Starting phenix.real_space_refine on Sat Mar 7 06:52:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y1z_33576/03_2026/7y1z_33576.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y1z_33576/03_2026/7y1z_33576.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y1z_33576/03_2026/7y1z_33576.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y1z_33576/03_2026/7y1z_33576.map" model { file = "/net/cci-nas-00/data/ceres_data/7y1z_33576/03_2026/7y1z_33576.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y1z_33576/03_2026/7y1z_33576.cif" } resolution = 3.4 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= 0.082 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 25240 2.51 5 N 6435 2.21 5 O 7713 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39583 Number of models: 1 Model: "" Number of chains: 50 Chain: "A" Number of atoms: 7843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 999, 7843 Classifications: {'peptide': 999} Link IDs: {'PTRANS': 54, 'TRANS': 944} Chain breaks: 9 Chain: "B" Number of atoms: 7837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7837 Classifications: {'peptide': 998} Link IDs: {'PTRANS': 54, 'TRANS': 943} Chain breaks: 9 Chain: "C" Number of atoms: 7837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7837 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: 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: "B" 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: "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: 9.30, per 1000 atoms: 0.23 Number of scatterers: 39583 At special positions: 0 Unit cell: (184.79, 195.66, 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 7713 8.00 N 6435 7.00 C 25240 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=1.94 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.41 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=1.88 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=2.12 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.18 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.07 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.14 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=1.95 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=1.94 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=2.26 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=1.97 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.17 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.10 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=1.98 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=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=1.89 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=1.91 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=2.08 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.04 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.20 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.04 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.02 Simple disulfide: pdb=" SG CYS F 133 " - pdb=" SG CYS F 141 " distance=2.04 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=2.04 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 A1409 " - " ASN A 709 " " 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 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 717 " " NAG J 1 " - " ASN A 801 " " NAG K 1 " - " ASN A1074 " " NAG L 1 " - " ASN A1098 " " NAG M 1 " - " ASN A1134 " " NAG N 1 " - " ASN B 331 " " NAG O 1 " - " ASN B 343 " " NAG P 1 " - " ASN B 709 " " 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: 3.60 Conformation dependent library (CDL) restraints added in 1.7 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: 9014 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 49 sheets defined 39.4% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.708A pdb=" N GLU A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.681A 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: 4.018A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.803A 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 403 through 410 removed outlier: 3.693A pdb=" N GLU A 406 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ARG A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.529A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.791A pdb=" N LYS A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.701A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.252A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 932 Processing helix chain 'A' and resid 933 through 940 Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.761A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 968 removed outlier: 3.703A pdb=" N SER A 968 " --> pdb=" O GLN A 965 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 965 through 968' Processing helix chain 'A' and resid 976 through 981 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.757A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.983A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.679A 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: 4.018A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.803A 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 403 through 410 removed outlier: 3.693A pdb=" N GLU B 406 " --> pdb=" O ARG B 403 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ARG B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 754 removed outlier: 4.087A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (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: 3.985A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 removed outlier: 3.590A pdb=" N LEU B 821 " --> pdb=" O PRO B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.516A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.576A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.650A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.591A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 4.078A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.758A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 983 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.323A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.680A 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: 4.018A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.804A 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 403 through 410 removed outlier: 3.693A pdb=" N GLU C 406 " --> pdb=" O ARG C 403 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ARG C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 753 Processing helix chain 'C' and resid 754 through 756 No H-bonds generated for 'chain 'C' and resid 754 through 756' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.612A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.655A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 933 Processing helix chain 'C' and resid 933 through 939 Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.321A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 981 removed outlier: 3.810A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.931A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 Processing helix chain 'D' and resid 22 through 53 removed outlier: 4.096A pdb=" N LYS D 31 " --> pdb=" O THR D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 81 removed outlier: 4.154A pdb=" N GLN D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN D 64 " --> pdb=" O GLN D 60 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA D 65 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLN D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 101 Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 147 through 155 Processing helix chain 'D' and resid 157 through 192 removed outlier: 3.910A pdb=" N TRP D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LYS D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU D 176 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG D 177 " --> pdb=" O GLY D 173 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 4.190A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 205 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 220 through 252 removed outlier: 3.733A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLU D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS D 234 " --> pdb=" O PHE D 230 " (cutoff:3.500A) Proline residue: D 235 - end of helix removed outlier: 4.084A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ASN D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR D 252 " --> pdb=" O LEU D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 281 removed outlier: 4.178A pdb=" N SER D 280 " --> pdb=" O ASN D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 299 removed outlier: 3.785A pdb=" N VAL D 298 " --> pdb=" O THR D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 319 removed outlier: 3.728A pdb=" N ILE D 307 " --> pdb=" O ASP D 303 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL D 318 " --> pdb=" O PHE D 314 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY D 319 " --> pdb=" O PHE D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 331 removed outlier: 3.653A pdb=" N ASN D 330 " --> pdb=" O GLY D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.691A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 399 through 413 removed outlier: 3.564A pdb=" N ILE D 407 " --> pdb=" O ALA D 403 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 420 Processing helix chain 'D' and resid 431 through 444 Processing helix chain 'D' and resid 448 through 466 removed outlier: 4.607A pdb=" N PHE D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) 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 531 removed outlier: 4.535A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 548 through 559 removed outlier: 3.973A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG D 559 " --> pdb=" O PHE D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 removed outlier: 3.743A pdb=" N GLU D 571 " --> pdb=" O THR D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 598 Proline residue: D 590 - end of helix removed outlier: 3.599A pdb=" N ASP D 597 " --> pdb=" O THR D 593 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 53 removed outlier: 4.096A pdb=" N LYS F 31 " --> pdb=" O THR F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 81 removed outlier: 4.155A pdb=" N GLN F 60 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN F 64 " --> pdb=" O GLN F 60 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA F 65 " --> pdb=" O ASN F 61 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLN F 81 " --> pdb=" O SER F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 101 Processing helix chain 'F' and resid 109 through 129 Processing helix chain 'F' and resid 147 through 155 Processing helix chain 'F' and resid 157 through 192 removed outlier: 3.909A pdb=" N TRP F 168 " --> pdb=" O ALA F 164 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG F 169 " --> pdb=" O TRP F 165 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LYS F 174 " --> pdb=" O SER F 170 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN F 175 " --> pdb=" O GLU F 171 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU F 176 " --> pdb=" O VAL F 172 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG F 177 " --> pdb=" O GLY F 173 " (cutoff:3.500A) Proline residue: F 178 - end of helix removed outlier: 4.189A pdb=" N GLU F 182 " --> pdb=" O PRO F 178 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL F 185 " --> pdb=" O GLU F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 205 Processing helix chain 'F' and resid 206 through 208 No H-bonds generated for 'chain 'F' and resid 206 through 208' Processing helix chain 'F' and resid 220 through 252 removed outlier: 3.731A pdb=" N GLU F 224 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLU F 231 " --> pdb=" O GLU F 227 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLU F 232 " --> pdb=" O HIS F 228 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE F 233 " --> pdb=" O THR F 229 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS F 234 " --> pdb=" O PHE F 230 " (cutoff:3.500A) Proline residue: F 235 - end of helix removed outlier: 4.084A pdb=" N HIS F 239 " --> pdb=" O PRO F 235 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ASN F 250 " --> pdb=" O ALA F 246 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA F 251 " --> pdb=" O LYS F 247 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR F 252 " --> pdb=" O LEU F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 267 No H-bonds generated for 'chain 'F' and resid 265 through 267' Processing helix chain 'F' and resid 275 through 281 removed outlier: 4.178A pdb=" N SER F 280 " --> pdb=" O ASN F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 299 removed outlier: 3.785A pdb=" N VAL F 298 " --> pdb=" O THR F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 319 removed outlier: 3.729A pdb=" N ILE F 307 " --> pdb=" O ASP F 303 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE F 308 " --> pdb=" O ALA F 304 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL F 318 " --> pdb=" O PHE F 314 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY F 319 " --> pdb=" O PHE F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 331 removed outlier: 3.652A pdb=" N ASN F 330 " --> pdb=" O GLY F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 385 removed outlier: 3.691A pdb=" N HIS F 373 " --> pdb=" O PHE F 369 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N HIS F 378 " --> pdb=" O HIS F 374 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N TYR F 385 " --> pdb=" O TYR F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 393 Processing helix chain 'F' and resid 399 through 413 removed outlier: 3.563A pdb=" N ILE F 407 " --> pdb=" O ALA F 403 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER F 409 " --> pdb=" O GLY F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 420 Processing helix chain 'F' and resid 431 through 444 Processing helix chain 'F' and resid 448 through 466 removed outlier: 4.607A pdb=" N PHE F 452 " --> pdb=" O GLY F 448 " (cutoff:3.500A) 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 531 removed outlier: 4.534A pdb=" N THR F 519 " --> pdb=" O TYR F 515 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU F 520 " --> pdb=" O TYR F 516 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N PHE F 523 " --> pdb=" O THR F 519 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 542 Processing helix chain 'F' and resid 548 through 559 removed outlier: 3.973A pdb=" N MET F 557 " --> pdb=" O LYS F 553 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG F 559 " --> pdb=" O PHE F 555 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 572 removed outlier: 3.743A pdb=" N GLU F 571 " --> pdb=" O THR F 567 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 598 Proline residue: F 590 - end of helix removed outlier: 3.599A pdb=" N ASP F 597 " --> pdb=" O THR F 593 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 53 removed outlier: 4.096A pdb=" N LYS H 31 " --> pdb=" O THR H 27 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 81 removed outlier: 4.154A pdb=" N GLN H 60 " --> pdb=" O GLU H 56 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN H 64 " --> pdb=" O GLN H 60 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA H 65 " --> pdb=" O ASN H 61 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLN H 81 " --> pdb=" O SER H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 101 Processing helix chain 'H' and resid 109 through 129 Processing helix chain 'H' and resid 147 through 155 Processing helix chain 'H' and resid 157 through 192 removed outlier: 3.909A pdb=" N TRP H 168 " --> pdb=" O ALA H 164 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG H 169 " --> pdb=" O TRP H 165 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LYS H 174 " --> pdb=" O SER H 170 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN H 175 " --> pdb=" O GLU H 171 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU H 176 " --> pdb=" O VAL H 172 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG H 177 " --> pdb=" O GLY H 173 " (cutoff:3.500A) Proline residue: H 178 - end of helix removed outlier: 4.189A pdb=" N GLU H 182 " --> pdb=" O PRO H 178 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL H 185 " --> pdb=" O GLU H 181 " (cutoff:3.500A) Processing helix chain 'H' and resid 199 through 205 Processing helix chain 'H' and resid 206 through 208 No H-bonds generated for 'chain 'H' and resid 206 through 208' Processing helix chain 'H' and resid 220 through 252 removed outlier: 3.731A pdb=" N GLU H 224 " --> pdb=" O GLY H 220 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLU H 231 " --> pdb=" O GLU H 227 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLU H 232 " --> pdb=" O HIS H 228 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE H 233 " --> pdb=" O THR H 229 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS H 234 " --> pdb=" O PHE H 230 " (cutoff:3.500A) Proline residue: H 235 - end of helix removed outlier: 4.083A pdb=" N HIS H 239 " --> pdb=" O PRO H 235 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ASN H 250 " --> pdb=" O ALA H 246 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA H 251 " --> pdb=" O LYS H 247 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR H 252 " --> pdb=" O LEU H 248 " (cutoff:3.500A) Processing helix chain 'H' and resid 265 through 267 No H-bonds generated for 'chain 'H' and resid 265 through 267' Processing helix chain 'H' and resid 275 through 281 removed outlier: 4.179A pdb=" N SER H 280 " --> pdb=" O ASN H 277 " (cutoff:3.500A) Processing helix chain 'H' and resid 294 through 299 removed outlier: 3.785A pdb=" N VAL H 298 " --> pdb=" O THR H 294 " (cutoff:3.500A) Processing helix chain 'H' and resid 303 through 319 removed outlier: 3.728A pdb=" N ILE H 307 " --> pdb=" O ASP H 303 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE H 308 " --> pdb=" O ALA H 304 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL H 318 " --> pdb=" O PHE H 314 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY H 319 " --> pdb=" O PHE H 315 " (cutoff:3.500A) Processing helix chain 'H' and resid 326 through 331 removed outlier: 3.652A pdb=" N ASN H 330 " --> pdb=" O GLY H 326 " (cutoff:3.500A) Processing helix chain 'H' and resid 365 through 385 removed outlier: 3.691A pdb=" N HIS H 373 " --> pdb=" O PHE H 369 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N HIS H 378 " --> pdb=" O HIS H 374 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TYR H 385 " --> pdb=" O TYR H 381 " (cutoff:3.500A) Processing helix chain 'H' and resid 389 through 393 Processing helix chain 'H' and resid 399 through 413 removed outlier: 3.564A pdb=" N ILE H 407 " --> pdb=" O ALA H 403 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N MET H 408 " --> pdb=" O VAL H 404 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER H 409 " --> pdb=" O GLY H 405 " (cutoff:3.500A) Processing helix chain 'H' and resid 414 through 420 Processing helix chain 'H' and resid 431 through 444 Processing helix chain 'H' and resid 448 through 466 removed outlier: 4.606A pdb=" N PHE H 452 " --> pdb=" O GLY H 448 " (cutoff:3.500A) 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 531 removed outlier: 4.534A pdb=" N THR H 519 " --> pdb=" O TYR H 515 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU H 520 " --> pdb=" O TYR H 516 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N PHE H 523 " --> pdb=" O THR H 519 " (cutoff:3.500A) Processing helix chain 'H' and resid 538 through 542 Processing helix chain 'H' and resid 548 through 559 removed outlier: 3.973A pdb=" N MET H 557 " --> pdb=" O LYS H 553 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG H 559 " --> pdb=" O PHE H 555 " (cutoff:3.500A) Processing helix chain 'H' and resid 565 through 572 removed outlier: 3.743A pdb=" N GLU H 571 " --> pdb=" O THR H 567 " (cutoff:3.500A) Processing helix chain 'H' and resid 581 through 598 Proline residue: H 590 - end of helix removed outlier: 3.599A 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: 4.410A 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: 4.845A 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: 5.162A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 6.608A 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: 3.765A 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: 5.059A pdb=" N GLU A 132 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ASN A 165 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N GLN A 134 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.983A 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: 3.740A 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: 5.333A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.432A 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 325 through 328 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 357 removed outlier: 3.797A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.811A pdb=" N ARG A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.076A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE A 693 " --> pdb=" O SER A 673 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.752A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.752A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.484A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.770A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.850A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.686A 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=AB8, 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=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.925A 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: 6.630A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 5.161A 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: 5.352A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 5.059A 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=AC1, 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=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.329A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY B 593 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 323 through 328 removed outlier: 5.612A 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=AC4, first strand: chain 'B' and resid 354 through 357 removed outlier: 3.796A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 removed outlier: 3.811A pdb=" N ARG B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 659 through 660 removed outlier: 4.530A pdb=" N TYR B 660 " --> pdb=" O THR B 696 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 664 through 667 removed outlier: 6.473A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 702 through 704 removed outlier: 3.546A pdb=" N ASN B 703 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.152A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.152A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.499A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.943A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD4, 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=AD5, first strand: chain 'C' and resid 49 through 55 removed outlier: 7.499A 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: 6.421A 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=AD6, 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: 4.845A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU C 117 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 6.345A 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: 8.339A pdb=" N GLN C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ALA C 163 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD7, 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=AD8, first strand: chain 'C' and resid 311 through 318 removed outlier: 5.049A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.560A pdb=" N ASN C 542 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 5.612A 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=AE1, first strand: chain 'C' and resid 354 through 357 removed outlier: 3.796A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 454 removed outlier: 3.811A pdb=" N ARG C 493 " --> pdb=" O TYR C 453 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.108A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.892A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.892A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.301A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE8, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.805A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'D' and resid 347 through 350 Processing sheet with id=AF1, first strand: chain 'F' and resid 262 through 263 removed outlier: 5.805A pdb=" N LEU F 262 " --> pdb=" O VAL F 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'F' and resid 347 through 350 Processing sheet with id=AF3, first strand: chain 'H' and resid 262 through 263 removed outlier: 5.805A pdb=" N LEU H 262 " --> pdb=" O VAL H 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'H' and resid 347 through 350 1564 hydrogen bonds defined for protein. 4386 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: 9.22 Time building geometry restraints manager: 4.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 8630 1.33 - 1.45: 10902 1.45 - 1.58: 20726 1.58 - 1.71: 0 1.71 - 1.83: 285 Bond restraints: 40543 Sorted by residual: bond pdb=" CA SER A 698 " pdb=" C SER A 698 " ideal model delta sigma weight residual 1.522 1.443 0.080 1.20e-02 6.94e+03 4.40e+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 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 2.33e+01 bond pdb=" C THR C 208 " pdb=" N PRO C 209 " ideal model delta sigma weight residual 1.329 1.387 -0.058 1.20e-02 6.94e+03 2.33e+01 bond pdb=" N PRO A1143 " pdb=" CD PRO A1143 " ideal model delta sigma weight residual 1.473 1.412 0.061 1.40e-02 5.10e+03 1.92e+01 ... (remaining 40538 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 54168 2.70 - 5.41: 837 5.41 - 8.11: 80 8.11 - 10.81: 23 10.81 - 13.52: 6 Bond angle restraints: 55114 Sorted by residual: angle pdb=" N PHE H 28 " pdb=" CA PHE H 28 " pdb=" C PHE H 28 " ideal model delta sigma weight residual 111.24 101.82 9.42 1.29e+00 6.01e-01 5.34e+01 angle pdb=" N PHE F 28 " pdb=" CA PHE F 28 " pdb=" C PHE F 28 " ideal model delta sigma weight residual 111.24 101.84 9.40 1.29e+00 6.01e-01 5.31e+01 angle pdb=" N PHE D 28 " pdb=" CA PHE D 28 " pdb=" C PHE D 28 " ideal model delta sigma weight residual 111.24 101.85 9.39 1.29e+00 6.01e-01 5.29e+01 angle pdb=" N LEU F 45 " pdb=" CA LEU F 45 " pdb=" C LEU F 45 " ideal model delta sigma weight residual 111.07 103.93 7.14 1.07e+00 8.73e-01 4.46e+01 angle pdb=" N LEU D 45 " pdb=" CA LEU D 45 " pdb=" C LEU D 45 " ideal model delta sigma weight residual 111.07 103.95 7.12 1.07e+00 8.73e-01 4.43e+01 ... (remaining 55109 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 23376 17.88 - 35.77: 1516 35.77 - 53.65: 397 53.65 - 71.54: 87 71.54 - 89.42: 65 Dihedral angle restraints: 25441 sinusoidal: 11452 harmonic: 13989 Sorted by residual: dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual -86.00 3.42 -89.42 1 1.00e+01 1.00e-02 9.50e+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 -16.73 -69.27 1 1.00e+01 1.00e-02 6.20e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual 93.00 25.65 67.35 1 1.00e+01 1.00e-02 5.90e+01 ... (remaining 25438 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.331: 6339 0.331 - 0.661: 7 0.661 - 0.992: 5 0.992 - 1.323: 0 1.323 - 1.653: 2 Chirality restraints: 6353 Sorted by residual: chirality pdb=" C1 NAG W 2 " pdb=" O4 NAG W 1 " pdb=" C2 NAG W 2 " pdb=" O5 NAG W 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-02 2.50e+03 5.04e+02 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-02 2.50e+03 5.02e+02 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-02 2.50e+03 5.00e+02 ... (remaining 6350 not shown) Planarity restraints: 7050 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 331 " 0.239 2.00e-02 2.50e+03 3.35e-01 1.40e+03 pdb=" CG ASN B 331 " -0.113 2.00e-02 2.50e+03 pdb=" OD1 ASN B 331 " 0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN B 331 " -0.563 2.00e-02 2.50e+03 pdb=" C1 NAG N 1 " 0.418 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 801 " 0.142 2.00e-02 2.50e+03 1.63e-01 3.34e+02 pdb=" CG ASN A 801 " -0.056 2.00e-02 2.50e+03 pdb=" OD1 ASN A 801 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A 801 " -0.271 2.00e-02 2.50e+03 pdb=" C1 NAG J 1 " 0.191 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " 0.105 2.00e-02 2.50e+03 1.19e-01 1.76e+02 pdb=" CG ASN A 331 " -0.039 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " -0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " -0.196 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " 0.140 2.00e-02 2.50e+03 ... (remaining 7047 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 233 2.52 - 3.12: 30471 3.12 - 3.71: 55966 3.71 - 4.31: 81226 4.31 - 4.90: 133628 Nonbonded interactions: 301524 Sorted by model distance: nonbonded pdb=" O ARG A 328 " pdb=" CD1 PHE A 329 " model vdw 1.926 3.340 nonbonded pdb=" O ASP B 40 " pdb=" O LYS B 41 " model vdw 1.995 3.040 nonbonded pdb=" O VAL C 445 " pdb=" OG SER C 446 " model vdw 2.034 3.040 nonbonded pdb=" O VAL B 445 " pdb=" OG SER B 446 " model vdw 2.035 3.040 nonbonded pdb=" O VAL A 445 " pdb=" OG SER A 446 " model vdw 2.035 3.040 ... (remaining 301519 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' and (resid 27 through 939 or resid 944 through 1408)) selection = chain 'B' 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: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.660 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 37.720 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.260 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:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5057 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 0.376 40695 Z= 0.459 Angle : 1.124 61.444 55522 Z= 0.606 Chirality : 0.069 1.653 6353 Planarity : 0.005 0.106 6984 Dihedral : 13.261 88.438 16283 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 1.65 % Allowed : 6.76 % Favored : 91.59 % Rotamer: Outliers : 1.54 % Allowed : 4.72 % Favored : 93.73 % 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: -3.20 (0.11), residues: 4720 helix: -1.64 (0.11), residues: 1645 sheet: -1.15 (0.19), residues: 649 loop : -2.81 (0.11), residues: 2426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 161 TYR 0.014 0.001 TYR C 369 PHE 0.013 0.001 PHE C 456 TRP 0.013 0.001 TRP H 594 HIS 0.003 0.001 HIS D 241 Details of bonding type rmsd covalent geometry : bond 0.00732 (40543) covalent geometry : angle 0.89175 (55114) SS BOND : bond 0.09061 ( 48) SS BOND : angle 12.07086 ( 96) hydrogen bonds : bond 0.20043 ( 1535) hydrogen bonds : angle 7.87873 ( 4386) link_BETA1-4 : bond 0.00890 ( 38) link_BETA1-4 : angle 4.96467 ( 114) link_NAG-ASN : bond 0.03892 ( 66) link_NAG-ASN : angle 6.94588 ( 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 842 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 777 time to evaluate : 1.111 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: 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 306 PHE cc_start: 0.5924 (m-80) cc_final: 0.5619 (m-80) REVERT: A 332 ILE cc_start: 0.3761 (OUTLIER) cc_final: 0.3325 (tt) REVERT: A 371 PHE cc_start: 0.0628 (OUTLIER) cc_final: 0.0053 (t80) REVERT: A 800 PHE cc_start: 0.6115 (m-80) cc_final: 0.5049 (m-80) REVERT: B 909 ILE cc_start: 0.7729 (pt) cc_final: 0.7195 (pt) REVERT: B 1143 PRO cc_start: 0.8092 (Cg_endo) cc_final: 0.7459 (Cg_exo) REVERT: C 1031 GLU cc_start: 0.7201 (mt-10) cc_final: 0.6992 (tt0) REVERT: D 85 LEU cc_start: -0.1612 (tp) cc_final: -0.1826 (pt) REVERT: D 189 GLU cc_start: 0.4969 (mt-10) cc_final: 0.4574 (mm-30) REVERT: D 221 GLN cc_start: 0.3678 (tt0) cc_final: 0.3295 (mm-40) REVERT: F 31 LYS cc_start: 0.0371 (OUTLIER) cc_final: 0.0159 (tptt) REVERT: F 474 MET cc_start: -0.2123 (mmp) cc_final: -0.2789 (ttt) REVERT: H 39 LEU cc_start: 0.4931 (OUTLIER) cc_final: 0.4672 (mt) REVERT: H 270 MET cc_start: 0.2103 (tpt) cc_final: 0.1050 (tpp) outliers start: 65 outliers final: 17 residues processed: 831 average time/residue: 0.2342 time to fit residues: 317.5753 Evaluate side-chains 378 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 357 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 498 ARG Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 493 ARG Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain H residue 39 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 432 optimal weight: 50.0000 chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 30.0000 chunk 455 optimal weight: 30.0000 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 6.9990 chunk 470 optimal weight: 50.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 314 GLN A 417 ASN A 422 ASN A 690 GLN A1135 ASN B 30 ASN B 271 GLN B 314 GLN B 334 ASN B 417 ASN B 450 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN C 121 ASN C 417 ASN C 755 GLN C 762 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS D 24 GLN D 34 HIS D 101 GLN D 137 ASN D 210 ASN D 374 HIS D 472 GLN D 599 ASN F 24 GLN F 101 GLN F 137 ASN F 277 ASN F 374 HIS F 417 HIS F 472 GLN F 599 ASN H 24 GLN H 101 GLN H 137 ASN H 277 ASN H 373 HIS H 417 HIS H 472 GLN H 580 ASN H 599 ASN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4924 r_free = 0.4924 target = 0.257677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.217653 restraints weight = 60244.290| |-----------------------------------------------------------------------------| r_work (start): 0.4549 rms_B_bonded: 2.94 r_work: 0.3627 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.093 40695 Z= 0.375 Angle : 0.973 20.398 55522 Z= 0.480 Chirality : 0.057 0.428 6353 Planarity : 0.006 0.083 6984 Dihedral : 8.004 59.558 7375 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.33 % Favored : 93.20 % Rotamer: Outliers : 2.75 % Allowed : 11.37 % Favored : 85.88 % 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: -2.69 (0.11), residues: 4720 helix: -0.82 (0.12), residues: 1675 sheet: -1.50 (0.18), residues: 699 loop : -2.65 (0.11), residues: 2346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 493 TYR 0.034 0.002 TYR B 501 PHE 0.037 0.003 PHE A1052 TRP 0.046 0.002 TRP F 461 HIS 0.015 0.002 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00905 (40543) covalent geometry : angle 0.92176 (55114) SS BOND : bond 0.01796 ( 48) SS BOND : angle 3.14127 ( 96) hydrogen bonds : bond 0.06699 ( 1535) hydrogen bonds : angle 5.69324 ( 4386) link_BETA1-4 : bond 0.01034 ( 38) link_BETA1-4 : angle 2.84069 ( 114) link_NAG-ASN : bond 0.00885 ( 66) link_NAG-ASN : angle 4.44245 ( 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 494 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 378 time to evaluate : 1.321 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 205 SER cc_start: 0.8661 (p) cc_final: 0.8439 (p) REVERT: A 523 THR cc_start: 0.1905 (OUTLIER) cc_final: 0.1656 (m) REVERT: A 535 LYS cc_start: 0.7347 (ttpt) cc_final: 0.7048 (ttmm) REVERT: A 559 PHE cc_start: 0.7728 (m-10) cc_final: 0.7514 (m-10) REVERT: A 756 TYR cc_start: 0.7299 (OUTLIER) cc_final: 0.5809 (t80) REVERT: A 855 PHE cc_start: 0.6423 (t80) cc_final: 0.5037 (m-80) REVERT: A 1111 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8143 (pp20) REVERT: B 329 PHE cc_start: 0.7424 (m-80) cc_final: 0.7100 (m-10) REVERT: B 523 THR cc_start: 0.5089 (OUTLIER) cc_final: 0.4850 (m) REVERT: C 121 ASN cc_start: 0.6303 (OUTLIER) cc_final: 0.6082 (p0) REVERT: C 200 TYR cc_start: 0.7239 (m-80) cc_final: 0.7015 (m-80) REVERT: C 266 TYR cc_start: 0.7899 (OUTLIER) cc_final: 0.7490 (m-80) REVERT: C 307 THR cc_start: 0.8867 (m) cc_final: 0.8588 (p) REVERT: C 917 TYR cc_start: 0.8650 (m-80) cc_final: 0.8381 (m-80) REVERT: D 85 LEU cc_start: -0.0679 (tp) cc_final: -0.1053 (pt) REVERT: D 189 GLU cc_start: 0.5266 (mt-10) cc_final: 0.4914 (mm-30) REVERT: D 190 MET cc_start: -0.1567 (tmm) cc_final: -0.2382 (ttp) REVERT: D 455 MET cc_start: 0.0818 (tmm) cc_final: 0.0337 (ttp) REVERT: F 150 GLU cc_start: 0.2764 (tm-30) cc_final: 0.1727 (mm-30) REVERT: F 152 MET cc_start: 0.0338 (mmt) cc_final: -0.0349 (mmp) REVERT: F 323 MET cc_start: -0.1390 (mmp) cc_final: -0.1972 (ppp) REVERT: F 474 MET cc_start: -0.1708 (mmp) cc_final: -0.3176 (ttt) REVERT: H 39 LEU cc_start: 0.4299 (OUTLIER) cc_final: 0.3947 (mt) REVERT: H 82 MET cc_start: 0.3205 (mtp) cc_final: 0.2787 (mpp) REVERT: H 270 MET cc_start: 0.0498 (tpt) cc_final: 0.0214 (mmm) REVERT: H 383 MET cc_start: 0.0982 (mtp) cc_final: 0.0039 (tmm) outliers start: 116 outliers final: 55 residues processed: 479 average time/residue: 0.2012 time to fit residues: 165.3569 Evaluate side-chains 337 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 275 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 493 ARG Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 1057 PRO Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 557 MET Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 455 MET Chi-restraints excluded: chain H residue 510 TYR Chi-restraints excluded: chain H residue 563 SER Chi-restraints excluded: chain H residue 580 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 223 optimal weight: 20.0000 chunk 99 optimal weight: 6.9990 chunk 246 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 178 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 120 optimal weight: 0.9990 chunk 155 optimal weight: 0.8980 chunk 124 optimal weight: 6.9990 chunk 280 optimal weight: 8.9990 chunk 433 optimal weight: 30.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 450 ASN A 955 ASN B 87 ASN B 207 HIS B 506 GLN B1005 GLN D 101 GLN D 417 HIS ** F 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 378 HIS F 429 GLN F 442 GLN ** H 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4937 r_free = 0.4937 target = 0.259379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.209887 restraints weight = 60275.640| |-----------------------------------------------------------------------------| r_work (start): 0.4473 rms_B_bonded: 4.05 r_work: 0.3545 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.4806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 40695 Z= 0.164 Angle : 0.735 18.013 55522 Z= 0.352 Chirality : 0.047 0.481 6353 Planarity : 0.005 0.110 6984 Dihedral : 6.976 58.984 7332 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.55 % Favored : 94.17 % Rotamer: Outliers : 2.42 % Allowed : 13.29 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.41 % 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: -1.97 (0.11), residues: 4720 helix: -0.09 (0.13), residues: 1690 sheet: -1.15 (0.18), residues: 725 loop : -2.34 (0.11), residues: 2305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 460 TYR 0.024 0.001 TYR A 453 PHE 0.021 0.002 PHE B 43 TRP 0.019 0.001 TRP D 459 HIS 0.005 0.001 HIS D 373 Details of bonding type rmsd covalent geometry : bond 0.00375 (40543) covalent geometry : angle 0.67978 (55114) SS BOND : bond 0.00539 ( 48) SS BOND : angle 2.50642 ( 96) hydrogen bonds : bond 0.05021 ( 1535) hydrogen bonds : angle 5.16904 ( 4386) link_BETA1-4 : bond 0.00772 ( 38) link_BETA1-4 : angle 2.64905 ( 114) link_NAG-ASN : bond 0.00638 ( 66) link_NAG-ASN : angle 3.97633 ( 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 399 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 297 time to evaluate : 1.421 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 523 THR cc_start: 0.1953 (OUTLIER) cc_final: 0.1733 (m) REVERT: A 535 LYS cc_start: 0.7337 (ttpt) cc_final: 0.7102 (ttmm) REVERT: A 756 TYR cc_start: 0.7336 (OUTLIER) cc_final: 0.5793 (t80) REVERT: A 767 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.7929 (mm) REVERT: A 1010 GLN cc_start: 0.6997 (OUTLIER) cc_final: 0.6138 (tp40) REVERT: B 568 ASP cc_start: 0.7187 (p0) cc_final: 0.6982 (p0) REVERT: C 200 TYR cc_start: 0.7659 (m-80) cc_final: 0.7384 (m-80) REVERT: C 307 THR cc_start: 0.9014 (m) cc_final: 0.8768 (p) REVERT: C 859 THR cc_start: 0.8270 (m) cc_final: 0.7690 (p) REVERT: D 168 TRP cc_start: -0.1952 (t-100) cc_final: -0.2374 (t-100) REVERT: D 190 MET cc_start: -0.1602 (tmm) cc_final: -0.2328 (ttp) REVERT: D 213 ASP cc_start: 0.2014 (t0) cc_final: 0.1272 (m-30) REVERT: D 438 PHE cc_start: 0.0696 (t80) cc_final: -0.1076 (m-80) REVERT: F 150 GLU cc_start: 0.2497 (tm-30) cc_final: 0.1292 (mm-30) REVERT: F 154 ASN cc_start: 0.1524 (m-40) cc_final: 0.1127 (t0) REVERT: F 323 MET cc_start: -0.1465 (mmp) cc_final: -0.2275 (ppp) REVERT: H 141 CYS cc_start: -0.0229 (OUTLIER) cc_final: -0.0495 (p) REVERT: H 383 MET cc_start: 0.0699 (mtp) cc_final: -0.0027 (tmm) REVERT: H 587 TYR cc_start: 0.2025 (OUTLIER) cc_final: 0.1746 (m-80) outliers start: 102 outliers final: 47 residues processed: 377 average time/residue: 0.2067 time to fit residues: 135.2468 Evaluate side-chains 304 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 251 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 557 MET Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain F residue 542 CYS Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 141 CYS Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 455 MET Chi-restraints excluded: chain H residue 587 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 469 optimal weight: 0.6980 chunk 166 optimal weight: 0.0970 chunk 439 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 336 optimal weight: 50.0000 chunk 123 optimal weight: 2.9990 chunk 312 optimal weight: 20.0000 chunk 282 optimal weight: 5.9990 chunk 432 optimal weight: 40.0000 chunk 254 optimal weight: 0.2980 chunk 51 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 HIS C 450 ASN C 755 GLN C 762 GLN ** D 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 373 HIS H 101 GLN H 373 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4950 r_free = 0.4950 target = 0.259811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.211116 restraints weight = 60640.142| |-----------------------------------------------------------------------------| r_work (start): 0.4492 rms_B_bonded: 4.10 r_work: 0.3542 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.5168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 40695 Z= 0.116 Angle : 0.654 11.911 55522 Z= 0.313 Chirality : 0.046 0.550 6353 Planarity : 0.004 0.049 6984 Dihedral : 6.278 58.704 7324 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.15 % Favored : 94.58 % Rotamer: Outliers : 1.97 % Allowed : 14.38 % Favored : 83.65 % 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: -1.45 (0.12), residues: 4720 helix: 0.43 (0.13), residues: 1696 sheet: -0.79 (0.18), residues: 739 loop : -2.16 (0.12), residues: 2285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 319 TYR 0.020 0.001 TYR C1067 PHE 0.031 0.001 PHE C 970 TRP 0.022 0.001 TRP D 203 HIS 0.011 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00243 (40543) covalent geometry : angle 0.61867 (55114) SS BOND : bond 0.00414 ( 48) SS BOND : angle 1.93221 ( 96) hydrogen bonds : bond 0.04061 ( 1535) hydrogen bonds : angle 4.84474 ( 4386) link_BETA1-4 : bond 0.00679 ( 38) link_BETA1-4 : angle 2.37121 ( 114) link_NAG-ASN : bond 0.00531 ( 66) link_NAG-ASN : angle 2.92073 ( 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 383 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 300 time to evaluate : 1.261 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 64 TRP cc_start: 0.7882 (t60) cc_final: 0.7041 (t-100) REVERT: A 301 CYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7723 (m) REVERT: A 559 PHE cc_start: 0.7757 (m-10) cc_final: 0.7525 (m-10) REVERT: A 767 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.7788 (mm) REVERT: A 1010 GLN cc_start: 0.6974 (OUTLIER) cc_final: 0.6157 (tp40) REVERT: C 200 TYR cc_start: 0.7739 (m-80) cc_final: 0.7400 (m-80) REVERT: C 307 THR cc_start: 0.8905 (m) cc_final: 0.8668 (p) REVERT: C 859 THR cc_start: 0.8275 (m) cc_final: 0.7764 (p) REVERT: D 168 TRP cc_start: -0.1836 (t-100) cc_final: -0.2074 (t-100) REVERT: D 189 GLU cc_start: 0.5179 (pt0) cc_final: 0.4872 (mm-30) REVERT: D 190 MET cc_start: -0.1239 (tmm) cc_final: -0.1659 (ttp) REVERT: D 213 ASP cc_start: 0.2231 (t0) cc_final: 0.1351 (m-30) REVERT: D 438 PHE cc_start: 0.0789 (t80) cc_final: -0.0974 (m-80) REVERT: D 480 MET cc_start: -0.0614 (OUTLIER) cc_final: -0.0981 (mtt) REVERT: F 150 GLU cc_start: 0.2151 (tm-30) cc_final: 0.1454 (mm-30) REVERT: F 323 MET cc_start: -0.1812 (mmp) cc_final: -0.2300 (ppp) REVERT: F 351 LEU cc_start: 0.0599 (OUTLIER) cc_final: 0.0231 (mp) REVERT: H 165 TRP cc_start: 0.1753 (t60) cc_final: 0.1029 (t60) REVERT: H 270 MET cc_start: 0.0093 (tpp) cc_final: -0.1382 (ptp) REVERT: H 383 MET cc_start: 0.0664 (mtp) cc_final: 0.0012 (tmm) REVERT: H 587 TYR cc_start: 0.2496 (OUTLIER) cc_final: 0.2128 (m-80) outliers start: 83 outliers final: 41 residues processed: 369 average time/residue: 0.2031 time to fit residues: 130.9491 Evaluate side-chains 300 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 253 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 480 MET Chi-restraints excluded: chain D residue 542 CYS Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain F residue 542 CYS Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 587 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 83 optimal weight: 6.9990 chunk 371 optimal weight: 50.0000 chunk 179 optimal weight: 4.9990 chunk 332 optimal weight: 30.0000 chunk 471 optimal weight: 20.0000 chunk 257 optimal weight: 0.8980 chunk 330 optimal weight: 5.9990 chunk 361 optimal weight: 50.0000 chunk 367 optimal weight: 8.9990 chunk 129 optimal weight: 7.9990 chunk 341 optimal weight: 50.0000 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 644 GLN A 804 GLN B 207 HIS B 422 ASN B 544 ASN B1083 HIS C 121 ASN C 544 ASN C 935 GLN C1005 GLN ** D 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 GLN F 154 ASN ** F 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4887 r_free = 0.4887 target = 0.252914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.198849 restraints weight = 59290.144| |-----------------------------------------------------------------------------| r_work (start): 0.4364 rms_B_bonded: 4.12 r_work: 0.3396 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.6109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.113 40695 Z= 0.351 Angle : 0.880 16.181 55522 Z= 0.428 Chirality : 0.055 1.036 6353 Planarity : 0.005 0.077 6984 Dihedral : 6.892 59.402 7324 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.74 % Favored : 92.99 % Rotamer: Outliers : 3.44 % Allowed : 14.38 % Favored : 82.17 % 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: -1.84 (0.12), residues: 4720 helix: 0.03 (0.12), residues: 1691 sheet: -1.16 (0.18), residues: 762 loop : -2.26 (0.12), residues: 2267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 44 TYR 0.025 0.002 TYR B 707 PHE 0.035 0.003 PHE A 888 TRP 0.020 0.001 TRP B1102 HIS 0.013 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00866 (40543) covalent geometry : angle 0.84027 (55114) SS BOND : bond 0.00653 ( 48) SS BOND : angle 2.68142 ( 96) hydrogen bonds : bond 0.06053 ( 1535) hydrogen bonds : angle 5.33750 ( 4386) link_BETA1-4 : bond 0.01000 ( 38) link_BETA1-4 : angle 2.66430 ( 114) link_NAG-ASN : bond 0.00943 ( 66) link_NAG-ASN : angle 3.62146 ( 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 417 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 272 time to evaluate : 1.221 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 559 PHE cc_start: 0.8748 (m-10) cc_final: 0.8490 (m-10) REVERT: A 754 LEU cc_start: 0.8525 (tt) cc_final: 0.8157 (mp) REVERT: A 762 GLN cc_start: 0.8369 (mm110) cc_final: 0.7690 (mt0) REVERT: A 1010 GLN cc_start: 0.7023 (OUTLIER) cc_final: 0.6530 (tt0) REVERT: B 900 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.8124 (mtp) REVERT: B 949 GLN cc_start: 0.8736 (tp40) cc_final: 0.8112 (mt0) REVERT: B 1014 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.8625 (ttm170) REVERT: C 121 ASN cc_start: 0.6538 (OUTLIER) cc_final: 0.6147 (p0) REVERT: C 200 TYR cc_start: 0.7936 (m-80) cc_final: 0.7621 (m-80) REVERT: C 307 THR cc_start: 0.9089 (m) cc_final: 0.8877 (p) REVERT: C 917 TYR cc_start: 0.8934 (m-80) cc_final: 0.8629 (m-80) REVERT: D 189 GLU cc_start: 0.5071 (pt0) cc_final: 0.4786 (mm-30) REVERT: D 190 MET cc_start: -0.0578 (tmm) cc_final: -0.1077 (ttp) REVERT: D 213 ASP cc_start: 0.1893 (t0) cc_final: 0.1176 (m-30) REVERT: D 294 THR cc_start: 0.2181 (p) cc_final: 0.1887 (t) REVERT: D 438 PHE cc_start: 0.0702 (t80) cc_final: -0.0982 (m-80) REVERT: D 480 MET cc_start: -0.0638 (OUTLIER) cc_final: -0.0971 (mtt) REVERT: D 571 GLU cc_start: 0.2290 (OUTLIER) cc_final: 0.2026 (pt0) REVERT: F 150 GLU cc_start: 0.1361 (tm-30) cc_final: 0.1149 (mm-30) REVERT: F 351 LEU cc_start: 0.0925 (OUTLIER) cc_final: 0.0553 (mp) REVERT: F 587 TYR cc_start: -0.0824 (OUTLIER) cc_final: -0.1228 (m-10) REVERT: H 39 LEU cc_start: 0.4101 (OUTLIER) cc_final: 0.3713 (mt) REVERT: H 270 MET cc_start: 0.0316 (tpp) cc_final: -0.1054 (ptp) REVERT: H 383 MET cc_start: 0.0147 (mtp) cc_final: -0.0372 (tmm) REVERT: H 587 TYR cc_start: 0.2654 (OUTLIER) cc_final: 0.2370 (m-80) outliers start: 145 outliers final: 87 residues processed: 390 average time/residue: 0.2033 time to fit residues: 138.2140 Evaluate side-chains 340 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 243 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 498 ARG Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1014 ARG Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1057 PRO Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 480 MET Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 542 CYS Chi-restraints excluded: chain D residue 571 GLU Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain F residue 367 ASP Chi-restraints excluded: chain F residue 587 TYR Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 510 TYR Chi-restraints excluded: chain H residue 587 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 396 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 414 optimal weight: 9.9990 chunk 128 optimal weight: 0.5980 chunk 412 optimal weight: 8.9990 chunk 231 optimal weight: 8.9990 chunk 337 optimal weight: 7.9990 chunk 445 optimal weight: 0.0570 overall best weight: 0.9302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 207 HIS B 207 HIS B 506 GLN B 544 ASN C 314 GLN D 373 HIS ** F 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 330 ASN ** F 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 101 GLN H 210 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4921 r_free = 0.4921 target = 0.257689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.210573 restraints weight = 61654.709| |-----------------------------------------------------------------------------| r_work (start): 0.4479 rms_B_bonded: 3.95 r_work: 0.3531 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.6245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 40695 Z= 0.125 Angle : 0.665 14.921 55522 Z= 0.318 Chirality : 0.046 0.518 6353 Planarity : 0.004 0.058 6984 Dihedral : 6.218 59.077 7324 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.00 % Favored : 94.75 % Rotamer: Outliers : 1.99 % Allowed : 16.14 % Favored : 81.87 % 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: -1.34 (0.12), residues: 4720 helix: 0.58 (0.13), residues: 1687 sheet: -0.98 (0.18), residues: 737 loop : -2.04 (0.12), residues: 2296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 983 TYR 0.022 0.001 TYR A1067 PHE 0.022 0.001 PHE H 285 TRP 0.013 0.001 TRP A 64 HIS 0.008 0.001 HIS F 535 Details of bonding type rmsd covalent geometry : bond 0.00274 (40543) covalent geometry : angle 0.63025 (55114) SS BOND : bond 0.00431 ( 48) SS BOND : angle 2.25489 ( 96) hydrogen bonds : bond 0.04141 ( 1535) hydrogen bonds : angle 4.86643 ( 4386) link_BETA1-4 : bond 0.00572 ( 38) link_BETA1-4 : angle 2.21097 ( 114) link_NAG-ASN : bond 0.00459 ( 66) link_NAG-ASN : angle 2.85535 ( 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 353 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 269 time to evaluate : 1.463 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: A 301 CYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7778 (m) REVERT: A 379 CYS cc_start: 0.2531 (OUTLIER) cc_final: 0.1925 (p) REVERT: A 559 PHE cc_start: 0.8652 (m-10) cc_final: 0.8421 (m-10) REVERT: A 754 LEU cc_start: 0.8571 (tt) cc_final: 0.8283 (mp) REVERT: A 767 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8061 (mm) REVERT: A 950 ASP cc_start: 0.8367 (m-30) cc_final: 0.8014 (m-30) REVERT: A 1010 GLN cc_start: 0.6867 (OUTLIER) cc_final: 0.6023 (tp40) REVERT: B 788 ILE cc_start: 0.9069 (tp) cc_final: 0.8691 (pt) REVERT: B 856 ASN cc_start: 0.8559 (p0) cc_final: 0.8335 (p0) REVERT: C 105 ILE cc_start: 0.8412 (OUTLIER) cc_final: 0.7784 (tt) REVERT: C 200 TYR cc_start: 0.8019 (m-80) cc_final: 0.7725 (m-80) REVERT: C 307 THR cc_start: 0.8927 (m) cc_final: 0.8707 (p) REVERT: C 398 ASP cc_start: 0.4022 (OUTLIER) cc_final: 0.1559 (t0) REVERT: D 189 GLU cc_start: 0.5257 (pt0) cc_final: 0.4930 (mm-30) REVERT: D 190 MET cc_start: -0.0624 (tmm) cc_final: -0.0983 (ttp) REVERT: D 213 ASP cc_start: 0.1836 (t0) cc_final: 0.1131 (m-30) REVERT: D 294 THR cc_start: 0.2016 (p) cc_final: 0.1774 (t) REVERT: D 438 PHE cc_start: 0.0925 (t80) cc_final: -0.0664 (m-80) REVERT: D 559 ARG cc_start: 0.2339 (ptt90) cc_final: 0.1836 (tpt-90) REVERT: D 571 GLU cc_start: 0.2417 (OUTLIER) cc_final: 0.2071 (pt0) REVERT: F 351 LEU cc_start: 0.1015 (OUTLIER) cc_final: 0.0626 (mp) REVERT: F 376 MET cc_start: 0.1474 (mmm) cc_final: 0.1218 (mmt) REVERT: F 579 MET cc_start: -0.1727 (pmm) cc_final: -0.1974 (ttp) REVERT: H 166 GLU cc_start: 0.3878 (tp30) cc_final: 0.3170 (tt0) REVERT: H 270 MET cc_start: 0.0301 (tpp) cc_final: -0.1075 (ptp) REVERT: H 383 MET cc_start: 0.0286 (mtp) cc_final: -0.0323 (tmm) REVERT: H 587 TYR cc_start: 0.2650 (OUTLIER) cc_final: 0.2357 (m-80) outliers start: 84 outliers final: 49 residues processed: 337 average time/residue: 0.2020 time to fit residues: 119.2742 Evaluate side-chains 305 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 247 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 498 ARG Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 542 CYS Chi-restraints excluded: chain D residue 571 GLU Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 293 VAL Chi-restraints excluded: chain H residue 530 CYS Chi-restraints excluded: chain H residue 587 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 438 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 106 optimal weight: 20.0000 chunk 290 optimal weight: 0.5980 chunk 72 optimal weight: 0.6980 chunk 204 optimal weight: 5.9990 chunk 317 optimal weight: 8.9990 chunk 462 optimal weight: 20.0000 chunk 382 optimal weight: 5.9990 chunk 389 optimal weight: 30.0000 chunk 220 optimal weight: 0.9980 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 207 HIS B 207 HIS C 188 ASN ** F 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 505 HIS ** F 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 101 GLN H 442 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4904 r_free = 0.4904 target = 0.255669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.206828 restraints weight = 61455.104| |-----------------------------------------------------------------------------| r_work (start): 0.4434 rms_B_bonded: 3.95 r_work: 0.3473 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.6509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 40695 Z= 0.183 Angle : 0.686 14.280 55522 Z= 0.331 Chirality : 0.047 0.473 6353 Planarity : 0.004 0.063 6984 Dihedral : 6.091 59.003 7324 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.97 % Favored : 93.77 % Rotamer: Outliers : 2.47 % Allowed : 16.26 % Favored : 81.27 % 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: -1.28 (0.12), residues: 4720 helix: 0.60 (0.13), residues: 1685 sheet: -0.92 (0.19), residues: 727 loop : -1.98 (0.12), residues: 2308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 983 TYR 0.027 0.001 TYR D 454 PHE 0.024 0.002 PHE C 86 TRP 0.022 0.001 TRP D 459 HIS 0.006 0.001 HIS H 195 Details of bonding type rmsd covalent geometry : bond 0.00437 (40543) covalent geometry : angle 0.65402 (55114) SS BOND : bond 0.00361 ( 48) SS BOND : angle 2.16848 ( 96) hydrogen bonds : bond 0.04497 ( 1535) hydrogen bonds : angle 4.90440 ( 4386) link_BETA1-4 : bond 0.00630 ( 38) link_BETA1-4 : angle 2.17554 ( 114) link_NAG-ASN : bond 0.00499 ( 66) link_NAG-ASN : angle 2.84032 ( 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 364 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 260 time to evaluate : 1.415 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: A 55 PHE cc_start: 0.8041 (m-80) cc_final: 0.7814 (m-80) REVERT: A 301 CYS cc_start: 0.8373 (OUTLIER) cc_final: 0.8072 (m) REVERT: A 379 CYS cc_start: 0.2565 (OUTLIER) cc_final: 0.1668 (p) REVERT: A 559 PHE cc_start: 0.8756 (m-10) cc_final: 0.8481 (m-10) REVERT: A 754 LEU cc_start: 0.8734 (tt) cc_final: 0.8389 (mp) REVERT: A 762 GLN cc_start: 0.8169 (mm110) cc_final: 0.7493 (mt0) REVERT: A 767 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8126 (mm) REVERT: A 950 ASP cc_start: 0.8533 (m-30) cc_final: 0.8119 (m-30) REVERT: A 1010 GLN cc_start: 0.6879 (OUTLIER) cc_final: 0.6049 (tp40) REVERT: B 983 ARG cc_start: 0.7957 (ttp80) cc_final: 0.7598 (ttp80) REVERT: C 307 THR cc_start: 0.8897 (m) cc_final: 0.8669 (p) REVERT: C 895 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8143 (pm20) REVERT: C 917 TYR cc_start: 0.8693 (m-80) cc_final: 0.8435 (m-80) REVERT: C 975 SER cc_start: 0.7667 (p) cc_final: 0.6782 (m) REVERT: D 189 GLU cc_start: 0.5117 (pt0) cc_final: 0.4759 (mm-30) REVERT: D 190 MET cc_start: -0.0821 (tmm) cc_final: -0.1104 (ttp) REVERT: D 213 ASP cc_start: 0.1656 (t0) cc_final: 0.0961 (m-30) REVERT: D 294 THR cc_start: 0.2395 (p) cc_final: 0.2156 (t) REVERT: D 383 MET cc_start: 0.4176 (ptp) cc_final: 0.2687 (ppp) REVERT: D 438 PHE cc_start: 0.0902 (t80) cc_final: -0.0630 (m-80) REVERT: D 520 LEU cc_start: 0.3225 (tp) cc_final: 0.2903 (tp) REVERT: D 559 ARG cc_start: 0.2411 (ptt90) cc_final: 0.1853 (tpt-90) REVERT: D 571 GLU cc_start: 0.2253 (OUTLIER) cc_final: 0.1878 (pt0) REVERT: D 581 VAL cc_start: 0.0944 (OUTLIER) cc_final: 0.0665 (m) REVERT: F 266 LEU cc_start: 0.3292 (pp) cc_final: 0.2948 (mt) REVERT: F 323 MET cc_start: -0.2129 (tpt) cc_final: -0.2886 (ppp) REVERT: F 351 LEU cc_start: 0.1108 (OUTLIER) cc_final: 0.0612 (mp) REVERT: F 459 TRP cc_start: 0.0371 (t60) cc_final: -0.0337 (t60) REVERT: F 474 MET cc_start: -0.1792 (mmp) cc_final: -0.3390 (ttm) REVERT: F 587 TYR cc_start: -0.0481 (OUTLIER) cc_final: -0.1350 (m-80) REVERT: H 270 MET cc_start: 0.0371 (tpp) cc_final: -0.1045 (ptp) REVERT: H 285 PHE cc_start: 0.1455 (m-10) cc_final: 0.1088 (m-80) REVERT: H 383 MET cc_start: 0.0314 (mtp) cc_final: -0.0378 (tmm) REVERT: H 579 MET cc_start: 0.2764 (mmt) cc_final: 0.1482 (mmm) REVERT: H 587 TYR cc_start: 0.2383 (OUTLIER) cc_final: 0.2087 (m-80) outliers start: 104 outliers final: 69 residues processed: 342 average time/residue: 0.2130 time to fit residues: 126.1095 Evaluate side-chains 324 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 245 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 498 ARG Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1142 GLN Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 542 CYS Chi-restraints excluded: chain D residue 571 GLU Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain F residue 587 TYR Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 293 VAL Chi-restraints excluded: chain H residue 587 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 144 optimal weight: 2.9990 chunk 203 optimal weight: 10.0000 chunk 107 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 429 optimal weight: 8.9990 chunk 135 optimal weight: 7.9990 chunk 102 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 175 optimal weight: 0.7980 chunk 253 optimal weight: 4.9990 chunk 241 optimal weight: 9.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 207 HIS B 207 HIS C 87 ASN F 265 HIS F 505 HIS F 524 GLN H 101 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4918 r_free = 0.4918 target = 0.257477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.210033 restraints weight = 62140.393| |-----------------------------------------------------------------------------| r_work (start): 0.4471 rms_B_bonded: 3.97 r_work: 0.3522 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.6664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 40695 Z= 0.130 Angle : 0.637 11.965 55522 Z= 0.305 Chirality : 0.045 0.508 6353 Planarity : 0.004 0.073 6984 Dihedral : 5.814 59.583 7324 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.00 % Favored : 94.72 % Rotamer: Outliers : 2.04 % Allowed : 16.64 % Favored : 81.32 % 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: -1.05 (0.12), residues: 4720 helix: 0.80 (0.13), residues: 1690 sheet: -0.75 (0.19), residues: 704 loop : -1.86 (0.12), residues: 2326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.000 ARG F 245 TYR 0.020 0.001 TYR C1067 PHE 0.022 0.001 PHE B 86 TRP 0.030 0.001 TRP D 478 HIS 0.006 0.001 HIS H 195 Details of bonding type rmsd covalent geometry : bond 0.00300 (40543) covalent geometry : angle 0.60846 (55114) SS BOND : bond 0.00352 ( 48) SS BOND : angle 1.89407 ( 96) hydrogen bonds : bond 0.03918 ( 1535) hydrogen bonds : angle 4.75773 ( 4386) link_BETA1-4 : bond 0.00598 ( 38) link_BETA1-4 : angle 2.10769 ( 114) link_NAG-ASN : bond 0.00384 ( 66) link_NAG-ASN : angle 2.53736 ( 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 343 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 257 time to evaluate : 1.352 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 55 PHE cc_start: 0.8115 (m-80) cc_final: 0.7911 (m-80) REVERT: A 301 CYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7874 (m) REVERT: A 379 CYS cc_start: 0.2610 (OUTLIER) cc_final: 0.1861 (p) REVERT: A 754 LEU cc_start: 0.8803 (tt) cc_final: 0.8573 (mp) REVERT: A 767 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8051 (mm) REVERT: A 950 ASP cc_start: 0.8386 (m-30) cc_final: 0.8019 (m-30) REVERT: A 1010 GLN cc_start: 0.6777 (OUTLIER) cc_final: 0.5942 (tp40) REVERT: B 309 GLU cc_start: 0.8000 (tp30) cc_final: 0.7613 (tt0) REVERT: C 307 THR cc_start: 0.8821 (m) cc_final: 0.8577 (p) REVERT: C 955 ASN cc_start: 0.7344 (m-40) cc_final: 0.6783 (t0) REVERT: C 975 SER cc_start: 0.7816 (p) cc_final: 0.6973 (m) REVERT: D 213 ASP cc_start: 0.1486 (t0) cc_final: 0.0923 (m-30) REVERT: D 287 GLN cc_start: 0.5343 (tp40) cc_final: 0.4092 (pp30) REVERT: D 383 MET cc_start: 0.4167 (ptp) cc_final: 0.2594 (ppp) REVERT: D 473 TRP cc_start: 0.0536 (m-10) cc_final: -0.0173 (t60) REVERT: D 480 MET cc_start: -0.1061 (OUTLIER) cc_final: -0.1489 (mtt) REVERT: D 520 LEU cc_start: 0.2982 (tp) cc_final: 0.2757 (tp) REVERT: D 559 ARG cc_start: 0.2419 (ptt90) cc_final: 0.1862 (tpt-90) REVERT: D 571 GLU cc_start: 0.2254 (OUTLIER) cc_final: 0.1872 (pt0) REVERT: D 581 VAL cc_start: 0.0827 (OUTLIER) cc_final: 0.0496 (m) REVERT: F 266 LEU cc_start: 0.3295 (pp) cc_final: 0.2839 (mt) REVERT: F 323 MET cc_start: -0.1941 (tpt) cc_final: -0.2754 (ppp) REVERT: F 351 LEU cc_start: 0.1121 (OUTLIER) cc_final: 0.0680 (mp) REVERT: F 459 TRP cc_start: 0.0138 (t60) cc_final: -0.0488 (t60) REVERT: F 474 MET cc_start: -0.1731 (mmp) cc_final: -0.3280 (ttm) REVERT: F 587 TYR cc_start: -0.0610 (OUTLIER) cc_final: -0.1250 (m-80) REVERT: H 270 MET cc_start: 0.0306 (tpp) cc_final: -0.1082 (ptp) REVERT: H 285 PHE cc_start: 0.1483 (m-80) cc_final: 0.1109 (m-80) REVERT: H 383 MET cc_start: 0.0341 (mtp) cc_final: -0.0318 (tmm) REVERT: H 579 MET cc_start: 0.2739 (mmt) cc_final: 0.1491 (mmm) REVERT: H 587 TYR cc_start: 0.2179 (OUTLIER) cc_final: 0.1947 (m-80) outliers start: 86 outliers final: 58 residues processed: 329 average time/residue: 0.2047 time to fit residues: 117.7874 Evaluate side-chains 312 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 244 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 498 ARG Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1142 GLN Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 480 MET Chi-restraints excluded: chain D residue 542 CYS Chi-restraints excluded: chain D residue 571 GLU Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain F residue 587 TYR Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 293 VAL Chi-restraints excluded: chain H residue 587 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 317 optimal weight: 4.9990 chunk 213 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 301 optimal weight: 6.9990 chunk 274 optimal weight: 1.9990 chunk 299 optimal weight: 7.9990 chunk 294 optimal weight: 0.0770 chunk 379 optimal weight: 20.0000 chunk 313 optimal weight: 10.0000 chunk 157 optimal weight: 6.9990 chunk 468 optimal weight: 8.9990 overall best weight: 2.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS B 207 HIS C 913 GLN F 442 GLN F 505 HIS F 524 GLN H 101 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4905 r_free = 0.4905 target = 0.253909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.202896 restraints weight = 58940.538| |-----------------------------------------------------------------------------| r_work (start): 0.4440 rms_B_bonded: 4.05 r_work: 0.3464 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.6830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 40695 Z= 0.169 Angle : 0.662 12.116 55522 Z= 0.320 Chirality : 0.046 0.516 6353 Planarity : 0.004 0.062 6984 Dihedral : 5.823 59.487 7322 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.81 % Favored : 93.92 % Rotamer: Outliers : 2.09 % Allowed : 16.81 % Favored : 81.11 % 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: -1.03 (0.12), residues: 4720 helix: 0.81 (0.13), residues: 1691 sheet: -0.78 (0.19), residues: 712 loop : -1.83 (0.12), residues: 2317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 983 TYR 0.021 0.001 TYR C1067 PHE 0.023 0.001 PHE A 86 TRP 0.028 0.001 TRP D 478 HIS 0.006 0.001 HIS H 195 Details of bonding type rmsd covalent geometry : bond 0.00405 (40543) covalent geometry : angle 0.63358 (55114) SS BOND : bond 0.00363 ( 48) SS BOND : angle 1.92380 ( 96) hydrogen bonds : bond 0.04236 ( 1535) hydrogen bonds : angle 4.80420 ( 4386) link_BETA1-4 : bond 0.00612 ( 38) link_BETA1-4 : angle 2.10596 ( 114) link_NAG-ASN : bond 0.00392 ( 66) link_NAG-ASN : angle 2.59697 ( 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 339 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 251 time to evaluate : 1.240 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 55 PHE cc_start: 0.8163 (m-80) cc_final: 0.7960 (m-80) REVERT: A 301 CYS cc_start: 0.8320 (OUTLIER) cc_final: 0.8044 (m) REVERT: A 767 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8123 (mm) REVERT: A 950 ASP cc_start: 0.8602 (m-30) cc_final: 0.8148 (m-30) REVERT: A 1010 GLN cc_start: 0.6851 (OUTLIER) cc_final: 0.6004 (tp40) REVERT: B 47 VAL cc_start: 0.8487 (t) cc_final: 0.8270 (p) REVERT: B 281 GLU cc_start: 0.8591 (pt0) cc_final: 0.8358 (tm-30) REVERT: B 309 GLU cc_start: 0.8063 (tp30) cc_final: 0.7721 (tt0) REVERT: B 949 GLN cc_start: 0.8706 (tp40) cc_final: 0.8011 (mt0) REVERT: B 983 ARG cc_start: 0.8028 (ttp80) cc_final: 0.7572 (ttp80) REVERT: C 307 THR cc_start: 0.8919 (m) cc_final: 0.8684 (p) REVERT: C 895 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8165 (pm20) REVERT: C 917 TYR cc_start: 0.8632 (m-80) cc_final: 0.8358 (m-80) REVERT: D 189 GLU cc_start: 0.3016 (tp30) cc_final: 0.2568 (pt0) REVERT: D 213 ASP cc_start: 0.1506 (t0) cc_final: 0.0981 (m-30) REVERT: D 221 GLN cc_start: 0.0366 (OUTLIER) cc_final: -0.0426 (mm-40) REVERT: D 287 GLN cc_start: 0.5450 (tp40) cc_final: 0.4106 (pp30) REVERT: D 383 MET cc_start: 0.4103 (ptp) cc_final: 0.2399 (ppp) REVERT: D 473 TRP cc_start: 0.0650 (m-10) cc_final: 0.0013 (t60) REVERT: D 480 MET cc_start: -0.1321 (ptt) cc_final: -0.1589 (mtt) REVERT: D 520 LEU cc_start: 0.2923 (tp) cc_final: 0.2709 (tp) REVERT: D 571 GLU cc_start: 0.2524 (OUTLIER) cc_final: 0.2129 (pt0) REVERT: D 581 VAL cc_start: 0.0710 (OUTLIER) cc_final: 0.0402 (m) REVERT: F 152 MET cc_start: 0.0884 (ttp) cc_final: 0.0560 (tpt) REVERT: F 266 LEU cc_start: 0.3317 (pp) cc_final: 0.2892 (mt) REVERT: F 351 LEU cc_start: 0.1277 (OUTLIER) cc_final: 0.0846 (mp) REVERT: F 459 TRP cc_start: 0.0026 (t60) cc_final: -0.0576 (t60) REVERT: F 474 MET cc_start: -0.1623 (mmp) cc_final: -0.3069 (ttm) REVERT: F 587 TYR cc_start: -0.0699 (OUTLIER) cc_final: -0.1345 (m-80) REVERT: H 270 MET cc_start: 0.0323 (tpp) cc_final: -0.1100 (ptp) REVERT: H 285 PHE cc_start: 0.1435 (m-80) cc_final: 0.1039 (m-80) REVERT: H 383 MET cc_start: 0.0487 (mtp) cc_final: -0.0244 (tmm) REVERT: H 587 TYR cc_start: 0.2242 (OUTLIER) cc_final: 0.1993 (m-80) outliers start: 88 outliers final: 64 residues processed: 328 average time/residue: 0.2045 time to fit residues: 117.3809 Evaluate side-chains 316 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 242 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 498 ARG Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1142 GLN Chi-restraints excluded: chain D residue 221 GLN Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 542 CYS Chi-restraints excluded: chain D residue 571 GLU Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain F residue 462 MET Chi-restraints excluded: chain F residue 587 TYR Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 293 VAL Chi-restraints excluded: chain H residue 587 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 50 optimal weight: 6.9990 chunk 157 optimal weight: 0.2980 chunk 322 optimal weight: 0.9980 chunk 427 optimal weight: 0.7980 chunk 399 optimal weight: 30.0000 chunk 372 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 266 optimal weight: 1.9990 chunk 318 optimal weight: 8.9990 chunk 293 optimal weight: 0.4980 chunk 286 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 HIS C 907 ASN C 955 ASN H 101 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4933 r_free = 0.4933 target = 0.258101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.211464 restraints weight = 61387.816| |-----------------------------------------------------------------------------| r_work (start): 0.4474 rms_B_bonded: 3.89 r_work: 0.3500 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.6913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 40695 Z= 0.108 Angle : 0.618 11.741 55522 Z= 0.296 Chirality : 0.044 0.474 6353 Planarity : 0.004 0.052 6984 Dihedral : 5.538 59.876 7322 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.77 % Favored : 94.96 % Rotamer: Outliers : 1.57 % Allowed : 17.33 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.12), residues: 4720 helix: 0.95 (0.13), residues: 1725 sheet: -0.60 (0.19), residues: 694 loop : -1.77 (0.12), residues: 2301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 983 TYR 0.021 0.001 TYR A1067 PHE 0.023 0.001 PHE B 86 TRP 0.032 0.001 TRP D 478 HIS 0.006 0.001 HIS H 195 Details of bonding type rmsd covalent geometry : bond 0.00232 (40543) covalent geometry : angle 0.59353 (55114) SS BOND : bond 0.00489 ( 48) SS BOND : angle 1.66516 ( 96) hydrogen bonds : bond 0.03554 ( 1535) hydrogen bonds : angle 4.63104 ( 4386) link_BETA1-4 : bond 0.00562 ( 38) link_BETA1-4 : angle 2.02566 ( 114) link_NAG-ASN : bond 0.00370 ( 66) link_NAG-ASN : angle 2.32330 ( 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 316 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 250 time to evaluate : 1.454 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 379 CYS cc_start: 0.2645 (OUTLIER) cc_final: 0.2014 (p) REVERT: A 767 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7971 (mm) REVERT: A 1010 GLN cc_start: 0.6765 (OUTLIER) cc_final: 0.5943 (tp40) REVERT: B 281 GLU cc_start: 0.8547 (pt0) cc_final: 0.8198 (tm-30) REVERT: B 309 GLU cc_start: 0.8101 (tp30) cc_final: 0.7714 (tt0) REVERT: B 983 ARG cc_start: 0.7909 (ttp80) cc_final: 0.7574 (ttp80) REVERT: C 65 PHE cc_start: 0.7331 (m-80) cc_final: 0.7093 (m-80) REVERT: C 200 TYR cc_start: 0.7944 (m-80) cc_final: 0.7623 (m-80) REVERT: C 307 THR cc_start: 0.8846 (m) cc_final: 0.8630 (p) REVERT: C 858 LEU cc_start: 0.8271 (mt) cc_final: 0.8063 (mt) REVERT: C 895 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.8037 (pm20) REVERT: D 189 GLU cc_start: 0.3011 (tp30) cc_final: 0.2690 (pt0) REVERT: D 221 GLN cc_start: 0.0134 (OUTLIER) cc_final: -0.0630 (mm-40) REVERT: D 287 GLN cc_start: 0.5365 (tp40) cc_final: 0.4250 (tm-30) REVERT: D 383 MET cc_start: 0.4113 (ptp) cc_final: 0.2341 (ppp) REVERT: D 473 TRP cc_start: 0.0628 (m-10) cc_final: 0.0060 (t60) REVERT: D 480 MET cc_start: -0.1071 (ptt) cc_final: -0.1350 (mtt) REVERT: D 559 ARG cc_start: 0.2381 (ptt90) cc_final: 0.1814 (tpt-90) REVERT: D 571 GLU cc_start: 0.2250 (OUTLIER) cc_final: 0.1954 (pt0) REVERT: D 581 VAL cc_start: 0.0618 (OUTLIER) cc_final: 0.0300 (m) REVERT: F 152 MET cc_start: 0.0573 (ttp) cc_final: 0.0131 (tpp) REVERT: F 266 LEU cc_start: 0.3313 (pp) cc_final: 0.2918 (mt) REVERT: F 351 LEU cc_start: 0.1108 (OUTLIER) cc_final: 0.0677 (mp) REVERT: F 376 MET cc_start: 0.1104 (mmm) cc_final: 0.0652 (mmt) REVERT: F 459 TRP cc_start: 0.0057 (t60) cc_final: -0.0521 (t60) REVERT: F 474 MET cc_start: -0.1592 (mmp) cc_final: -0.3122 (ttm) REVERT: F 587 TYR cc_start: -0.0872 (OUTLIER) cc_final: -0.1475 (m-80) REVERT: H 270 MET cc_start: 0.0288 (tpp) cc_final: -0.1144 (ptp) REVERT: H 285 PHE cc_start: 0.1417 (m-80) cc_final: 0.1047 (m-80) REVERT: H 383 MET cc_start: 0.0290 (mtp) cc_final: -0.0311 (tmm) REVERT: H 587 TYR cc_start: 0.2193 (OUTLIER) cc_final: 0.1946 (m-80) outliers start: 66 outliers final: 51 residues processed: 305 average time/residue: 0.2061 time to fit residues: 109.4612 Evaluate side-chains 297 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 236 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1142 GLN Chi-restraints excluded: chain D residue 221 GLN Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 542 CYS Chi-restraints excluded: chain D residue 571 GLU Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 579 MET Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain F residue 462 MET Chi-restraints excluded: chain F residue 587 TYR Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 293 VAL Chi-restraints excluded: chain H residue 587 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 304 optimal weight: 8.9990 chunk 112 optimal weight: 9.9990 chunk 251 optimal weight: 2.9990 chunk 387 optimal weight: 50.0000 chunk 119 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 421 optimal weight: 0.0970 chunk 15 optimal weight: 0.8980 chunk 302 optimal weight: 6.9990 chunk 188 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 HIS C 563 GLN F 154 ASN H 101 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4934 r_free = 0.4934 target = 0.258173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.212307 restraints weight = 61890.496| |-----------------------------------------------------------------------------| r_work (start): 0.4464 rms_B_bonded: 3.87 r_work: 0.3556 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.7035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 40695 Z= 0.109 Angle : 0.606 10.464 55522 Z= 0.290 Chirality : 0.044 0.468 6353 Planarity : 0.004 0.053 6984 Dihedral : 5.352 59.804 7322 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.94 % Favored : 94.79 % Rotamer: Outliers : 1.59 % Allowed : 17.33 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.12), residues: 4720 helix: 1.06 (0.13), residues: 1731 sheet: -0.46 (0.19), residues: 741 loop : -1.73 (0.12), residues: 2248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 983 TYR 0.023 0.001 TYR F 454 PHE 0.023 0.001 PHE B 86 TRP 0.026 0.001 TRP D 478 HIS 0.006 0.001 HIS H 195 Details of bonding type rmsd covalent geometry : bond 0.00240 (40543) covalent geometry : angle 0.58160 (55114) SS BOND : bond 0.00296 ( 48) SS BOND : angle 1.61934 ( 96) hydrogen bonds : bond 0.03483 ( 1535) hydrogen bonds : angle 4.55242 ( 4386) link_BETA1-4 : bond 0.00572 ( 38) link_BETA1-4 : angle 1.99113 ( 114) link_NAG-ASN : bond 0.00348 ( 66) link_NAG-ASN : angle 2.29062 ( 198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11123.06 seconds wall clock time: 190 minutes 29.87 seconds (11429.87 seconds total)