Starting phenix.real_space_refine on Tue Aug 26 17:01:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i9b_35264/08_2025/8i9b_35264.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i9b_35264/08_2025/8i9b_35264.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8i9b_35264/08_2025/8i9b_35264.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i9b_35264/08_2025/8i9b_35264.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8i9b_35264/08_2025/8i9b_35264.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i9b_35264/08_2025/8i9b_35264.map" } resolution = 3.5 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= 0.006 sd= 0.050 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 25211 2.51 5 N 6425 2.21 5 O 7708 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 162 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: 39539 Number of models: 1 Model: "" Number of chains: 49 Chain: "A" Number of atoms: 7833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 999, 7833 Classifications: {'peptide': 999} Link IDs: {'PTRANS': 54, 'TRANS': 944} Chain breaks: 9 Chain: "B" Number of atoms: 7827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7827 Classifications: {'peptide': 998} Link IDs: {'PTRANS': 54, 'TRANS': 943} Chain breaks: 9 Chain: "C" Number of atoms: 7827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7827 Classifications: {'peptide': 998} Link IDs: {'PTRANS': 54, 'TRANS': 943} 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: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 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: 8.38, per 1000 atoms: 0.21 Number of scatterers: 39539 At special positions: 0 Unit cell: (184.79, 198.921, 246.749, 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 7708 8.00 N 6425 7.00 C 25211 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=2.08 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 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=2.06 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=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.06 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=2.37 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.06 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=2.04 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=2.01 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=2.06 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=2.06 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=2.06 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-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 A1410 " - " ASN A 801 " " 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 A1074 " " NAG K 1 " - " ASN A1098 " " NAG L 1 " - " ASN A1134 " " NAG M 1 " - " ASN B 331 " " NAG N 1 " - " ASN B 343 " " NAG O 1 " - " ASN B 709 " " NAG P 1 " - " ASN B 717 " " NAG Q 1 " - " ASN B 801 " " NAG R 1 " - " ASN B1074 " " NAG S 1 " - " ASN B1098 " " NAG T 1 " - " ASN B1134 " " NAG U 1 " - " ASN C 331 " " NAG V 1 " - " ASN C 343 " " NAG W 1 " - " ASN C 709 " " NAG X 1 " - " ASN C 717 " " NAG Y 1 " - " ASN C 801 " " NAG Z 1 " - " ASN C1074 " " NAG a 1 " - " ASN C1098 " " NAG b 1 " - " ASN C1134 " " NAG c 1 " - " ASN F 53 " " NAG d 1 " - " ASN F 90 " " NAG e 1 " - " ASN F 103 " " NAG f 1 " - " ASN F 432 " " NAG g 1 " - " ASN F 546 " " NAG h 1 " - " ASN D 53 " " NAG i 1 " - " ASN D 90 " " NAG j 1 " - " ASN D 103 " " NAG k 1 " - " ASN D 432 " " NAG l 1 " - " ASN D 546 " " NAG m 1 " - " ASN E 53 " " NAG n 1 " - " ASN E 90 " " NAG o 1 " - " ASN E 103 " " NAG p 1 " - " ASN E 432 " " NAG q 1 " - " ASN E 546 " Time building additional restraints: 3.13 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 476.8 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: 154 helices and 54 sheets defined 40.0% alpha, 18.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 342 removed outlier: 4.216A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 366 No H-bonds generated for 'chain 'A' and resid 364 through 366' Processing helix chain 'A' and resid 367 through 372 removed outlier: 4.431A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.709A pdb=" N GLU A 406 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.706A pdb=" N TYR A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.613A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) 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: 3.641A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.558A 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: 3.537A 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: 3.552A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.573A 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: 3.627A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.879A 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: 4.631A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.650A 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: 3.647A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.678A 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 342 removed outlier: 4.215A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 368 removed outlier: 3.673A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.709A pdb=" N GLU B 406 " --> pdb=" O ARG B 403 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.706A pdb=" N TYR B 421 " --> pdb=" O ASN B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.613A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 754 removed outlier: 3.695A 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: 3.648A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.638A 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: 3.602A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.021A 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: 4.009A 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: 3.703A 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: 4.269A 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: 4.210A 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: 3.506A 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 342 removed outlier: 4.215A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 368 removed outlier: 3.673A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.708A pdb=" N GLU C 406 " --> pdb=" O ARG C 403 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.706A pdb=" N TYR C 421 " --> pdb=" O ASN C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.613A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) 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: 3.559A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.720A 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: 3.552A 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: 3.591A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.358A 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: 3.740A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.636A 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: 3.816A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.605A 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 53 removed outlier: 3.613A pdb=" N LYS F 31 " --> pdb=" O THR F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 80 removed outlier: 3.737A pdb=" N GLN F 60 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 3.848A 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: 3.884A 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: 3.940A pdb=" N ALA F 153 " --> pdb=" O ASN F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 172 removed outlier: 3.672A pdb=" N ARG F 169 " --> pdb=" O TRP F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 175 No H-bonds generated for 'chain 'F' and resid 173 through 175' Processing helix chain 'F' and resid 176 through 193 removed outlier: 3.738A pdb=" N GLU F 182 " --> pdb=" O PRO F 178 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL F 185 " --> pdb=" O GLU F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 205 Processing helix chain 'F' and resid 220 through 252 removed outlier: 3.758A pdb=" N GLU F 224 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU F 231 " --> pdb=" O GLU F 227 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLU F 232 " --> pdb=" O HIS F 228 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE F 233 " --> pdb=" O THR F 229 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS F 234 " --> pdb=" O PHE F 230 " (cutoff:3.500A) Proline residue: F 235 - end of helix removed outlier: 3.670A pdb=" N HIS F 239 " --> pdb=" O PRO F 235 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ASN F 250 " --> pdb=" O ALA F 246 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA F 251 " --> pdb=" O LYS F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 267 No H-bonds generated for 'chain 'F' and resid 265 through 267' Processing helix chain 'F' and resid 275 through 279 removed outlier: 3.728A 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 303 through 318 removed outlier: 3.797A pdb=" N PHE F 308 " --> pdb=" O ALA F 304 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL F 318 " --> pdb=" O PHE F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 331 removed outlier: 3.502A pdb=" N SER F 331 " --> pdb=" O PHE F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 366 through 385 removed outlier: 3.817A pdb=" N HIS F 373 " --> pdb=" O PHE F 369 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N HIS F 378 " --> pdb=" O HIS F 374 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR F 385 " --> pdb=" O TYR F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 393 removed outlier: 3.580A pdb=" N ARG F 393 " --> pdb=" O PHE F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 412 removed outlier: 3.702A pdb=" N ALA F 403 " --> pdb=" O GLY F 399 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER F 409 " --> pdb=" O GLY F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 422 removed outlier: 3.505A pdb=" N SER F 420 " --> pdb=" O LYS F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 447 removed outlier: 3.600A pdb=" N GLU F 435 " --> pdb=" O ASP F 431 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR F 445 " --> pdb=" O LYS F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 466 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: 3.856A pdb=" N THR F 519 " --> pdb=" O TYR F 515 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU F 520 " --> pdb=" O TYR F 516 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE F 523 " --> pdb=" O THR F 519 " (cutoff:3.500A) removed outlier: 3.704A 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: 3.779A pdb=" N GLY F 551 " --> pdb=" O SER F 547 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET F 557 " --> pdb=" O LYS F 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 572 removed outlier: 3.612A pdb=" N GLU F 571 " --> pdb=" O THR F 567 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 588 Processing helix chain 'F' and resid 588 through 599 Processing helix chain 'D' and resid 22 through 53 removed outlier: 3.613A pdb=" N LYS D 31 " --> pdb=" O THR D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 80 removed outlier: 3.737A pdb=" N GLN D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 3.849A 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: 3.885A 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: 3.939A pdb=" N ALA D 153 " --> pdb=" O ASN D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 172 removed outlier: 3.672A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 175 No H-bonds generated for 'chain 'D' and resid 173 through 175' Processing helix chain 'D' and resid 176 through 193 removed outlier: 3.737A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 220 through 252 removed outlier: 3.758A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS D 234 " --> pdb=" O PHE D 230 " (cutoff:3.500A) Proline residue: D 235 - end of helix removed outlier: 3.670A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ASN D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 279 removed outlier: 3.729A 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 303 through 318 removed outlier: 3.796A pdb=" N PHE D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL D 318 " --> pdb=" O PHE D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 331 removed outlier: 3.503A pdb=" N SER D 331 " --> pdb=" O PHE D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 385 removed outlier: 3.816A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 removed outlier: 3.579A pdb=" N ARG D 393 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 412 removed outlier: 3.702A pdb=" N ALA D 403 " --> pdb=" O GLY D 399 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 422 removed outlier: 3.505A pdb=" N SER D 420 " --> pdb=" O LYS D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.600A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 466 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: 3.856A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) removed outlier: 3.704A 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: 3.779A pdb=" N GLY D 551 " --> pdb=" O SER D 547 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 removed outlier: 3.612A pdb=" N GLU D 571 " --> pdb=" O THR D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 599 Processing helix chain 'E' and resid 22 through 53 removed outlier: 3.613A pdb=" N LYS E 31 " --> pdb=" O THR E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 80 removed outlier: 3.736A pdb=" N GLN E 60 " --> pdb=" O GLU E 56 " (cutoff:3.500A) removed outlier: 3.849A 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: 3.884A 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: 3.940A pdb=" N ALA E 153 " --> pdb=" O ASN E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 172 removed outlier: 3.672A pdb=" N ARG E 169 " --> pdb=" O TRP E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 175 No H-bonds generated for 'chain 'E' and resid 173 through 175' Processing helix chain 'E' and resid 176 through 193 removed outlier: 3.737A pdb=" N GLU E 182 " --> pdb=" O PRO E 178 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL E 185 " --> pdb=" O GLU E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 205 Processing helix chain 'E' and resid 220 through 252 removed outlier: 3.759A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU E 231 " --> pdb=" O GLU E 227 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLU E 232 " --> pdb=" O HIS E 228 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE E 233 " --> pdb=" O THR E 229 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS E 234 " --> pdb=" O PHE E 230 " (cutoff:3.500A) Proline residue: E 235 - end of helix removed outlier: 3.670A pdb=" N HIS E 239 " --> pdb=" O PRO E 235 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ASN E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA E 251 " --> pdb=" O LYS E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 267 No H-bonds generated for 'chain 'E' and resid 265 through 267' Processing helix chain 'E' and resid 275 through 279 removed outlier: 3.729A 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 303 through 318 removed outlier: 3.796A pdb=" N PHE E 308 " --> pdb=" O ALA E 304 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL E 318 " --> pdb=" O PHE E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 331 removed outlier: 3.502A pdb=" N SER E 331 " --> pdb=" O PHE E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 385 removed outlier: 3.817A pdb=" N HIS E 373 " --> pdb=" O PHE E 369 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N HIS E 378 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 393 removed outlier: 3.579A pdb=" N ARG E 393 " --> pdb=" O PHE E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 412 removed outlier: 3.701A pdb=" N ALA E 403 " --> pdb=" O GLY E 399 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N SER E 409 " --> pdb=" O GLY E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 422 removed outlier: 3.505A pdb=" N SER E 420 " --> pdb=" O LYS E 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 447 removed outlier: 3.600A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR E 445 " --> pdb=" O LYS E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 466 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: 3.856A pdb=" N THR E 519 " --> pdb=" O TYR E 515 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU E 520 " --> pdb=" O TYR E 516 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) removed outlier: 3.704A 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: 3.778A pdb=" N GLY E 551 " --> pdb=" O SER E 547 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 572 removed outlier: 3.612A pdb=" N GLU E 571 " --> pdb=" O THR E 567 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 588 Processing helix chain 'E' and resid 588 through 599 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: 6.440A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.680A 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: 6.948A 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: 3.729A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 7.476A 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: 7.211A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.589A 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: 4.047A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 317 removed outlier: 5.849A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.338A 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=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.890A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 448 through 454 removed outlier: 5.892A pdb=" N TYR A 449 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N PHE A 497 " --> pdb=" O TYR A 449 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR A 453 " --> pdb=" O GLN A 493 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 653 through 655 removed outlier: 6.207A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 664 through 665 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.588A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.604A 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: 3.530A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.588A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.604A 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: 4.730A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.699A 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=AB5, 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=AB6, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB7, 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=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.061A 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: 3.678A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.437A 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=AB9, first strand: chain 'B' and resid 49 through 55 removed outlier: 3.857A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC2, first strand: chain 'B' and resid 116 through 121 removed outlier: 3.730A 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: 7.211A 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: 4.047A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 317 removed outlier: 5.658A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.128A 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=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.338A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.891A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 448 through 454 removed outlier: 5.892A pdb=" N TYR B 449 " --> pdb=" O PHE B 497 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N PHE B 497 " --> pdb=" O TYR B 449 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N TYR B 451 " --> pdb=" O TYR B 495 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR B 453 " --> pdb=" O GLN B 493 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.557A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.937A 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=AC9, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.541A 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: 6.526A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.210A 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=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.541A 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: 6.526A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.210A 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: 4.595A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.578A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD5, 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: 3.679A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (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=AD6, first strand: chain 'C' and resid 49 through 55 removed outlier: 3.856A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD8, first strand: chain 'C' and resid 116 through 121 removed outlier: 3.731A 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=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.488A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.364A 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=AE1, 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: 6.444A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.890A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 448 through 454 removed outlier: 5.891A pdb=" N TYR C 449 " --> pdb=" O PHE C 497 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N PHE C 497 " --> pdb=" O TYR C 449 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR C 453 " --> pdb=" O GLN C 493 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'C' and resid 664 through 665 Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.591A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.759A 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: 6.147A 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=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.591A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.759A 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: 6.147A 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: 3.881A 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=AE8, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.568A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF1, first strand: chain 'F' and resid 131 through 132 Processing sheet with id=AF2, first strand: chain 'F' and resid 262 through 263 removed outlier: 5.914A pdb=" N LEU F 262 " --> pdb=" O VAL F 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'F' and resid 347 through 352 removed outlier: 6.140A pdb=" N ASP F 355 " --> pdb=" O LEU F 351 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 131 through 132 Processing sheet with id=AF5, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.914A 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: 6.139A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 131 through 132 Processing sheet with id=AF8, first strand: chain 'E' and resid 262 through 263 removed outlier: 5.914A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'E' and resid 347 through 352 removed outlier: 6.139A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 1613 hydrogen bonds defined for protein. 4545 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: 8.75 Time building geometry restraints manager: 4.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 12439 1.34 - 1.47: 10848 1.47 - 1.60: 16927 1.60 - 1.74: 0 1.74 - 1.87: 285 Bond restraints: 40499 Sorted by residual: bond pdb=" C HIS B1088 " pdb=" N PHE B1089 " ideal model delta sigma weight residual 1.331 1.264 0.068 1.59e-02 3.96e+03 1.80e+01 bond pdb=" N PRO C 209 " pdb=" CD PRO C 209 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.63e+01 bond pdb=" N PRO A 209 " pdb=" CD PRO A 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 B 217 " pdb=" CD PRO B 217 " ideal model delta sigma weight residual 1.473 1.529 -0.056 1.40e-02 5.10e+03 1.59e+01 ... (remaining 40494 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 53938 2.72 - 5.44: 1006 5.44 - 8.16: 90 8.16 - 10.88: 9 10.88 - 13.59: 13 Bond angle restraints: 55056 Sorted by residual: angle pdb=" N LYS C 529 " pdb=" CA LYS C 529 " pdb=" C LYS C 529 " ideal model delta sigma weight residual 108.24 119.72 -11.48 1.32e+00 5.74e-01 7.56e+01 angle pdb=" N LEU A 157 " pdb=" CA LEU A 157 " pdb=" C LEU A 157 " ideal model delta sigma weight residual 111.74 123.23 -11.49 1.35e+00 5.49e-01 7.24e+01 angle pdb=" N LEU B 157 " pdb=" CA LEU B 157 " pdb=" C LEU B 157 " ideal model delta sigma weight residual 111.74 123.19 -11.45 1.35e+00 5.49e-01 7.19e+01 angle pdb=" N LEU C 157 " pdb=" CA LEU C 157 " pdb=" C LEU C 157 " ideal model delta sigma weight residual 111.74 123.18 -11.44 1.35e+00 5.49e-01 7.18e+01 angle pdb=" N THR C 531 " pdb=" CA THR C 531 " pdb=" C THR C 531 " ideal model delta sigma weight residual 107.88 118.85 -10.97 1.41e+00 5.03e-01 6.05e+01 ... (remaining 55051 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 21836 17.94 - 35.87: 2450 35.87 - 53.81: 816 53.81 - 71.75: 224 71.75 - 89.69: 58 Dihedral angle restraints: 25384 sinusoidal: 11395 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 21.09 71.91 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 21.10 71.90 1 1.00e+01 1.00e-02 6.62e+01 ... (remaining 25381 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.338: 6340 0.338 - 0.675: 4 0.675 - 1.012: 2 1.012 - 1.350: 0 1.350 - 1.687: 2 Chirality restraints: 6348 Sorted by residual: chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-02 2.50e+03 7.94e+02 chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.76 0.36 2.00e-02 2.50e+03 3.21e+02 chirality pdb=" C1 NAG b 1 " pdb=" ND2 ASN C1134 " pdb=" C2 NAG b 1 " pdb=" O5 NAG b 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.71 -1.69 2.00e-01 2.50e+01 7.12e+01 ... (remaining 6345 not shown) Planarity restraints: 7040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 801 " 0.131 2.00e-02 2.50e+03 2.03e-01 5.15e+02 pdb=" CG ASN A 801 " -0.064 2.00e-02 2.50e+03 pdb=" OD1 ASN A 801 " 0.057 2.00e-02 2.50e+03 pdb=" ND2 ASN A 801 " -0.357 2.00e-02 2.50e+03 pdb=" C1 NAG A1410 " 0.233 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " -0.130 2.00e-02 2.50e+03 1.49e-01 2.78e+02 pdb=" CG ASN C 331 " 0.051 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " 0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " 0.242 2.00e-02 2.50e+03 pdb=" C1 NAG U 1 " -0.182 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " -0.088 2.00e-02 2.50e+03 9.53e-02 1.14e+02 pdb=" CG ASN A 331 " 0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " 0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " 0.150 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " -0.116 2.00e-02 2.50e+03 ... (remaining 7037 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 305 2.50 - 3.10: 27652 3.10 - 3.70: 56165 3.70 - 4.30: 86447 4.30 - 4.90: 143479 Nonbonded interactions: 314048 Sorted by model distance: nonbonded pdb=" O GLN A 690 " pdb=" OG SER A 691 " model vdw 1.899 3.040 nonbonded pdb=" O GLY B 799 " pdb=" O PHE B 800 " model vdw 2.107 3.040 nonbonded pdb=" N GLU B 748 " pdb=" OE1 GLU B 748 " model vdw 2.141 3.120 nonbonded pdb=" O PHE B 375 " pdb=" O ALA B 376 " model vdw 2.145 3.040 nonbonded pdb=" O GLY A 700 " pdb=" O ALA A 701 " model vdw 2.167 3.040 ... (remaining 314043 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' } 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: 1.350 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: 0.480 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 33.670 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.180 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:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3708 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 0.343 40644 Z= 0.409 Angle : 1.089 48.854 55449 Z= 0.586 Chirality : 0.067 1.687 6348 Planarity : 0.006 0.091 6974 Dihedral : 17.466 89.687 16244 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 19.27 Ramachandran Plot: Outliers : 1.76 % Allowed : 8.16 % Favored : 90.08 % Rotamer: Outliers : 9.83 % Allowed : 18.06 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.51 (0.10), residues: 4720 helix: -1.42 (0.11), residues: 1652 sheet: -2.00 (0.17), residues: 757 loop : -3.19 (0.10), residues: 2311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 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 0.010 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00886 (40499) covalent geometry : angle 0.93162 (55056) SS BOND : bond 0.05503 ( 42) SS BOND : angle 9.83285 ( 84) hydrogen bonds : bond 0.19168 ( 1577) hydrogen bonds : angle 7.28528 ( 4545) link_BETA1-4 : bond 0.00905 ( 37) link_BETA1-4 : angle 3.94430 ( 111) link_NAG-ASN : bond 0.00897 ( 66) link_NAG-ASN : angle 6.41405 ( 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 1022 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 414 poor density : 608 time to evaluate : 1.293 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: A 216 LEU cc_start: -0.0118 (OUTLIER) cc_final: -0.0445 (mp) REVERT: A 660 TYR cc_start: 0.0657 (OUTLIER) cc_final: 0.0454 (p90) REVERT: B 615 VAL cc_start: 0.6257 (t) cc_final: 0.5815 (t) REVERT: C 122 ASN cc_start: -0.1410 (OUTLIER) cc_final: -0.1617 (t0) REVERT: C 164 ASN cc_start: 0.0509 (OUTLIER) cc_final: 0.0138 (p0) REVERT: C 216 LEU cc_start: 0.4162 (OUTLIER) cc_final: 0.3791 (pt) REVERT: E 474 MET cc_start: -0.1809 (mmp) cc_final: -0.2556 (tpp) outliers start: 414 outliers final: 64 residues processed: 963 average time/residue: 0.2037 time to fit residues: 327.8598 Evaluate side-chains 370 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 301 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain B residue 217 PRO Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 912 THR 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 48 LEU Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 217 PRO Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 133 CYS Chi-restraints excluded: chain F residue 353 LYS Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 247 LYS Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 409 SER Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain E residue 133 CYS Chi-restraints excluded: chain E residue 247 LYS Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 353 LYS Chi-restraints excluded: chain E residue 409 SER Chi-restraints excluded: chain E residue 548 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 432 optimal weight: 20.0000 chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 20.0000 chunk 455 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 40.0000 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.9990 chunk 470 optimal weight: 50.0000 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 134 GLN A 137 ASN A 188 ASN A 196 ASN A 239 GLN A 339 HIS A 360 ASN A 422 ASN ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 ASN A 644 GLN A 658 ASN A 762 GLN A 784 GLN A 787 GLN A 901 GLN A 914 ASN A 919 ASN A 955 ASN A 957 GLN A 992 GLN A1005 GLN A1101 HIS B 134 GLN B 137 ASN B 164 ASN B 188 ASN B 317 ASN B 339 HIS B 360 ASN B 422 ASN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN B 644 GLN B 658 ASN B 901 GLN B 914 ASN B 919 ASN B 926 GLN B 992 GLN B1054 GLN B1119 ASN C 134 GLN C 137 ASN C 188 ASN C 239 GLN C 339 HIS C 360 ASN C 422 ASN C 658 ASN C 703 ASN C 751 ASN C 901 GLN C 914 ASN C 919 ASN C 926 GLN C 954 HIS C 965 GLN C 992 GLN C1002 GLN C1010 GLN C1071 GLN C1101 HIS C1142 GLN F 42 GLN F 58 ASN F 102 GLN F 117 ASN F 137 ASN F 210 ASN F 305 GLN F 374 HIS F 437 ASN ** F 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 505 HIS F 522 GLN D 34 HIS D 42 GLN D 51 ASN D 58 ASN D 102 GLN D 117 ASN D 210 ASN D 374 HIS D 437 ASN D 505 HIS D 522 GLN ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 GLN E 51 ASN E 58 ASN E 102 GLN E 117 ASN E 137 ASN E 210 ASN E 437 ASN E 472 GLN E 493 HIS Total number of N/Q/H flips: 95 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5162 r_free = 0.5162 target = 0.191776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.151148 restraints weight = 140593.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.150303 restraints weight = 76385.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.152619 restraints weight = 46109.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.152504 restraints weight = 34815.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.152689 restraints weight = 33212.065| |-----------------------------------------------------------------------------| r_work (final): 0.4497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5569 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 40644 Z= 0.181 Angle : 0.830 22.637 55449 Z= 0.402 Chirality : 0.051 0.803 6348 Planarity : 0.006 0.069 6974 Dihedral : 8.939 71.057 7417 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.21 % Favored : 93.47 % Rotamer: Outliers : 5.03 % Allowed : 20.82 % Favored : 74.15 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.11 (0.11), residues: 4720 helix: 0.02 (0.13), residues: 1701 sheet: -1.20 (0.18), residues: 722 loop : -2.66 (0.11), residues: 2297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 983 TYR 0.029 0.002 TYR A1067 PHE 0.042 0.002 PHE B 374 TRP 0.030 0.001 TRP A1102 HIS 0.012 0.001 HIS C 954 Details of bonding type rmsd covalent geometry : bond 0.00400 (40499) covalent geometry : angle 0.77903 (55056) SS BOND : bond 0.00784 ( 42) SS BOND : angle 2.84695 ( 84) hydrogen bonds : bond 0.05103 ( 1577) hydrogen bonds : angle 5.39153 ( 4545) link_BETA1-4 : bond 0.00696 ( 37) link_BETA1-4 : angle 2.46191 ( 111) link_NAG-ASN : bond 0.00835 ( 66) link_NAG-ASN : angle 4.15017 ( 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 535 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 212 poor density : 323 time to evaluate : 1.142 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 30 ASN cc_start: 0.8024 (OUTLIER) cc_final: 0.7354 (m-40) REVERT: A 153 MET cc_start: 0.2583 (tpt) cc_final: 0.2351 (tpt) REVERT: A 204 TYR cc_start: 0.3242 (m-80) cc_final: 0.2980 (m-10) REVERT: A 231 ILE cc_start: 0.4562 (OUTLIER) cc_final: 0.4278 (mt) REVERT: A 296 LEU cc_start: 0.7586 (mt) cc_final: 0.7338 (mp) REVERT: A 562 PHE cc_start: 0.7368 (m-80) cc_final: 0.6795 (m-80) REVERT: A 765 ARG cc_start: 0.8161 (tpp80) cc_final: 0.7756 (tpp-160) REVERT: A 823 PHE cc_start: 0.8020 (t80) cc_final: 0.7794 (t80) REVERT: B 191 GLU cc_start: 0.6733 (pm20) cc_final: 0.6498 (pm20) REVERT: B 273 ARG cc_start: 0.4491 (mmt180) cc_final: 0.4223 (mmt180) REVERT: B 984 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8259 (mp) REVERT: C 53 ASP cc_start: 0.5810 (t70) cc_final: 0.5406 (t70) REVERT: C 54 LEU cc_start: 0.7192 (mt) cc_final: 0.6268 (tp) REVERT: C 55 PHE cc_start: 0.6073 (m-80) cc_final: 0.5397 (m-10) REVERT: C 122 ASN cc_start: 0.3615 (OUTLIER) cc_final: 0.0648 (t0) REVERT: C 563 GLN cc_start: 0.4739 (mm110) cc_final: 0.4151 (mm-40) REVERT: C 917 TYR cc_start: 0.7968 (m-80) cc_final: 0.7695 (m-10) REVERT: C 945 LEU cc_start: 0.7698 (mt) cc_final: 0.7490 (tp) REVERT: C 959 LEU cc_start: 0.7235 (mp) cc_final: 0.6612 (tt) REVERT: F 323 MET cc_start: 0.2332 (mtp) cc_final: 0.1896 (mtt) REVERT: F 383 MET cc_start: 0.5685 (mtp) cc_final: 0.5168 (mtt) REVERT: F 427 ASP cc_start: 0.2147 (OUTLIER) cc_final: 0.1855 (t70) REVERT: F 455 MET cc_start: 0.5596 (tmm) cc_final: 0.5267 (ppp) REVERT: D 270 MET cc_start: 0.4376 (ttm) cc_final: 0.3928 (ttm) REVERT: D 323 MET cc_start: 0.1923 (mmt) cc_final: 0.1394 (tpp) REVERT: D 360 MET cc_start: 0.3180 (tmm) cc_final: 0.2796 (ttt) REVERT: E 474 MET cc_start: -0.1174 (mmp) cc_final: -0.1680 (tpp) outliers start: 212 outliers final: 111 residues processed: 504 average time/residue: 0.1925 time to fit residues: 168.0940 Evaluate side-chains 369 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 253 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 690 GLN Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain F residue 49 ASN Chi-restraints excluded: chain F residue 256 ILE Chi-restraints excluded: chain F residue 353 LYS Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 596 LYS Chi-restraints excluded: chain F residue 597 ASP Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain D residue 530 CYS Chi-restraints excluded: chain D residue 555 PHE Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 353 LYS Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 383 MET Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 530 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 405 optimal weight: 10.0000 chunk 73 optimal weight: 0.6980 chunk 383 optimal weight: 8.9990 chunk 40 optimal weight: 30.0000 chunk 61 optimal weight: 2.9990 chunk 304 optimal weight: 20.0000 chunk 5 optimal weight: 6.9990 chunk 178 optimal weight: 6.9990 chunk 285 optimal weight: 8.9990 chunk 152 optimal weight: 10.0000 chunk 311 optimal weight: 50.0000 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN A 536 ASN A 613 GLN A 784 GLN A 965 GLN ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN B 493 GLN B 613 GLN B 856 ASN ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 ASN C 935 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 51 ASN F 472 GLN F 493 HIS D 305 GLN D 599 ASN E 34 HIS E 599 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5045 r_free = 0.5045 target = 0.181030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.133632 restraints weight = 136193.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.132415 restraints weight = 80910.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.132619 restraints weight = 63322.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.132795 restraints weight = 49266.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.133135 restraints weight = 40556.835| |-----------------------------------------------------------------------------| r_work (final): 0.4179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6190 moved from start: 0.4832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.149 40644 Z= 0.276 Angle : 0.890 18.601 55449 Z= 0.440 Chirality : 0.053 0.803 6348 Planarity : 0.006 0.067 6974 Dihedral : 8.018 59.230 7346 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.22 % Favored : 92.50 % Rotamer: Outliers : 5.82 % Allowed : 21.15 % 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: -2.02 (0.11), residues: 4720 helix: -0.03 (0.12), residues: 1733 sheet: -1.29 (0.18), residues: 760 loop : -2.48 (0.11), residues: 2227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 559 TYR 0.052 0.002 TYR A 660 PHE 0.040 0.003 PHE C1052 TRP 0.034 0.002 TRP C 104 HIS 0.013 0.002 HIS D 239 Details of bonding type rmsd covalent geometry : bond 0.00631 (40499) covalent geometry : angle 0.85672 (55056) SS BOND : bond 0.02503 ( 42) SS BOND : angle 2.45401 ( 84) hydrogen bonds : bond 0.05764 ( 1577) hydrogen bonds : angle 5.62307 ( 4545) link_BETA1-4 : bond 0.00730 ( 37) link_BETA1-4 : angle 2.29167 ( 111) link_NAG-ASN : bond 0.00936 ( 66) link_NAG-ASN : angle 3.48161 ( 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 514 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 245 poor density : 269 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.2682 (OUTLIER) cc_final: 0.1587 (t0) REVERT: A 227 VAL cc_start: 0.7714 (OUTLIER) cc_final: 0.7062 (p) REVERT: A 231 ILE cc_start: 0.4698 (OUTLIER) cc_final: 0.4019 (mt) REVERT: A 277 LEU cc_start: 0.1238 (OUTLIER) cc_final: 0.0533 (mt) REVERT: A 765 ARG cc_start: 0.8264 (tpp80) cc_final: 0.7978 (tpp-160) REVERT: A 775 ASP cc_start: 0.8737 (OUTLIER) cc_final: 0.8081 (t70) REVERT: A 786 LYS cc_start: 0.8181 (pttt) cc_final: 0.7976 (pttm) REVERT: B 133 PHE cc_start: 0.8311 (m-80) cc_final: 0.7832 (m-80) REVERT: B 139 PRO cc_start: 0.7344 (Cg_endo) cc_final: 0.7032 (Cg_exo) REVERT: B 140 PHE cc_start: 0.4877 (p90) cc_final: 0.4650 (p90) REVERT: B 569 ILE cc_start: 0.7569 (OUTLIER) cc_final: 0.7272 (pt) REVERT: B 699 LEU cc_start: 0.7249 (OUTLIER) cc_final: 0.6947 (mp) REVERT: B 808 ASP cc_start: 0.7322 (OUTLIER) cc_final: 0.6467 (m-30) REVERT: B 854 LYS cc_start: 0.6042 (OUTLIER) cc_final: 0.5485 (tmtt) REVERT: B 1005 GLN cc_start: 0.8055 (tp40) cc_final: 0.7724 (tm-30) REVERT: B 1067 TYR cc_start: 0.8222 (OUTLIER) cc_final: 0.7686 (t80) REVERT: C 122 ASN cc_start: 0.6095 (OUTLIER) cc_final: 0.3419 (t0) REVERT: C 238 PHE cc_start: 0.7411 (p90) cc_final: 0.7006 (p90) REVERT: C 339 HIS cc_start: 0.9372 (OUTLIER) cc_final: 0.8743 (t70) REVERT: C 695 TYR cc_start: 0.7925 (OUTLIER) cc_final: 0.6838 (p90) REVERT: C 733 LYS cc_start: 0.6131 (OUTLIER) cc_final: 0.5616 (mtpt) REVERT: C 869 MET cc_start: 0.7779 (mtp) cc_final: 0.7514 (mtp) REVERT: C 935 GLN cc_start: 0.7114 (pt0) cc_final: 0.6830 (tm-30) REVERT: F 323 MET cc_start: 0.4018 (mtp) cc_final: 0.3674 (mtt) REVERT: F 427 ASP cc_start: 0.2633 (OUTLIER) cc_final: 0.2370 (t0) REVERT: D 47 SER cc_start: 0.2975 (OUTLIER) cc_final: 0.2504 (t) REVERT: D 270 MET cc_start: 0.2883 (ttm) cc_final: 0.2484 (tpp) REVERT: D 323 MET cc_start: 0.2818 (mmt) cc_final: 0.1766 (tpp) REVERT: D 383 MET cc_start: 0.7078 (ptp) cc_final: 0.6205 (ppp) REVERT: E 123 MET cc_start: -0.4808 (ptt) cc_final: -0.5015 (ptm) REVERT: E 455 MET cc_start: 0.2826 (tmm) cc_final: 0.2418 (tmm) REVERT: E 474 MET cc_start: -0.0614 (mmp) cc_final: -0.1091 (tpp) REVERT: E 579 MET cc_start: 0.7608 (mpp) cc_final: 0.6852 (ttm) outliers start: 245 outliers final: 137 residues processed: 479 average time/residue: 0.1802 time to fit residues: 152.5855 Evaluate side-chains 386 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 233 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 576 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 788 ILE Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1075 PHE Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 917 TYR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1067 TYR 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 B residue 1130 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 221 SER 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 339 HIS Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 733 LYS Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain F residue 170 SER Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 256 ILE Chi-restraints excluded: chain F residue 408 MET Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 597 ASP Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 530 CYS Chi-restraints excluded: chain E residue 139 GLN Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 530 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 183 optimal weight: 0.9990 chunk 207 optimal weight: 5.9990 chunk 161 optimal weight: 4.9990 chunk 31 optimal weight: 30.0000 chunk 232 optimal weight: 50.0000 chunk 454 optimal weight: 30.0000 chunk 112 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 177 optimal weight: 0.9980 chunk 129 optimal weight: 8.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 317 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1071 GLN A1106 GLN ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN C1002 GLN C1036 GLN E 134 ASN E 374 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5062 r_free = 0.5062 target = 0.182581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.134454 restraints weight = 135836.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.133629 restraints weight = 74857.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.135131 restraints weight = 49233.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.135367 restraints weight = 35513.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.135623 restraints weight = 31031.377| |-----------------------------------------------------------------------------| r_work (final): 0.4212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6154 moved from start: 0.5180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 40644 Z= 0.146 Angle : 0.718 19.144 55449 Z= 0.344 Chirality : 0.047 0.589 6348 Planarity : 0.004 0.068 6974 Dihedral : 7.214 59.379 7322 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.04 % Favored : 93.73 % Rotamer: Outliers : 4.39 % Allowed : 21.74 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (0.12), residues: 4720 helix: 0.59 (0.13), residues: 1721 sheet: -0.98 (0.19), residues: 717 loop : -2.28 (0.11), residues: 2282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 815 TYR 0.032 0.001 TYR A 660 PHE 0.041 0.002 PHE B 338 TRP 0.017 0.001 TRP E 271 HIS 0.005 0.001 HIS D 34 Details of bonding type rmsd covalent geometry : bond 0.00329 (40499) covalent geometry : angle 0.68392 (55056) SS BOND : bond 0.00522 ( 42) SS BOND : angle 2.19167 ( 84) hydrogen bonds : bond 0.04313 ( 1577) hydrogen bonds : angle 5.08780 ( 4545) link_BETA1-4 : bond 0.00491 ( 37) link_BETA1-4 : angle 2.13023 ( 111) link_NAG-ASN : bond 0.00647 ( 66) link_NAG-ASN : angle 3.14160 ( 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 442 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 257 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.2046 (OUTLIER) cc_final: 0.0993 (t0) REVERT: A 748 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7741 (pp20) REVERT: A 765 ARG cc_start: 0.8192 (tpp80) cc_final: 0.7923 (tpp-160) REVERT: A 917 TYR cc_start: 0.6356 (OUTLIER) cc_final: 0.5767 (m-10) REVERT: B 117 LEU cc_start: 0.8847 (tp) cc_final: 0.8546 (mt) REVERT: B 338 PHE cc_start: 0.7358 (m-80) cc_final: 0.7000 (m-80) REVERT: B 673 SER cc_start: 0.8834 (t) cc_final: 0.8632 (p) REVERT: B 854 LYS cc_start: 0.6145 (OUTLIER) cc_final: 0.5523 (tmtt) REVERT: B 1067 TYR cc_start: 0.7864 (OUTLIER) cc_final: 0.7009 (t80) REVERT: C 62 VAL cc_start: 0.7648 (m) cc_final: 0.7232 (p) REVERT: C 122 ASN cc_start: 0.5571 (OUTLIER) cc_final: 0.3169 (t0) REVERT: C 238 PHE cc_start: 0.7294 (p90) cc_final: 0.6935 (p90) REVERT: C 339 HIS cc_start: 0.9124 (OUTLIER) cc_final: 0.8722 (t70) REVERT: C 695 TYR cc_start: 0.7659 (OUTLIER) cc_final: 0.6083 (p90) REVERT: C 872 GLN cc_start: 0.6727 (OUTLIER) cc_final: 0.6273 (tt0) REVERT: C 900 MET cc_start: 0.7897 (tpp) cc_final: 0.7686 (tpp) REVERT: C 959 LEU cc_start: 0.7222 (OUTLIER) cc_final: 0.6487 (tt) REVERT: F 427 ASP cc_start: 0.2873 (OUTLIER) cc_final: 0.2581 (t0) REVERT: D 323 MET cc_start: 0.2581 (mmt) cc_final: 0.1163 (tpp) REVERT: D 383 MET cc_start: 0.6991 (ptp) cc_final: 0.6318 (ppp) REVERT: E 123 MET cc_start: -0.4731 (ptt) cc_final: -0.4936 (ptm) REVERT: E 270 MET cc_start: 0.0202 (tmm) cc_final: -0.0312 (tmm) REVERT: E 455 MET cc_start: 0.2352 (tmm) cc_final: 0.2052 (tmm) REVERT: E 474 MET cc_start: -0.0765 (mmp) cc_final: -0.1094 (tpp) REVERT: E 579 MET cc_start: 0.7484 (mpp) cc_final: 0.6838 (ttm) outliers start: 185 outliers final: 111 residues processed: 414 average time/residue: 0.1803 time to fit residues: 130.8866 Evaluate side-chains 352 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 230 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 917 TYR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 122 ASN 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 339 HIS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 872 GLN Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1047 TYR Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain F residue 256 ILE Chi-restraints excluded: chain F residue 408 MET Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 597 ASP Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 530 CYS Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 530 CYS Chi-restraints excluded: chain E residue 547 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 447 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 305 optimal weight: 40.0000 chunk 259 optimal weight: 0.2980 chunk 236 optimal weight: 40.0000 chunk 436 optimal weight: 50.0000 chunk 6 optimal weight: 6.9990 chunk 165 optimal weight: 3.9990 chunk 422 optimal weight: 50.0000 chunk 393 optimal weight: 50.0000 chunk 34 optimal weight: 6.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 417 ASN A 755 GLN A1106 GLN ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 GLN D 599 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5028 r_free = 0.5028 target = 0.179475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.130666 restraints weight = 134869.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.129791 restraints weight = 72985.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.131059 restraints weight = 50657.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.131370 restraints weight = 37111.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.131474 restraints weight = 32790.781| |-----------------------------------------------------------------------------| r_work (final): 0.4160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6176 moved from start: 0.5800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 40644 Z= 0.184 Angle : 0.744 18.298 55449 Z= 0.356 Chirality : 0.048 0.624 6348 Planarity : 0.005 0.071 6974 Dihedral : 6.882 59.570 7314 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.80 % Favored : 92.97 % Rotamer: Outliers : 4.87 % Allowed : 21.86 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.30 (0.12), residues: 4720 helix: 0.71 (0.13), residues: 1723 sheet: -0.79 (0.19), residues: 703 loop : -2.19 (0.12), residues: 2294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 237 TYR 0.031 0.002 TYR A 660 PHE 0.037 0.002 PHE B 374 TRP 0.015 0.001 TRP C 104 HIS 0.005 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00421 (40499) covalent geometry : angle 0.71361 (55056) SS BOND : bond 0.00740 ( 42) SS BOND : angle 1.83028 ( 84) hydrogen bonds : bond 0.04497 ( 1577) hydrogen bonds : angle 5.10272 ( 4545) link_BETA1-4 : bond 0.00506 ( 37) link_BETA1-4 : angle 2.09827 ( 111) link_NAG-ASN : bond 0.00617 ( 66) link_NAG-ASN : angle 3.09932 ( 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 448 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 243 time to evaluate : 1.301 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 81 ASN cc_start: -0.0300 (OUTLIER) cc_final: -0.0659 (t0) REVERT: A 697 MET cc_start: 0.7109 (tmm) cc_final: 0.6579 (tpt) REVERT: A 917 TYR cc_start: 0.6329 (OUTLIER) cc_final: 0.5698 (m-10) REVERT: B 117 LEU cc_start: 0.8824 (tp) cc_final: 0.8533 (mp) REVERT: B 338 PHE cc_start: 0.7523 (m-80) cc_final: 0.7187 (m-80) REVERT: B 554 GLU cc_start: 0.7427 (tp30) cc_final: 0.7224 (tp30) REVERT: B 673 SER cc_start: 0.8891 (t) cc_final: 0.8685 (p) REVERT: B 854 LYS cc_start: 0.6363 (OUTLIER) cc_final: 0.5606 (tmtt) REVERT: B 954 HIS cc_start: 0.7295 (OUTLIER) cc_final: 0.6821 (m-70) REVERT: B 1067 TYR cc_start: 0.8034 (OUTLIER) cc_final: 0.7431 (t80) REVERT: C 104 TRP cc_start: 0.5187 (t-100) cc_final: 0.4953 (t-100) REVERT: C 122 ASN cc_start: 0.5421 (OUTLIER) cc_final: 0.2690 (t0) REVERT: C 229 LEU cc_start: 0.7163 (mt) cc_final: 0.6385 (tp) REVERT: C 238 PHE cc_start: 0.7541 (p90) cc_final: 0.7337 (p90) REVERT: C 339 HIS cc_start: 0.9046 (OUTLIER) cc_final: 0.8806 (t70) REVERT: C 695 TYR cc_start: 0.7876 (OUTLIER) cc_final: 0.6415 (p90) REVERT: C 869 MET cc_start: 0.7714 (mtp) cc_final: 0.7410 (mtp) REVERT: C 872 GLN cc_start: 0.6794 (OUTLIER) cc_final: 0.6323 (tt0) REVERT: C 1111 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8417 (mm-30) REVERT: F 323 MET cc_start: 0.3723 (mtt) cc_final: 0.0197 (tpt) REVERT: F 383 MET cc_start: 0.4805 (mmm) cc_final: 0.4580 (mmm) REVERT: F 427 ASP cc_start: 0.3042 (OUTLIER) cc_final: 0.2763 (t0) REVERT: D 323 MET cc_start: 0.1705 (mmt) cc_final: 0.0526 (tpp) REVERT: D 383 MET cc_start: 0.6840 (ptp) cc_final: 0.6280 (ppp) REVERT: D 557 MET cc_start: 0.4674 (ppp) cc_final: 0.4082 (ptt) REVERT: E 408 MET cc_start: 0.4749 (mmt) cc_final: 0.4473 (mmm) REVERT: E 474 MET cc_start: -0.1193 (mmp) cc_final: -0.1469 (tpp) REVERT: E 579 MET cc_start: 0.7327 (mpp) cc_final: 0.6664 (ttm) outliers start: 205 outliers final: 140 residues processed: 415 average time/residue: 0.1888 time to fit residues: 138.1832 Evaluate side-chains 385 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 234 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 917 TYR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1075 PHE Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 954 HIS Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 221 SER 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 328 ARG Chi-restraints excluded: chain C residue 339 HIS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 872 GLN Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1111 GLU Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 597 ASP Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain D residue 530 CYS Chi-restraints excluded: chain D residue 607 SER Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 480 MET Chi-restraints excluded: chain E residue 530 CYS Chi-restraints excluded: chain E residue 547 SER Chi-restraints excluded: chain E residue 581 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 254 optimal weight: 5.9990 chunk 395 optimal weight: 50.0000 chunk 196 optimal weight: 7.9990 chunk 304 optimal weight: 9.9990 chunk 428 optimal weight: 40.0000 chunk 440 optimal weight: 50.0000 chunk 164 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 262 optimal weight: 0.6980 chunk 179 optimal weight: 0.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 417 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 GLN B 115 GLN ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 HIS E 96 GLN E 149 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5035 r_free = 0.5035 target = 0.179752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.133885 restraints weight = 135445.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.131807 restraints weight = 74781.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.132801 restraints weight = 56201.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.132938 restraints weight = 48248.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.133290 restraints weight = 37877.776| |-----------------------------------------------------------------------------| r_work (final): 0.4208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6129 moved from start: 0.6050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 40644 Z= 0.136 Angle : 0.680 18.926 55449 Z= 0.322 Chirality : 0.046 0.572 6348 Planarity : 0.004 0.076 6974 Dihedral : 6.579 59.512 7312 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.02 % Favored : 93.77 % Rotamer: Outliers : 3.82 % Allowed : 22.98 % Favored : 73.20 % 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: -1.06 (0.12), residues: 4720 helix: 0.98 (0.13), residues: 1717 sheet: -0.73 (0.19), residues: 694 loop : -2.08 (0.12), residues: 2309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 237 TYR 0.024 0.001 TYR A1067 PHE 0.037 0.001 PHE B 374 TRP 0.016 0.001 TRP C 104 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00306 (40499) covalent geometry : angle 0.65061 (55056) SS BOND : bond 0.00414 ( 42) SS BOND : angle 1.43440 ( 84) hydrogen bonds : bond 0.04017 ( 1577) hydrogen bonds : angle 4.91111 ( 4545) link_BETA1-4 : bond 0.00519 ( 37) link_BETA1-4 : angle 2.01933 ( 111) link_NAG-ASN : bond 0.00556 ( 66) link_NAG-ASN : angle 2.93522 ( 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 416 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 255 time to evaluate : 1.645 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 227 VAL cc_start: 0.8197 (OUTLIER) cc_final: 0.7929 (p) REVERT: A 697 MET cc_start: 0.7235 (tmm) cc_final: 0.6756 (tpt) REVERT: A 917 TYR cc_start: 0.6359 (OUTLIER) cc_final: 0.5636 (m-10) REVERT: B 338 PHE cc_start: 0.7624 (m-80) cc_final: 0.7311 (m-80) REVERT: B 577 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.7141 (ttm170) REVERT: B 854 LYS cc_start: 0.6262 (OUTLIER) cc_final: 0.5735 (tmtt) REVERT: C 45 SER cc_start: 0.8077 (m) cc_final: 0.7872 (p) REVERT: C 62 VAL cc_start: 0.7736 (m) cc_final: 0.7355 (p) REVERT: C 104 TRP cc_start: 0.5197 (t-100) cc_final: 0.4926 (t-100) REVERT: C 122 ASN cc_start: 0.5068 (OUTLIER) cc_final: 0.2098 (t0) REVERT: C 339 HIS cc_start: 0.9011 (OUTLIER) cc_final: 0.8787 (t70) REVERT: C 695 TYR cc_start: 0.7603 (OUTLIER) cc_final: 0.6201 (p90) REVERT: C 872 GLN cc_start: 0.6569 (OUTLIER) cc_final: 0.6135 (tt0) REVERT: C 959 LEU cc_start: 0.7336 (mp) cc_final: 0.6839 (tt) REVERT: F 323 MET cc_start: 0.2238 (mtt) cc_final: -0.0066 (tpt) REVERT: F 427 ASP cc_start: 0.3022 (OUTLIER) cc_final: 0.2757 (t0) REVERT: D 323 MET cc_start: 0.1814 (mmt) cc_final: 0.0733 (tpp) REVERT: D 383 MET cc_start: 0.6770 (ptp) cc_final: 0.6244 (ppp) REVERT: D 557 MET cc_start: 0.4741 (ppp) cc_final: 0.4173 (ptt) REVERT: E 474 MET cc_start: -0.1200 (mmp) cc_final: -0.1467 (tpp) REVERT: E 579 MET cc_start: 0.7197 (mpp) cc_final: 0.6629 (ttm) outliers start: 161 outliers final: 121 residues processed: 388 average time/residue: 0.2137 time to fit residues: 144.3790 Evaluate side-chains 367 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 237 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 576 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 788 ILE Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 917 TYR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1075 PHE Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 577 ARG Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 339 HIS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 872 GLN Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1013 ILE Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 597 ASP Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 480 MET Chi-restraints excluded: chain E residue 530 CYS Chi-restraints excluded: chain E residue 581 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 3 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 194 optimal weight: 0.6980 chunk 152 optimal weight: 9.9990 chunk 181 optimal weight: 0.0770 chunk 467 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 chunk 179 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 430 optimal weight: 50.0000 chunk 266 optimal weight: 0.9990 overall best weight: 1.5544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN F 149 ASN F 524 GLN D 374 HIS D 442 GLN E 522 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5038 r_free = 0.5038 target = 0.180042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.134983 restraints weight = 135652.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.131529 restraints weight = 81959.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.132435 restraints weight = 64031.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.132855 restraints weight = 44651.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.133315 restraints weight = 38155.639| |-----------------------------------------------------------------------------| r_work (final): 0.4206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6101 moved from start: 0.6263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 40644 Z= 0.121 Angle : 0.663 19.227 55449 Z= 0.311 Chirality : 0.045 0.531 6348 Planarity : 0.004 0.077 6974 Dihedral : 6.349 59.443 7312 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.42 % Favored : 93.37 % Rotamer: Outliers : 3.82 % Allowed : 23.05 % Favored : 73.13 % 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: -0.88 (0.12), residues: 4720 helix: 1.20 (0.13), residues: 1695 sheet: -0.71 (0.19), residues: 710 loop : -1.99 (0.12), residues: 2315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 582 TYR 0.021 0.001 TYR A1067 PHE 0.033 0.001 PHE B 374 TRP 0.016 0.001 TRP C 104 HIS 0.003 0.001 HIS F 241 Details of bonding type rmsd covalent geometry : bond 0.00267 (40499) covalent geometry : angle 0.63428 (55056) SS BOND : bond 0.00362 ( 42) SS BOND : angle 1.30497 ( 84) hydrogen bonds : bond 0.03750 ( 1577) hydrogen bonds : angle 4.78783 ( 4545) link_BETA1-4 : bond 0.00492 ( 37) link_BETA1-4 : angle 2.02812 ( 111) link_NAG-ASN : bond 0.00537 ( 66) link_NAG-ASN : angle 2.86344 ( 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 410 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 249 time to evaluate : 1.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.7639 (m-10) cc_final: 0.7195 (m-10) REVERT: A 227 VAL cc_start: 0.8251 (OUTLIER) cc_final: 0.8032 (t) REVERT: A 917 TYR cc_start: 0.6273 (OUTLIER) cc_final: 0.5565 (m-10) REVERT: B 117 LEU cc_start: 0.9020 (tp) cc_final: 0.8703 (mt) REVERT: B 338 PHE cc_start: 0.7656 (m-80) cc_final: 0.7354 (m-80) REVERT: B 374 PHE cc_start: 0.6800 (OUTLIER) cc_final: 0.5625 (p90) REVERT: B 554 GLU cc_start: 0.7655 (tp30) cc_final: 0.7429 (tp30) REVERT: B 577 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.7163 (ttm170) REVERT: B 854 LYS cc_start: 0.6256 (OUTLIER) cc_final: 0.5778 (tmtt) REVERT: B 912 THR cc_start: 0.8635 (OUTLIER) cc_final: 0.8330 (p) REVERT: B 954 HIS cc_start: 0.7074 (OUTLIER) cc_final: 0.6591 (m-70) REVERT: B 1067 TYR cc_start: 0.7433 (OUTLIER) cc_final: 0.6870 (t80) REVERT: C 62 VAL cc_start: 0.7732 (m) cc_final: 0.7362 (p) REVERT: C 104 TRP cc_start: 0.5244 (t-100) cc_final: 0.4921 (t-100) REVERT: C 122 ASN cc_start: 0.5256 (OUTLIER) cc_final: 0.2351 (t0) REVERT: C 229 LEU cc_start: 0.6005 (OUTLIER) cc_final: 0.5438 (mm) REVERT: C 328 ARG cc_start: 0.7221 (OUTLIER) cc_final: 0.6878 (tpt-90) REVERT: C 339 HIS cc_start: 0.9058 (OUTLIER) cc_final: 0.8826 (t70) REVERT: C 695 TYR cc_start: 0.7391 (OUTLIER) cc_final: 0.6292 (p90) REVERT: C 872 GLN cc_start: 0.6907 (OUTLIER) cc_final: 0.6467 (tt0) REVERT: C 959 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.6821 (tt) REVERT: F 323 MET cc_start: 0.2538 (mtt) cc_final: -0.0007 (tpt) REVERT: F 427 ASP cc_start: 0.3283 (OUTLIER) cc_final: 0.3049 (t0) REVERT: F 455 MET cc_start: 0.6823 (ppp) cc_final: 0.6411 (ppp) REVERT: D 323 MET cc_start: 0.2282 (mmt) cc_final: 0.1357 (tpp) REVERT: D 383 MET cc_start: 0.6777 (ptp) cc_final: 0.6314 (ppp) REVERT: D 557 MET cc_start: 0.4815 (ppp) cc_final: 0.4257 (ptt) REVERT: E 408 MET cc_start: 0.4850 (mmt) cc_final: 0.4516 (mmm) REVERT: E 474 MET cc_start: -0.1151 (mmp) cc_final: -0.1422 (tpp) REVERT: E 579 MET cc_start: 0.7167 (mpp) cc_final: 0.6606 (ttm) outliers start: 161 outliers final: 116 residues processed: 378 average time/residue: 0.2182 time to fit residues: 143.4174 Evaluate side-chains 373 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 241 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 695 TYR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 917 TYR Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1075 PHE Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 577 ARG Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 954 HIS Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 229 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 328 ARG Chi-restraints excluded: chain C residue 339 HIS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 872 GLN Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain F residue 408 MET Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 597 ASP Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 607 SER Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 581 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 383 optimal weight: 30.0000 chunk 421 optimal weight: 7.9990 chunk 472 optimal weight: 50.0000 chunk 266 optimal weight: 0.0980 chunk 405 optimal weight: 20.0000 chunk 54 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 149 optimal weight: 8.9990 chunk 430 optimal weight: 50.0000 chunk 453 optimal weight: 50.0000 overall best weight: 3.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 GLN C 919 ASN F 442 GLN D 374 HIS E 139 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5002 r_free = 0.5002 target = 0.176867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.128649 restraints weight = 135482.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.127140 restraints weight = 80540.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.127935 restraints weight = 54122.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.128076 restraints weight = 46389.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.128270 restraints weight = 36681.802| |-----------------------------------------------------------------------------| r_work (final): 0.4121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6288 moved from start: 0.6754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 40644 Z= 0.182 Angle : 0.724 18.345 55449 Z= 0.346 Chirality : 0.047 0.591 6348 Planarity : 0.005 0.077 6974 Dihedral : 6.449 59.928 7310 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.10 % Favored : 92.71 % Rotamer: Outliers : 4.08 % Allowed : 22.93 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.12), residues: 4720 helix: 0.99 (0.13), residues: 1692 sheet: -0.82 (0.19), residues: 711 loop : -2.07 (0.12), residues: 2317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG B 246 TYR 0.034 0.001 TYR A1067 PHE 0.036 0.002 PHE A 192 TRP 0.019 0.001 TRP C 104 HIS 0.012 0.001 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00423 (40499) covalent geometry : angle 0.69697 (55056) SS BOND : bond 0.00391 ( 42) SS BOND : angle 1.42455 ( 84) hydrogen bonds : bond 0.04378 ( 1577) hydrogen bonds : angle 5.07399 ( 4545) link_BETA1-4 : bond 0.00454 ( 37) link_BETA1-4 : angle 2.03901 ( 111) link_NAG-ASN : bond 0.00598 ( 66) link_NAG-ASN : angle 2.94900 ( 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 417 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 245 time to evaluate : 1.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 VAL cc_start: 0.8417 (OUTLIER) cc_final: 0.8197 (t) REVERT: A 775 ASP cc_start: 0.8762 (OUTLIER) cc_final: 0.8335 (t70) REVERT: A 917 TYR cc_start: 0.6370 (OUTLIER) cc_final: 0.5597 (m-10) REVERT: B 117 LEU cc_start: 0.8986 (tp) cc_final: 0.8696 (mt) REVERT: B 338 PHE cc_start: 0.7704 (m-80) cc_final: 0.7408 (m-80) REVERT: B 374 PHE cc_start: 0.6798 (OUTLIER) cc_final: 0.5886 (p90) REVERT: B 577 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.7249 (ttm170) REVERT: B 854 LYS cc_start: 0.6364 (OUTLIER) cc_final: 0.5853 (tmtt) REVERT: B 912 THR cc_start: 0.8778 (OUTLIER) cc_final: 0.8504 (p) REVERT: B 954 HIS cc_start: 0.7308 (OUTLIER) cc_final: 0.6888 (m-70) REVERT: B 1067 TYR cc_start: 0.7923 (OUTLIER) cc_final: 0.7382 (t80) REVERT: C 122 ASN cc_start: 0.5552 (OUTLIER) cc_final: 0.5288 (p0) REVERT: C 328 ARG cc_start: 0.7532 (OUTLIER) cc_final: 0.7164 (tpt-90) REVERT: C 339 HIS cc_start: 0.9120 (OUTLIER) cc_final: 0.8881 (t70) REVERT: C 643 PHE cc_start: 0.7568 (t80) cc_final: 0.6777 (t80) REVERT: C 695 TYR cc_start: 0.7902 (OUTLIER) cc_final: 0.6509 (p90) REVERT: C 872 GLN cc_start: 0.6972 (OUTLIER) cc_final: 0.6483 (tt0) REVERT: C 900 MET cc_start: 0.8110 (tpp) cc_final: 0.7889 (tpp) REVERT: C 959 LEU cc_start: 0.7291 (OUTLIER) cc_final: 0.6666 (tt) REVERT: C 1111 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8304 (mm-30) REVERT: F 323 MET cc_start: 0.3519 (mtt) cc_final: 0.0327 (tpt) REVERT: F 427 ASP cc_start: 0.3183 (OUTLIER) cc_final: 0.2928 (t0) REVERT: F 572 ASN cc_start: 0.5029 (m-40) cc_final: 0.4412 (t0) REVERT: D 323 MET cc_start: 0.2678 (OUTLIER) cc_final: 0.2021 (tpp) REVERT: D 383 MET cc_start: 0.6828 (ptp) cc_final: 0.6283 (ppp) REVERT: D 557 MET cc_start: 0.4928 (ppp) cc_final: 0.4361 (ptt) REVERT: E 408 MET cc_start: 0.4857 (mmt) cc_final: 0.4522 (mmm) REVERT: E 474 MET cc_start: -0.1080 (mmp) cc_final: -0.1585 (tpp) REVERT: E 579 MET cc_start: 0.7195 (mpp) cc_final: 0.6541 (ttm) outliers start: 172 outliers final: 136 residues processed: 378 average time/residue: 0.2123 time to fit residues: 140.1935 Evaluate side-chains 386 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 232 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 695 TYR 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 875 SER Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 917 TYR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1075 PHE Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 577 ARG Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 954 HIS Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1067 TYR 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 B residue 1141 LEU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 276 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 328 ARG Chi-restraints excluded: chain C residue 339 HIS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 872 GLN Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1013 ILE Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1111 GLU Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 474 MET Chi-restraints excluded: chain F residue 597 ASP Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain D residue 607 SER Chi-restraints excluded: chain E residue 139 GLN Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 547 SER Chi-restraints excluded: chain E residue 581 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 57 optimal weight: 4.9990 chunk 189 optimal weight: 0.7980 chunk 377 optimal weight: 0.9980 chunk 161 optimal weight: 6.9990 chunk 432 optimal weight: 30.0000 chunk 183 optimal weight: 1.9990 chunk 114 optimal weight: 0.4980 chunk 455 optimal weight: 20.0000 chunk 222 optimal weight: 20.0000 chunk 31 optimal weight: 9.9990 chunk 169 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A 949 GLN D 374 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5030 r_free = 0.5030 target = 0.179204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.132913 restraints weight = 135686.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.130175 restraints weight = 81318.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.131205 restraints weight = 60014.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.131427 restraints weight = 43363.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.131842 restraints weight = 35897.110| |-----------------------------------------------------------------------------| r_work (final): 0.4180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6160 moved from start: 0.6819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 40644 Z= 0.115 Angle : 0.669 19.261 55449 Z= 0.314 Chirality : 0.045 0.509 6348 Planarity : 0.004 0.081 6974 Dihedral : 6.216 59.545 7308 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.97 % Favored : 93.83 % Rotamer: Outliers : 3.28 % Allowed : 23.69 % 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: -0.79 (0.12), residues: 4720 helix: 1.30 (0.13), residues: 1678 sheet: -0.63 (0.19), residues: 697 loop : -1.94 (0.12), residues: 2345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 995 TYR 0.019 0.001 TYR A1067 PHE 0.030 0.001 PHE B 374 TRP 0.019 0.001 TRP E 477 HIS 0.015 0.001 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00252 (40499) covalent geometry : angle 0.64089 (55056) SS BOND : bond 0.00517 ( 42) SS BOND : angle 1.67765 ( 84) hydrogen bonds : bond 0.03676 ( 1577) hydrogen bonds : angle 4.80009 ( 4545) link_BETA1-4 : bond 0.00514 ( 37) link_BETA1-4 : angle 1.99631 ( 111) link_NAG-ASN : bond 0.00541 ( 66) link_NAG-ASN : angle 2.76495 ( 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 382 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 244 time to evaluate : 1.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 VAL cc_start: 0.8410 (OUTLIER) cc_final: 0.8204 (t) REVERT: A 917 TYR cc_start: 0.6285 (OUTLIER) cc_final: 0.5523 (m-10) REVERT: B 48 LEU cc_start: 0.8348 (mm) cc_final: 0.8009 (mt) REVERT: B 105 ILE cc_start: 0.8761 (pt) cc_final: 0.8521 (tp) REVERT: B 338 PHE cc_start: 0.7539 (m-80) cc_final: 0.7252 (m-80) REVERT: B 374 PHE cc_start: 0.6751 (OUTLIER) cc_final: 0.5878 (p90) REVERT: B 577 ARG cc_start: 0.7583 (OUTLIER) cc_final: 0.7252 (ttm170) REVERT: B 854 LYS cc_start: 0.6213 (OUTLIER) cc_final: 0.5804 (tmtt) REVERT: B 912 THR cc_start: 0.8653 (OUTLIER) cc_final: 0.8346 (p) REVERT: B 954 HIS cc_start: 0.7166 (OUTLIER) cc_final: 0.6697 (m-70) REVERT: B 1067 TYR cc_start: 0.7826 (OUTLIER) cc_final: 0.7035 (t80) REVERT: C 62 VAL cc_start: 0.7623 (m) cc_final: 0.7286 (p) REVERT: C 122 ASN cc_start: 0.5631 (OUTLIER) cc_final: 0.5328 (p0) REVERT: C 229 LEU cc_start: 0.5701 (OUTLIER) cc_final: 0.5225 (mm) REVERT: C 339 HIS cc_start: 0.9113 (OUTLIER) cc_final: 0.8890 (t70) REVERT: C 643 PHE cc_start: 0.7433 (t80) cc_final: 0.6692 (t80) REVERT: C 695 TYR cc_start: 0.7401 (OUTLIER) cc_final: 0.6363 (p90) REVERT: C 872 GLN cc_start: 0.6517 (OUTLIER) cc_final: 0.6086 (tt0) REVERT: C 959 LEU cc_start: 0.7065 (OUTLIER) cc_final: 0.6584 (tt) REVERT: F 323 MET cc_start: 0.3373 (mtt) cc_final: 0.0259 (tpt) REVERT: F 427 ASP cc_start: 0.2981 (OUTLIER) cc_final: 0.2766 (t0) REVERT: F 455 MET cc_start: 0.6834 (ppp) cc_final: 0.6393 (ppp) REVERT: F 572 ASN cc_start: 0.5039 (m-40) cc_final: 0.4431 (t0) REVERT: D 323 MET cc_start: 0.2772 (OUTLIER) cc_final: 0.2147 (tpp) REVERT: D 383 MET cc_start: 0.6981 (ptp) cc_final: 0.6462 (ppp) REVERT: D 557 MET cc_start: 0.4958 (ppp) cc_final: 0.4354 (ptt) REVERT: E 82 MET cc_start: 0.6502 (ptp) cc_final: 0.6283 (pmm) REVERT: E 408 MET cc_start: 0.4837 (mmt) cc_final: 0.4507 (mmm) REVERT: E 579 MET cc_start: 0.7085 (mpp) cc_final: 0.6458 (ttm) outliers start: 138 outliers final: 113 residues processed: 357 average time/residue: 0.2232 time to fit residues: 138.1990 Evaluate side-chains 367 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 238 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 695 TYR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 917 TYR Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1075 PHE Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 577 ARG Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 954 HIS Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 339 HIS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 872 GLN Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain F residue 408 MET Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 597 ASP Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain D residue 607 SER Chi-restraints excluded: chain E residue 270 MET Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 581 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 76 optimal weight: 3.9990 chunk 249 optimal weight: 7.9990 chunk 297 optimal weight: 30.0000 chunk 22 optimal weight: 2.9990 chunk 182 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 chunk 329 optimal weight: 30.0000 chunk 92 optimal weight: 0.7980 chunk 188 optimal weight: 1.9990 chunk 327 optimal weight: 50.0000 chunk 429 optimal weight: 50.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5017 r_free = 0.5017 target = 0.177959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.130878 restraints weight = 135358.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.128648 restraints weight = 82398.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.129728 restraints weight = 53515.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.129757 restraints weight = 48641.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.130100 restraints weight = 39012.814| |-----------------------------------------------------------------------------| r_work (final): 0.4155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6225 moved from start: 0.7034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 40644 Z= 0.135 Angle : 0.681 13.662 55449 Z= 0.322 Chirality : 0.046 0.518 6348 Planarity : 0.004 0.085 6974 Dihedral : 6.263 59.597 7308 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.50 % Favored : 93.31 % Rotamer: Outliers : 3.32 % Allowed : 23.64 % Favored : 73.04 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.74 (0.12), residues: 4720 helix: 1.29 (0.13), residues: 1681 sheet: -0.52 (0.19), residues: 713 loop : -1.91 (0.12), residues: 2326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 328 TYR 0.024 0.001 TYR A1067 PHE 0.031 0.002 PHE B 92 TRP 0.019 0.001 TRP E 477 HIS 0.006 0.001 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00308 (40499) covalent geometry : angle 0.65988 (55056) SS BOND : bond 0.00354 ( 42) SS BOND : angle 1.47116 ( 84) hydrogen bonds : bond 0.03815 ( 1577) hydrogen bonds : angle 4.83795 ( 4545) link_BETA1-4 : bond 0.00499 ( 37) link_BETA1-4 : angle 1.99791 ( 111) link_NAG-ASN : bond 0.00424 ( 66) link_NAG-ASN : angle 2.39925 ( 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 382 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 242 time to evaluate : 1.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 VAL cc_start: 0.8610 (OUTLIER) cc_final: 0.8387 (t) REVERT: A 917 TYR cc_start: 0.6351 (OUTLIER) cc_final: 0.5476 (m-10) REVERT: B 338 PHE cc_start: 0.7543 (m-80) cc_final: 0.7296 (m-80) REVERT: B 374 PHE cc_start: 0.5993 (OUTLIER) cc_final: 0.5464 (p90) REVERT: B 577 ARG cc_start: 0.7635 (OUTLIER) cc_final: 0.7295 (ttm170) REVERT: B 854 LYS cc_start: 0.6274 (OUTLIER) cc_final: 0.5944 (tmtt) REVERT: B 954 HIS cc_start: 0.7235 (OUTLIER) cc_final: 0.6765 (m-70) REVERT: B 1067 TYR cc_start: 0.7831 (OUTLIER) cc_final: 0.7165 (t80) REVERT: C 62 VAL cc_start: 0.7623 (m) cc_final: 0.7280 (p) REVERT: C 122 ASN cc_start: 0.5583 (OUTLIER) cc_final: 0.5287 (p0) REVERT: C 238 PHE cc_start: 0.7965 (p90) cc_final: 0.7519 (p90) REVERT: C 643 PHE cc_start: 0.7499 (t80) cc_final: 0.6522 (t80) REVERT: C 644 GLN cc_start: 0.8192 (mm-40) cc_final: 0.7488 (tm-30) REVERT: C 695 TYR cc_start: 0.7503 (OUTLIER) cc_final: 0.6208 (p90) REVERT: C 872 GLN cc_start: 0.6886 (OUTLIER) cc_final: 0.6389 (tt0) REVERT: C 959 LEU cc_start: 0.7147 (OUTLIER) cc_final: 0.6668 (tt) REVERT: C 1111 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8150 (mm-30) REVERT: F 323 MET cc_start: 0.2981 (mtt) cc_final: 0.0015 (tpt) REVERT: F 455 MET cc_start: 0.6924 (ppp) cc_final: 0.6442 (ppp) REVERT: D 323 MET cc_start: 0.2305 (OUTLIER) cc_final: 0.1675 (tpp) REVERT: D 383 MET cc_start: 0.6697 (ptp) cc_final: 0.6217 (ppp) REVERT: D 557 MET cc_start: 0.5028 (ppp) cc_final: 0.4444 (ptt) REVERT: E 82 MET cc_start: 0.6544 (ptp) cc_final: 0.6316 (pmm) REVERT: E 408 MET cc_start: 0.4936 (mmt) cc_final: 0.4627 (mmm) REVERT: E 480 MET cc_start: 0.1245 (tmm) cc_final: 0.0913 (ppp) REVERT: E 579 MET cc_start: 0.7108 (mpp) cc_final: 0.6470 (ttm) outliers start: 140 outliers final: 117 residues processed: 350 average time/residue: 0.2202 time to fit residues: 134.0639 Evaluate side-chains 364 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 234 time to evaluate : 1.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 695 TYR Chi-restraints excluded: chain A residue 697 MET 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 788 ILE Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 917 TYR Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1075 PHE Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 577 ARG Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 954 HIS Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 229 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 377 PHE Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 872 GLN Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1111 GLU Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 408 MET Chi-restraints excluded: chain F residue 597 ASP Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain D residue 607 SER Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 581 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 112 optimal weight: 5.9990 chunk 352 optimal weight: 40.0000 chunk 150 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 395 optimal weight: 2.9990 chunk 372 optimal weight: 10.0000 chunk 210 optimal weight: 10.0000 chunk 381 optimal weight: 30.0000 chunk 11 optimal weight: 10.0000 chunk 132 optimal weight: 50.0000 chunk 186 optimal weight: 5.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 49 ASN D 374 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4997 r_free = 0.4997 target = 0.176181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.131282 restraints weight = 135813.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.127181 restraints weight = 81584.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.127527 restraints weight = 72303.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.127984 restraints weight = 52420.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.128275 restraints weight = 43336.619| |-----------------------------------------------------------------------------| r_work (final): 0.4126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6296 moved from start: 0.7403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 40644 Z= 0.174 Angle : 0.719 14.358 55449 Z= 0.343 Chirality : 0.047 0.556 6348 Planarity : 0.005 0.080 6974 Dihedral : 6.375 59.841 7308 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.10 % Favored : 92.71 % Rotamer: Outliers : 3.63 % Allowed : 23.45 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.90 (0.12), residues: 4720 helix: 1.12 (0.13), residues: 1686 sheet: -0.71 (0.19), residues: 695 loop : -1.93 (0.12), residues: 2339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 237 TYR 0.033 0.001 TYR A1067 PHE 0.031 0.002 PHE B 374 TRP 0.037 0.001 TRP E 271 HIS 0.007 0.001 HIS C 339 Details of bonding type rmsd covalent geometry : bond 0.00402 (40499) covalent geometry : angle 0.69764 (55056) SS BOND : bond 0.00377 ( 42) SS BOND : angle 1.56027 ( 84) hydrogen bonds : bond 0.04170 ( 1577) hydrogen bonds : angle 5.02225 ( 4545) link_BETA1-4 : bond 0.00456 ( 37) link_BETA1-4 : angle 1.98701 ( 111) link_NAG-ASN : bond 0.00441 ( 66) link_NAG-ASN : angle 2.46923 ( 198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12400.51 seconds wall clock time: 212 minutes 23.60 seconds (12743.60 seconds total)