3354 (p0) REVERT: H 297 MET cc_start: -0.3075 (OUTLIER) cc_final: -0.3615 (mtp) REVERT: H 332 MET cc_start: 0.0613 (mtt) cc_final: -0.0016 (tpp) REVERT: H 428 PHE cc_start: 0.1318 (t80) cc_final: 0.0022 (t80) REVERT: H 534 LYS cc_start: 0.4141 (mtmm) cc_final: 0.3500 (pttm) outliers start: 152 outliers final: 89 residues processed: 354 average time/residue: 0.5963 time to fit residues: 268.9564 Evaluate side-chains 329 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 219 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 933 LYS Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 273 ARG Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 530 CYS Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 183 TYR Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 333 LEU Chi-restraints excluded: chain F residue 376 MET Chi-restraints excluded: chain F residue 416 LYS Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 584 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 291 ILE Chi-restraints excluded: chain H residue 297 MET Chi-restraints excluded: chain H residue 334 THR Chi-restraints excluded: chain H residue 343 VAL Chi-restraints excluded: chain H residue 357 ARG Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 366 MET Chi-restraints excluded: chain H residue 504 PHE Chi-restraints excluded: chain H residue 548 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 45 optimal weight: 7.9990 chunk 192 optimal weight: 6.9990 chunk 357 optimal weight: 30.0000 chunk 189 optimal weight: 0.8980 chunk 208 optimal weight: 1.9990 chunk 284 optimal weight: 1.9990 chunk 403 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 335 optimal weight: 6.9990 chunk 181 optimal weight: 9.9990 chunk 449 optimal weight: 9.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 949 GLN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN B1106 GLN C 314 GLN C 762 GLN C 784 GLN D 599 ASN H 42 GLN H 117 ASN H 378 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5046 r_free = 0.5046 target = 0.275419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.225040 restraints weight = 53404.420| |-----------------------------------------------------------------------------| r_work (start): 0.4622 rms_B_bonded: 3.55 r_work: 0.3911 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.5710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 40656 Z= 0.221 Angle : 0.764 19.599 55471 Z= 0.370 Chirality : 0.050 0.791 6347 Planarity : 0.005 0.072 6981 Dihedral : 6.649 58.742 7329 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.86 % Favored : 92.97 % Rotamer: Outliers : 3.71 % Allowed : 20.05 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.12), residues: 4720 helix: -0.16 (0.12), residues: 1757 sheet: -0.74 (0.19), residues: 677 loop : -1.99 (0.12), residues: 2286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 237 TYR 0.024 0.002 TYR A1067 PHE 0.031 0.002 PHE B 86 TRP 0.077 0.002 TRP D 461 HIS 0.013 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00531 (40504) covalent geometry : angle 0.71968 (55063) SS BOND : bond 0.00505 ( 48) SS BOND : angle 2.08566 ( 96) hydrogen bonds : bond 0.05673 ( 1482) hydrogen bonds : angle 5.28679 ( 4263) link_BETA1-4 : bond 0.00622 ( 38) link_BETA1-4 : angle 1.79965 ( 114) link_NAG-ASN : bond 0.00566 ( 66) link_NAG-ASN : angle 3.95174 ( 198) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 231 time to evaluate : 1.362 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 REVERT: A 314 GLN cc_start: 0.7997 (pt0) cc_final: 0.7791 (tm-30) REVERT: A 358 ILE cc_start: 0.1114 (OUTLIER) cc_final: 0.0435 (tp) REVERT: A 361 CYS cc_start: 0.3029 (OUTLIER) cc_final: 0.2646 (m) REVERT: A 580 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7542 (mp-120) REVERT: B 104 TRP cc_start: 0.7769 (m-90) cc_final: 0.7430 (m-90) REVERT: B 118 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7725 (pp) REVERT: B 237 ARG cc_start: 0.7921 (mtm180) cc_final: 0.7407 (mmm-85) REVERT: B 319 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.7099 (ttp80) REVERT: B 646 ARG cc_start: 0.7684 (OUTLIER) cc_final: 0.7043 (mpp-170) REVERT: B 752 LEU cc_start: 0.8373 (mt) cc_final: 0.8109 (tt) REVERT: C 122 ASN cc_start: 0.5984 (OUTLIER) cc_final: 0.5414 (p0) REVERT: C 226 LEU cc_start: 0.7071 (OUTLIER) cc_final: 0.6684 (mp) REVERT: C 273 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.5281 (mtt-85) REVERT: C 324 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.7090 (tt0) REVERT: C 332 ILE cc_start: 0.6061 (OUTLIER) cc_final: 0.5531 (mt) REVERT: C 517 LEU cc_start: 0.2943 (OUTLIER) cc_final: 0.2012 (tt) REVERT: C 549 THR cc_start: 0.8449 (m) cc_final: 0.8229 (t) REVERT: D 62 MET cc_start: -0.0890 (mmm) cc_final: -0.1378 (tpt) REVERT: D 360 MET cc_start: 0.1935 (mtp) cc_final: 0.1395 (mtp) REVERT: D 366 MET cc_start: 0.2128 (ttt) cc_final: 0.0713 (tmt) REVERT: D 431 ASP cc_start: 0.1229 (t70) cc_final: 0.0794 (OUTLIER) REVERT: D 462 MET cc_start: 0.2552 (ptm) cc_final: 0.1445 (mmm) REVERT: D 478 TRP cc_start: 0.0966 (m100) cc_final: -0.1023 (OUTLIER) REVERT: D 480 MET cc_start: 0.0791 (mtp) cc_final: 0.0523 (mtm) REVERT: D 524 GLN cc_start: 0.2621 (mt0) cc_final: 0.2102 (mt0) REVERT: D 529 LEU cc_start: 0.1505 (pp) cc_final: 0.0667 (tp) REVERT: F 62 MET cc_start: 0.2299 (ttp) cc_final: 0.0163 (tmt) REVERT: F 108 LEU cc_start: -0.1103 (OUTLIER) cc_final: -0.1363 (pp) REVERT: F 183 TYR cc_start: -0.1135 (OUTLIER) cc_final: -0.1739 (t80) REVERT: F 332 MET cc_start: 0.3212 (ttm) cc_final: 0.2498 (ptm) REVERT: F 470 LYS cc_start: -0.0137 (mmtt) cc_final: -0.1231 (mmmt) REVERT: F 474 MET cc_start: -0.0538 (mmp) cc_final: -0.0909 (mmm) REVERT: H 82 MET cc_start: 0.4322 (mtt) cc_final: 0.3962 (mtt) REVERT: H 85 LEU cc_start: 0.0503 (OUTLIER) cc_final: 0.0113 (tt) REVERT: H 291 ILE cc_start: -0.0482 (OUTLIER) cc_final: -0.0747 (tt) REVERT: H 297 MET cc_start: -0.3236 (OUTLIER) cc_final: -0.3991 (mtp) REVERT: H 332 MET cc_start: 0.0562 (mtt) cc_final: -0.0119 (tpp) REVERT: H 534 LYS cc_start: 0.3984 (mtmm) cc_final: 0.3364 (pttm) outliers start: 156 outliers final: 100 residues processed: 360 average time/residue: 0.5566 time to fit residues: 257.0204 Evaluate side-chains 332 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 217 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 273 ARG Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 530 CYS Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 183 TYR Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 333 LEU Chi-restraints excluded: chain F residue 584 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 291 ILE Chi-restraints excluded: chain H residue 297 MET Chi-restraints excluded: chain H residue 334 THR Chi-restraints excluded: chain H residue 343 VAL Chi-restraints excluded: chain H residue 357 ARG Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 366 MET Chi-restraints excluded: chain H residue 504 PHE Chi-restraints excluded: chain H residue 548 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 270 optimal weight: 1.9990 chunk 238 optimal weight: 40.0000 chunk 58 optimal weight: 8.9990 chunk 5 optimal weight: 20.0000 chunk 207 optimal weight: 20.0000 chunk 300 optimal weight: 2.9990 chunk 235 optimal weight: 20.0000 chunk 179 optimal weight: 0.6980 chunk 185 optimal weight: 0.9990 chunk 126 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 949 GLN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 784 GLN D 305 GLN F 239 HIS F 442 GLN H 51 ASN H 378 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5050 r_free = 0.5050 target = 0.275837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.225591 restraints weight = 53668.185| |-----------------------------------------------------------------------------| r_work (start): 0.4629 rms_B_bonded: 3.51 r_work: 0.3934 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.5874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 40656 Z= 0.179 Angle : 0.719 19.613 55471 Z= 0.347 Chirality : 0.048 0.769 6347 Planarity : 0.005 0.082 6981 Dihedral : 6.425 57.114 7329 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.17 % Favored : 93.67 % Rotamer: Outliers : 3.40 % Allowed : 20.57 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.12), residues: 4720 helix: 0.05 (0.12), residues: 1739 sheet: -0.71 (0.19), residues: 675 loop : -1.94 (0.12), residues: 2306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 237 TYR 0.023 0.001 TYR A1067 PHE 0.029 0.002 PHE B 86 TRP 0.049 0.002 TRP D 461 HIS 0.011 0.001 HIS F 239 Details of bonding type rmsd covalent geometry : bond 0.00427 (40504) covalent geometry : angle 0.67422 (55063) SS BOND : bond 0.00433 ( 48) SS BOND : angle 1.95861 ( 96) hydrogen bonds : bond 0.05046 ( 1482) hydrogen bonds : angle 5.14498 ( 4263) link_BETA1-4 : bond 0.00575 ( 38) link_BETA1-4 : angle 1.74404 ( 114) link_NAG-ASN : bond 0.00595 ( 66) link_NAG-ASN : angle 3.87261 ( 198) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 224 time to evaluate : 1.366 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 revert: symmetry clash revert: symmetry clash REVERT: A 314 GLN cc_start: 0.8010 (pt0) cc_final: 0.7739 (tm-30) REVERT: A 321 GLN cc_start: 0.7272 (OUTLIER) cc_final: 0.6532 (mp10) REVERT: A 358 ILE cc_start: 0.1280 (OUTLIER) cc_final: 0.0522 (tp) REVERT: A 361 CYS cc_start: 0.3000 (OUTLIER) cc_final: 0.2671 (m) REVERT: A 580 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.7541 (mp-120) REVERT: B 104 TRP cc_start: 0.7805 (m-90) cc_final: 0.7392 (m-90) REVERT: B 118 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7828 (pp) REVERT: B 237 ARG cc_start: 0.7957 (mtm180) cc_final: 0.7452 (mmm-85) REVERT: B 319 ARG cc_start: 0.7559 (OUTLIER) cc_final: 0.7070 (ttp80) REVERT: B 646 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.7042 (mpp-170) REVERT: B 752 LEU cc_start: 0.8234 (mt) cc_final: 0.7989 (tt) REVERT: B 821 LEU cc_start: 0.8149 (tm) cc_final: 0.7933 (tt) REVERT: C 226 LEU cc_start: 0.7012 (OUTLIER) cc_final: 0.6716 (mp) REVERT: C 273 ARG cc_start: 0.7528 (OUTLIER) cc_final: 0.5393 (mtt-85) REVERT: C 324 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.7128 (tt0) REVERT: C 332 ILE cc_start: 0.5836 (OUTLIER) cc_final: 0.5392 (mt) REVERT: C 549 THR cc_start: 0.8414 (m) cc_final: 0.8122 (t) REVERT: C 562 PHE cc_start: 0.6819 (p90) cc_final: 0.6577 (p90) REVERT: C 661 GLU cc_start: 0.7061 (mm-30) cc_final: 0.6692 (mm-30) REVERT: D 62 MET cc_start: -0.0783 (mmm) cc_final: -0.1265 (tpt) REVERT: D 297 MET cc_start: -0.0492 (OUTLIER) cc_final: -0.0733 (ttp) REVERT: D 360 MET cc_start: 0.1825 (mtp) cc_final: 0.1239 (mtp) REVERT: D 366 MET cc_start: 0.1807 (ttt) cc_final: 0.0507 (tmt) REVERT: D 462 MET cc_start: 0.2607 (ptm) cc_final: 0.1579 (mmm) REVERT: D 477 TRP cc_start: -0.0345 (OUTLIER) cc_final: -0.1093 (m100) REVERT: D 478 TRP cc_start: 0.0738 (m100) cc_final: -0.1056 (OUTLIER) REVERT: D 480 MET cc_start: 0.0767 (mtp) cc_final: 0.0539 (mtm) REVERT: D 524 GLN cc_start: 0.2627 (mt0) cc_final: 0.2125 (mt0) REVERT: D 529 LEU cc_start: 0.1459 (pp) cc_final: 0.0618 (tp) REVERT: F 62 MET cc_start: 0.2279 (ttp) cc_final: 0.0140 (tmt) REVERT: F 108 LEU cc_start: -0.1056 (OUTLIER) cc_final: -0.1316 (pp) REVERT: F 183 TYR cc_start: -0.1065 (OUTLIER) cc_final: -0.1596 (t80) REVERT: F 332 MET cc_start: 0.3266 (ttm) cc_final: 0.2570 (ptm) REVERT: F 408 MET cc_start: 0.2568 (tpp) cc_final: 0.1644 (mtt) REVERT: F 416 LYS cc_start: -0.0091 (OUTLIER) cc_final: -0.0977 (mttt) REVERT: F 470 LYS cc_start: -0.0177 (mmtt) cc_final: -0.1250 (mmmt) REVERT: F 474 MET cc_start: -0.0561 (mmp) cc_final: -0.0931 (mmm) REVERT: H 82 MET cc_start: 0.4397 (mtt) cc_final: 0.4054 (mtt) REVERT: H 85 LEU cc_start: 0.0484 (OUTLIER) cc_final: 0.0078 (tt) REVERT: H 291 ILE cc_start: -0.0652 (OUTLIER) cc_final: -0.0859 (pt) REVERT: H 332 MET cc_start: 0.0917 (mtt) cc_final: 0.0066 (tpp) REVERT: H 428 PHE cc_start: 0.1126 (t80) cc_final: 0.0064 (t80) REVERT: H 534 LYS cc_start: 0.3942 (mtmm) cc_final: 0.3323 (pttm) outliers start: 143 outliers final: 101 residues processed: 341 average time/residue: 0.5505 time to fit residues: 243.1115 Evaluate side-chains 336 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 218 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 273 ARG Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 477 TRP Chi-restraints excluded: chain D residue 530 CYS Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 183 TYR Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 333 LEU Chi-restraints excluded: chain F residue 416 LYS Chi-restraints excluded: chain F residue 584 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 291 ILE Chi-restraints excluded: chain H residue 334 THR Chi-restraints excluded: chain H residue 343 VAL Chi-restraints excluded: chain H residue 357 ARG Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 504 PHE Chi-restraints excluded: chain H residue 548 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 196 optimal weight: 0.8980 chunk 458 optimal weight: 50.0000 chunk 451 optimal weight: 50.0000 chunk 81 optimal weight: 0.7980 chunk 14 optimal weight: 0.0570 chunk 266 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 396 optimal weight: 20.0000 chunk 318 optimal weight: 6.9990 chunk 287 optimal weight: 0.7980 chunk 185 optimal weight: 0.8980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 913 GLN A 949 GLN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1125 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN C 762 GLN F 239 HIS H 378 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5078 r_free = 0.5078 target = 0.278690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.222469 restraints weight = 52630.601| |-----------------------------------------------------------------------------| r_work (start): 0.4563 rms_B_bonded: 3.60 r_work: 0.3879 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.5915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 40656 Z= 0.116 Angle : 0.664 19.659 55471 Z= 0.317 Chirality : 0.045 0.542 6347 Planarity : 0.004 0.075 6981 Dihedral : 6.068 57.250 7328 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.78 % Favored : 94.07 % Rotamer: Outliers : 2.07 % Allowed : 22.02 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.12), residues: 4720 helix: 0.39 (0.13), residues: 1738 sheet: -0.44 (0.19), residues: 679 loop : -1.79 (0.12), residues: 2303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 237 TYR 0.016 0.001 TYR A1067 PHE 0.027 0.001 PHE B 855 TRP 0.054 0.001 TRP D 461 HIS 0.012 0.001 HIS F 239 Details of bonding type rmsd covalent geometry : bond 0.00252 (40504) covalent geometry : angle 0.62060 (55063) SS BOND : bond 0.00387 ( 48) SS BOND : angle 1.75046 ( 96) hydrogen bonds : bond 0.04047 ( 1482) hydrogen bonds : angle 4.87532 ( 4263) link_BETA1-4 : bond 0.00597 ( 38) link_BETA1-4 : angle 1.73983 ( 114) link_NAG-ASN : bond 0.00581 ( 66) link_NAG-ASN : angle 3.61016 ( 198) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 226 time to evaluate : 1.154 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: A 194 PHE cc_start: 0.6131 (m-80) cc_final: 0.5858 (m-80) REVERT: A 314 GLN cc_start: 0.8019 (pt0) cc_final: 0.7583 (tm-30) REVERT: A 321 GLN cc_start: 0.7366 (OUTLIER) cc_final: 0.6645 (mp10) REVERT: A 358 ILE cc_start: 0.0816 (OUTLIER) cc_final: 0.0188 (tp) REVERT: A 361 CYS cc_start: 0.3052 (OUTLIER) cc_final: 0.2643 (m) REVERT: A 580 GLN cc_start: 0.7614 (OUTLIER) cc_final: 0.7377 (mp-120) REVERT: A 855 PHE cc_start: 0.4751 (OUTLIER) cc_final: 0.3664 (m-80) REVERT: B 104 TRP cc_start: 0.7819 (m-90) cc_final: 0.7344 (m-90) REVERT: B 118 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7815 (pp) REVERT: B 169 GLU cc_start: 0.7542 (mt-10) cc_final: 0.7260 (mp0) REVERT: B 237 ARG cc_start: 0.7844 (mtm180) cc_final: 0.7302 (mmm-85) REVERT: B 319 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.7062 (ttp80) REVERT: B 646 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.6958 (mpp-170) REVERT: C 122 ASN cc_start: 0.6329 (OUTLIER) cc_final: 0.5735 (p0) REVERT: C 226 LEU cc_start: 0.6912 (OUTLIER) cc_final: 0.6709 (mp) REVERT: C 324 GLU cc_start: 0.7475 (tt0) cc_final: 0.7129 (tt0) REVERT: C 332 ILE cc_start: 0.5715 (OUTLIER) cc_final: 0.5351 (mt) REVERT: C 549 THR cc_start: 0.8261 (m) cc_final: 0.7983 (t) REVERT: C 562 PHE cc_start: 0.6767 (p90) cc_final: 0.6518 (p90) REVERT: C 565 PHE cc_start: 0.7404 (p90) cc_final: 0.7099 (p90) REVERT: C 780 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7746 (pt0) REVERT: D 62 MET cc_start: -0.0846 (mmm) cc_final: -0.1172 (tpt) REVERT: D 360 MET cc_start: 0.1475 (mtp) cc_final: 0.0931 (mtp) REVERT: D 366 MET cc_start: 0.1758 (ttt) cc_final: 0.0430 (tmt) REVERT: D 462 MET cc_start: 0.2293 (ptm) cc_final: 0.1379 (mmm) REVERT: D 477 TRP cc_start: -0.0785 (OUTLIER) cc_final: -0.1368 (m100) REVERT: D 478 TRP cc_start: 0.0572 (m100) cc_final: -0.1268 (m-90) REVERT: D 524 GLN cc_start: 0.2438 (mt0) cc_final: 0.1996 (mt0) REVERT: D 529 LEU cc_start: 0.1726 (pp) cc_final: 0.0899 (tp) REVERT: D 557 MET cc_start: 0.3065 (tmm) cc_final: 0.2831 (tmm) REVERT: F 62 MET cc_start: 0.2243 (ttp) cc_final: 0.0323 (tmt) REVERT: F 108 LEU cc_start: -0.0881 (OUTLIER) cc_final: -0.1278 (pp) REVERT: F 332 MET cc_start: 0.2977 (ttm) cc_final: 0.2394 (ptm) REVERT: F 408 MET cc_start: 0.2506 (tpp) cc_final: 0.1577 (mtt) REVERT: F 416 LYS cc_start: -0.0150 (OUTLIER) cc_final: -0.0794 (mttt) REVERT: F 455 MET cc_start: -0.0392 (pp-130) cc_final: -0.0624 (ppp) REVERT: F 470 LYS cc_start: -0.0332 (mmtt) cc_final: -0.1155 (mmmt) REVERT: F 474 MET cc_start: -0.0440 (mmp) cc_final: -0.0817 (mmm) REVERT: H 82 MET cc_start: 0.4205 (mtt) cc_final: 0.3959 (mtt) REVERT: H 85 LEU cc_start: 0.0449 (OUTLIER) cc_final: 0.0037 (tt) REVERT: H 270 MET cc_start: 0.2058 (ptm) cc_final: 0.1805 (ptp) REVERT: H 297 MET cc_start: -0.4011 (mmt) cc_final: -0.4642 (mtp) REVERT: H 332 MET cc_start: 0.0611 (mtt) cc_final: -0.0017 (tpp) REVERT: H 428 PHE cc_start: 0.1300 (t80) cc_final: 0.0329 (t80) REVERT: H 534 LYS cc_start: 0.4151 (mtmm) cc_final: 0.3532 (pttm) outliers start: 87 outliers final: 53 residues processed: 295 average time/residue: 0.6234 time to fit residues: 235.0160 Evaluate side-chains 286 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 218 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 477 TRP Chi-restraints excluded: chain D residue 530 CYS Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 333 LEU Chi-restraints excluded: chain F residue 400 PHE Chi-restraints excluded: chain F residue 416 LYS Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 343 VAL Chi-restraints excluded: chain H residue 357 ARG Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 504 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 316 optimal weight: 40.0000 chunk 333 optimal weight: 10.0000 chunk 89 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 364 optimal weight: 2.9990 chunk 130 optimal weight: 40.0000 chunk 21 optimal weight: 3.9990 chunk 266 optimal weight: 0.6980 chunk 239 optimal weight: 50.0000 chunk 148 optimal weight: 4.9990 chunk 336 optimal weight: 30.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 913 GLN A 949 GLN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1135 ASN C 784 GLN F 239 HIS H 60 GLN H 378 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5062 r_free = 0.5062 target = 0.276480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.221412 restraints weight = 52378.377| |-----------------------------------------------------------------------------| r_work (start): 0.4555 rms_B_bonded: 3.61 r_work: 0.3830 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.6051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 40656 Z= 0.164 Angle : 0.706 19.588 55471 Z= 0.339 Chirality : 0.048 0.695 6347 Planarity : 0.005 0.094 6981 Dihedral : 6.105 57.605 7328 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.23 % Favored : 93.64 % Rotamer: Outliers : 2.42 % Allowed : 21.64 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.12), residues: 4720 helix: 0.29 (0.13), residues: 1739 sheet: -0.54 (0.19), residues: 679 loop : -1.84 (0.12), residues: 2302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 237 TYR 0.021 0.001 TYR A1067 PHE 0.033 0.002 PHE C 58 TRP 0.051 0.001 TRP H 478 HIS 0.012 0.001 HIS F 239 Details of bonding type rmsd covalent geometry : bond 0.00389 (40504) covalent geometry : angle 0.66457 (55063) SS BOND : bond 0.00402 ( 48) SS BOND : angle 1.80436 ( 96) hydrogen bonds : bond 0.04883 ( 1482) hydrogen bonds : angle 5.01562 ( 4263) link_BETA1-4 : bond 0.00599 ( 38) link_BETA1-4 : angle 1.69721 ( 114) link_NAG-ASN : bond 0.00588 ( 66) link_NAG-ASN : angle 3.70158 ( 198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16771.68 seconds wall clock time: 285 minutes 45.13 seconds (17145.13 seconds total)