Starting phenix.real_space_refine on Tue Aug 26 17:12:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i9d_35267/08_2025/8i9d_35267.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i9d_35267/08_2025/8i9d_35267.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8i9d_35267/08_2025/8i9d_35267.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i9d_35267/08_2025/8i9d_35267.map" model { file = "/net/cci-nas-00/data/ceres_data/8i9d_35267/08_2025/8i9d_35267.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i9d_35267/08_2025/8i9d_35267.cif" } resolution = 3.95 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= 0.004 sd= 0.055 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 25183 2.51 5 N 6417 2.21 5 O 7722 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 153 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39517 Number of models: 1 Model: "" Number of chains: 50 Chain: "A" Number of atoms: 7821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 999, 7821 Classifications: {'peptide': 999} Link IDs: {'PTRANS': 55, 'TRANS': 943} Chain breaks: 9 Chain: "B" Number of atoms: 7815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7815 Classifications: {'peptide': 998} Link IDs: {'PTRANS': 55, 'TRANS': 942} Chain breaks: 9 Chain: "C" Number of atoms: 7815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7815 Classifications: {'peptide': 998} Link IDs: {'PTRANS': 55, 'TRANS': 942} Chain breaks: 9 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: "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: "E" 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: "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: "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: "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: "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: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.56, per 1000 atoms: 0.22 Number of scatterers: 39517 At special positions: 0 Unit cell: (193.486, 204.356, 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 7722 8.00 N 6417 7.00 C 25183 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.09 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.06 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.05 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.45 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.05 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.21 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.05 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=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.09 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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 D 133 " - pdb=" SG CYS D 141 " distance=2.05 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.04 Simple disulfide: pdb=" SG CYS E 344 " - pdb=" SG CYS E 361 " 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 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 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 701 " - " ASN E 322 " " NAG F 701 " - " ASN F 322 " " NAG G 1 " - " ASN A 331 " " NAG H 1 " - " ASN A 343 " " 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 F 53 " " NAG e 1 " - " ASN F 90 " " NAG f 1 " - " ASN F 103 " " NAG g 1 " - " ASN F 432 " " NAG h 1 " - " ASN F 546 " " NAG i 1 " - " ASN D 53 " " NAG j 1 " - " ASN D 90 " " NAG k 1 " - " ASN D 103 " " NAG l 1 " - " ASN D 432 " " NAG m 1 " - " ASN D 546 " " NAG n 1 " - " ASN E 53 " " NAG o 1 " - " ASN E 90 " " NAG p 1 " - " ASN E 103 " " NAG q 1 " - " ASN E 432 " " NAG r 1 " - " ASN E 546 " Time building additional restraints: 3.62 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 150 helices and 53 sheets defined 38.6% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 341 Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.636A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 removed outlier: 3.776A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.521A pdb=" N ASP A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) No H-bonds generated for '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: 3.630A 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: 3.773A pdb=" N LYS A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.589A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 removed outlier: 3.634A pdb=" N LYS A 814 " --> pdb=" O LYS A 811 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG A 815 " --> pdb=" O PRO A 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 811 through 815' Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.773A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.572A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 3.993A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.626A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.799A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 981 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.633A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.646A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 341 Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.636A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 390 removed outlier: 3.776A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.521A pdb=" N ASP B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) No H-bonds generated for '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: 3.694A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.631A 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: 3.964A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.545A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.603A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.020A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 983 removed outlier: 4.268A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.245A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.584A 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 337 through 341 Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.637A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 390 removed outlier: 3.777A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.521A pdb=" N ASP C 442 " --> pdb=" O SER C 438 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 438 through 443' Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.717A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.561A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.700A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 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 939 removed outlier: 3.589A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.360A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR C 961 " --> pdb=" O GLN C 957 " (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: 3.738A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 976 through 981' Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.221A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 Processing helix chain 'F' and resid 22 through 52 removed outlier: 3.737A pdb=" N LYS F 26 " --> pdb=" O GLU F 22 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR F 27 " --> pdb=" O GLU F 23 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS F 31 " --> pdb=" O THR F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 80 removed outlier: 3.825A pdb=" N GLN F 60 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA F 65 " --> pdb=" O ASN F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 83 No H-bonds generated for 'chain 'F' and resid 81 through 83' Processing helix chain 'F' and resid 90 through 102 removed outlier: 3.779A pdb=" N GLN F 102 " --> pdb=" O GLN F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 129 Processing helix chain 'F' and resid 147 through 155 removed outlier: 3.618A pdb=" N ALA F 153 " --> pdb=" O ASN F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 171 removed outlier: 3.724A pdb=" N ARG F 169 " --> pdb=" O TRP F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 175 removed outlier: 3.507A pdb=" N GLN F 175 " --> pdb=" O VAL F 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 172 through 175' Processing helix chain 'F' and resid 176 through 193 removed outlier: 4.340A pdb=" N GLU F 182 " --> pdb=" O PRO F 178 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N VAL F 185 " --> pdb=" O GLU F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 205 removed outlier: 3.687A pdb=" N TYR F 202 " --> pdb=" O ASP F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 230 removed outlier: 4.143A pdb=" N GLU F 224 " --> pdb=" O GLY F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 249 removed outlier: 4.359A pdb=" N HIS F 239 " --> pdb=" O PRO F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 279 removed outlier: 3.513A pdb=" N TYR F 279 " --> pdb=" O THR F 276 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 300 Processing helix chain 'F' and resid 305 through 319 removed outlier: 3.801A pdb=" N VAL F 318 " --> pdb=" O PHE F 314 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY F 319 " --> pdb=" O PHE F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 331 removed outlier: 3.984A pdb=" N ASN F 330 " --> pdb=" O GLY F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 366 through 385 removed outlier: 3.969A pdb=" N HIS F 373 " --> pdb=" O PHE F 369 " (cutoff:3.500A) removed outlier: 3.548A 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 412 removed outlier: 3.708A pdb=" N ALA F 403 " --> pdb=" O GLY F 399 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N SER F 409 " --> pdb=" O GLY F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 422 removed outlier: 3.753A pdb=" N SER F 420 " --> pdb=" O LYS F 416 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY F 422 " --> pdb=" O LEU F 418 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 447 removed outlier: 3.554A pdb=" N GLU F 435 " --> pdb=" O ASP F 431 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N THR F 445 " --> pdb=" O LYS F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 465 Processing helix chain 'F' and resid 472 through 484 Processing helix chain 'F' and resid 499 through 502 Processing helix chain 'F' and resid 503 through 508 Processing helix chain 'F' and resid 513 through 533 removed outlier: 4.112A pdb=" N THR F 519 " --> pdb=" O TYR F 515 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU F 520 " --> pdb=" O TYR F 516 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N PHE F 523 " --> pdb=" O THR F 519 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA F 532 " --> pdb=" O ALA F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 542 Processing helix chain 'F' and resid 547 through 559 removed outlier: 3.896A pdb=" N GLY F 551 " --> pdb=" O SER F 547 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N MET F 557 " --> pdb=" O LYS F 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 570 Processing helix chain 'F' and resid 581 through 597 removed outlier: 3.545A pdb=" N LEU F 585 " --> pdb=" O VAL F 581 " (cutoff:3.500A) Proline residue: F 590 - end of helix Processing helix chain 'D' and resid 22 through 52 removed outlier: 3.736A pdb=" N LYS D 26 " --> pdb=" O GLU D 22 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR D 27 " --> pdb=" O GLU D 23 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS D 31 " --> pdb=" O THR D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 80 removed outlier: 3.826A pdb=" N GLN D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA D 65 " --> pdb=" O ASN D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 83 No H-bonds generated for 'chain 'D' and resid 81 through 83' Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.778A pdb=" N GLN D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 147 through 155 removed outlier: 3.617A pdb=" N ALA D 153 " --> pdb=" O ASN D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 171 removed outlier: 3.723A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 175 removed outlier: 3.507A pdb=" N GLN D 175 " --> pdb=" O VAL D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 172 through 175' Processing helix chain 'D' and resid 176 through 193 removed outlier: 4.341A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.686A pdb=" N TYR D 202 " --> pdb=" O ASP D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 230 removed outlier: 4.143A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 249 removed outlier: 4.360A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 279 removed outlier: 3.512A pdb=" N TYR D 279 " --> pdb=" O THR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 300 Processing helix chain 'D' and resid 305 through 319 removed outlier: 3.802A pdb=" N VAL D 318 " --> pdb=" O PHE D 314 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY D 319 " --> pdb=" O PHE D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 331 removed outlier: 3.985A pdb=" N ASN D 330 " --> pdb=" O GLY D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 385 removed outlier: 3.969A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 3.549A 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 412 removed outlier: 3.708A pdb=" N ALA D 403 " --> pdb=" O GLY D 399 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 422 removed outlier: 3.752A pdb=" N SER D 420 " --> pdb=" O LYS D 416 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY D 422 " --> pdb=" O LEU D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.553A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 465 Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 499 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 533 removed outlier: 4.113A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA D 532 " --> pdb=" O ALA D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.896A pdb=" N GLY D 551 " --> pdb=" O SER D 547 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 570 Processing helix chain 'D' and resid 581 through 597 removed outlier: 3.544A pdb=" N LEU D 585 " --> pdb=" O VAL D 581 " (cutoff:3.500A) Proline residue: D 590 - end of helix Processing helix chain 'E' and resid 22 through 52 removed outlier: 3.736A pdb=" N LYS E 26 " --> pdb=" O GLU E 22 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR E 27 " --> pdb=" O GLU E 23 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS E 31 " --> pdb=" O THR E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 80 removed outlier: 3.826A pdb=" N GLN E 60 " --> pdb=" O GLU E 56 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA E 65 " --> pdb=" O ASN E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 83 No H-bonds generated for 'chain 'E' and resid 81 through 83' Processing helix chain 'E' and resid 90 through 102 removed outlier: 3.779A pdb=" N GLN E 102 " --> pdb=" O GLN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 129 Processing helix chain 'E' and resid 147 through 155 removed outlier: 3.618A pdb=" N ALA E 153 " --> pdb=" O ASN E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 171 removed outlier: 3.723A pdb=" N ARG E 169 " --> pdb=" O TRP E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 175 removed outlier: 3.507A pdb=" N GLN E 175 " --> pdb=" O VAL E 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 172 through 175' Processing helix chain 'E' and resid 176 through 193 removed outlier: 4.340A pdb=" N GLU E 182 " --> pdb=" O PRO E 178 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N VAL E 185 " --> pdb=" O GLU E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 205 removed outlier: 3.686A pdb=" N TYR E 202 " --> pdb=" O ASP E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 230 removed outlier: 4.143A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 249 removed outlier: 4.359A pdb=" N HIS E 239 " --> pdb=" O PRO E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 279 removed outlier: 3.514A pdb=" N TYR E 279 " --> pdb=" O THR E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 300 Processing helix chain 'E' and resid 305 through 319 removed outlier: 3.802A pdb=" N VAL E 318 " --> pdb=" O PHE E 314 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY E 319 " --> pdb=" O PHE E 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 331 removed outlier: 3.986A pdb=" N ASN E 330 " --> pdb=" O GLY E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 385 removed outlier: 3.969A pdb=" N HIS E 373 " --> pdb=" O PHE E 369 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 393 Processing helix chain 'E' and resid 399 through 412 removed outlier: 3.707A pdb=" N ALA E 403 " --> pdb=" O GLY E 399 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER E 409 " --> pdb=" O GLY E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 422 removed outlier: 3.752A pdb=" N SER E 420 " --> pdb=" O LYS E 416 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY E 422 " --> pdb=" O LEU E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 447 removed outlier: 3.553A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N THR E 445 " --> pdb=" O LYS E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 465 Processing helix chain 'E' and resid 472 through 484 Processing helix chain 'E' and resid 499 through 502 Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 513 through 533 removed outlier: 4.112A pdb=" N THR E 519 " --> pdb=" O TYR E 515 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU E 520 " --> pdb=" O TYR E 516 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA E 532 " --> pdb=" O ALA E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 Processing helix chain 'E' and resid 547 through 559 removed outlier: 3.896A pdb=" N GLY E 551 " --> pdb=" O SER E 547 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 570 Processing helix chain 'E' and resid 581 through 597 removed outlier: 3.544A pdb=" N LEU E 585 " --> pdb=" O VAL E 581 " (cutoff:3.500A) Proline residue: E 590 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.061A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 55 removed outlier: 3.856A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 116 through 121 removed outlier: 3.730A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN A 134 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 188 through 189 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 317 removed outlier: 6.060A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 326 through 328 removed outlier: 7.030A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 357 removed outlier: 3.570A pdb=" N ILE A 434 " --> pdb=" O VAL A 511 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.704A pdb=" N GLN A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 551 through 554 removed outlier: 5.338A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.581A pdb=" N GLU A 654 " --> pdb=" O ILE A 692 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.590A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.590A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.505A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.713A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.060A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 49 through 55 removed outlier: 3.858A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC3, first strand: chain 'B' and resid 116 through 121 removed outlier: 3.729A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN B 134 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 188 through 189 Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.870A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 323 through 326 removed outlier: 5.339A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 357 removed outlier: 3.570A pdb=" N ILE B 434 " --> pdb=" O VAL B 511 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 removed outlier: 3.704A pdb=" N GLN B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.563A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.893A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.542A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.542A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.579A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD7, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.061A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 49 through 55 removed outlier: 3.857A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE1, first strand: chain 'C' and resid 116 through 121 removed outlier: 3.730A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ILE C 128 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE C 168 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N VAL C 130 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N CYS C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN C 134 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.621A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.338A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 357 removed outlier: 3.571A pdb=" N ILE C 434 " --> pdb=" O VAL C 511 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 454 removed outlier: 3.704A pdb=" N GLN C 493 " --> pdb=" O TYR C 453 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE7, first strand: chain 'C' and resid 653 through 655 removed outlier: 6.417A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.592A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.592A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.569A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF3, first strand: chain 'F' and resid 262 through 263 removed outlier: 6.231A pdb=" N LEU F 262 " --> pdb=" O VAL F 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'F' and resid 347 through 352 removed outlier: 3.647A pdb=" N ARG F 357 " --> pdb=" O TRP F 349 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ASP F 355 " --> pdb=" O LEU F 351 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.229A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'D' and resid 347 through 352 removed outlier: 3.646A pdb=" N ARG D 357 " --> pdb=" O TRP D 349 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 262 through 263 removed outlier: 6.230A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'E' and resid 347 through 352 removed outlier: 3.648A pdb=" N ARG E 357 " --> pdb=" O TRP E 349 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 1565 hydrogen bonds defined for protein. 4356 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: 8.86 Time building geometry restraints manager: 4.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 8227 1.33 - 1.45: 10531 1.45 - 1.58: 21434 1.58 - 1.70: 0 1.70 - 1.83: 285 Bond restraints: 40477 Sorted by residual: bond pdb=" CA SER A 698 " pdb=" C SER A 698 " ideal model delta sigma weight residual 1.522 1.443 0.079 1.20e-02 6.94e+03 4.32e+01 bond pdb=" C HIS B1088 " pdb=" N PHE B1089 " ideal model delta sigma weight residual 1.331 1.264 0.067 1.59e-02 3.96e+03 1.79e+01 bond pdb=" N PRO C 209 " pdb=" CD PRO C 209 " ideal model delta sigma weight residual 1.473 1.529 -0.056 1.40e-02 5.10e+03 1.62e+01 bond pdb=" N PRO B 209 " pdb=" CD PRO B 209 " ideal model delta sigma weight residual 1.473 1.529 -0.056 1.40e-02 5.10e+03 1.62e+01 bond pdb=" N PRO A 209 " pdb=" CD PRO A 209 " ideal model delta sigma weight residual 1.473 1.528 -0.055 1.40e-02 5.10e+03 1.56e+01 ... (remaining 40472 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 53360 2.26 - 4.53: 1504 4.53 - 6.79: 135 6.79 - 9.05: 27 9.05 - 11.32: 4 Bond angle restraints: 55030 Sorted by residual: angle pdb=" C PHE A 86 " pdb=" N ASN A 87 " pdb=" CA ASN A 87 " ideal model delta sigma weight residual 121.54 132.86 -11.32 1.91e+00 2.74e-01 3.51e+01 angle pdb=" C PHE C 86 " pdb=" N ASN C 87 " pdb=" CA ASN C 87 " ideal model delta sigma weight residual 121.54 132.86 -11.32 1.91e+00 2.74e-01 3.51e+01 angle pdb=" C PHE B 86 " pdb=" N ASN B 87 " pdb=" CA ASN B 87 " ideal model delta sigma weight residual 121.54 132.81 -11.27 1.91e+00 2.74e-01 3.48e+01 angle pdb=" C ASP C 985 " pdb=" N PRO C 986 " pdb=" CA PRO C 986 " ideal model delta sigma weight residual 120.38 114.52 5.86 1.03e+00 9.43e-01 3.23e+01 angle pdb=" C CYS B 590 " pdb=" N SER B 591 " pdb=" CA SER B 591 " ideal model delta sigma weight residual 122.65 114.78 7.87 1.49e+00 4.50e-01 2.79e+01 ... (remaining 55025 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.67: 23265 25.67 - 51.35: 1768 51.35 - 77.02: 321 77.02 - 102.69: 36 102.69 - 128.36: 3 Dihedral angle restraints: 25393 sinusoidal: 11404 harmonic: 13989 Sorted by residual: dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.04 71.96 1 1.00e+01 1.00e-02 6.63e+01 dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.07 71.93 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.08 71.92 1 1.00e+01 1.00e-02 6.62e+01 ... (remaining 25390 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.256: 6323 0.256 - 0.512: 20 0.512 - 0.768: 2 0.768 - 1.024: 1 1.024 - 1.280: 1 Chirality restraints: 6347 Sorted by residual: chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-02 2.50e+03 1.92e+02 chirality pdb=" C1 NAG c 2 " pdb=" O4 NAG c 1 " pdb=" C2 NAG c 2 " pdb=" O5 NAG c 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 8.07e+01 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN A 801 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.12 -1.28 2.00e-01 2.50e+01 4.09e+01 ... (remaining 6344 not shown) Planarity restraints: 7038 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 801 " 0.051 2.00e-02 2.50e+03 6.72e-02 5.64e+01 pdb=" CG ASN A 801 " -0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN A 801 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN A 801 " -0.116 2.00e-02 2.50e+03 pdb=" C1 NAG J 1 " 0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 709 " -0.047 2.00e-02 2.50e+03 5.82e-02 4.24e+01 pdb=" CG ASN A 709 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN A 709 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN A 709 " 0.099 2.00e-02 2.50e+03 pdb=" C1 NAG A1409 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " -0.050 2.00e-02 2.50e+03 5.27e-02 3.47e+01 pdb=" CG ASN A 331 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " 0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " 0.077 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " -0.068 2.00e-02 2.50e+03 ... (remaining 7035 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 243 2.48 - 3.08: 27044 3.08 - 3.69: 55202 3.69 - 4.29: 82500 4.29 - 4.90: 137806 Nonbonded interactions: 302795 Sorted by model distance: nonbonded pdb=" O GLY B 799 " pdb=" O PHE B 800 " model vdw 1.871 3.040 nonbonded pdb=" N GLU B 748 " pdb=" OE1 GLU B 748 " model vdw 2.141 3.120 nonbonded pdb=" O GLN B 675 " pdb=" OG1 THR B 676 " model vdw 2.148 3.040 nonbonded pdb=" O GLY A 700 " pdb=" O ALA A 701 " model vdw 2.167 3.040 nonbonded pdb=" O SER A 813 " pdb=" OG SER A 813 " model vdw 2.184 3.040 ... (remaining 302790 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 'E' selection = chain 'F' } ncs_group { reference = 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' 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 group one per residue 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: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.690 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 35.200 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.190 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4933 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 : 0.009 0.421 40623 Z= 0.393 Angle : 1.037 48.913 55426 Z= 0.545 Chirality : 0.062 1.280 6347 Planarity : 0.006 0.086 6972 Dihedral : 17.444 128.363 16253 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 1.59 % Allowed : 7.63 % Favored : 90.78 % Rotamer: Outliers : 9.03 % Allowed : 17.51 % Favored : 73.47 % 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 aren not related in a simple way. whole: -3.78 (0.10), residues: 4720 helix: -1.54 (0.11), residues: 1652 sheet: -2.24 (0.16), residues: 745 loop : -3.40 (0.10), residues: 2323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1039 TYR 0.027 0.002 TYR B1067 PHE 0.025 0.002 PHE A 898 TRP 0.025 0.002 TRP B 104 HIS 0.009 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00831 (40477) covalent geometry : angle 0.87341 (55030) SS BOND : bond 0.07220 ( 42) SS BOND : angle 8.94658 ( 84) hydrogen bonds : bond 0.19467 ( 1529) hydrogen bonds : angle 7.13203 ( 4356) link_BETA1-4 : bond 0.00680 ( 38) link_BETA1-4 : angle 3.93007 ( 114) link_NAG-ASN : bond 0.00872 ( 66) link_NAG-ASN : angle 6.81117 ( 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 881 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 380 poor density : 501 time to evaluate : 1.520 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: 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 48 LEU cc_start: 0.6696 (OUTLIER) cc_final: 0.6488 (mp) REVERT: A 205 SER cc_start: 0.6948 (OUTLIER) cc_final: 0.5799 (t) REVERT: B 207 HIS cc_start: 0.6497 (OUTLIER) cc_final: 0.6091 (m90) REVERT: B 480 CYS cc_start: -0.0441 (OUTLIER) cc_final: -0.3431 (t) REVERT: B 531 THR cc_start: 0.2568 (OUTLIER) cc_final: 0.1966 (t) REVERT: B 541 PHE cc_start: 0.6148 (OUTLIER) cc_final: 0.5626 (p90) REVERT: C 373 PRO cc_start: 0.7819 (Cg_exo) cc_final: 0.7617 (Cg_endo) REVERT: C 480 CYS cc_start: 0.2827 (OUTLIER) cc_final: 0.2083 (m) REVERT: C 530 SER cc_start: 0.5277 (OUTLIER) cc_final: 0.4765 (m) REVERT: D 20 THR cc_start: 0.0792 (OUTLIER) cc_final: 0.0187 (m) REVERT: D 297 MET cc_start: 0.0586 (mtp) cc_final: 0.0085 (ptm) REVERT: D 360 MET cc_start: 0.0791 (ptm) cc_final: -0.0324 (tpt) REVERT: D 376 MET cc_start: 0.2186 (mtp) cc_final: 0.1598 (mtm) REVERT: E 323 MET cc_start: 0.0076 (mmp) cc_final: -0.1174 (mmt) REVERT: E 360 MET cc_start: 0.5676 (ptm) cc_final: 0.5339 (ptp) outliers start: 380 outliers final: 72 residues processed: 840 average time/residue: 0.2072 time to fit residues: 292.7553 Evaluate side-chains 334 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 253 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 217 PRO Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 217 PRO Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 217 PRO Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 133 CYS Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 343 VAL Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 133 CYS Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain E residue 133 CYS Chi-restraints excluded: chain E residue 141 CYS Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 343 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 432 optimal weight: 4.9990 chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 0.9990 chunk 455 optimal weight: 8.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 40.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 7.9990 chunk 470 optimal weight: 50.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 134 GLN A 137 ASN A 188 ASN A 239 GLN A 317 ASN A 334 ASN A 339 HIS A 542 ASN A 613 GLN A 644 GLN A 658 ASN A 784 GLN A 872 GLN A 901 GLN A 914 ASN A 919 ASN A 954 HIS ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 GLN A1071 GLN A1101 HIS ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN B 137 ASN B 188 ASN B 239 GLN B 334 ASN B 339 HIS B 542 ASN B 613 GLN B 644 GLN B 658 ASN B 901 GLN B 914 ASN B 919 ASN B 954 HIS B 992 GLN B1054 GLN B1106 GLN C 134 GLN C 137 ASN C 188 ASN C 239 GLN C 317 ASN C 450 ASN C 542 ASN C 644 GLN C 658 ASN C 703 ASN C 751 ASN C 901 GLN C 914 ASN C 992 GLN C1071 GLN C1101 HIS C1135 ASN F 96 GLN F 102 GLN F 239 HIS F 305 GLN F 340 GLN F 378 HIS F 472 GLN F 505 HIS F 531 GLN ** F 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 599 ASN D 61 ASN D 96 GLN D 102 GLN D 239 HIS D 305 GLN D 340 GLN D 378 HIS D 472 GLN D 505 HIS D 599 ASN E 42 GLN E 102 GLN E 305 GLN E 340 GLN ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 472 GLN E 505 HIS Total number of N/Q/H flips: 81 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.125638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.077360 restraints weight = 176532.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.075364 restraints weight = 118043.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.075347 restraints weight = 99578.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.075097 restraints weight = 73823.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.075071 restraints weight = 70943.725| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.114 40623 Z= 0.225 Angle : 0.842 13.922 55426 Z= 0.409 Chirality : 0.050 0.732 6347 Planarity : 0.006 0.077 6972 Dihedral : 9.470 107.669 7443 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.02 % Favored : 93.75 % Rotamer: Outliers : 5.18 % Allowed : 21.21 % Favored : 73.61 % 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 aren not related in a simple way. whole: -2.26 (0.11), residues: 4720 helix: -0.02 (0.13), residues: 1662 sheet: -1.56 (0.17), residues: 754 loop : -2.66 (0.11), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B1019 TYR 0.027 0.002 TYR D 50 PHE 0.026 0.002 PHE C1042 TRP 0.031 0.001 TRP B 104 HIS 0.011 0.002 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00498 (40477) covalent geometry : angle 0.81199 (55030) SS BOND : bond 0.00489 ( 42) SS BOND : angle 2.69662 ( 84) hydrogen bonds : bond 0.04977 ( 1529) hydrogen bonds : angle 5.41547 ( 4356) link_BETA1-4 : bond 0.00697 ( 38) link_BETA1-4 : angle 2.35078 ( 114) link_NAG-ASN : bond 0.00689 ( 66) link_NAG-ASN : angle 2.96475 ( 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 453 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 218 poor density : 235 time to evaluate : 1.056 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: A 63 THR cc_start: 0.4363 (OUTLIER) cc_final: 0.3953 (p) REVERT: A 90 VAL cc_start: 0.8553 (OUTLIER) cc_final: 0.8335 (t) REVERT: A 122 ASN cc_start: 0.6397 (OUTLIER) cc_final: 0.5983 (p0) REVERT: A 276 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8827 (tp) REVERT: A 740 MET cc_start: 0.8735 (mmp) cc_final: 0.8405 (tpt) REVERT: A 869 MET cc_start: 0.9078 (mtt) cc_final: 0.8868 (mtt) REVERT: A 902 MET cc_start: 0.9038 (tpt) cc_final: 0.8678 (tpp) REVERT: A 950 ASP cc_start: 0.8789 (m-30) cc_final: 0.8588 (m-30) REVERT: B 988 GLU cc_start: 0.9182 (tp30) cc_final: 0.8861 (pt0) REVERT: C 62 VAL cc_start: 0.8116 (m) cc_final: 0.7887 (p) REVERT: C 97 LYS cc_start: 0.6844 (OUTLIER) cc_final: 0.6139 (tppt) REVERT: C 122 ASN cc_start: 0.5620 (OUTLIER) cc_final: 0.5307 (p0) REVERT: C 226 LEU cc_start: 0.9258 (tp) cc_final: 0.8677 (mp) REVERT: C 697 MET cc_start: 0.8266 (ptm) cc_final: 0.7794 (ttp) REVERT: C 740 MET cc_start: 0.9382 (tmm) cc_final: 0.8935 (tmm) REVERT: C 780 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8060 (mt-10) REVERT: C 820 ASP cc_start: 0.8657 (OUTLIER) cc_final: 0.8293 (m-30) REVERT: C 953 ASN cc_start: 0.9211 (m-40) cc_final: 0.8692 (m110) REVERT: F 62 MET cc_start: 0.8748 (tmm) cc_final: 0.8382 (ttp) REVERT: F 581 VAL cc_start: 0.5393 (OUTLIER) cc_final: 0.5117 (p) REVERT: F 584 LEU cc_start: 0.3021 (OUTLIER) cc_final: 0.2604 (mp) REVERT: D 270 MET cc_start: 0.2676 (ttm) cc_final: 0.1884 (ttp) REVERT: D 297 MET cc_start: 0.6062 (mtp) cc_final: 0.5150 (ptm) REVERT: D 360 MET cc_start: 0.3720 (ptm) cc_final: 0.1720 (tpt) REVERT: D 366 MET cc_start: -0.0738 (tpt) cc_final: -0.0958 (tpt) REVERT: E 358 ILE cc_start: 0.1098 (OUTLIER) cc_final: 0.0836 (tp) outliers start: 218 outliers final: 95 residues processed: 436 average time/residue: 0.1876 time to fit residues: 139.6727 Evaluate side-chains 290 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 184 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 797 PHE Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 343 VAL Chi-restraints excluded: chain F residue 408 MET Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 581 VAL Chi-restraints excluded: chain F residue 584 LEU Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 133 CYS Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 510 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 450 optimal weight: 50.0000 chunk 247 optimal weight: 7.9990 chunk 373 optimal weight: 40.0000 chunk 14 optimal weight: 9.9990 chunk 469 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 409 optimal weight: 20.0000 chunk 367 optimal weight: 50.0000 chunk 36 optimal weight: 50.0000 chunk 237 optimal weight: 20.0000 chunk 218 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 703 ASN ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN A 824 ASN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN A1135 ASN B 115 GLN B 317 ASN B 751 ASN ** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 HIS B1108 ASN C 81 ASN C 690 GLN ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 ASN ** F 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.122755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.068007 restraints weight = 179013.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.068380 restraints weight = 102606.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.068090 restraints weight = 70598.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.068742 restraints weight = 62330.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.068717 restraints weight = 51070.481| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.138 40623 Z= 0.240 Angle : 0.792 14.088 55426 Z= 0.383 Chirality : 0.048 0.665 6347 Planarity : 0.005 0.063 6972 Dihedral : 8.247 103.325 7353 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.40 % Favored : 93.47 % Rotamer: Outliers : 5.13 % Allowed : 21.64 % Favored : 73.23 % 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 aren not related in a simple way. whole: -1.74 (0.12), residues: 4720 helix: 0.42 (0.13), residues: 1681 sheet: -1.21 (0.18), residues: 738 loop : -2.41 (0.11), residues: 2301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 905 TYR 0.031 0.002 TYR A1067 PHE 0.037 0.002 PHE C1052 TRP 0.030 0.001 TRP B 104 HIS 0.010 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00533 (40477) covalent geometry : angle 0.76240 (55030) SS BOND : bond 0.00495 ( 42) SS BOND : angle 1.86981 ( 84) hydrogen bonds : bond 0.04618 ( 1529) hydrogen bonds : angle 5.28362 ( 4356) link_BETA1-4 : bond 0.00513 ( 38) link_BETA1-4 : angle 2.42910 ( 114) link_NAG-ASN : bond 0.00830 ( 66) link_NAG-ASN : angle 3.01586 ( 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 411 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 216 poor density : 195 time to evaluate : 1.089 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: A 122 ASN cc_start: 0.7038 (OUTLIER) cc_final: 0.6653 (p0) REVERT: A 133 PHE cc_start: 0.7282 (m-80) cc_final: 0.6872 (m-80) REVERT: A 153 MET cc_start: 0.5790 (tpt) cc_final: 0.5191 (tpp) REVERT: A 207 HIS cc_start: 0.8422 (OUTLIER) cc_final: 0.8163 (m-70) REVERT: A 297 SER cc_start: 0.8920 (m) cc_final: 0.8658 (p) REVERT: A 869 MET cc_start: 0.9230 (mtt) cc_final: 0.8888 (mtt) REVERT: A 901 GLN cc_start: 0.9191 (OUTLIER) cc_final: 0.8702 (tm-30) REVERT: A 902 MET cc_start: 0.9274 (tpt) cc_final: 0.8756 (tpp) REVERT: B 114 THR cc_start: 0.3623 (OUTLIER) cc_final: 0.3007 (t) REVERT: B 518 LEU cc_start: 0.6790 (OUTLIER) cc_final: 0.6488 (pt) REVERT: B 869 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.8401 (mmp) REVERT: B 901 GLN cc_start: 0.8894 (OUTLIER) cc_final: 0.8588 (tm-30) REVERT: B 902 MET cc_start: 0.9193 (tpp) cc_final: 0.8891 (tpp) REVERT: C 62 VAL cc_start: 0.8221 (m) cc_final: 0.8002 (p) REVERT: C 122 ASN cc_start: 0.5324 (OUTLIER) cc_final: 0.4887 (p0) REVERT: C 226 LEU cc_start: 0.9255 (tp) cc_final: 0.8733 (mp) REVERT: C 319 ARG cc_start: 0.6282 (OUTLIER) cc_final: 0.5989 (ptm160) REVERT: C 731 MET cc_start: 0.8435 (ppp) cc_final: 0.7701 (ppp) REVERT: C 740 MET cc_start: 0.9506 (tmm) cc_final: 0.9077 (tmm) REVERT: C 821 LEU cc_start: 0.9594 (OUTLIER) cc_final: 0.9044 (tp) REVERT: C 900 MET cc_start: 0.8780 (mtp) cc_final: 0.8562 (ttm) REVERT: F 62 MET cc_start: 0.8758 (tmm) cc_final: 0.8376 (ttp) REVERT: F 480 MET cc_start: 0.7388 (mmp) cc_final: 0.7021 (ptp) REVERT: D 297 MET cc_start: 0.6194 (mtp) cc_final: 0.5417 (ptm) REVERT: D 360 MET cc_start: 0.3470 (ptm) cc_final: 0.1216 (tpp) outliers start: 216 outliers final: 119 residues processed: 390 average time/residue: 0.1802 time to fit residues: 121.4562 Evaluate side-chains 302 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 173 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 690 GLN Chi-restraints excluded: chain C residue 733 LYS Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1142 GLN Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 343 VAL Chi-restraints excluded: chain F residue 408 MET Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 481 LYS Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain E residue 133 CYS Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 409 SER Chi-restraints excluded: chain E residue 510 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 198 optimal weight: 20.0000 chunk 364 optimal weight: 5.9990 chunk 159 optimal weight: 3.9990 chunk 46 optimal weight: 10.0000 chunk 174 optimal weight: 2.9990 chunk 456 optimal weight: 30.0000 chunk 213 optimal weight: 6.9990 chunk 201 optimal weight: 0.3980 chunk 161 optimal weight: 0.9990 chunk 2 optimal weight: 8.9990 chunk 335 optimal weight: 50.0000 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 755 GLN ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1002 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN C 804 GLN C1011 GLN ** F 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 522 GLN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 340 GLN ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.129036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.085674 restraints weight = 251337.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.086297 restraints weight = 127392.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.085017 restraints weight = 78394.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.085552 restraints weight = 71412.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.085596 restraints weight = 53337.879| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.4543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 40623 Z= 0.141 Angle : 0.683 13.244 55426 Z= 0.324 Chirality : 0.046 0.569 6347 Planarity : 0.004 0.053 6972 Dihedral : 7.614 102.726 7344 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.70 % Favored : 94.22 % Rotamer: Outliers : 3.87 % Allowed : 22.00 % Favored : 74.13 % 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 aren not related in a simple way. whole: -1.29 (0.12), residues: 4720 helix: 0.75 (0.13), residues: 1683 sheet: -0.82 (0.18), residues: 748 loop : -2.18 (0.11), residues: 2289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 983 TYR 0.022 0.001 TYR A1067 PHE 0.018 0.001 PHE A 55 TRP 0.014 0.001 TRP B 104 HIS 0.008 0.001 HIS D 239 Details of bonding type rmsd covalent geometry : bond 0.00309 (40477) covalent geometry : angle 0.65750 (55030) SS BOND : bond 0.00388 ( 42) SS BOND : angle 1.54773 ( 84) hydrogen bonds : bond 0.03849 ( 1529) hydrogen bonds : angle 4.85845 ( 4356) link_BETA1-4 : bond 0.00485 ( 38) link_BETA1-4 : angle 2.20036 ( 114) link_NAG-ASN : bond 0.00438 ( 66) link_NAG-ASN : angle 2.56455 ( 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 343 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 180 time to evaluate : 1.495 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: A 122 ASN cc_start: 0.7149 (OUTLIER) cc_final: 0.6902 (p0) REVERT: A 133 PHE cc_start: 0.6488 (m-80) cc_final: 0.6118 (m-80) REVERT: A 207 HIS cc_start: 0.8382 (OUTLIER) cc_final: 0.8156 (m-70) REVERT: A 297 SER cc_start: 0.8857 (m) cc_final: 0.8621 (p) REVERT: A 861 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8888 (mp) REVERT: A 869 MET cc_start: 0.9180 (mtt) cc_final: 0.8931 (mtt) REVERT: A 1029 MET cc_start: 0.9267 (tpp) cc_final: 0.9056 (ttm) REVERT: B 114 THR cc_start: 0.3236 (OUTLIER) cc_final: 0.2690 (t) REVERT: B 452 LEU cc_start: 0.7145 (OUTLIER) cc_final: 0.6901 (tt) REVERT: B 819 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7969 (mm-30) REVERT: B 901 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8610 (tm-30) REVERT: B 902 MET cc_start: 0.9173 (tpp) cc_final: 0.8899 (tpp) REVERT: B 1029 MET cc_start: 0.9458 (tpp) cc_final: 0.8955 (tpp) REVERT: C 62 VAL cc_start: 0.8261 (m) cc_final: 0.8005 (p) REVERT: C 122 ASN cc_start: 0.6555 (OUTLIER) cc_final: 0.6239 (p0) REVERT: C 226 LEU cc_start: 0.9236 (tp) cc_final: 0.8674 (mp) REVERT: C 319 ARG cc_start: 0.6464 (OUTLIER) cc_final: 0.6175 (ptm160) REVERT: C 328 ARG cc_start: 0.9189 (OUTLIER) cc_final: 0.8635 (tpp80) REVERT: C 697 MET cc_start: 0.8565 (ttp) cc_final: 0.8217 (ttp) REVERT: C 731 MET cc_start: 0.8449 (ppp) cc_final: 0.7724 (ppp) REVERT: C 740 MET cc_start: 0.9397 (tmm) cc_final: 0.9087 (tmm) REVERT: C 820 ASP cc_start: 0.8858 (OUTLIER) cc_final: 0.8422 (m-30) REVERT: C 821 LEU cc_start: 0.9585 (OUTLIER) cc_final: 0.8895 (tp) REVERT: F 474 MET cc_start: 0.6614 (tpp) cc_final: 0.6111 (tpp) REVERT: D 152 MET cc_start: 0.0499 (ptp) cc_final: 0.0074 (ptp) REVERT: D 293 VAL cc_start: 0.1853 (OUTLIER) cc_final: 0.1097 (m) REVERT: D 297 MET cc_start: 0.6112 (mtp) cc_final: 0.5305 (ptm) REVERT: D 360 MET cc_start: 0.3081 (ptm) cc_final: 0.0642 (tpp) outliers start: 163 outliers final: 96 residues processed: 326 average time/residue: 0.1834 time to fit residues: 104.7032 Evaluate side-chains 275 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 166 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 797 PHE Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 343 VAL Chi-restraints excluded: chain F residue 408 MET Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 481 LYS Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 360 MET Chi-restraints excluded: chain E residue 487 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 405 optimal weight: 50.0000 chunk 5 optimal weight: 20.0000 chunk 52 optimal weight: 2.9990 chunk 396 optimal weight: 9.9990 chunk 295 optimal weight: 0.0470 chunk 133 optimal weight: 20.0000 chunk 176 optimal weight: 0.0570 chunk 180 optimal weight: 0.9980 chunk 173 optimal weight: 8.9990 chunk 388 optimal weight: 30.0000 chunk 446 optimal weight: 40.0000 overall best weight: 2.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 422 ASN C 422 ASN ** F 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 522 GLN ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.128881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.085614 restraints weight = 251612.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.085029 restraints weight = 124226.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.085028 restraints weight = 78494.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.084944 restraints weight = 60814.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.085356 restraints weight = 48937.326| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.4824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 40623 Z= 0.133 Angle : 0.665 13.340 55426 Z= 0.313 Chirality : 0.045 0.519 6347 Planarity : 0.004 0.053 6972 Dihedral : 7.199 102.606 7338 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.59 % Favored : 94.32 % Rotamer: Outliers : 3.73 % Allowed : 22.47 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.12), residues: 4720 helix: 0.97 (0.13), residues: 1673 sheet: -0.70 (0.18), residues: 725 loop : -2.05 (0.11), residues: 2322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 319 TYR 0.019 0.001 TYR A1067 PHE 0.021 0.001 PHE C 201 TRP 0.011 0.001 TRP B 104 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00295 (40477) covalent geometry : angle 0.63985 (55030) SS BOND : bond 0.00431 ( 42) SS BOND : angle 1.41305 ( 84) hydrogen bonds : bond 0.03683 ( 1529) hydrogen bonds : angle 4.72435 ( 4356) link_BETA1-4 : bond 0.00458 ( 38) link_BETA1-4 : angle 2.11608 ( 114) link_NAG-ASN : bond 0.00592 ( 66) link_NAG-ASN : angle 2.57793 ( 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 329 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 172 time to evaluate : 1.582 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: A 133 PHE cc_start: 0.7206 (m-80) cc_final: 0.6715 (m-80) REVERT: A 153 MET cc_start: 0.5500 (tpt) cc_final: 0.5033 (tpp) REVERT: A 207 HIS cc_start: 0.8295 (OUTLIER) cc_final: 0.8046 (m-70) REVERT: A 297 SER cc_start: 0.8885 (m) cc_final: 0.8640 (p) REVERT: A 781 VAL cc_start: 0.9397 (OUTLIER) cc_final: 0.9118 (p) REVERT: A 861 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8887 (mp) REVERT: A 869 MET cc_start: 0.9133 (mtt) cc_final: 0.8828 (mtt) REVERT: A 922 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8202 (tt) REVERT: A 926 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.8577 (mp10) REVERT: B 452 LEU cc_start: 0.7137 (OUTLIER) cc_final: 0.6908 (tt) REVERT: B 819 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7709 (mp0) REVERT: B 901 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.8626 (tm-30) REVERT: B 902 MET cc_start: 0.9171 (tpp) cc_final: 0.8882 (tpp) REVERT: B 1029 MET cc_start: 0.9480 (tpp) cc_final: 0.8984 (tpp) REVERT: C 62 VAL cc_start: 0.8263 (m) cc_final: 0.8045 (p) REVERT: C 122 ASN cc_start: 0.6025 (OUTLIER) cc_final: 0.5631 (p0) REVERT: C 201 PHE cc_start: 0.9364 (t80) cc_final: 0.9100 (t80) REVERT: C 226 LEU cc_start: 0.9191 (tp) cc_final: 0.8651 (mp) REVERT: C 319 ARG cc_start: 0.6704 (OUTLIER) cc_final: 0.6376 (ptm160) REVERT: C 328 ARG cc_start: 0.9242 (OUTLIER) cc_final: 0.8688 (tpp80) REVERT: C 697 MET cc_start: 0.8610 (ttp) cc_final: 0.8285 (ttp) REVERT: C 721 SER cc_start: 0.8469 (OUTLIER) cc_final: 0.8237 (p) REVERT: C 731 MET cc_start: 0.8378 (ppp) cc_final: 0.7631 (ppp) REVERT: C 740 MET cc_start: 0.9396 (tmm) cc_final: 0.9096 (tmm) REVERT: F 579 MET cc_start: -0.1511 (ptp) cc_final: -0.2442 (ptm) REVERT: D 293 VAL cc_start: 0.1238 (OUTLIER) cc_final: 0.0358 (m) REVERT: D 297 MET cc_start: 0.5989 (mtp) cc_final: 0.4306 (ptm) REVERT: D 360 MET cc_start: 0.2926 (ptm) cc_final: 0.0244 (tpp) REVERT: E 297 MET cc_start: 0.4172 (mmm) cc_final: 0.3906 (mmt) REVERT: E 325 GLN cc_start: 0.9091 (tp40) cc_final: 0.8822 (mp10) REVERT: E 408 MET cc_start: 0.4812 (mpp) cc_final: 0.4569 (pmm) outliers start: 157 outliers final: 107 residues processed: 313 average time/residue: 0.2043 time to fit residues: 112.7916 Evaluate side-chains 281 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 161 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 926 GLN Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 797 PHE Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 327 PHE Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 343 VAL Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain F residue 408 MET Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 481 LYS Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 487 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 121 optimal weight: 9.9990 chunk 357 optimal weight: 50.0000 chunk 453 optimal weight: 40.0000 chunk 390 optimal weight: 10.0000 chunk 71 optimal weight: 20.0000 chunk 147 optimal weight: 0.0050 chunk 285 optimal weight: 1.9990 chunk 434 optimal weight: 50.0000 chunk 63 optimal weight: 6.9990 chunk 157 optimal weight: 9.9990 chunk 300 optimal weight: 20.0000 overall best weight: 5.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 121 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 953 ASN ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN C 965 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 437 ASN D 524 GLN ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 599 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.121844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.065375 restraints weight = 179205.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.066303 restraints weight = 105475.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.065352 restraints weight = 85868.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.066161 restraints weight = 73131.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.066148 restraints weight = 57342.406| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.5487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 40623 Z= 0.223 Angle : 0.735 13.314 55426 Z= 0.351 Chirality : 0.046 0.574 6347 Planarity : 0.004 0.072 6972 Dihedral : 7.093 102.882 7331 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.36 % Favored : 93.56 % Rotamer: Outliers : 4.37 % Allowed : 22.66 % Favored : 72.97 % 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 aren not related in a simple way. whole: -1.09 (0.12), residues: 4720 helix: 0.95 (0.13), residues: 1668 sheet: -0.84 (0.18), residues: 718 loop : -1.99 (0.12), residues: 2334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 319 TYR 0.035 0.002 TYR A1067 PHE 0.024 0.002 PHE A 797 TRP 0.013 0.001 TRP B 104 HIS 0.008 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00495 (40477) covalent geometry : angle 0.71054 (55030) SS BOND : bond 0.00366 ( 42) SS BOND : angle 1.40209 ( 84) hydrogen bonds : bond 0.04021 ( 1529) hydrogen bonds : angle 5.00027 ( 4356) link_BETA1-4 : bond 0.00423 ( 38) link_BETA1-4 : angle 2.16092 ( 114) link_NAG-ASN : bond 0.00674 ( 66) link_NAG-ASN : angle 2.73908 ( 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 341 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 157 time to evaluate : 1.200 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: A 133 PHE cc_start: 0.6692 (m-80) cc_final: 0.6437 (m-80) REVERT: A 207 HIS cc_start: 0.8519 (OUTLIER) cc_final: 0.8315 (m-70) REVERT: A 270 LEU cc_start: 0.9392 (mp) cc_final: 0.9166 (mp) REVERT: A 297 SER cc_start: 0.8920 (m) cc_final: 0.8705 (p) REVERT: A 765 ARG cc_start: 0.8767 (ttm110) cc_final: 0.8476 (ttm110) REVERT: A 861 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8976 (mp) REVERT: A 869 MET cc_start: 0.9224 (mtt) cc_final: 0.8915 (mtt) REVERT: A 922 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8145 (tt) REVERT: A 923 ILE cc_start: 0.9178 (OUTLIER) cc_final: 0.8859 (tp) REVERT: A 926 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8602 (mp10) REVERT: B 104 TRP cc_start: 0.8998 (OUTLIER) cc_final: 0.8339 (m-90) REVERT: B 229 LEU cc_start: 0.8224 (mt) cc_final: 0.8003 (mp) REVERT: B 452 LEU cc_start: 0.6973 (OUTLIER) cc_final: 0.6768 (tt) REVERT: B 471 GLU cc_start: 0.3270 (OUTLIER) cc_final: 0.3026 (pm20) REVERT: B 878 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9156 (mm) REVERT: B 901 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8626 (tm-30) REVERT: B 902 MET cc_start: 0.9290 (tpp) cc_final: 0.8965 (tpp) REVERT: C 62 VAL cc_start: 0.8208 (m) cc_final: 0.7948 (p) REVERT: C 122 ASN cc_start: 0.6030 (OUTLIER) cc_final: 0.5662 (p0) REVERT: C 201 PHE cc_start: 0.9374 (t80) cc_final: 0.9013 (t80) REVERT: C 226 LEU cc_start: 0.9215 (tp) cc_final: 0.8705 (mp) REVERT: C 319 ARG cc_start: 0.7026 (OUTLIER) cc_final: 0.6707 (ptm160) REVERT: C 326 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8500 (mt) REVERT: C 328 ARG cc_start: 0.9403 (OUTLIER) cc_final: 0.8766 (tpp80) REVERT: C 546 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8563 (tp) REVERT: C 697 MET cc_start: 0.8708 (ttp) cc_final: 0.8391 (ttp) REVERT: C 731 MET cc_start: 0.8461 (ppp) cc_final: 0.7641 (ppp) REVERT: C 740 MET cc_start: 0.9593 (tmm) cc_final: 0.9234 (tmm) REVERT: C 820 ASP cc_start: 0.8932 (OUTLIER) cc_final: 0.8476 (m-30) REVERT: C 821 LEU cc_start: 0.9679 (OUTLIER) cc_final: 0.9311 (tp) REVERT: C 1094 VAL cc_start: 0.8749 (OUTLIER) cc_final: 0.8513 (m) REVERT: F 62 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.7827 (tpt) REVERT: F 249 MET cc_start: 0.0029 (mtt) cc_final: -0.0514 (mmt) REVERT: F 579 MET cc_start: -0.1541 (ptp) cc_final: -0.2287 (ptt) REVERT: D 293 VAL cc_start: 0.1717 (OUTLIER) cc_final: 0.0806 (m) REVERT: D 297 MET cc_start: 0.5920 (mtp) cc_final: 0.5150 (ptm) REVERT: D 322 ASN cc_start: 0.4937 (m-40) cc_final: 0.4671 (t0) REVERT: D 360 MET cc_start: 0.3608 (ptm) cc_final: 0.1140 (tpt) REVERT: D 364 VAL cc_start: 0.2748 (OUTLIER) cc_final: 0.2358 (m) REVERT: E 455 MET cc_start: 0.0481 (tmm) cc_final: -0.0126 (tmm) outliers start: 184 outliers final: 118 residues processed: 321 average time/residue: 0.2005 time to fit residues: 112.5312 Evaluate side-chains 292 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 153 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 543 PHE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 926 GLN Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 797 PHE Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 327 PHE Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 343 VAL Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain F residue 408 MET Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 481 LYS Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 360 MET Chi-restraints excluded: chain E residue 487 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 339 optimal weight: 40.0000 chunk 472 optimal weight: 50.0000 chunk 245 optimal weight: 9.9990 chunk 329 optimal weight: 6.9990 chunk 400 optimal weight: 5.9990 chunk 385 optimal weight: 7.9990 chunk 208 optimal weight: 0.9990 chunk 220 optimal weight: 2.9990 chunk 288 optimal weight: 0.9990 chunk 407 optimal weight: 40.0000 chunk 463 optimal weight: 30.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 703 ASN A 872 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN F 210 ASN ** F 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 599 ASN ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.127182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.083004 restraints weight = 254430.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.082778 restraints weight = 134975.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.082107 restraints weight = 90090.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.082524 restraints weight = 57989.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.082636 restraints weight = 57821.589| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.5704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 40623 Z= 0.150 Angle : 0.671 12.741 55426 Z= 0.316 Chirality : 0.045 0.467 6347 Planarity : 0.004 0.052 6972 Dihedral : 6.767 103.679 7327 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.28 % Favored : 94.64 % Rotamer: Outliers : 3.56 % Allowed : 23.49 % Favored : 72.95 % 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 aren not related in a simple way. whole: -0.87 (0.12), residues: 4720 helix: 1.14 (0.13), residues: 1672 sheet: -0.64 (0.19), residues: 701 loop : -1.91 (0.12), residues: 2347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 983 TYR 0.024 0.001 TYR A1067 PHE 0.019 0.001 PHE A 133 TRP 0.013 0.001 TRP D 271 HIS 0.005 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00331 (40477) covalent geometry : angle 0.64860 (55030) SS BOND : bond 0.00338 ( 42) SS BOND : angle 1.53152 ( 84) hydrogen bonds : bond 0.03587 ( 1529) hydrogen bonds : angle 4.74340 ( 4356) link_BETA1-4 : bond 0.00464 ( 38) link_BETA1-4 : angle 2.02022 ( 114) link_NAG-ASN : bond 0.00406 ( 66) link_NAG-ASN : angle 2.40177 ( 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 309 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 159 time to evaluate : 1.521 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: A 133 PHE cc_start: 0.6997 (m-80) cc_final: 0.6576 (m-10) REVERT: A 153 MET cc_start: 0.5763 (tpt) cc_final: 0.5359 (tpp) REVERT: A 270 LEU cc_start: 0.9478 (mp) cc_final: 0.9260 (mp) REVERT: A 297 SER cc_start: 0.8844 (m) cc_final: 0.8605 (p) REVERT: A 765 ARG cc_start: 0.8733 (ttm110) cc_final: 0.8422 (ttm110) REVERT: A 861 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.9016 (mp) REVERT: A 869 MET cc_start: 0.9192 (mtt) cc_final: 0.8913 (mtp) REVERT: B 104 TRP cc_start: 0.8800 (OUTLIER) cc_final: 0.8253 (m-90) REVERT: B 471 GLU cc_start: 0.3232 (OUTLIER) cc_final: 0.2980 (pm20) REVERT: B 878 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.9129 (mm) REVERT: B 902 MET cc_start: 0.9177 (tpp) cc_final: 0.8899 (tpp) REVERT: B 1029 MET cc_start: 0.9500 (tpp) cc_final: 0.8996 (tpp) REVERT: C 122 ASN cc_start: 0.6843 (OUTLIER) cc_final: 0.6574 (p0) REVERT: C 201 PHE cc_start: 0.9278 (t80) cc_final: 0.8866 (t80) REVERT: C 319 ARG cc_start: 0.7206 (OUTLIER) cc_final: 0.6913 (ptm160) REVERT: C 326 ILE cc_start: 0.8665 (OUTLIER) cc_final: 0.8269 (mt) REVERT: C 328 ARG cc_start: 0.9297 (OUTLIER) cc_final: 0.8889 (tpp80) REVERT: C 528 LYS cc_start: 0.7606 (OUTLIER) cc_final: 0.7285 (ptmm) REVERT: C 583 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8716 (pp20) REVERT: C 731 MET cc_start: 0.8343 (ppp) cc_final: 0.7581 (ppp) REVERT: C 740 MET cc_start: 0.9346 (tmm) cc_final: 0.9138 (tmm) REVERT: C 820 ASP cc_start: 0.8771 (OUTLIER) cc_final: 0.8325 (m-30) REVERT: C 821 LEU cc_start: 0.9545 (OUTLIER) cc_final: 0.9188 (tp) REVERT: C 1094 VAL cc_start: 0.8735 (OUTLIER) cc_final: 0.8493 (m) REVERT: F 62 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7747 (tpt) REVERT: F 249 MET cc_start: 0.0193 (mtt) cc_final: -0.0059 (mmt) REVERT: F 297 MET cc_start: 0.1154 (mmt) cc_final: 0.0914 (mmt) REVERT: F 579 MET cc_start: -0.1290 (ptp) cc_final: -0.2008 (ptt) REVERT: D 293 VAL cc_start: 0.1840 (OUTLIER) cc_final: 0.1133 (m) REVERT: D 297 MET cc_start: 0.5856 (mtp) cc_final: 0.5270 (ptm) REVERT: D 360 MET cc_start: 0.3458 (ptm) cc_final: 0.1364 (tpt) REVERT: D 364 VAL cc_start: 0.2505 (OUTLIER) cc_final: 0.2151 (m) REVERT: D 366 MET cc_start: -0.0868 (tpt) cc_final: -0.1351 (tpt) REVERT: D 462 MET cc_start: 0.3125 (mmt) cc_final: 0.1410 (tmm) outliers start: 150 outliers final: 104 residues processed: 293 average time/residue: 0.2061 time to fit residues: 105.4477 Evaluate side-chains 271 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 151 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 543 PHE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 797 PHE Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 327 PHE Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 343 VAL Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain F residue 408 MET Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 481 LYS Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 360 MET Chi-restraints excluded: chain E residue 487 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 238 optimal weight: 50.0000 chunk 15 optimal weight: 9.9990 chunk 198 optimal weight: 20.0000 chunk 252 optimal weight: 5.9990 chunk 181 optimal weight: 1.9990 chunk 377 optimal weight: 50.0000 chunk 37 optimal weight: 0.8980 chunk 82 optimal weight: 0.0030 chunk 300 optimal weight: 6.9990 chunk 191 optimal weight: 6.9990 chunk 308 optimal weight: 20.0000 overall best weight: 3.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1064 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 HIS ** F 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 599 ASN ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.127077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.082629 restraints weight = 254119.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.081471 restraints weight = 134264.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.081621 restraints weight = 89171.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.081567 restraints weight = 60045.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.081190 restraints weight = 51258.207| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.5925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 40623 Z= 0.143 Angle : 0.672 12.902 55426 Z= 0.314 Chirality : 0.045 0.464 6347 Planarity : 0.004 0.051 6972 Dihedral : 6.658 102.263 7325 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.64 % Favored : 94.28 % Rotamer: Outliers : 3.30 % Allowed : 23.54 % Favored : 73.16 % 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 aren not related in a simple way. whole: -0.72 (0.12), residues: 4720 helix: 1.27 (0.13), residues: 1664 sheet: -0.56 (0.19), residues: 694 loop : -1.82 (0.12), residues: 2362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 983 TYR 0.023 0.001 TYR A1067 PHE 0.024 0.001 PHE A 927 TRP 0.013 0.001 TRP D 271 HIS 0.005 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00316 (40477) covalent geometry : angle 0.64908 (55030) SS BOND : bond 0.00372 ( 42) SS BOND : angle 1.80384 ( 84) hydrogen bonds : bond 0.03531 ( 1529) hydrogen bonds : angle 4.66794 ( 4356) link_BETA1-4 : bond 0.00431 ( 38) link_BETA1-4 : angle 2.00859 ( 114) link_NAG-ASN : bond 0.00407 ( 66) link_NAG-ASN : angle 2.33840 ( 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 297 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 158 time to evaluate : 1.556 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: A 133 PHE cc_start: 0.6360 (m-80) cc_final: 0.6032 (m-80) REVERT: A 153 MET cc_start: 0.6012 (tpt) cc_final: 0.5593 (tpp) REVERT: A 270 LEU cc_start: 0.9459 (mp) cc_final: 0.9244 (mp) REVERT: A 297 SER cc_start: 0.8762 (m) cc_final: 0.8562 (p) REVERT: A 765 ARG cc_start: 0.8703 (ttm110) cc_final: 0.8385 (ttm110) REVERT: A 861 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8973 (mp) REVERT: A 869 MET cc_start: 0.9119 (mtt) cc_final: 0.8855 (mtp) REVERT: B 104 TRP cc_start: 0.8916 (OUTLIER) cc_final: 0.8592 (m-90) REVERT: B 191 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7566 (mp0) REVERT: B 471 GLU cc_start: 0.3234 (OUTLIER) cc_final: 0.2980 (pm20) REVERT: B 758 SER cc_start: 0.8785 (OUTLIER) cc_final: 0.8267 (t) REVERT: B 878 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9124 (mm) REVERT: B 1029 MET cc_start: 0.9500 (tpp) cc_final: 0.8999 (tpp) REVERT: C 201 PHE cc_start: 0.9406 (t80) cc_final: 0.9052 (t80) REVERT: C 319 ARG cc_start: 0.7264 (OUTLIER) cc_final: 0.6998 (ptm160) REVERT: C 326 ILE cc_start: 0.8754 (OUTLIER) cc_final: 0.8499 (mt) REVERT: C 528 LYS cc_start: 0.7856 (OUTLIER) cc_final: 0.7455 (ptmm) REVERT: C 583 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8628 (pp20) REVERT: C 731 MET cc_start: 0.8313 (ppp) cc_final: 0.7554 (ppp) REVERT: C 740 MET cc_start: 0.9385 (tmm) cc_final: 0.9156 (tmm) REVERT: C 820 ASP cc_start: 0.8855 (OUTLIER) cc_final: 0.8418 (m-30) REVERT: C 821 LEU cc_start: 0.9562 (OUTLIER) cc_final: 0.9236 (tp) REVERT: C 1094 VAL cc_start: 0.8696 (OUTLIER) cc_final: 0.8461 (m) REVERT: F 62 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.8266 (tpt) REVERT: F 297 MET cc_start: 0.2133 (mmt) cc_final: 0.1815 (mmt) REVERT: F 360 MET cc_start: 0.2671 (tpp) cc_final: 0.2433 (tpp) REVERT: F 579 MET cc_start: -0.1311 (ptp) cc_final: -0.2003 (ptt) REVERT: D 293 VAL cc_start: 0.1947 (OUTLIER) cc_final: 0.1221 (m) REVERT: D 297 MET cc_start: 0.5708 (mtp) cc_final: 0.5085 (ptm) REVERT: D 360 MET cc_start: 0.3691 (ptm) cc_final: 0.1598 (tpt) REVERT: D 364 VAL cc_start: 0.2309 (OUTLIER) cc_final: 0.1979 (m) REVERT: D 366 MET cc_start: -0.0834 (tpt) cc_final: -0.1301 (tpt) REVERT: D 462 MET cc_start: 0.3042 (mmt) cc_final: 0.1348 (tmm) REVERT: E 455 MET cc_start: -0.0049 (tmm) cc_final: -0.0758 (tmm) outliers start: 139 outliers final: 105 residues processed: 285 average time/residue: 0.2262 time to fit residues: 112.1101 Evaluate side-chains 275 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 155 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 543 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 797 PHE Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 327 PHE Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 343 VAL Chi-restraints excluded: chain F residue 408 MET Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 481 LYS Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 360 MET Chi-restraints excluded: chain E residue 487 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 159 optimal weight: 7.9990 chunk 334 optimal weight: 30.0000 chunk 305 optimal weight: 40.0000 chunk 52 optimal weight: 6.9990 chunk 390 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 145 optimal weight: 20.0000 chunk 306 optimal weight: 6.9990 chunk 198 optimal weight: 20.0000 chunk 469 optimal weight: 6.9990 chunk 38 optimal weight: 30.0000 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 920 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 599 ASN ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.121886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.063408 restraints weight = 179324.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.064212 restraints weight = 102079.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.063651 restraints weight = 73094.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.064185 restraints weight = 68793.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.064441 restraints weight = 55530.274| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.6363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 40623 Z= 0.199 Angle : 0.725 13.862 55426 Z= 0.342 Chirality : 0.046 0.494 6347 Planarity : 0.004 0.060 6972 Dihedral : 6.765 102.051 7322 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.31 % Favored : 93.58 % Rotamer: Outliers : 3.44 % Allowed : 23.59 % Favored : 72.97 % 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 aren not related in a simple way. whole: -0.84 (0.12), residues: 4720 helix: 1.15 (0.13), residues: 1670 sheet: -0.64 (0.19), residues: 706 loop : -1.86 (0.12), residues: 2344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 983 TYR 0.034 0.001 TYR A1067 PHE 0.027 0.002 PHE B 201 TRP 0.016 0.001 TRP D 271 HIS 0.008 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00442 (40477) covalent geometry : angle 0.70243 (55030) SS BOND : bond 0.00330 ( 42) SS BOND : angle 1.66569 ( 84) hydrogen bonds : bond 0.03842 ( 1529) hydrogen bonds : angle 4.90569 ( 4356) link_BETA1-4 : bond 0.00395 ( 38) link_BETA1-4 : angle 2.07765 ( 114) link_NAG-ASN : bond 0.00603 ( 66) link_NAG-ASN : angle 2.51210 ( 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 297 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 152 time to evaluate : 1.847 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: A 133 PHE cc_start: 0.7149 (m-80) cc_final: 0.6665 (m-80) REVERT: A 153 MET cc_start: 0.5859 (tpt) cc_final: 0.5436 (tpp) REVERT: A 270 LEU cc_start: 0.9512 (mp) cc_final: 0.9263 (mp) REVERT: A 765 ARG cc_start: 0.8801 (ttm110) cc_final: 0.8475 (ttm110) REVERT: A 861 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.9035 (mp) REVERT: A 869 MET cc_start: 0.9220 (mtt) cc_final: 0.8886 (mtt) REVERT: B 104 TRP cc_start: 0.8809 (OUTLIER) cc_final: 0.8475 (m-90) REVERT: B 191 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7738 (mp0) REVERT: B 471 GLU cc_start: 0.3382 (OUTLIER) cc_final: 0.3119 (pm20) REVERT: B 878 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9179 (mm) REVERT: B 1029 MET cc_start: 0.9509 (tpp) cc_final: 0.8991 (tpp) REVERT: C 201 PHE cc_start: 0.9297 (t80) cc_final: 0.9011 (t80) REVERT: C 319 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.7143 (ptm160) REVERT: C 326 ILE cc_start: 0.8876 (OUTLIER) cc_final: 0.8589 (mt) REVERT: C 697 MET cc_start: 0.8963 (ttp) cc_final: 0.8523 (tpt) REVERT: C 731 MET cc_start: 0.8400 (ppp) cc_final: 0.7560 (ppp) REVERT: C 740 MET cc_start: 0.9639 (tmm) cc_final: 0.9315 (tmm) REVERT: C 820 ASP cc_start: 0.8918 (OUTLIER) cc_final: 0.8470 (m-30) REVERT: C 821 LEU cc_start: 0.9656 (OUTLIER) cc_final: 0.9334 (tp) REVERT: C 1094 VAL cc_start: 0.8778 (OUTLIER) cc_final: 0.8530 (m) REVERT: F 62 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8412 (tpt) REVERT: F 249 MET cc_start: -0.1518 (mtt) cc_final: -0.2109 (mmt) REVERT: F 297 MET cc_start: -0.0851 (mmt) cc_final: -0.1634 (mmt) REVERT: D 293 VAL cc_start: 0.2114 (OUTLIER) cc_final: 0.1333 (m) REVERT: D 297 MET cc_start: 0.5727 (mtp) cc_final: 0.5078 (ptm) REVERT: D 360 MET cc_start: 0.4094 (ptm) cc_final: 0.1832 (tpt) REVERT: D 364 VAL cc_start: 0.2325 (OUTLIER) cc_final: 0.2027 (m) REVERT: D 366 MET cc_start: -0.0823 (tpt) cc_final: -0.1308 (tpt) REVERT: D 408 MET cc_start: 0.5217 (mmt) cc_final: 0.4835 (mpp) REVERT: D 462 MET cc_start: 0.3046 (mmt) cc_final: 0.1472 (ttt) REVERT: E 455 MET cc_start: 0.0190 (tmm) cc_final: -0.0460 (tmm) outliers start: 145 outliers final: 113 residues processed: 283 average time/residue: 0.2276 time to fit residues: 112.0872 Evaluate side-chains 274 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 149 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 543 PHE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1075 PHE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 797 PHE Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 327 PHE Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 408 MET Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 481 LYS Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 360 MET Chi-restraints excluded: chain E residue 487 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 63 optimal weight: 5.9990 chunk 382 optimal weight: 0.0370 chunk 81 optimal weight: 8.9990 chunk 369 optimal weight: 9.9990 chunk 68 optimal weight: 6.9990 chunk 389 optimal weight: 30.0000 chunk 9 optimal weight: 3.9990 chunk 458 optimal weight: 8.9990 chunk 295 optimal weight: 0.7980 chunk 119 optimal weight: 6.9990 chunk 346 optimal weight: 50.0000 overall best weight: 3.5664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.123783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.074528 restraints weight = 202568.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.067000 restraints weight = 136685.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.066815 restraints weight = 95266.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.067565 restraints weight = 77402.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.067330 restraints weight = 58661.177| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.6472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 40623 Z= 0.154 Angle : 0.698 18.057 55426 Z= 0.327 Chirality : 0.045 0.441 6347 Planarity : 0.004 0.051 6972 Dihedral : 6.638 102.749 7321 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.55 % Favored : 94.36 % Rotamer: Outliers : 2.97 % Allowed : 23.99 % Favored : 73.04 % 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 aren not related in a simple way. whole: -0.69 (0.12), residues: 4720 helix: 1.26 (0.13), residues: 1674 sheet: -0.44 (0.19), residues: 679 loop : -1.81 (0.12), residues: 2367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 983 TYR 0.026 0.001 TYR A1067 PHE 0.023 0.001 PHE B 201 TRP 0.015 0.001 TRP F 478 HIS 0.006 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00340 (40477) covalent geometry : angle 0.67104 (55030) SS BOND : bond 0.00479 ( 42) SS BOND : angle 1.92186 ( 84) hydrogen bonds : bond 0.03580 ( 1529) hydrogen bonds : angle 4.74703 ( 4356) link_BETA1-4 : bond 0.00419 ( 38) link_BETA1-4 : angle 1.99669 ( 114) link_NAG-ASN : bond 0.00410 ( 66) link_NAG-ASN : angle 2.70841 ( 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 280 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 155 time to evaluate : 1.624 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: A 133 PHE cc_start: 0.6982 (m-80) cc_final: 0.6565 (m-80) REVERT: A 153 MET cc_start: 0.6082 (tpt) cc_final: 0.5612 (tpp) REVERT: A 191 GLU cc_start: 0.8919 (mt-10) cc_final: 0.8606 (mt-10) REVERT: A 270 LEU cc_start: 0.9461 (mp) cc_final: 0.9188 (mp) REVERT: A 765 ARG cc_start: 0.8729 (ttm110) cc_final: 0.8389 (ttm110) REVERT: A 869 MET cc_start: 0.9211 (mtt) cc_final: 0.8916 (mtt) REVERT: B 191 GLU cc_start: 0.8351 (mt-10) cc_final: 0.7852 (mp0) REVERT: B 471 GLU cc_start: 0.3246 (OUTLIER) cc_final: 0.2990 (pm20) REVERT: B 878 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9133 (mm) REVERT: B 1029 MET cc_start: 0.9522 (tpp) cc_final: 0.9028 (tpp) REVERT: C 201 PHE cc_start: 0.9468 (t80) cc_final: 0.9224 (t80) REVERT: C 319 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.7205 (ptm160) REVERT: C 326 ILE cc_start: 0.8876 (OUTLIER) cc_final: 0.8528 (mt) REVERT: C 697 MET cc_start: 0.8835 (ttp) cc_final: 0.8469 (tpt) REVERT: C 731 MET cc_start: 0.8335 (ppp) cc_final: 0.7688 (ppp) REVERT: C 820 ASP cc_start: 0.8894 (OUTLIER) cc_final: 0.8456 (m-30) REVERT: C 821 LEU cc_start: 0.9641 (OUTLIER) cc_final: 0.9303 (tp) REVERT: C 1094 VAL cc_start: 0.8804 (OUTLIER) cc_final: 0.8569 (m) REVERT: F 62 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.8635 (tpt) REVERT: F 249 MET cc_start: -0.2617 (mtt) cc_final: -0.3193 (mmt) REVERT: F 360 MET cc_start: 0.1920 (mmm) cc_final: 0.1493 (mmm) REVERT: F 557 MET cc_start: 0.5885 (mmt) cc_final: 0.5625 (mmt) REVERT: F 579 MET cc_start: -0.1400 (mtm) cc_final: -0.2318 (ptt) REVERT: D 293 VAL cc_start: 0.1734 (OUTLIER) cc_final: 0.0836 (m) REVERT: D 297 MET cc_start: 0.5712 (mtp) cc_final: 0.4515 (ptm) REVERT: D 360 MET cc_start: 0.4027 (ptm) cc_final: 0.1728 (tpt) REVERT: D 364 VAL cc_start: 0.1972 (OUTLIER) cc_final: 0.1620 (m) REVERT: D 366 MET cc_start: -0.1072 (tpt) cc_final: -0.1577 (tpt) REVERT: D 462 MET cc_start: 0.3052 (mmt) cc_final: 0.1502 (ttt) outliers start: 125 outliers final: 107 residues processed: 268 average time/residue: 0.2265 time to fit residues: 105.4224 Evaluate side-chains 267 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 150 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 543 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 327 PHE Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 408 MET Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 481 LYS Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 360 MET Chi-restraints excluded: chain E residue 487 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 245 optimal weight: 0.8980 chunk 202 optimal weight: 30.0000 chunk 388 optimal weight: 0.3980 chunk 7 optimal weight: 50.0000 chunk 167 optimal weight: 3.9990 chunk 405 optimal weight: 40.0000 chunk 463 optimal weight: 8.9990 chunk 385 optimal weight: 5.9990 chunk 390 optimal weight: 30.0000 chunk 359 optimal weight: 50.0000 chunk 30 optimal weight: 5.9990 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.123887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.072349 restraints weight = 205197.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.067740 restraints weight = 157299.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.066030 restraints weight = 126281.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.065509 restraints weight = 90072.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.065694 restraints weight = 84768.407| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.6577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 40623 Z= 0.151 Angle : 0.701 21.785 55426 Z= 0.327 Chirality : 0.045 0.429 6347 Planarity : 0.004 0.051 6972 Dihedral : 6.648 102.457 7320 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.76 % Favored : 94.13 % Rotamer: Outliers : 3.04 % Allowed : 24.16 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.12), residues: 4720 helix: 1.27 (0.13), residues: 1671 sheet: -0.47 (0.19), residues: 689 loop : -1.76 (0.12), residues: 2360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 983 TYR 0.024 0.001 TYR A1067 PHE 0.022 0.001 PHE B 201 TRP 0.013 0.001 TRP D 271 HIS 0.006 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00334 (40477) covalent geometry : angle 0.67379 (55030) SS BOND : bond 0.00368 ( 42) SS BOND : angle 1.82319 ( 84) hydrogen bonds : bond 0.03535 ( 1529) hydrogen bonds : angle 4.71444 ( 4356) link_BETA1-4 : bond 0.00441 ( 38) link_BETA1-4 : angle 1.97831 ( 114) link_NAG-ASN : bond 0.00438 ( 66) link_NAG-ASN : angle 2.77263 ( 198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15268.92 seconds wall clock time: 260 minutes 35.25 seconds (15635.25 seconds total)