Starting phenix.real_space_refine on Mon Jul 6 21:11:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7y1y_33575/07_2026/7y1y_33575.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y1y_33575/07_2026/7y1y_33575.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7y1y_33575/07_2026/7y1y_33575.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y1y_33575/07_2026/7y1y_33575.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7y1y_33575/07_2026/7y1y_33575.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y1y_33575/07_2026/7y1y_33575.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7y1y_33575/07_2026/7y1y_33575.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7y1y_33575/07_2026/7y1y_33575.cif" } resolution = 3.3 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= 0.009 sd= 0.087 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 25219 2.51 5 N 6426 2.21 5 O 7716 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 82 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 39556 Number of models: 1 Model: "" Number of chains: 50 Chain: "A" Number of atoms: 7834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 999, 7834 Classifications: {'peptide': 999} Link IDs: {'PTRANS': 54, 'TRANS': 944} Chain breaks: 9 Chain: "B" Number of atoms: 7828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7828 Classifications: {'peptide': 998} Link IDs: {'PTRANS': 54, 'TRANS': 943} Chain breaks: 9 Chain: "C" Number of atoms: 7828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7828 Classifications: {'peptide': 998} Link IDs: {'PTRANS': 54, 'TRANS': 943} Chain breaks: 9 Chain: "D" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 27, 'TRANS': 569} Chain: "F" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 27, 'TRANS': 569} Chain: "H" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 27, 'TRANS': 569} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen 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 chiralities: 8 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 10.17, per 1000 atoms: 0.26 Number of scatterers: 39556 At special positions: 0 Unit cell: (183.703, 202.182, 247.836, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 195 16.00 O 7716 8.00 N 6426 7.00 C 25219 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.09 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=1.82 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=1.92 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.06 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.05 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.12 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.18 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.07 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.14 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.09 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=1.95 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=1.85 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=1.95 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.06 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.05 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.26 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=1.97 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.17 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.10 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.09 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.06 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=1.86 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.44 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.06 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.05 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.08 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.04 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.20 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.04 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS F 133 " - pdb=" SG CYS F 141 " distance=2.04 Simple disulfide: pdb=" SG CYS F 344 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 530 " - pdb=" SG CYS F 542 " distance=2.03 Simple disulfide: pdb=" SG CYS H 133 " - pdb=" SG CYS H 141 " distance=2.04 Simple disulfide: pdb=" SG CYS H 344 " - pdb=" SG CYS H 361 " distance=2.03 Simple disulfide: pdb=" SG CYS H 530 " - pdb=" SG CYS H 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 165 " " NAG A1404 " - " ASN A 234 " " NAG A1405 " - " ASN A 282 " " NAG A1406 " - " ASN A 603 " " NAG A1407 " - " ASN A 616 " " NAG A1408 " - " ASN A 657 " " NAG A1409 " - " ASN A 709 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 122 " " NAG B1403 " - " ASN B 165 " " NAG B1404 " - " ASN B 234 " " NAG B1405 " - " ASN B 282 " " NAG B1406 " - " ASN B 603 " " NAG B1407 " - " ASN B 616 " " NAG B1408 " - " ASN B 657 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 122 " " NAG C1403 " - " ASN C 165 " " NAG C1404 " - " ASN C 234 " " NAG C1405 " - " ASN C 282 " " NAG C1406 " - " ASN C 603 " " NAG C1407 " - " ASN C 616 " " NAG C1408 " - " ASN C 657 " " NAG D 701 " - " ASN D 322 " " NAG E 1 " - " ASN A 331 " " NAG F 701 " - " ASN F 322 " " NAG G 1 " - " ASN A 343 " " NAG H 701 " - " ASN H 322 " " NAG I 1 " - " ASN A 717 " " NAG J 1 " - " ASN A 801 " " NAG K 1 " - " ASN A1074 " " NAG L 1 " - " ASN A1098 " " NAG M 1 " - " ASN A1134 " " NAG N 1 " - " ASN B 331 " " NAG O 1 " - " ASN B 343 " " NAG P 1 " - " ASN B 709 " " NAG Q 1 " - " ASN B 717 " " NAG R 1 " - " ASN B 801 " " NAG S 1 " - " ASN B1074 " " NAG T 1 " - " ASN B1098 " " NAG U 1 " - " ASN B1134 " " NAG V 1 " - " ASN C 331 " " NAG W 1 " - " ASN C 343 " " NAG X 1 " - " ASN C 709 " " NAG Y 1 " - " ASN C 717 " " NAG Z 1 " - " ASN C 801 " " NAG a 1 " - " ASN C1074 " " NAG b 1 " - " ASN C1098 " " NAG c 1 " - " ASN C1134 " " NAG d 1 " - " ASN D 53 " " NAG e 1 " - " ASN D 90 " " NAG f 1 " - " ASN D 103 " " NAG g 1 " - " ASN D 432 " " NAG h 1 " - " ASN D 546 " " NAG i 1 " - " ASN F 53 " " NAG j 1 " - " ASN F 90 " " NAG k 1 " - " ASN F 103 " " NAG l 1 " - " ASN F 432 " " NAG m 1 " - " ASN F 546 " " NAG n 1 " - " ASN H 53 " " NAG o 1 " - " ASN H 90 " " NAG p 1 " - " ASN H 103 " " NAG q 1 " - " ASN H 432 " " NAG r 1 " - " ASN H 546 " Time building additional restraints: 3.73 Conformation dependent library (CDL) restraints added in 1.6 seconds 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9008 Finding SS restraints... Secondary structure from input PDB file: 149 helices and 48 sheets defined 39.4% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 299 through 304 Processing helix chain 'A' and resid 337 through 342 removed outlier: 4.509A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.680A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 385 through 389 removed outlier: 4.018A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 385 through 389' Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.693A pdb=" N GLU A 406 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.529A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.791A pdb=" N LYS A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.701A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.252A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 932 Processing helix chain 'A' and resid 933 through 940 Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.761A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 968 removed outlier: 3.703A pdb=" N SER A 968 " --> pdb=" O GLN A 965 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 965 through 968' Processing helix chain 'A' and resid 976 through 981 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.758A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.982A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 4.046A pdb=" N GLU B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.680A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 385 through 389 removed outlier: 4.018A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 385 through 389' Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.694A pdb=" N GLU B 406 " --> pdb=" O ARG B 403 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 754 removed outlier: 4.088A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.985A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 removed outlier: 3.589A pdb=" N LEU B 821 " --> pdb=" O PRO B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.516A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.576A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.649A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.591A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 4.078A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.758A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 983 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.322A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 296 through 304 removed outlier: 3.519A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.681A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 385 through 389 removed outlier: 4.018A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 385 through 389' Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.693A pdb=" N GLU C 406 " --> pdb=" O ARG C 403 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 753 Processing helix chain 'C' and resid 754 through 756 No H-bonds generated for 'chain 'C' and resid 754 through 756' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.612A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.655A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.793A pdb=" N LEU C 877 " --> pdb=" O TYR C 873 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 933 Processing helix chain 'C' and resid 933 through 939 Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.322A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 981 removed outlier: 3.810A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.931A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 Processing helix chain 'D' and resid 22 through 53 removed outlier: 3.726A pdb=" N PHE D 28 " --> pdb=" O GLN D 24 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LYS D 31 " --> pdb=" O THR D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 81 removed outlier: 4.155A pdb=" N GLN D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN D 64 " --> pdb=" O GLN D 60 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA D 65 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLN D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 101 Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 147 through 155 Processing helix chain 'D' and resid 157 through 192 removed outlier: 3.909A pdb=" N TRP D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LYS D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU D 176 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG D 177 " --> pdb=" O GLY D 173 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 4.189A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 205 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 220 through 252 removed outlier: 3.730A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLU D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS D 234 " --> pdb=" O PHE D 230 " (cutoff:3.500A) Proline residue: D 235 - end of helix removed outlier: 4.083A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ASN D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR D 252 " --> pdb=" O LEU D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 281 removed outlier: 4.178A pdb=" N SER D 280 " --> pdb=" O ASN D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 299 removed outlier: 3.785A pdb=" N VAL D 298 " --> pdb=" O THR D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 319 removed outlier: 3.729A pdb=" N ILE D 307 " --> pdb=" O ASP D 303 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL D 318 " --> pdb=" O PHE D 314 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY D 319 " --> pdb=" O PHE D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 331 removed outlier: 3.653A pdb=" N ASN D 330 " --> pdb=" O GLY D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.691A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 399 through 413 removed outlier: 3.564A pdb=" N ILE D 407 " --> pdb=" O ALA D 403 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 420 Processing helix chain 'D' and resid 431 through 444 Processing helix chain 'D' and resid 448 through 466 removed outlier: 4.606A pdb=" N PHE D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 499 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 531 removed outlier: 4.535A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 548 through 559 removed outlier: 3.973A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG D 559 " --> pdb=" O PHE D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 removed outlier: 3.743A pdb=" N GLU D 571 " --> pdb=" O THR D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 598 Proline residue: D 590 - end of helix removed outlier: 3.599A pdb=" N ASP D 597 " --> pdb=" O THR D 593 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 53 removed outlier: 3.553A pdb=" N THR F 27 " --> pdb=" O GLU F 23 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N PHE F 28 " --> pdb=" O GLN F 24 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LYS F 31 " --> pdb=" O THR F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 81 removed outlier: 4.155A pdb=" N GLN F 60 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN F 64 " --> pdb=" O GLN F 60 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA F 65 " --> pdb=" O ASN F 61 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLN F 81 " --> pdb=" O SER F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 101 Processing helix chain 'F' and resid 109 through 129 Processing helix chain 'F' and resid 147 through 155 Processing helix chain 'F' and resid 157 through 192 removed outlier: 3.909A pdb=" N TRP F 168 " --> pdb=" O ALA F 164 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG F 169 " --> pdb=" O TRP F 165 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LYS F 174 " --> pdb=" O SER F 170 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN F 175 " --> pdb=" O GLU F 171 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU F 176 " --> pdb=" O VAL F 172 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG F 177 " --> pdb=" O GLY F 173 " (cutoff:3.500A) Proline residue: F 178 - end of helix removed outlier: 4.189A pdb=" N GLU F 182 " --> pdb=" O PRO F 178 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL F 185 " --> pdb=" O GLU F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 205 Processing helix chain 'F' and resid 206 through 208 No H-bonds generated for 'chain 'F' and resid 206 through 208' Processing helix chain 'F' and resid 220 through 252 removed outlier: 3.732A pdb=" N GLU F 224 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLU F 231 " --> pdb=" O GLU F 227 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLU F 232 " --> pdb=" O HIS F 228 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE F 233 " --> pdb=" O THR F 229 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS F 234 " --> pdb=" O PHE F 230 " (cutoff:3.500A) Proline residue: F 235 - end of helix removed outlier: 4.083A pdb=" N HIS F 239 " --> pdb=" O PRO F 235 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ASN F 250 " --> pdb=" O ALA F 246 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA F 251 " --> pdb=" O LYS F 247 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR F 252 " --> pdb=" O LEU F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 267 No H-bonds generated for 'chain 'F' and resid 265 through 267' Processing helix chain 'F' and resid 275 through 281 removed outlier: 4.178A pdb=" N SER F 280 " --> pdb=" O ASN F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 299 removed outlier: 3.784A pdb=" N VAL F 298 " --> pdb=" O THR F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 319 removed outlier: 3.728A pdb=" N ILE F 307 " --> pdb=" O ASP F 303 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE F 308 " --> pdb=" O ALA F 304 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL F 318 " --> pdb=" O PHE F 314 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY F 319 " --> pdb=" O PHE F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 331 removed outlier: 3.652A pdb=" N ASN F 330 " --> pdb=" O GLY F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 385 removed outlier: 3.690A pdb=" N HIS F 373 " --> pdb=" O PHE F 369 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N HIS F 378 " --> pdb=" O HIS F 374 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N TYR F 385 " --> pdb=" O TYR F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 393 Processing helix chain 'F' and resid 399 through 413 removed outlier: 3.563A pdb=" N ILE F 407 " --> pdb=" O ALA F 403 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER F 409 " --> pdb=" O GLY F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 420 Processing helix chain 'F' and resid 431 through 444 Processing helix chain 'F' and resid 448 through 466 removed outlier: 4.607A pdb=" N PHE F 452 " --> pdb=" O GLY F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 484 Processing helix chain 'F' and resid 499 through 502 Processing helix chain 'F' and resid 503 through 508 Processing helix chain 'F' and resid 513 through 531 removed outlier: 4.534A pdb=" N THR F 519 " --> pdb=" O TYR F 515 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU F 520 " --> pdb=" O TYR F 516 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE F 523 " --> pdb=" O THR F 519 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 542 Processing helix chain 'F' and resid 548 through 559 removed outlier: 3.972A pdb=" N MET F 557 " --> pdb=" O LYS F 553 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG F 559 " --> pdb=" O PHE F 555 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 572 removed outlier: 3.743A pdb=" N GLU F 571 " --> pdb=" O THR F 567 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 598 Proline residue: F 590 - end of helix removed outlier: 3.598A pdb=" N ASP F 597 " --> pdb=" O THR F 593 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 53 removed outlier: 3.992A pdb=" N PHE H 28 " --> pdb=" O GLN H 24 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LYS H 31 " --> pdb=" O THR H 27 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 81 removed outlier: 4.156A pdb=" N GLN H 60 " --> pdb=" O GLU H 56 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN H 64 " --> pdb=" O GLN H 60 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA H 65 " --> pdb=" O ASN H 61 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLN H 81 " --> pdb=" O SER H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 101 Processing helix chain 'H' and resid 109 through 129 Processing helix chain 'H' and resid 147 through 155 Processing helix chain 'H' and resid 157 through 192 removed outlier: 3.910A pdb=" N TRP H 168 " --> pdb=" O ALA H 164 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG H 169 " --> pdb=" O TRP H 165 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LYS H 174 " --> pdb=" O SER H 170 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN H 175 " --> pdb=" O GLU H 171 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU H 176 " --> pdb=" O VAL H 172 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG H 177 " --> pdb=" O GLY H 173 " (cutoff:3.500A) Proline residue: H 178 - end of helix removed outlier: 4.189A pdb=" N GLU H 182 " --> pdb=" O PRO H 178 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL H 185 " --> pdb=" O GLU H 181 " (cutoff:3.500A) Processing helix chain 'H' and resid 199 through 205 Processing helix chain 'H' and resid 206 through 208 No H-bonds generated for 'chain 'H' and resid 206 through 208' Processing helix chain 'H' and resid 220 through 252 removed outlier: 3.731A pdb=" N GLU H 224 " --> pdb=" O GLY H 220 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLU H 231 " --> pdb=" O GLU H 227 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLU H 232 " --> pdb=" O HIS H 228 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE H 233 " --> pdb=" O THR H 229 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS H 234 " --> pdb=" O PHE H 230 " (cutoff:3.500A) Proline residue: H 235 - end of helix removed outlier: 4.084A pdb=" N HIS H 239 " --> pdb=" O PRO H 235 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ASN H 250 " --> pdb=" O ALA H 246 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA H 251 " --> pdb=" O LYS H 247 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR H 252 " --> pdb=" O LEU H 248 " (cutoff:3.500A) Processing helix chain 'H' and resid 265 through 267 No H-bonds generated for 'chain 'H' and resid 265 through 267' Processing helix chain 'H' and resid 275 through 281 removed outlier: 4.177A pdb=" N SER H 280 " --> pdb=" O ASN H 277 " (cutoff:3.500A) Processing helix chain 'H' and resid 294 through 299 removed outlier: 3.785A pdb=" N VAL H 298 " --> pdb=" O THR H 294 " (cutoff:3.500A) Processing helix chain 'H' and resid 303 through 319 removed outlier: 3.729A pdb=" N ILE H 307 " --> pdb=" O ASP H 303 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE H 308 " --> pdb=" O ALA H 304 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL H 318 " --> pdb=" O PHE H 314 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY H 319 " --> pdb=" O PHE H 315 " (cutoff:3.500A) Processing helix chain 'H' and resid 326 through 331 removed outlier: 3.653A pdb=" N ASN H 330 " --> pdb=" O GLY H 326 " (cutoff:3.500A) Processing helix chain 'H' and resid 365 through 385 removed outlier: 3.691A pdb=" N HIS H 373 " --> pdb=" O PHE H 369 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N HIS H 378 " --> pdb=" O HIS H 374 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N TYR H 385 " --> pdb=" O TYR H 381 " (cutoff:3.500A) Processing helix chain 'H' and resid 389 through 393 Processing helix chain 'H' and resid 399 through 413 removed outlier: 3.563A pdb=" N ILE H 407 " --> pdb=" O ALA H 403 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N MET H 408 " --> pdb=" O VAL H 404 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER H 409 " --> pdb=" O GLY H 405 " (cutoff:3.500A) Processing helix chain 'H' and resid 414 through 420 Processing helix chain 'H' and resid 431 through 444 Processing helix chain 'H' and resid 448 through 466 removed outlier: 4.607A pdb=" N PHE H 452 " --> pdb=" O GLY H 448 " (cutoff:3.500A) Processing helix chain 'H' and resid 472 through 484 Processing helix chain 'H' and resid 499 through 502 Processing helix chain 'H' and resid 503 through 508 Processing helix chain 'H' and resid 513 through 531 removed outlier: 4.535A pdb=" N THR H 519 " --> pdb=" O TYR H 515 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU H 520 " --> pdb=" O TYR H 516 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N PHE H 523 " --> pdb=" O THR H 519 " (cutoff:3.500A) Processing helix chain 'H' and resid 538 through 542 Processing helix chain 'H' and resid 548 through 559 removed outlier: 3.972A pdb=" N MET H 557 " --> pdb=" O LYS H 553 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG H 559 " --> pdb=" O PHE H 555 " (cutoff:3.500A) Processing helix chain 'H' and resid 565 through 572 removed outlier: 3.742A pdb=" N GLU H 571 " --> pdb=" O THR H 567 " (cutoff:3.500A) Processing helix chain 'H' and resid 581 through 598 Proline residue: H 590 - end of helix removed outlier: 3.599A pdb=" N ASP H 597 " --> pdb=" O THR H 593 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 removed outlier: 3.686A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 55 removed outlier: 7.498A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.924A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU A 117 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N GLU A 132 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ASN A 165 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N GLN A 134 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ALA A 163 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 90 through 92 removed outlier: 3.740A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 318 removed outlier: 5.428A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.545A 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: 3.777A pdb=" N LEU A 546 " --> pdb=" O PHE A 543 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 357 removed outlier: 3.797A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.803A pdb=" N ARG A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.972A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 693 " --> pdb=" O SER A 673 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.752A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.752A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.485A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.769A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.851A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 29 through 30 removed outlier: 3.852A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 49 through 55 removed outlier: 7.498A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.925A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N GLU B 132 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 90 through 92 removed outlier: 3.739A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 317 removed outlier: 5.344A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 323 through 328 removed outlier: 5.610A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 357 removed outlier: 3.797A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 removed outlier: 3.802A pdb=" N ARG B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 659 removed outlier: 5.674A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE B 693 " --> pdb=" O SER B 673 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N CYS B 671 " --> pdb=" O TYR B 695 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 703 through 704 removed outlier: 7.685A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.151A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.151A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.499A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.943A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.686A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 49 through 55 removed outlier: 7.497A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.925A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU C 117 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLU C 132 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ASN C 165 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N GLN C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ALA C 163 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 90 through 92 removed outlier: 3.739A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 316 removed outlier: 7.056A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.545A pdb=" N ASN C 542 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 357 removed outlier: 3.797A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 454 removed outlier: 3.803A pdb=" N ARG C 493 " --> pdb=" O TYR C 453 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.167A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.891A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.891A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.301A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE7, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.806A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'D' and resid 347 through 350 Processing sheet with id=AE9, first strand: chain 'F' and resid 262 through 263 removed outlier: 5.806A pdb=" N LEU F 262 " --> pdb=" O VAL F 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'F' and resid 347 through 350 Processing sheet with id=AF2, first strand: chain 'H' and resid 262 through 263 removed outlier: 5.805A pdb=" N LEU H 262 " --> pdb=" O VAL H 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'H' and resid 347 through 350 1549 hydrogen bonds defined for protein. 4335 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.70 Time building geometry restraints manager: 4.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 8727 1.33 - 1.45: 10831 1.45 - 1.58: 20673 1.58 - 1.71: 0 1.71 - 1.83: 285 Bond restraints: 40516 Sorted by residual: bond pdb=" CA SER A 698 " pdb=" C SER A 698 " ideal model delta sigma weight residual 1.522 1.442 0.080 1.20e-02 6.94e+03 4.41e+01 bond pdb=" C THR B 208 " pdb=" N PRO B 209 " ideal model delta sigma weight residual 1.329 1.387 -0.058 1.20e-02 6.94e+03 2.35e+01 bond pdb=" C THR A 208 " pdb=" N PRO A 209 " ideal model delta sigma weight residual 1.329 1.386 -0.058 1.20e-02 6.94e+03 2.30e+01 bond pdb=" C THR C 208 " pdb=" N PRO C 209 " ideal model delta sigma weight residual 1.329 1.386 -0.057 1.20e-02 6.94e+03 2.29e+01 bond pdb=" N PRO A1143 " pdb=" CD PRO A1143 " ideal model delta sigma weight residual 1.473 1.412 0.061 1.40e-02 5.10e+03 1.88e+01 ... (remaining 40511 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 54090 2.76 - 5.51: 871 5.51 - 8.27: 81 8.27 - 11.02: 25 11.02 - 13.78: 11 Bond angle restraints: 55078 Sorted by residual: angle pdb=" N CYS C 291 " pdb=" CA CYS C 291 " pdb=" C CYS C 291 " ideal model delta sigma weight residual 109.71 120.49 -10.78 1.41e+00 5.03e-01 5.85e+01 angle pdb=" N PHE H 28 " pdb=" CA PHE H 28 " pdb=" C PHE H 28 " ideal model delta sigma weight residual 111.56 100.42 11.14 1.53e+00 4.27e-01 5.30e+01 angle pdb=" N PHE F 28 " pdb=" CA PHE F 28 " pdb=" C PHE F 28 " ideal model delta sigma weight residual 111.24 102.25 8.99 1.29e+00 6.01e-01 4.85e+01 angle pdb=" N SER C 530 " pdb=" CA SER C 530 " pdb=" C SER C 530 " ideal model delta sigma weight residual 108.19 116.99 -8.80 1.29e+00 6.01e-01 4.65e+01 angle pdb=" N LEU F 45 " pdb=" CA LEU F 45 " pdb=" C LEU F 45 " ideal model delta sigma weight residual 111.07 103.90 7.17 1.07e+00 8.73e-01 4.50e+01 ... (remaining 55073 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 21230 17.68 - 35.35: 1500 35.35 - 53.03: 347 53.03 - 70.70: 85 70.70 - 88.38: 71 Dihedral angle restraints: 23233 sinusoidal: 9250 harmonic: 13983 Sorted by residual: dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual 93.00 5.37 87.63 1 1.00e+01 1.00e-02 9.20e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 166.80 -73.80 1 1.00e+01 1.00e-02 6.92e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -16.74 -69.26 1 1.00e+01 1.00e-02 6.20e+01 ... (remaining 23230 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.330: 6328 0.330 - 0.661: 12 0.661 - 0.991: 5 0.991 - 1.322: 0 1.322 - 1.652: 2 Chirality restraints: 6347 Sorted by residual: chirality pdb=" C1 NAG e 2 " pdb=" O4 NAG e 1 " pdb=" C2 NAG e 2 " pdb=" O5 NAG e 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.06 -1.34 2.00e-02 2.50e+03 4.51e+03 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.64 -0.76 2.00e-02 2.50e+03 1.43e+03 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.65 -0.75 2.00e-02 2.50e+03 1.42e+03 ... (remaining 6344 not shown) Planarity restraints: 7047 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 90 " 0.218 2.00e-02 2.50e+03 2.68e-01 8.97e+02 pdb=" CG ASN D 90 " -0.088 2.00e-02 2.50e+03 pdb=" OD1 ASN D 90 " -0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN D 90 " -0.443 2.00e-02 2.50e+03 pdb=" C1 NAG e 1 " 0.328 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 61 " 0.233 2.00e-02 2.50e+03 2.47e-01 7.60e+02 pdb=" CG ASN A 61 " -0.087 2.00e-02 2.50e+03 pdb=" OD1 ASN A 61 " -0.082 2.00e-02 2.50e+03 pdb=" ND2 ASN A 61 " -0.373 2.00e-02 2.50e+03 pdb=" C1 NAG A1401 " 0.310 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 165 " -0.146 2.00e-02 2.50e+03 2.06e-01 5.30e+02 pdb=" CG ASN C 165 " 0.067 2.00e-02 2.50e+03 pdb=" OD1 ASN C 165 " -0.045 2.00e-02 2.50e+03 pdb=" ND2 ASN C 165 " 0.359 2.00e-02 2.50e+03 pdb=" C1 NAG C1403 " -0.235 2.00e-02 2.50e+03 ... (remaining 7044 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 265 2.52 - 3.12: 30723 3.12 - 3.71: 55846 3.71 - 4.31: 81153 4.31 - 4.90: 133436 Nonbonded interactions: 301423 Sorted by model distance: nonbonded pdb=" O ILE A 332 " pdb=" OG1 THR A 333 " model vdw 1.930 3.040 nonbonded pdb=" O PRO B 527 " pdb=" NZ LYS B 528 " model vdw 2.071 3.120 nonbonded pdb=" O PHE B 497 " pdb=" CG ARG B 498 " model vdw 2.138 3.440 nonbonded pdb=" O ILE B 332 " pdb=" OG1 THR B 333 " model vdw 2.175 3.040 nonbonded pdb=" OG SER A 45 " pdb=" N SER A 46 " model vdw 2.201 3.120 ... (remaining 301418 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 939 or resid 944 through 1408)) selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.340 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: 0.050 Extract box with map and model: 0.920 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 39.840 Find NCS groups from input model: 1.590 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5444 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.405 40668 Z= 0.470 Angle : 1.234 54.469 55486 Z= 0.638 Chirality : 0.071 1.652 6347 Planarity : 0.005 0.082 6981 Dihedral : 13.791 88.377 14081 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 1.89 % Allowed : 7.12 % Favored : 91.00 % Rotamer: Outliers : 2.16 % Allowed : 5.18 % Favored : 92.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.28 (0.11), residues: 4720 helix: -1.68 (0.11), residues: 1635 sheet: -1.23 (0.19), residues: 674 loop : -2.88 (0.11), residues: 2411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 457 TYR 0.021 0.001 TYR A 495 PHE 0.016 0.001 PHE A 592 TRP 0.013 0.001 TRP H 594 HIS 0.003 0.001 HIS H 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00741 / 0.43 (40516) covalent geometry : angle 0.92020 / 0.55 (55078) SS BOND : bond 0.09864 / 5.87 ( 48) SS BOND : angle 11.96158 / 8.35 ( 96) hydrogen bonds : bond 0.20255 / 13.07 ( 1520) hydrogen bonds : angle 7.98178 / 5.42 ( 4335) link_BETA1-4 : bond 0.02362 / 1.18 ( 38) link_BETA1-4 : angle 8.32821 / 5.24 ( 114) link_NAG-ASN : bond 0.03399 / 2.03 ( 66) link_NAG-ASN : angle 9.03986 / 5.88 ( 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 852 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 761 time to evaluate : 1.553 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 615 VAL cc_start: 0.6550 (t) cc_final: 0.6346 (t) REVERT: A 1052 PHE cc_start: 0.6531 (m-80) cc_final: 0.5930 (m-80) REVERT: B 28 TYR cc_start: 0.6875 (OUTLIER) cc_final: 0.6515 (m-10) REVERT: F 29 LEU cc_start: 0.2126 (OUTLIER) cc_final: 0.1524 (tt) REVERT: F 190 MET cc_start: 0.1298 (tmm) cc_final: 0.1088 (ttp) REVERT: F 383 MET cc_start: 0.0212 (mtp) cc_final: -0.1231 (tmm) REVERT: H 474 MET cc_start: -0.3008 (mmp) cc_final: -0.3307 (tpp) outliers start: 91 outliers final: 23 residues processed: 837 average time/residue: 0.2525 time to fit residues: 344.4085 Evaluate side-chains 390 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 365 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 695 TYR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 497 PHE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 35 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 432 optimal weight: 10.0000 chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 0.7980 chunk 455 optimal weight: 9.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 6.9990 chunk 470 optimal weight: 20.0000 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN A 207 HIS A 334 ASN A 417 ASN A 477 ASN A 690 GLN A 901 GLN B 321 GLN B 417 ASN B 450 ASN B 477 ASN B 487 ASN B 506 GLN ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B1119 ASN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN C 417 ASN C 751 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN D 101 GLN D 137 ASN D 277 ASN D 442 GLN D 472 GLN F 24 GLN F 96 GLN F 101 GLN F 137 ASN F 277 ASN F 442 GLN F 472 GLN F 599 ASN H 60 GLN H 101 GLN H 137 ASN H 277 ASN H 373 HIS H 417 HIS H 442 GLN H 472 GLN H 572 ASN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4886 r_free = 0.4886 target = 0.211639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.173952 restraints weight = 91766.095| |-----------------------------------------------------------------------------| r_work (start): 0.4445 rms_B_bonded: 3.98 r_work: 0.3729 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.108 40668 Z= 0.314 Angle : 0.958 18.869 55486 Z= 0.460 Chirality : 0.055 0.454 6347 Planarity : 0.006 0.113 6981 Dihedral : 6.233 75.514 5174 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.57 % Favored : 93.01 % Rotamer: Outliers : 2.97 % Allowed : 10.93 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.54 (0.11), residues: 4720 helix: -0.70 (0.12), residues: 1692 sheet: -1.39 (0.18), residues: 642 loop : -2.57 (0.11), residues: 2386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 905 TYR 0.048 0.002 TYR A1067 PHE 0.039 0.003 PHE A 797 TRP 0.031 0.001 TRP A 64 HIS 0.012 0.002 HIS H 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00734 / 0.31 (40516) covalent geometry : angle 0.91232 / 0.45 (55078) SS BOND : bond 0.00588 / 0.36 ( 48) SS BOND : angle 2.31737 / 1.50 ( 96) hydrogen bonds : bond 0.06191 / 4.03 ( 1520) hydrogen bonds : angle 5.58981 / 3.78 ( 4335) link_BETA1-4 : bond 0.01094 / 0.65 ( 38) link_BETA1-4 : angle 2.76541 / 1.89 ( 114) link_NAG-ASN : bond 0.01266 / 0.64 ( 66) link_NAG-ASN : angle 4.32151 / 2.61 ( 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 478 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 353 time to evaluate : 1.435 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 269 TYR cc_start: 0.6177 (m-80) cc_final: 0.5578 (m-80) REVERT: A 523 THR cc_start: 0.5149 (OUTLIER) cc_final: 0.4893 (m) REVERT: A 584 ILE cc_start: 0.8746 (mp) cc_final: 0.8292 (mm) REVERT: A 725 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7609 (tt0) REVERT: A 1012 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8825 (mp) REVERT: B 49 HIS cc_start: 0.8409 (t70) cc_final: 0.8092 (t70) REVERT: B 327 VAL cc_start: 0.9095 (t) cc_final: 0.8795 (t) REVERT: B 904 TYR cc_start: 0.8325 (m-10) cc_final: 0.8115 (m-10) REVERT: C 153 MET cc_start: 0.2171 (ppp) cc_final: 0.1939 (ppp) REVERT: C 994 ASP cc_start: 0.8588 (OUTLIER) cc_final: 0.8347 (m-30) REVERT: C 1129 VAL cc_start: 0.8047 (OUTLIER) cc_final: 0.7668 (t) REVERT: D 323 MET cc_start: 0.1408 (mmm) cc_final: 0.0993 (mmm) REVERT: D 474 MET cc_start: -0.1013 (OUTLIER) cc_final: -0.1605 (tpp) REVERT: F 29 LEU cc_start: 0.2352 (OUTLIER) cc_final: 0.1743 (tt) REVERT: F 383 MET cc_start: 0.0896 (mtp) cc_final: -0.1027 (tmm) REVERT: F 582 ARG cc_start: 0.4281 (mmm160) cc_final: 0.3920 (mmt90) REVERT: H 228 HIS cc_start: 0.3032 (OUTLIER) cc_final: 0.1156 (t70) REVERT: H 249 MET cc_start: 0.3848 (mtt) cc_final: 0.3428 (ptp) REVERT: H 474 MET cc_start: -0.3664 (mmp) cc_final: -0.3989 (tpp) outliers start: 125 outliers final: 59 residues processed: 455 average time/residue: 0.2059 time to fit residues: 159.4424 Evaluate side-chains 310 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 244 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 695 TYR Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1146 ASP Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 504 PHE Chi-restraints excluded: chain D residue 557 MET Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain H residue 228 HIS Chi-restraints excluded: chain H residue 351 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 428 optimal weight: 30.0000 chunk 313 optimal weight: 40.0000 chunk 409 optimal weight: 30.0000 chunk 327 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 173 optimal weight: 0.9980 chunk 217 optimal weight: 0.9980 chunk 270 optimal weight: 0.6980 chunk 358 optimal weight: 30.0000 chunk 140 optimal weight: 30.0000 chunk 239 optimal weight: 8.9990 overall best weight: 2.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN B 134 GLN B 188 ASN B 506 GLN B1119 ASN C 87 ASN D 101 GLN F 265 HIS H 51 ASN H 58 ASN H 493 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4868 r_free = 0.4868 target = 0.209492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.171275 restraints weight = 91440.663| |-----------------------------------------------------------------------------| r_work (start): 0.4406 rms_B_bonded: 3.87 r_work: 0.3685 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.4881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 40668 Z= 0.195 Angle : 0.737 12.515 55486 Z= 0.355 Chirality : 0.048 0.475 6347 Planarity : 0.005 0.092 6981 Dihedral : 5.218 67.296 5145 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.83 % Favored : 93.86 % Rotamer: Outliers : 3.02 % Allowed : 13.33 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.11), residues: 4720 helix: -0.06 (0.13), residues: 1697 sheet: -1.13 (0.18), residues: 655 loop : -2.31 (0.11), residues: 2368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 995 TYR 0.021 0.001 TYR A1067 PHE 0.021 0.002 PHE A 802 TRP 0.019 0.001 TRP D 165 HIS 0.008 0.001 HIS A 954 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.19 (40516) covalent geometry : angle 0.69994 / 0.35 (55078) SS BOND : bond 0.00556 / 0.33 ( 48) SS BOND : angle 2.39925 / 1.64 ( 96) hydrogen bonds : bond 0.05188 / 3.37 ( 1520) hydrogen bonds : angle 5.10790 / 3.45 ( 4335) link_BETA1-4 : bond 0.00678 / 0.38 ( 38) link_BETA1-4 : angle 2.39693 / 1.72 ( 114) link_NAG-ASN : bond 0.00905 / 0.44 ( 66) link_NAG-ASN : angle 3.15235 / 1.94 ( 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 404 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 277 time to evaluate : 1.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7482 (p90) cc_final: 0.7279 (p90) REVERT: A 269 TYR cc_start: 0.6271 (m-80) cc_final: 0.5810 (m-80) REVERT: A 313 TYR cc_start: 0.8724 (m-80) cc_final: 0.8499 (m-80) REVERT: A 325 SER cc_start: 0.8080 (t) cc_final: 0.7657 (p) REVERT: A 334 ASN cc_start: 0.5570 (OUTLIER) cc_final: 0.5251 (t0) REVERT: A 523 THR cc_start: 0.4937 (OUTLIER) cc_final: 0.4607 (m) REVERT: A 725 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7570 (tt0) REVERT: A 813 SER cc_start: 0.8117 (OUTLIER) cc_final: 0.6697 (m) REVERT: A 1012 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8965 (mp) REVERT: B 49 HIS cc_start: 0.8479 (t70) cc_final: 0.8264 (t70) REVERT: B 238 PHE cc_start: 0.6632 (p90) cc_final: 0.6314 (p90) REVERT: B 699 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8771 (mt) REVERT: B 785 VAL cc_start: 0.8098 (OUTLIER) cc_final: 0.7609 (m) REVERT: B 917 TYR cc_start: 0.8797 (m-80) cc_final: 0.8422 (m-80) REVERT: C 153 MET cc_start: 0.2328 (ppp) cc_final: 0.1829 (ppp) REVERT: C 165 ASN cc_start: 0.5057 (OUTLIER) cc_final: 0.4673 (m-40) REVERT: C 237 ARG cc_start: 0.6951 (mmm-85) cc_final: 0.6550 (mtp85) REVERT: C 858 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8565 (pp) REVERT: D 249 MET cc_start: 0.4827 (mpp) cc_final: 0.3529 (tpp) REVERT: D 297 MET cc_start: -0.1932 (mtm) cc_final: -0.2260 (mtm) REVERT: D 579 MET cc_start: 0.1057 (mtp) cc_final: 0.0412 (mtp) REVERT: F 29 LEU cc_start: 0.2369 (OUTLIER) cc_final: 0.1746 (tt) REVERT: F 332 MET cc_start: -0.1460 (tpp) cc_final: -0.1684 (tpp) REVERT: F 383 MET cc_start: 0.0931 (mtp) cc_final: -0.1025 (tmm) REVERT: F 531 GLN cc_start: 0.3015 (OUTLIER) cc_final: 0.2608 (pt0) REVERT: F 582 ARG cc_start: 0.4211 (mmm160) cc_final: 0.3873 (mmt90) REVERT: H 166 GLU cc_start: 0.5524 (OUTLIER) cc_final: 0.4711 (mm-30) REVERT: H 366 MET cc_start: 0.0407 (mmm) cc_final: -0.0645 (mmm) REVERT: H 474 MET cc_start: -0.3533 (mmp) cc_final: -0.3831 (tpp) outliers start: 127 outliers final: 59 residues processed: 387 average time/residue: 0.2088 time to fit residues: 138.8549 Evaluate side-chains 311 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 241 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 695 TYR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1146 ASP Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 287 GLN Chi-restraints excluded: chain F residue 531 GLN Chi-restraints excluded: chain H residue 115 ARG Chi-restraints excluded: chain H residue 166 GLU Chi-restraints excluded: chain H residue 228 HIS Chi-restraints excluded: chain H residue 351 LEU Chi-restraints excluded: chain H residue 572 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 377 optimal weight: 40.0000 chunk 121 optimal weight: 0.9990 chunk 40 optimal weight: 30.0000 chunk 354 optimal weight: 50.0000 chunk 112 optimal weight: 7.9990 chunk 286 optimal weight: 1.9990 chunk 264 optimal weight: 1.9990 chunk 408 optimal weight: 6.9990 chunk 284 optimal weight: 0.5980 chunk 472 optimal weight: 20.0000 chunk 384 optimal weight: 30.0000 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN B 774 GLN C 751 ASN D 330 ASN D 417 HIS D 505 HIS ** H 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 599 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4862 r_free = 0.4862 target = 0.210103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.171605 restraints weight = 89776.026| |-----------------------------------------------------------------------------| r_work (start): 0.4397 rms_B_bonded: 3.91 r_work: 0.3646 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.5517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 40668 Z= 0.176 Angle : 0.707 15.476 55486 Z= 0.341 Chirality : 0.048 1.022 6347 Planarity : 0.005 0.100 6981 Dihedral : 5.000 59.128 5141 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.93 % Favored : 93.73 % Rotamer: Outliers : 2.61 % Allowed : 13.94 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.12), residues: 4720 helix: 0.21 (0.13), residues: 1721 sheet: -0.91 (0.18), residues: 695 loop : -2.19 (0.12), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 177 TYR 0.024 0.001 TYR A1067 PHE 0.031 0.002 PHE C 86 TRP 0.016 0.001 TRP C 436 HIS 0.005 0.001 HIS H 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 (40516) covalent geometry : angle 0.66925 / 0.33 (55078) SS BOND : bond 0.00705 / 0.43 ( 48) SS BOND : angle 1.95925 / 1.35 ( 96) hydrogen bonds : bond 0.04713 / 3.07 ( 1520) hydrogen bonds : angle 4.87700 / 3.29 ( 4335) link_BETA1-4 : bond 0.00582 / 0.36 ( 38) link_BETA1-4 : angle 2.09646 / 1.53 ( 114) link_NAG-ASN : bond 0.00469 / 0.26 ( 66) link_NAG-ASN : angle 3.33730 / 2.20 ( 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 364 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 254 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7715 (p90) cc_final: 0.7335 (p90) REVERT: A 325 SER cc_start: 0.8262 (t) cc_final: 0.7850 (p) REVERT: A 523 THR cc_start: 0.4913 (OUTLIER) cc_final: 0.4615 (m) REVERT: A 584 ILE cc_start: 0.8807 (mp) cc_final: 0.8365 (mm) REVERT: A 916 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8710 (tm) REVERT: A 1012 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8825 (mp) REVERT: B 49 HIS cc_start: 0.8518 (t70) cc_final: 0.8279 (t70) REVERT: B 134 GLN cc_start: 0.6932 (tm130) cc_final: 0.6700 (tm-30) REVERT: B 238 PHE cc_start: 0.7088 (p90) cc_final: 0.6710 (p90) REVERT: D 249 MET cc_start: 0.4773 (OUTLIER) cc_final: 0.3505 (tpp) REVERT: D 297 MET cc_start: -0.2025 (mtm) cc_final: -0.2434 (mtm) REVERT: D 579 MET cc_start: 0.0475 (mtp) cc_final: -0.0290 (mtp) REVERT: F 29 LEU cc_start: 0.1929 (OUTLIER) cc_final: 0.1301 (tt) REVERT: F 383 MET cc_start: 0.1035 (mtp) cc_final: -0.1019 (tmm) REVERT: F 474 MET cc_start: 0.0002 (mmm) cc_final: -0.1210 (mmm) REVERT: F 582 ARG cc_start: 0.4233 (mmm160) cc_final: 0.3920 (mmt90) REVERT: H 249 MET cc_start: 0.3272 (mtt) cc_final: 0.2729 (ptp) REVERT: H 366 MET cc_start: 0.0750 (mmm) cc_final: 0.0086 (tpt) REVERT: H 462 MET cc_start: 0.2232 (ptt) cc_final: 0.0975 (mmp) REVERT: H 474 MET cc_start: -0.3605 (mmp) cc_final: -0.3856 (tpp) REVERT: H 557 MET cc_start: 0.5650 (tmm) cc_final: 0.5329 (ppp) outliers start: 110 outliers final: 72 residues processed: 346 average time/residue: 0.2229 time to fit residues: 134.4543 Evaluate side-chains 301 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 224 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 695 TYR Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1146 ASP Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 152 MET Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 455 MET Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 228 HIS Chi-restraints excluded: chain H residue 351 LEU Chi-restraints excluded: chain H residue 572 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 212 optimal weight: 9.9990 chunk 189 optimal weight: 0.9980 chunk 111 optimal weight: 10.0000 chunk 324 optimal weight: 50.0000 chunk 27 optimal weight: 8.9990 chunk 78 optimal weight: 1.9990 chunk 289 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 114 optimal weight: 6.9990 chunk 453 optimal weight: 50.0000 chunk 384 optimal weight: 20.0000 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 544 ASN B 321 GLN ** B 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 GLN B 856 ASN C 30 ASN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN D 51 ASN F 417 HIS ** H 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 524 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4839 r_free = 0.4839 target = 0.207014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.166477 restraints weight = 89734.093| |-----------------------------------------------------------------------------| r_work (start): 0.4342 rms_B_bonded: 3.87 r_work: 0.3600 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.6123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 40668 Z= 0.203 Angle : 0.720 15.285 55486 Z= 0.345 Chirality : 0.048 0.467 6347 Planarity : 0.004 0.064 6981 Dihedral : 4.984 59.105 5141 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.66 % Favored : 94.00 % Rotamer: Outliers : 2.90 % Allowed : 14.49 % Favored : 82.61 % 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 are not related in a simple way. whole: -1.42 (0.12), residues: 4720 helix: 0.35 (0.13), residues: 1730 sheet: -0.77 (0.18), residues: 698 loop : -2.07 (0.12), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 482 TYR 0.029 0.001 TYR A1067 PHE 0.026 0.002 PHE B 898 TRP 0.016 0.001 TRP C 436 HIS 0.007 0.001 HIS C1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.20 (40516) covalent geometry : angle 0.68366 / 0.34 (55078) SS BOND : bond 0.00497 / 0.28 ( 48) SS BOND : angle 2.06556 / 1.36 ( 96) hydrogen bonds : bond 0.04749 / 3.10 ( 1520) hydrogen bonds : angle 4.85986 / 3.28 ( 4335) link_BETA1-4 : bond 0.00647 / 0.38 ( 38) link_BETA1-4 : angle 2.07695 / 1.51 ( 114) link_NAG-ASN : bond 0.00450 / 0.25 ( 66) link_NAG-ASN : angle 3.29198 / 2.03 ( 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 363 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 241 time to evaluate : 1.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7870 (p90) cc_final: 0.7466 (p90) REVERT: A 325 SER cc_start: 0.8448 (t) cc_final: 0.8005 (p) REVERT: A 329 PHE cc_start: 0.7715 (OUTLIER) cc_final: 0.7513 (m-10) REVERT: A 584 ILE cc_start: 0.8843 (mp) cc_final: 0.8401 (mm) REVERT: A 756 TYR cc_start: 0.7782 (m-10) cc_final: 0.7556 (m-80) REVERT: A 916 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8766 (tm) REVERT: A 1012 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8883 (mp) REVERT: B 238 PHE cc_start: 0.7187 (p90) cc_final: 0.6900 (p90) REVERT: C 153 MET cc_start: 0.2588 (ppp) cc_final: 0.2235 (ppp) REVERT: C 994 ASP cc_start: 0.8606 (m-30) cc_final: 0.8387 (m-30) REVERT: D 249 MET cc_start: 0.4781 (OUTLIER) cc_final: 0.3453 (tpp) REVERT: D 265 HIS cc_start: 0.1721 (p-80) cc_final: 0.1324 (p90) REVERT: D 531 GLN cc_start: 0.5220 (OUTLIER) cc_final: 0.4645 (mm-40) REVERT: D 579 MET cc_start: 0.0307 (mtp) cc_final: -0.0007 (mtp) REVERT: F 29 LEU cc_start: 0.2037 (OUTLIER) cc_final: 0.1364 (tt) REVERT: F 287 GLN cc_start: -0.0350 (OUTLIER) cc_final: -0.0593 (tp40) REVERT: F 327 PHE cc_start: -0.1169 (OUTLIER) cc_final: -0.1547 (t80) REVERT: F 383 MET cc_start: 0.1099 (mtp) cc_final: -0.1021 (tmm) REVERT: F 474 MET cc_start: 0.0163 (mmm) cc_final: -0.1028 (mmm) REVERT: F 582 ARG cc_start: 0.3975 (mmm160) cc_final: 0.3708 (mmt90) REVERT: H 366 MET cc_start: 0.0759 (mmm) cc_final: 0.0275 (mmt) REVERT: H 474 MET cc_start: -0.3458 (mmp) cc_final: -0.3862 (mmp) outliers start: 122 outliers final: 84 residues processed: 343 average time/residue: 0.2138 time to fit residues: 128.4731 Evaluate side-chains 310 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 218 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 695 TYR Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1146 ASP Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 504 PHE Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 152 MET Chi-restraints excluded: chain F residue 287 GLN Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 327 PHE Chi-restraints excluded: chain F residue 455 MET Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 203 TRP Chi-restraints excluded: chain H residue 228 HIS Chi-restraints excluded: chain H residue 351 LEU Chi-restraints excluded: chain H residue 530 CYS Chi-restraints excluded: chain H residue 572 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 244 optimal weight: 1.9990 chunk 221 optimal weight: 0.9990 chunk 464 optimal weight: 0.0970 chunk 400 optimal weight: 50.0000 chunk 318 optimal weight: 20.0000 chunk 149 optimal weight: 2.9990 chunk 157 optimal weight: 0.9990 chunk 327 optimal weight: 4.9990 chunk 217 optimal weight: 4.9990 chunk 309 optimal weight: 0.9980 chunk 210 optimal weight: 9.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 658 ASN A 978 ASN B 196 ASN ** B 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 599 ASN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4843 r_free = 0.4843 target = 0.207935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.163111 restraints weight = 88589.515| |-----------------------------------------------------------------------------| r_work (start): 0.4277 rms_B_bonded: 3.86 r_work: 0.3575 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.6321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 40668 Z= 0.116 Angle : 0.635 11.448 55486 Z= 0.304 Chirality : 0.045 0.504 6347 Planarity : 0.004 0.065 6981 Dihedral : 4.703 59.362 5141 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.00 % Favored : 94.68 % Rotamer: Outliers : 2.09 % Allowed : 15.75 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.12), residues: 4720 helix: 0.67 (0.13), residues: 1725 sheet: -0.61 (0.18), residues: 708 loop : -1.92 (0.12), residues: 2287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 482 TYR 0.022 0.001 TYR B 660 PHE 0.034 0.001 PHE C 86 TRP 0.018 0.001 TRP C 436 HIS 0.004 0.001 HIS H 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (40516) covalent geometry : angle 0.60658 / 0.30 (55078) SS BOND : bond 0.00400 / 0.22 ( 48) SS BOND : angle 1.70332 / 1.09 ( 96) hydrogen bonds : bond 0.03915 / 2.55 ( 1520) hydrogen bonds : angle 4.64935 / 3.14 ( 4335) link_BETA1-4 : bond 0.00594 / 0.35 ( 38) link_BETA1-4 : angle 1.90891 / 1.40 ( 114) link_NAG-ASN : bond 0.00406 / 0.24 ( 66) link_NAG-ASN : angle 2.66348 / 1.67 ( 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 325 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 237 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7568 (p90) cc_final: 0.7211 (p90) REVERT: A 730 SER cc_start: 0.9311 (OUTLIER) cc_final: 0.9081 (p) REVERT: B 203 ILE cc_start: 0.8770 (OUTLIER) cc_final: 0.8558 (pt) REVERT: B 238 PHE cc_start: 0.7167 (p90) cc_final: 0.6943 (p90) REVERT: B 487 ASN cc_start: -0.2856 (OUTLIER) cc_final: -0.3226 (m-40) REVERT: B 784 GLN cc_start: 0.9016 (OUTLIER) cc_final: 0.8756 (mt0) REVERT: C 153 MET cc_start: 0.2391 (ppp) cc_final: 0.2028 (ppp) REVERT: C 453 TYR cc_start: 0.6524 (p90) cc_final: 0.6259 (p90) REVERT: D 248 LEU cc_start: -0.1504 (mt) cc_final: -0.1904 (tp) REVERT: D 249 MET cc_start: 0.4714 (OUTLIER) cc_final: 0.3517 (tpp) REVERT: D 265 HIS cc_start: 0.1898 (p-80) cc_final: 0.1446 (p90) REVERT: D 531 GLN cc_start: 0.5398 (OUTLIER) cc_final: 0.4745 (mm-40) REVERT: D 579 MET cc_start: 0.0520 (mtp) cc_final: 0.0230 (mtp) REVERT: F 29 LEU cc_start: 0.2153 (OUTLIER) cc_final: 0.1567 (tt) REVERT: F 62 MET cc_start: -0.0571 (tpt) cc_final: -0.0874 (tpt) REVERT: F 287 GLN cc_start: -0.0429 (OUTLIER) cc_final: -0.0661 (tp40) REVERT: F 327 PHE cc_start: -0.1105 (OUTLIER) cc_final: -0.1434 (t80) REVERT: F 383 MET cc_start: 0.1358 (mtp) cc_final: -0.0698 (tmm) REVERT: F 474 MET cc_start: 0.0314 (mmm) cc_final: -0.0911 (mmm) REVERT: F 582 ARG cc_start: 0.3938 (mmm160) cc_final: 0.3641 (mmt90) REVERT: H 249 MET cc_start: 0.3272 (mtt) cc_final: 0.2848 (ptp) REVERT: H 366 MET cc_start: 0.0935 (mmm) cc_final: 0.0536 (mmt) REVERT: H 462 MET cc_start: 0.2599 (ptt) cc_final: 0.1558 (mmp) REVERT: H 474 MET cc_start: -0.3559 (mmp) cc_final: -0.3923 (mmp) outliers start: 88 outliers final: 60 residues processed: 308 average time/residue: 0.1931 time to fit residues: 103.8993 Evaluate side-chains 282 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 213 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 487 ASN Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 695 TYR Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1146 ASP Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 504 PHE Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 557 MET Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 152 MET Chi-restraints excluded: chain F residue 287 GLN Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 327 PHE Chi-restraints excluded: chain F residue 455 MET Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 228 HIS Chi-restraints excluded: chain H residue 293 VAL Chi-restraints excluded: chain H residue 351 LEU Chi-restraints excluded: chain H residue 425 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 64 optimal weight: 0.0980 chunk 151 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 378 optimal weight: 30.0000 chunk 140 optimal weight: 7.9990 chunk 176 optimal weight: 0.8980 chunk 164 optimal weight: 0.9990 chunk 321 optimal weight: 40.0000 chunk 52 optimal weight: 1.9990 chunk 333 optimal weight: 20.0000 chunk 43 optimal weight: 7.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 196 ASN B 580 GLN ** B 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 505 HIS F 531 GLN ** H 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4837 r_free = 0.4837 target = 0.207290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.163344 restraints weight = 88070.200| |-----------------------------------------------------------------------------| r_work (start): 0.4284 rms_B_bonded: 4.25 r_work: 0.3539 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.6545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 40668 Z= 0.130 Angle : 0.627 10.296 55486 Z= 0.301 Chirality : 0.044 0.413 6347 Planarity : 0.004 0.067 6981 Dihedral : 4.574 59.651 5139 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.13 % Favored : 94.60 % Rotamer: Outliers : 2.21 % Allowed : 15.94 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.12), residues: 4720 helix: 0.79 (0.13), residues: 1725 sheet: -0.50 (0.19), residues: 688 loop : -1.85 (0.12), residues: 2307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 482 TYR 0.021 0.001 TYR A1067 PHE 0.027 0.001 PHE C 86 TRP 0.018 0.001 TRP C 436 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (40516) covalent geometry : angle 0.60105 / 0.29 (55078) SS BOND : bond 0.00379 / 0.23 ( 48) SS BOND : angle 1.58859 / 1.02 ( 96) hydrogen bonds : bond 0.03941 / 2.57 ( 1520) hydrogen bonds : angle 4.58917 / 3.10 ( 4335) link_BETA1-4 : bond 0.00553 / 0.33 ( 38) link_BETA1-4 : angle 1.89656 / 1.39 ( 114) link_NAG-ASN : bond 0.00369 / 0.21 ( 66) link_NAG-ASN : angle 2.53394 / 1.58 ( 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 315 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 222 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7616 (p90) cc_final: 0.7190 (p90) REVERT: B 203 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8494 (pt) REVERT: B 487 ASN cc_start: -0.2405 (OUTLIER) cc_final: -0.2850 (m110) REVERT: B 816 SER cc_start: 0.8379 (p) cc_final: 0.8150 (p) REVERT: C 153 MET cc_start: 0.2502 (ppp) cc_final: 0.2070 (ppp) REVERT: C 453 TYR cc_start: 0.6592 (p90) cc_final: 0.6305 (p90) REVERT: D 248 LEU cc_start: -0.1567 (mt) cc_final: -0.1945 (tp) REVERT: D 249 MET cc_start: 0.4607 (OUTLIER) cc_final: 0.3415 (tpp) REVERT: D 265 HIS cc_start: 0.1698 (p-80) cc_final: 0.1212 (p90) REVERT: D 531 GLN cc_start: 0.5414 (OUTLIER) cc_final: 0.4635 (mm-40) REVERT: D 579 MET cc_start: 0.0341 (mtp) cc_final: 0.0041 (mtp) REVERT: F 29 LEU cc_start: 0.2068 (OUTLIER) cc_final: 0.1497 (tt) REVERT: F 327 PHE cc_start: -0.1309 (OUTLIER) cc_final: -0.1709 (t80) REVERT: F 383 MET cc_start: 0.1335 (mtp) cc_final: -0.0787 (tmm) REVERT: F 474 MET cc_start: 0.0400 (mmm) cc_final: -0.0743 (mmm) REVERT: F 582 ARG cc_start: 0.3937 (mmm160) cc_final: 0.3637 (mmt90) REVERT: H 366 MET cc_start: 0.0765 (mmm) cc_final: 0.0288 (mmt) REVERT: H 462 MET cc_start: 0.2707 (ptt) cc_final: 0.1640 (mmp) outliers start: 93 outliers final: 71 residues processed: 298 average time/residue: 0.2141 time to fit residues: 112.5769 Evaluate side-chains 286 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 209 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 487 ASN Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 695 TYR Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 504 PHE Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 557 MET Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 152 MET Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 327 PHE Chi-restraints excluded: chain F residue 455 MET Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 228 HIS Chi-restraints excluded: chain H residue 351 LEU Chi-restraints excluded: chain H residue 425 SER Chi-restraints excluded: chain H residue 572 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 392 optimal weight: 50.0000 chunk 427 optimal weight: 8.9990 chunk 104 optimal weight: 3.9990 chunk 373 optimal weight: 50.0000 chunk 423 optimal weight: 8.9990 chunk 387 optimal weight: 40.0000 chunk 370 optimal weight: 9.9990 chunk 216 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 323 optimal weight: 20.0000 chunk 255 optimal weight: 0.5980 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 957 GLN A 978 ASN B 196 ASN B 607 GLN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 89 GLN ** H 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4808 r_free = 0.4808 target = 0.205067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.159882 restraints weight = 86968.454| |-----------------------------------------------------------------------------| r_work (start): 0.4238 rms_B_bonded: 4.27 r_work: 0.3478 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.7023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 40668 Z= 0.211 Angle : 0.704 11.065 55486 Z= 0.340 Chirality : 0.047 0.393 6347 Planarity : 0.004 0.069 6981 Dihedral : 4.828 59.921 5139 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.95 % Favored : 93.81 % Rotamer: Outliers : 2.61 % Allowed : 15.51 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.12), residues: 4720 helix: 0.72 (0.13), residues: 1721 sheet: -0.61 (0.19), residues: 681 loop : -1.86 (0.12), residues: 2318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 482 TYR 0.031 0.001 TYR A1067 PHE 0.034 0.002 PHE B 238 TRP 0.021 0.001 TRP D 203 HIS 0.007 0.001 HIS C1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.21 (40516) covalent geometry : angle 0.67716 / 0.33 (55078) SS BOND : bond 0.00458 / 0.28 ( 48) SS BOND : angle 1.74985 / 1.13 ( 96) hydrogen bonds : bond 0.04833 / 3.16 ( 1520) hydrogen bonds : angle 4.86998 / 3.29 ( 4335) link_BETA1-4 : bond 0.00547 / 0.34 ( 38) link_BETA1-4 : angle 1.97647 / 1.43 ( 114) link_NAG-ASN : bond 0.00448 / 0.25 ( 66) link_NAG-ASN : angle 2.72548 / 1.70 ( 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 331 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 221 time to evaluate : 1.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.8367 (tt) cc_final: 0.7975 (mt) REVERT: A 238 PHE cc_start: 0.7987 (p90) cc_final: 0.7649 (p90) REVERT: A 266 TYR cc_start: 0.8287 (OUTLIER) cc_final: 0.8038 (m-10) REVERT: B 203 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8564 (pt) REVERT: B 784 GLN cc_start: 0.9067 (OUTLIER) cc_final: 0.8708 (mt0) REVERT: B 816 SER cc_start: 0.8546 (p) cc_final: 0.8332 (p) REVERT: B 878 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8047 (mt) REVERT: B 996 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8339 (mp) REVERT: C 153 MET cc_start: 0.2589 (ppp) cc_final: 0.1976 (ppp) REVERT: C 273 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.8108 (mmt-90) REVERT: C 453 TYR cc_start: 0.6737 (p90) cc_final: 0.6411 (p90) REVERT: C 654 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.7909 (pm20) REVERT: D 248 LEU cc_start: -0.1563 (mt) cc_final: -0.1988 (tp) REVERT: D 249 MET cc_start: 0.4568 (OUTLIER) cc_final: 0.3377 (tpp) REVERT: D 265 HIS cc_start: 0.1170 (p-80) cc_final: 0.0780 (p90) REVERT: D 531 GLN cc_start: 0.5457 (OUTLIER) cc_final: 0.4783 (mm-40) REVERT: D 579 MET cc_start: 0.0536 (mtp) cc_final: -0.0364 (mtp) REVERT: F 29 LEU cc_start: 0.2186 (OUTLIER) cc_final: 0.1600 (tt) REVERT: F 327 PHE cc_start: -0.1444 (OUTLIER) cc_final: -0.1932 (t80) REVERT: F 383 MET cc_start: 0.1378 (mtp) cc_final: -0.0564 (tmm) REVERT: F 474 MET cc_start: 0.0559 (mmm) cc_final: -0.0609 (mmm) REVERT: F 582 ARG cc_start: 0.4201 (mmm160) cc_final: 0.3897 (mmt180) REVERT: H 366 MET cc_start: 0.0799 (mmm) cc_final: 0.0486 (mmt) REVERT: H 462 MET cc_start: 0.2683 (ptt) cc_final: 0.1688 (mmp) outliers start: 110 outliers final: 80 residues processed: 312 average time/residue: 0.2224 time to fit residues: 121.1082 Evaluate side-chains 294 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 203 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 695 TYR Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1146 ASP Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 273 ARG Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 504 PHE Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 557 MET Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 152 MET Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 327 PHE Chi-restraints excluded: chain F residue 455 MET Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 203 TRP Chi-restraints excluded: chain H residue 228 HIS Chi-restraints excluded: chain H residue 351 LEU Chi-restraints excluded: chain H residue 400 PHE Chi-restraints excluded: chain H residue 425 SER Chi-restraints excluded: chain H residue 572 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 461 optimal weight: 7.9990 chunk 305 optimal weight: 7.9990 chunk 423 optimal weight: 8.9990 chunk 44 optimal weight: 20.0000 chunk 150 optimal weight: 1.9990 chunk 316 optimal weight: 50.0000 chunk 313 optimal weight: 40.0000 chunk 263 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 447 optimal weight: 7.9990 chunk 352 optimal weight: 10.0000 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 271 GLN B 394 ASN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN H 290 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4811 r_free = 0.4811 target = 0.204276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.163939 restraints weight = 87619.601| |-----------------------------------------------------------------------------| r_work (start): 0.4314 rms_B_bonded: 4.01 r_work: 0.3532 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.7351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 40668 Z= 0.234 Angle : 0.708 10.981 55486 Z= 0.342 Chirality : 0.047 0.355 6347 Planarity : 0.004 0.068 6981 Dihedral : 4.875 57.836 5139 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.00 % Favored : 93.79 % Rotamer: Outliers : 2.35 % Allowed : 16.06 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.12), residues: 4720 helix: 0.67 (0.13), residues: 1735 sheet: -0.67 (0.19), residues: 681 loop : -1.83 (0.12), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 559 TYR 0.033 0.002 TYR A1067 PHE 0.030 0.002 PHE C 86 TRP 0.024 0.001 TRP B 886 HIS 0.007 0.001 HIS C1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.23 (40516) covalent geometry : angle 0.68166 / 0.34 (55078) SS BOND : bond 0.00599 / 0.34 ( 48) SS BOND : angle 1.72609 / 1.12 ( 96) hydrogen bonds : bond 0.04740 / 3.09 ( 1520) hydrogen bonds : angle 4.92805 / 3.34 ( 4335) link_BETA1-4 : bond 0.00567 / 0.34 ( 38) link_BETA1-4 : angle 1.96658 / 1.43 ( 114) link_NAG-ASN : bond 0.00402 / 0.22 ( 66) link_NAG-ASN : angle 2.71512 / 1.68 ( 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 311 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 212 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.8288 (mm-30) cc_final: 0.7536 (mm-30) REVERT: A 238 PHE cc_start: 0.8048 (p90) cc_final: 0.7688 (p90) REVERT: B 203 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8666 (pt) REVERT: B 878 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8038 (mt) REVERT: B 990 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7025 (tp30) REVERT: C 153 MET cc_start: 0.2786 (ppp) cc_final: 0.2076 (ppp) REVERT: C 453 TYR cc_start: 0.6755 (p90) cc_final: 0.6492 (p90) REVERT: C 654 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.7993 (pm20) REVERT: D 248 LEU cc_start: -0.1684 (mt) cc_final: -0.2010 (tp) REVERT: D 249 MET cc_start: 0.4786 (OUTLIER) cc_final: 0.3456 (tpp) REVERT: D 265 HIS cc_start: 0.1124 (p-80) cc_final: 0.0787 (p90) REVERT: D 531 GLN cc_start: 0.5236 (OUTLIER) cc_final: 0.4575 (mm-40) REVERT: D 579 MET cc_start: 0.0412 (mtp) cc_final: -0.0440 (mtp) REVERT: F 474 MET cc_start: 0.0174 (mmm) cc_final: -0.0783 (mmm) REVERT: F 560 LEU cc_start: 0.4641 (mt) cc_final: 0.4377 (pp) REVERT: F 582 ARG cc_start: 0.4441 (mmm160) cc_final: 0.4125 (mmt180) REVERT: H 366 MET cc_start: 0.0834 (mmm) cc_final: 0.0497 (mmt) REVERT: H 462 MET cc_start: 0.2241 (ptt) cc_final: 0.1377 (mmp) outliers start: 99 outliers final: 82 residues processed: 295 average time/residue: 0.2150 time to fit residues: 111.7760 Evaluate side-chains 287 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 199 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 695 TYR Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1146 ASP Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 504 PHE Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 557 MET Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 152 MET Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 455 MET Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 203 TRP Chi-restraints excluded: chain H residue 228 HIS Chi-restraints excluded: chain H residue 400 PHE Chi-restraints excluded: chain H residue 425 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 119 optimal weight: 0.5980 chunk 455 optimal weight: 0.0470 chunk 117 optimal weight: 2.9990 chunk 318 optimal weight: 8.9990 chunk 468 optimal weight: 7.9990 chunk 466 optimal weight: 7.9990 chunk 439 optimal weight: 10.0000 chunk 196 optimal weight: 0.7980 chunk 291 optimal weight: 5.9990 chunk 415 optimal weight: 5.9990 chunk 161 optimal weight: 0.8980 overall best weight: 1.0680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 340 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4845 r_free = 0.4845 target = 0.206545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.167209 restraints weight = 88113.411| |-----------------------------------------------------------------------------| r_work (start): 0.4328 rms_B_bonded: 3.79 r_work: 0.3593 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.7411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 40668 Z= 0.116 Angle : 0.631 12.754 55486 Z= 0.302 Chirality : 0.044 0.299 6347 Planarity : 0.004 0.067 6981 Dihedral : 4.442 55.120 5136 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.06 % Favored : 94.72 % Rotamer: Outliers : 1.78 % Allowed : 16.70 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.12), residues: 4720 helix: 0.88 (0.13), residues: 1739 sheet: -0.52 (0.19), residues: 709 loop : -1.66 (0.13), residues: 2272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 482 TYR 0.019 0.001 TYR A1067 PHE 0.034 0.001 PHE B 238 TRP 0.025 0.001 TRP B 436 HIS 0.004 0.001 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (40516) covalent geometry : angle 0.60888 / 0.30 (55078) SS BOND : bond 0.00474 / 0.23 ( 48) SS BOND : angle 1.57640 / 0.98 ( 96) hydrogen bonds : bond 0.03781 / 2.47 ( 1520) hydrogen bonds : angle 4.69197 / 3.18 ( 4335) link_BETA1-4 : bond 0.00555 / 0.33 ( 38) link_BETA1-4 : angle 1.81603 / 1.34 ( 114) link_NAG-ASN : bond 0.00336 / 0.20 ( 66) link_NAG-ASN : angle 2.31401 / 1.43 ( 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 294 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 219 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 LEU cc_start: 0.7551 (pp) cc_final: 0.7089 (tp) REVERT: A 238 PHE cc_start: 0.7985 (p90) cc_final: 0.7651 (p90) REVERT: B 203 ILE cc_start: 0.8621 (OUTLIER) cc_final: 0.8401 (pt) REVERT: B 784 GLN cc_start: 0.9015 (OUTLIER) cc_final: 0.8737 (mt0) REVERT: B 990 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.6735 (tp30) REVERT: C 153 MET cc_start: 0.2652 (OUTLIER) cc_final: 0.2003 (ppp) REVERT: C 453 TYR cc_start: 0.6579 (p90) cc_final: 0.6344 (p90) REVERT: C 654 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8026 (pm20) REVERT: D 248 LEU cc_start: -0.1675 (mt) cc_final: -0.2035 (tp) REVERT: D 249 MET cc_start: 0.4713 (OUTLIER) cc_final: 0.3440 (tpp) REVERT: D 265 HIS cc_start: 0.1101 (p-80) cc_final: 0.0785 (p90) REVERT: D 531 GLN cc_start: 0.5084 (OUTLIER) cc_final: 0.4486 (mm-40) REVERT: D 579 MET cc_start: 0.0359 (mtp) cc_final: -0.0460 (mtp) REVERT: F 474 MET cc_start: 0.0262 (mmm) cc_final: -0.0744 (mmm) REVERT: F 557 MET cc_start: 0.2526 (ttt) cc_final: 0.2301 (ttt) REVERT: F 560 LEU cc_start: 0.4578 (mt) cc_final: 0.4279 (pp) REVERT: F 582 ARG cc_start: 0.4372 (mmm160) cc_final: 0.4050 (mmt180) REVERT: H 366 MET cc_start: 0.0683 (mmm) cc_final: 0.0345 (mmt) REVERT: H 462 MET cc_start: 0.2417 (ptt) cc_final: 0.1739 (mmp) outliers start: 75 outliers final: 62 residues processed: 281 average time/residue: 0.2233 time to fit residues: 109.4307 Evaluate side-chains 271 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 202 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 695 TYR Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 504 PHE Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 557 MET Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 152 MET Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 455 MET Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 228 HIS Chi-restraints excluded: chain H residue 400 PHE Chi-restraints excluded: chain H residue 425 SER Chi-restraints excluded: chain H residue 572 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 180 optimal weight: 0.6980 chunk 241 optimal weight: 50.0000 chunk 16 optimal weight: 0.0870 chunk 26 optimal weight: 1.9990 chunk 367 optimal weight: 40.0000 chunk 446 optimal weight: 8.9990 chunk 13 optimal weight: 0.3980 chunk 12 optimal weight: 8.9990 chunk 32 optimal weight: 8.9990 chunk 470 optimal weight: 10.0000 chunk 400 optimal weight: 40.0000 overall best weight: 2.4362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4833 r_free = 0.4833 target = 0.205388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.166377 restraints weight = 88128.906| |-----------------------------------------------------------------------------| r_work (start): 0.4323 rms_B_bonded: 3.97 r_work: 0.3552 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.7536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 40668 Z= 0.158 Angle : 0.649 15.080 55486 Z= 0.311 Chirality : 0.045 0.306 6347 Planarity : 0.004 0.067 6981 Dihedral : 4.449 57.057 5136 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.59 % Favored : 94.19 % Rotamer: Outliers : 1.78 % Allowed : 16.86 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.12), residues: 4720 helix: 0.88 (0.13), residues: 1742 sheet: -0.50 (0.19), residues: 679 loop : -1.65 (0.13), residues: 2299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 102 TYR 0.024 0.001 TYR A1067 PHE 0.035 0.002 PHE B 238 TRP 0.020 0.001 TRP C 436 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (40516) covalent geometry : angle 0.62700 / 0.31 (55078) SS BOND : bond 0.00404 / 0.24 ( 48) SS BOND : angle 1.51501 / 0.96 ( 96) hydrogen bonds : bond 0.04136 / 2.69 ( 1520) hydrogen bonds : angle 4.72647 / 3.20 ( 4335) link_BETA1-4 : bond 0.00526 / 0.32 ( 38) link_BETA1-4 : angle 1.84464 / 1.36 ( 114) link_NAG-ASN : bond 0.00323 / 0.18 ( 66) link_NAG-ASN : angle 2.38438 / 1.47 ( 198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12479.67 seconds wall clock time: 213 minutes 40.26 seconds (12820.26 seconds total)