Starting phenix.real_space_refine on Fri Feb 6 18:40:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7krs_23012/02_2026/7krs_23012_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7krs_23012/02_2026/7krs_23012.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7krs_23012/02_2026/7krs_23012.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7krs_23012/02_2026/7krs_23012.map" model { file = "/net/cci-nas-00/data/ceres_data/7krs_23012/02_2026/7krs_23012_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7krs_23012/02_2026/7krs_23012_neut.cif" } resolution = 3.2 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= 0.000 sd= 0.002 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 118 5.16 5 C 17333 2.51 5 N 4415 2.21 5 O 5432 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27298 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 8665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1109, 8665 Classifications: {'peptide': 1109} Link IDs: {'PTRANS': 52, 'TRANS': 1056} Chain breaks: 4 Chain: "B" Number of atoms: 8590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8590 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 52, 'TRANS': 1045} Chain breaks: 5 Chain: "C" Number of atoms: 8678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1109, 8678 Classifications: {'peptide': 1109} Link IDs: {'PTRANS': 53, 'TRANS': 1055} Chain breaks: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "l" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 7.02, per 1000 atoms: 0.26 Number of scatterers: 27298 At special positions: 0 Unit cell: (148.5, 151.8, 202.125, 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 118 16.00 O 5432 8.00 N 4415 7.00 C 17333 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.01 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.95 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.99 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.00 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.68 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.12 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.01 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 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=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.00 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.79 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.04 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.01 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.94 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.05 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.01 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 ALPHA1-4 " NAG N 2 " - " MAN N 3 " " NAG Z 2 " - " MAN Z 3 " " NAG l 2 " - " MAN l 3 " BETA1-4 " 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 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 " BETA1-6 " NAG M 1 " - " FUC M 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG Y 1 " - " FUC Y 3 " " NAG k 1 " - " FUC k 3 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 149 " " NAG A1403 " - " ASN A 343 " " NAG A1404 " - " ASN A 603 " " NAG A1405 " - " ASN A 657 " " NAG A1406 " - " ASN A 709 " " NAG A1407 " - " ASN A1158 " " NAG B1401 " - " ASN B 61 " " NAG B1403 " - " ASN B 343 " " NAG B1404 " - " ASN B 603 " " NAG B1405 " - " ASN B 657 " " NAG B1406 " - " ASN B 709 " " NAG B1407 " - " ASN B1158 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 149 " " NAG C1403 " - " ASN C 343 " " NAG C1404 " - " ASN C 603 " " NAG C1405 " - " ASN C 657 " " NAG C1406 " - " ASN C 709 " " NAG C1407 " - " ASN C1158 " " NAG D 1 " - " ASN A 17 " " NAG E 1 " - " ASN A 122 " " NAG F 1 " - " ASN A 165 " " NAG G 1 " - " ASN A 234 " " NAG H 1 " - " ASN A 282 " " NAG I 1 " - " ASN A 331 " " NAG J 1 " - " ASN A 616 " " NAG K 1 " - " ASN A 717 " " NAG L 1 " - " ASN A 801 " " NAG M 1 " - " ASN A1074 " " NAG N 1 " - " ASN A1098 " " NAG O 1 " - " ASN A1134 " " NAG Q 1 " - " ASN B 122 " " NAG R 1 " - " ASN B 165 " " NAG S 1 " - " ASN B 234 " " NAG T 1 " - " ASN B 282 " " NAG U 1 " - " ASN B 331 " " NAG V 1 " - " ASN B 616 " " NAG W 1 " - " ASN B 717 " " NAG X 1 " - " ASN B 801 " " NAG Y 1 " - " ASN B1074 " " NAG Z 1 " - " ASN B1098 " " NAG a 1 " - " ASN B1134 " " NAG b 1 " - " ASN C 17 " " NAG c 1 " - " ASN C 122 " " NAG d 1 " - " ASN C 165 " " NAG e 1 " - " ASN C 234 " " NAG g 1 " - " ASN C 331 " " NAG h 1 " - " ASN C 616 " " NAG i 1 " - " ASN C 717 " " NAG j 1 " - " ASN C 801 " " NAG k 1 " - " ASN C1074 " " NAG l 1 " - " ASN C1098 " " NAG m 1 " - " ASN C1134 " Time building additional restraints: 2.54 Conformation dependent library (CDL) restraints added in 1.2 seconds 6568 Ramachandran restraints generated. 3284 Oldfield, 0 Emsley, 3284 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6208 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 50 sheets defined 27.2% alpha, 30.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.587A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 385 through 390 removed outlier: 4.076A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.912A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 623 Proline residue: A 621 - end of helix Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 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: 3.567A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 3.997A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.755A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 855 removed outlier: 3.787A pdb=" N ALA A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.817A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.624A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.526A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.146A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 987 through 1033 removed outlier: 3.955A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1160 removed outlier: 4.176A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE A1148 " --> pdb=" O GLU A1144 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR A1155 " --> pdb=" O GLU A1151 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.560A 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 383 through 389 removed outlier: 4.528A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 removed outlier: 3.876A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 634 through 639 removed outlier: 3.850A pdb=" N THR B 638 " --> pdb=" O VAL B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 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: 3.876A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.163A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.738A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS B 825 " --> pdb=" O LEU B 821 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 853 through 856 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.710A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.682A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.861A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.856A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA B1016 " --> pdb=" O LEU B1012 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1160 removed outlier: 4.099A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N PHE B1148 " --> pdb=" O GLU B1144 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU B1152 " --> pdb=" O PHE B1148 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 364 through 370 removed outlier: 3.829A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.309A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 411 removed outlier: 3.520A pdb=" N ILE C 410 " --> pdb=" O GLU C 406 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ALA C 411 " --> pdb=" O VAL C 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 406 through 411' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 618 through 623 Processing helix chain 'C' and resid 634 through 639 removed outlier: 3.849A pdb=" N THR C 638 " --> pdb=" O VAL C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.711A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 782 removed outlier: 4.579A pdb=" N THR C 761 " --> pdb=" O GLY C 757 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.447A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.567A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 856 removed outlier: 3.602A pdb=" N ASN C 856 " --> pdb=" O ALA C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.636A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.144A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.708A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (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 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.571A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1127 through 1129 No H-bonds generated for 'chain 'C' and resid 1127 through 1129' Processing helix chain 'C' and resid 1140 through 1159 removed outlier: 4.128A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N PHE C1148 " --> pdb=" O GLU C1144 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.129A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.129A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.432A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.860A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 removed outlier: 13.024A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 12.442A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 9.728A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N CYS A 136 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N SER A 161 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ASP A 138 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL A 159 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.710A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 3.627A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.119A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.714A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N ASN A 437 " --> pdb=" O PHE A 374 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N PHE A 374 " --> pdb=" O ASN A 437 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.313A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.651A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 removed outlier: 4.071A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.898A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.354A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.500A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.557A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.440A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.226A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 11.315A pdb=" N SER B 221 " --> pdb=" O PRO B 209 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ARG B 34 " --> pdb=" O SER B 221 " (cutoff:3.500A) removed outlier: 8.810A pdb=" N LEU B 223 " --> pdb=" O ARG B 34 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.844A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.493A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N CYS B 136 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N SER B 161 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 12.631A pdb=" N PHE B 238 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 12.571A pdb=" N PHE B 135 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 12.549A pdb=" N THR B 240 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 11.075A pdb=" N ASN B 137 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 11.404A pdb=" N LEU B 242 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N CYS B 136 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N SER B 161 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 3.966A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.144A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.144A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 357 removed outlier: 7.030A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 357 removed outlier: 6.798A pdb=" N GLU B 516 " --> pdb=" O THR B 393 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL B 395 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N SER B 514 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ALA B 397 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL B 512 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N SER B 399 " --> pdb=" O VAL B 510 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL B 510 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N VAL B 401 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N TYR B 508 " --> pdb=" O VAL B 401 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.103A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.970A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.046A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.212A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 5.419A pdb=" N VAL B1122 " --> pdb=" O PHE B1089 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N PHE B1089 " --> pdb=" O VAL B1122 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N GLY B1124 " --> pdb=" O ALA B1087 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.943A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.943A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.691A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 83 through 85 removed outlier: 12.568A pdb=" N PHE C 238 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 12.006A pdb=" N PHE C 135 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 12.508A pdb=" N THR C 240 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 10.717A pdb=" N ASN C 137 " --> pdb=" O THR C 240 " (cutoff:3.500A) removed outlier: 10.601A pdb=" N LEU C 242 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 10.172A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 10.769A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N HIS C 146 " --> pdb=" O TRP C 152 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N TRP C 152 " --> pdb=" O HIS C 146 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.601A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.275A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE7, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.143A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF1, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.057A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.515A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.744A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.212A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.615A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1127 hydrogen bonds defined for protein. 3093 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: 7.30 Time building geometry restraints manager: 3.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4739 1.31 - 1.44: 7332 1.44 - 1.57: 15673 1.57 - 1.70: 5 1.70 - 1.83: 148 Bond restraints: 27897 Sorted by residual: bond pdb=" C THR A 124 " pdb=" N ASN A 125 " ideal model delta sigma weight residual 1.331 1.395 -0.064 1.30e-02 5.92e+03 2.42e+01 bond pdb=" CA PRO A 792 " pdb=" C PRO A 792 " ideal model delta sigma weight residual 1.514 1.539 -0.024 5.50e-03 3.31e+04 1.98e+01 bond pdb=" N CYS A 391 " pdb=" CA CYS A 391 " ideal model delta sigma weight residual 1.454 1.509 -0.054 1.23e-02 6.61e+03 1.96e+01 bond pdb=" N ILE C 624 " pdb=" CA ILE C 624 " ideal model delta sigma weight residual 1.459 1.513 -0.054 1.25e-02 6.40e+03 1.85e+01 bond pdb=" C5 NAG m 2 " pdb=" O5 NAG m 2 " ideal model delta sigma weight residual 1.413 1.499 -0.086 2.00e-02 2.50e+03 1.83e+01 ... (remaining 27892 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 28704 2.05 - 4.10: 8108 4.10 - 6.15: 1022 6.15 - 8.21: 97 8.21 - 10.26: 14 Bond angle restraints: 37945 Sorted by residual: angle pdb=" CA ASN A 125 " pdb=" CB ASN A 125 " pdb=" CG ASN A 125 " ideal model delta sigma weight residual 112.60 121.79 -9.19 1.00e+00 1.00e+00 8.45e+01 angle pdb=" N ASN B 603 " pdb=" CA ASN B 603 " pdb=" C ASN B 603 " ideal model delta sigma weight residual 111.07 103.69 7.38 1.07e+00 8.73e-01 4.76e+01 angle pdb=" CA ASP A 796 " pdb=" CB ASP A 796 " pdb=" CG ASP A 796 " ideal model delta sigma weight residual 112.60 119.48 -6.88 1.00e+00 1.00e+00 4.73e+01 angle pdb=" N TYR C 421 " pdb=" CA TYR C 421 " pdb=" C TYR C 421 " ideal model delta sigma weight residual 113.97 122.50 -8.53 1.28e+00 6.10e-01 4.44e+01 angle pdb=" CA ASP C 985 " pdb=" CB ASP C 985 " pdb=" CG ASP C 985 " ideal model delta sigma weight residual 112.60 119.08 -6.48 1.00e+00 1.00e+00 4.20e+01 ... (remaining 37940 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.91: 16954 23.91 - 47.82: 733 47.82 - 71.73: 156 71.73 - 95.64: 31 95.64 - 119.55: 12 Dihedral angle restraints: 17886 sinusoidal: 8233 harmonic: 9653 Sorted by residual: dihedral pdb=" CB CYS C 15 " pdb=" SG CYS C 15 " pdb=" SG CYS C 136 " pdb=" CB CYS C 136 " ideal model delta sinusoidal sigma weight residual -86.00 -161.81 75.81 1 1.00e+01 1.00e-02 7.25e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -155.19 69.19 1 1.00e+01 1.00e-02 6.19e+01 dihedral pdb=" CB CYS A 840 " pdb=" SG CYS A 840 " pdb=" SG CYS A 851 " pdb=" CB CYS A 851 " ideal model delta sinusoidal sigma weight residual -86.00 -152.20 66.20 1 1.00e+01 1.00e-02 5.73e+01 ... (remaining 17883 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.866: 4564 0.866 - 1.732: 6 1.732 - 2.598: 2 2.598 - 3.464: 0 3.464 - 4.330: 1 Chirality restraints: 4573 Sorted by residual: chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN B 165 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 1.93 -4.33 2.00e-01 2.50e+01 4.69e+02 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.10 -2.30 2.00e-01 2.50e+01 1.33e+02 chirality pdb=" C1 NAG k 1 " pdb=" ND2 ASN C1074 " pdb=" C2 NAG k 1 " pdb=" O5 NAG k 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.61 -1.79 2.00e-01 2.50e+01 8.03e+01 ... (remaining 4570 not shown) Planarity restraints: 4829 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " 0.212 2.00e-02 2.50e+03 2.33e-01 6.81e+02 pdb=" CG ASN C 331 " -0.089 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " -0.036 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " -0.371 2.00e-02 2.50e+03 pdb=" C1 NAG g 1 " 0.285 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 17 " 0.238 2.00e-02 2.50e+03 2.12e-01 5.60e+02 pdb=" CG ASN C 17 " -0.073 2.00e-02 2.50e+03 pdb=" OD1 ASN C 17 " -0.108 2.00e-02 2.50e+03 pdb=" ND2 ASN C 17 " -0.301 2.00e-02 2.50e+03 pdb=" C1 NAG b 1 " 0.244 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C1158 " -0.186 2.00e-02 2.50e+03 1.80e-01 4.06e+02 pdb=" CG ASN C1158 " 0.059 2.00e-02 2.50e+03 pdb=" OD1 ASN C1158 " 0.081 2.00e-02 2.50e+03 pdb=" ND2 ASN C1158 " 0.264 2.00e-02 2.50e+03 pdb=" C1 NAG C1407 " -0.219 2.00e-02 2.50e+03 ... (remaining 4826 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.49: 52 2.49 - 3.09: 17858 3.09 - 3.69: 39321 3.69 - 4.30: 61703 4.30 - 4.90: 100326 Nonbonded interactions: 219260 Sorted by model distance: nonbonded pdb=" O THR A 108 " pdb=" NH2 ARG A 237 " model vdw 1.884 3.120 nonbonded pdb=" CE1 TYR A 28 " pdb=" OG1 THR A 63 " model vdw 1.941 3.340 nonbonded pdb=" OD1 ASP A 442 " pdb=" NH2 ARG A 509 " model vdw 1.986 3.120 nonbonded pdb=" OG1 THR B 645 " pdb=" O GLY B 648 " model vdw 2.017 3.040 nonbonded pdb=" ND2 ASN B 17 " pdb=" C1 NAG P 1 " model vdw 2.048 3.550 ... (remaining 219255 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 14 through 68 or resid 77 through 835 or resid 851 through \ 1407)) selection = (chain 'B' and (resid 14 through 623 or resid 636 through 1407)) selection = (chain 'C' and (resid 14 through 68 or resid 77 through 623 or resid 636 through \ 835 or resid 851 through 1407)) } ncs_group { reference = 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 '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 '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 'm' } ncs_group { reference = (chain 'M' and resid 1 through 2) selection = (chain 'N' and resid 1 through 2) selection = (chain 'Y' and resid 1 through 2) selection = (chain 'Z' and resid 1 through 2) selection = (chain 'k' and resid 1 through 2) selection = (chain 'l' and resid 1 through 2) } 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: 8.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.620 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 28.810 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.090 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 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 : 0.019 0.961 28036 Z= 1.021 Angle : 1.989 49.005 38319 Z= 1.239 Chirality : 0.136 4.330 4573 Planarity : 0.012 0.134 4775 Dihedral : 14.270 119.545 11549 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.79 % Allowed : 5.82 % Favored : 93.39 % Rotamer: Outliers : 2.28 % Allowed : 4.81 % Favored : 92.91 % Cbeta Deviations : 0.23 % 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: -1.98 (0.13), residues: 3284 helix: -1.76 (0.15), residues: 730 sheet: -0.03 (0.20), residues: 605 loop : -1.59 (0.13), residues: 1949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 403 TYR 0.113 0.019 TYR C 396 PHE 0.104 0.015 PHE B 592 TRP 0.091 0.022 TRP C 104 HIS 0.013 0.003 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.01339 (27897) covalent geometry : angle 1.82059 (37945) SS BOND : bond 0.28995 ( 43) SS BOND : angle 7.43875 ( 86) hydrogen bonds : bond 0.17554 ( 1101) hydrogen bonds : angle 9.27390 ( 3093) link_ALPHA1-4 : bond 0.02627 ( 3) link_ALPHA1-4 : angle 4.62155 ( 9) link_BETA1-4 : bond 0.01278 ( 36) link_BETA1-4 : angle 2.62316 ( 108) link_BETA1-6 : bond 0.01839 ( 3) link_BETA1-6 : angle 2.68694 ( 9) link_NAG-ASN : bond 0.16712 ( 54) link_NAG-ASN : angle 11.12172 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6568 Ramachandran restraints generated. 3284 Oldfield, 0 Emsley, 3284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6568 Ramachandran restraints generated. 3284 Oldfield, 0 Emsley, 3284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 493 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 ASN cc_start: 0.8381 (m110) cc_final: 0.7991 (m110) REVERT: B 738 CYS cc_start: 0.7647 (t) cc_final: 0.7365 (t) REVERT: B 776 LYS cc_start: 0.9086 (tttt) cc_final: 0.8763 (ttpt) REVERT: B 904 TYR cc_start: 0.8416 (m-10) cc_final: 0.8110 (m-10) REVERT: C 401 VAL cc_start: 0.7979 (t) cc_final: 0.7701 (t) REVERT: C 823 PHE cc_start: 0.8307 (m-80) cc_final: 0.8039 (m-80) REVERT: C 850 ILE cc_start: 0.6269 (mp) cc_final: 0.6026 (tp) REVERT: C 1142 GLN cc_start: 0.8325 (tp40) cc_final: 0.8032 (mm110) outliers start: 66 outliers final: 9 residues processed: 543 average time/residue: 0.2170 time to fit residues: 178.0170 Evaluate side-chains 236 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 227 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 613 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.5980 chunk 298 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 125 ASN A 137 ASN A 474 GLN A 519 HIS A 856 ASN A 913 GLN A 914 ASN A 965 GLN B 125 ASN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN B 563 GLN B 564 GLN B 613 GLN B 658 ASN B 779 GLN B 856 ASN B 965 GLN C 188 ASN C 282 ASN C 493 GLN C 519 HIS ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 ASN C 965 GLN C1119 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.173720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.121961 restraints weight = 43899.898| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 3.14 r_work: 0.3291 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 28036 Z= 0.166 Angle : 0.801 15.575 38319 Z= 0.396 Chirality : 0.050 0.649 4573 Planarity : 0.004 0.080 4775 Dihedral : 9.373 112.058 5634 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.17 % Favored : 96.77 % Rotamer: Outliers : 2.21 % Allowed : 9.41 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.81 (0.14), residues: 3284 helix: 0.52 (0.19), residues: 733 sheet: 0.04 (0.18), residues: 694 loop : -1.22 (0.13), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 567 TYR 0.023 0.002 TYR B 265 PHE 0.020 0.002 PHE C 79 TRP 0.014 0.002 TRP A 64 HIS 0.006 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00364 (27897) covalent geometry : angle 0.74600 (37945) SS BOND : bond 0.00383 ( 43) SS BOND : angle 1.83389 ( 86) hydrogen bonds : bond 0.05049 ( 1101) hydrogen bonds : angle 6.63124 ( 3093) link_ALPHA1-4 : bond 0.01679 ( 3) link_ALPHA1-4 : angle 3.16427 ( 9) link_BETA1-4 : bond 0.00636 ( 36) link_BETA1-4 : angle 1.85937 ( 108) link_BETA1-6 : bond 0.01330 ( 3) link_BETA1-6 : angle 2.16710 ( 9) link_NAG-ASN : bond 0.00756 ( 54) link_NAG-ASN : angle 4.06707 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6568 Ramachandran restraints generated. 3284 Oldfield, 0 Emsley, 3284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6568 Ramachandran restraints generated. 3284 Oldfield, 0 Emsley, 3284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 269 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 574 ASP cc_start: 0.7681 (t0) cc_final: 0.7412 (p0) REVERT: A 646 ARG cc_start: 0.8308 (mmt-90) cc_final: 0.7887 (mtt90) REVERT: B 125 ASN cc_start: 0.4168 (OUTLIER) cc_final: 0.3571 (m-40) REVERT: B 177 MET cc_start: 0.5445 (ppp) cc_final: 0.4253 (ppp) REVERT: B 237 ARG cc_start: 0.7464 (mtt180) cc_final: 0.7123 (mpp80) REVERT: B 451 TYR cc_start: 0.6345 (m-10) cc_final: 0.6120 (m-10) REVERT: B 776 LYS cc_start: 0.9232 (tttt) cc_final: 0.8902 (ttpt) REVERT: B 950 ASP cc_start: 0.8356 (t0) cc_final: 0.8119 (t0) REVERT: B 954 GLN cc_start: 0.8726 (mt0) cc_final: 0.8514 (mt0) REVERT: C 52 GLN cc_start: 0.8603 (tm-30) cc_final: 0.8340 (tm-30) REVERT: C 164 ASN cc_start: 0.6182 (t0) cc_final: 0.5964 (t0) REVERT: C 342 PHE cc_start: 0.7164 (m-80) cc_final: 0.6881 (m-80) REVERT: C 427 ASP cc_start: 0.8527 (m-30) cc_final: 0.8082 (m-30) REVERT: C 634 ARG cc_start: 0.6017 (tmt170) cc_final: 0.5476 (tpt170) REVERT: C 823 PHE cc_start: 0.8138 (m-80) cc_final: 0.7912 (m-80) REVERT: C 850 ILE cc_start: 0.5834 (mp) cc_final: 0.5551 (tp) REVERT: C 856 ASN cc_start: 0.8488 (m-40) cc_final: 0.8234 (m-40) REVERT: C 994 ASP cc_start: 0.8547 (t70) cc_final: 0.8213 (m-30) REVERT: C 1142 GLN cc_start: 0.8627 (tp40) cc_final: 0.7953 (tm-30) outliers start: 64 outliers final: 32 residues processed: 319 average time/residue: 0.1923 time to fit residues: 97.3934 Evaluate side-chains 236 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 203 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 613 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 160 optimal weight: 6.9990 chunk 128 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 233 optimal weight: 5.9990 chunk 189 optimal weight: 0.0030 chunk 296 optimal weight: 2.9990 chunk 155 optimal weight: 0.5980 chunk 58 optimal weight: 0.5980 chunk 142 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 252 optimal weight: 0.9980 overall best weight: 0.8392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 506 GLN A 856 ASN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN B 49 HIS ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 ASN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN B 317 ASN B 394 ASN B1119 ASN C 14 GLN C 49 HIS ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.171247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.117443 restraints weight = 43958.373| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.81 r_work: 0.3228 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28036 Z= 0.142 Angle : 0.690 14.713 38319 Z= 0.336 Chirality : 0.047 0.566 4573 Planarity : 0.004 0.069 4775 Dihedral : 8.519 106.166 5631 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.68 % Favored : 96.25 % Rotamer: Outliers : 2.21 % Allowed : 10.48 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.48 (0.14), residues: 3284 helix: 1.18 (0.19), residues: 741 sheet: 0.01 (0.18), residues: 719 loop : -1.10 (0.13), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 983 TYR 0.022 0.001 TYR C1067 PHE 0.023 0.002 PHE B1148 TRP 0.010 0.001 TRP B 104 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00323 (27897) covalent geometry : angle 0.64693 (37945) SS BOND : bond 0.00226 ( 43) SS BOND : angle 1.29563 ( 86) hydrogen bonds : bond 0.04278 ( 1101) hydrogen bonds : angle 6.10710 ( 3093) link_ALPHA1-4 : bond 0.01820 ( 3) link_ALPHA1-4 : angle 3.37334 ( 9) link_BETA1-4 : bond 0.00486 ( 36) link_BETA1-4 : angle 1.60288 ( 108) link_BETA1-6 : bond 0.01513 ( 3) link_BETA1-6 : angle 2.16570 ( 9) link_NAG-ASN : bond 0.00546 ( 54) link_NAG-ASN : angle 3.33788 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6568 Ramachandran restraints generated. 3284 Oldfield, 0 Emsley, 3284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6568 Ramachandran restraints generated. 3284 Oldfield, 0 Emsley, 3284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 224 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 646 ARG cc_start: 0.8386 (mmt-90) cc_final: 0.7948 (mtt90) REVERT: A 702 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7523 (mm-30) REVERT: B 237 ARG cc_start: 0.7494 (mtt180) cc_final: 0.7115 (mpp80) REVERT: B 776 LYS cc_start: 0.9233 (tttt) cc_final: 0.8810 (tttm) REVERT: B 950 ASP cc_start: 0.8451 (t0) cc_final: 0.8075 (t0) REVERT: B 977 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8522 (mp) REVERT: B 979 ASP cc_start: 0.7938 (t70) cc_final: 0.7724 (t70) REVERT: C 164 ASN cc_start: 0.6357 (t0) cc_final: 0.6054 (t0) REVERT: C 342 PHE cc_start: 0.7087 (m-80) cc_final: 0.6805 (m-80) REVERT: C 850 ILE cc_start: 0.5872 (mp) cc_final: 0.5550 (tp) REVERT: C 994 ASP cc_start: 0.8504 (t70) cc_final: 0.8185 (m-30) REVERT: C 1142 GLN cc_start: 0.8576 (tp40) cc_final: 0.7910 (tm-30) outliers start: 64 outliers final: 40 residues processed: 277 average time/residue: 0.1645 time to fit residues: 74.4851 Evaluate side-chains 232 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 191 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1148 PHE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 209 optimal weight: 0.5980 chunk 117 optimal weight: 9.9990 chunk 252 optimal weight: 0.6980 chunk 249 optimal weight: 1.9990 chunk 36 optimal weight: 30.0000 chunk 259 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 308 optimal weight: 3.9990 chunk 218 optimal weight: 5.9990 chunk 208 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 580 GLN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 914 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.169580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.115242 restraints weight = 43550.709| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.83 r_work: 0.3197 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 28036 Z= 0.166 Angle : 0.660 14.273 38319 Z= 0.320 Chirality : 0.046 0.528 4573 Planarity : 0.004 0.061 4775 Dihedral : 7.943 98.121 5628 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.23 % Favored : 96.71 % Rotamer: Outliers : 2.42 % Allowed : 11.66 % Favored : 85.92 % 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: -0.35 (0.14), residues: 3284 helix: 1.32 (0.19), residues: 762 sheet: 0.21 (0.18), residues: 705 loop : -1.11 (0.13), residues: 1817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 646 TYR 0.023 0.001 TYR C1067 PHE 0.031 0.002 PHE A 329 TRP 0.009 0.001 TRP B 436 HIS 0.004 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00388 (27897) covalent geometry : angle 0.62459 (37945) SS BOND : bond 0.00259 ( 43) SS BOND : angle 1.06998 ( 86) hydrogen bonds : bond 0.04047 ( 1101) hydrogen bonds : angle 5.83361 ( 3093) link_ALPHA1-4 : bond 0.01800 ( 3) link_ALPHA1-4 : angle 3.21569 ( 9) link_BETA1-4 : bond 0.00416 ( 36) link_BETA1-4 : angle 1.45566 ( 108) link_BETA1-6 : bond 0.01615 ( 3) link_BETA1-6 : angle 2.37317 ( 9) link_NAG-ASN : bond 0.00421 ( 54) link_NAG-ASN : angle 2.94556 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6568 Ramachandran restraints generated. 3284 Oldfield, 0 Emsley, 3284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6568 Ramachandran restraints generated. 3284 Oldfield, 0 Emsley, 3284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 212 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7169 (mmmt) REVERT: A 646 ARG cc_start: 0.8369 (mmt-90) cc_final: 0.7978 (mtt90) REVERT: B 125 ASN cc_start: 0.4045 (OUTLIER) cc_final: 0.3541 (m-40) REVERT: B 237 ARG cc_start: 0.7531 (mtt180) cc_final: 0.7231 (mpp80) REVERT: B 473 TYR cc_start: 0.7541 (t80) cc_final: 0.7104 (t80) REVERT: B 776 LYS cc_start: 0.9232 (tttt) cc_final: 0.8822 (tttm) REVERT: B 950 ASP cc_start: 0.8459 (t0) cc_final: 0.8090 (t0) REVERT: B 977 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8572 (mp) REVERT: B 979 ASP cc_start: 0.7804 (t70) cc_final: 0.7493 (t70) REVERT: C 66 HIS cc_start: 0.7175 (OUTLIER) cc_final: 0.6485 (t-90) REVERT: C 164 ASN cc_start: 0.6631 (t0) cc_final: 0.6259 (t0) REVERT: C 242 LEU cc_start: 0.8817 (mt) cc_final: 0.8578 (mt) REVERT: C 342 PHE cc_start: 0.7054 (m-80) cc_final: 0.6737 (m-80) REVERT: C 775 ASP cc_start: 0.8846 (m-30) cc_final: 0.8591 (m-30) REVERT: C 850 ILE cc_start: 0.5780 (mp) cc_final: 0.5464 (tp) REVERT: C 994 ASP cc_start: 0.8545 (t70) cc_final: 0.8248 (m-30) REVERT: C 1142 GLN cc_start: 0.8525 (tp40) cc_final: 0.8206 (mm-40) outliers start: 70 outliers final: 46 residues processed: 263 average time/residue: 0.1843 time to fit residues: 78.1280 Evaluate side-chains 240 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 190 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1148 PHE Chi-restraints excluded: chain B residue 1155 TYR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 238 optimal weight: 0.3980 chunk 186 optimal weight: 0.8980 chunk 164 optimal weight: 5.9990 chunk 179 optimal weight: 0.9990 chunk 252 optimal weight: 5.9990 chunk 224 optimal weight: 3.9990 chunk 180 optimal weight: 0.9980 chunk 263 optimal weight: 0.9980 chunk 321 optimal weight: 3.9990 chunk 208 optimal weight: 2.9990 chunk 280 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 787 GLN A 856 ASN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.170110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.115662 restraints weight = 43442.671| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.83 r_work: 0.3206 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 28036 Z= 0.135 Angle : 0.631 13.154 38319 Z= 0.305 Chirality : 0.045 0.498 4573 Planarity : 0.004 0.058 4775 Dihedral : 7.556 97.567 5624 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.20 % Favored : 96.74 % Rotamer: Outliers : 2.35 % Allowed : 12.59 % Favored : 85.06 % 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: -0.21 (0.14), residues: 3284 helix: 1.48 (0.19), residues: 763 sheet: 0.29 (0.18), residues: 705 loop : -1.05 (0.14), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 646 TYR 0.021 0.001 TYR C1067 PHE 0.020 0.001 PHE B1148 TRP 0.009 0.001 TRP B 436 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00311 (27897) covalent geometry : angle 0.59454 (37945) SS BOND : bond 0.00218 ( 43) SS BOND : angle 1.65599 ( 86) hydrogen bonds : bond 0.03774 ( 1101) hydrogen bonds : angle 5.73550 ( 3093) link_ALPHA1-4 : bond 0.01707 ( 3) link_ALPHA1-4 : angle 3.16647 ( 9) link_BETA1-4 : bond 0.00418 ( 36) link_BETA1-4 : angle 1.40041 ( 108) link_BETA1-6 : bond 0.01781 ( 3) link_BETA1-6 : angle 2.43007 ( 9) link_NAG-ASN : bond 0.00391 ( 54) link_NAG-ASN : angle 2.78099 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6568 Ramachandran restraints generated. 3284 Oldfield, 0 Emsley, 3284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6568 Ramachandran restraints generated. 3284 Oldfield, 0 Emsley, 3284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 214 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 LYS cc_start: 0.7893 (OUTLIER) cc_final: 0.7590 (tmtt) REVERT: A 392 PHE cc_start: -0.3563 (OUTLIER) cc_final: -0.3781 (m-80) REVERT: A 646 ARG cc_start: 0.8396 (mmt-90) cc_final: 0.7968 (mtt90) REVERT: B 15 CYS cc_start: 0.4169 (OUTLIER) cc_final: 0.3864 (p) REVERT: B 190 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7640 (tpp80) REVERT: B 237 ARG cc_start: 0.7572 (mtt180) cc_final: 0.7241 (mpp80) REVERT: B 473 TYR cc_start: 0.7576 (t80) cc_final: 0.7171 (t80) REVERT: B 745 ASP cc_start: 0.7750 (t0) cc_final: 0.7521 (p0) REVERT: B 776 LYS cc_start: 0.9230 (tttt) cc_final: 0.8828 (tttm) REVERT: B 950 ASP cc_start: 0.8394 (t0) cc_final: 0.8019 (t0) REVERT: B 977 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8563 (mp) REVERT: B 979 ASP cc_start: 0.7753 (t70) cc_final: 0.7429 (t70) REVERT: C 164 ASN cc_start: 0.6702 (t0) cc_final: 0.6306 (t0) REVERT: C 242 LEU cc_start: 0.8826 (mt) cc_final: 0.8577 (mt) REVERT: C 342 PHE cc_start: 0.7082 (m-80) cc_final: 0.6767 (m-80) REVERT: C 775 ASP cc_start: 0.8847 (m-30) cc_final: 0.8556 (m-30) REVERT: C 850 ILE cc_start: 0.5805 (mp) cc_final: 0.5464 (tp) REVERT: C 977 LEU cc_start: 0.8937 (tp) cc_final: 0.8458 (mp) REVERT: C 994 ASP cc_start: 0.8570 (t70) cc_final: 0.8260 (m-30) REVERT: C 1142 GLN cc_start: 0.8476 (tp40) cc_final: 0.8171 (mm-40) outliers start: 68 outliers final: 50 residues processed: 266 average time/residue: 0.1916 time to fit residues: 81.4435 Evaluate side-chains 244 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 189 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 15 CYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1148 PHE Chi-restraints excluded: chain B residue 1155 TYR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 185 optimal weight: 3.9990 chunk 295 optimal weight: 0.0030 chunk 164 optimal weight: 5.9990 chunk 235 optimal weight: 10.0000 chunk 189 optimal weight: 4.9990 chunk 290 optimal weight: 0.7980 chunk 110 optimal weight: 20.0000 chunk 25 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 73 optimal weight: 0.0570 chunk 230 optimal weight: 0.8980 overall best weight: 0.7510 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** 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 = 0.4217 r_free = 0.4217 target = 0.171726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.118711 restraints weight = 43625.210| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.84 r_work: 0.3224 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 28036 Z= 0.125 Angle : 0.608 12.102 38319 Z= 0.292 Chirality : 0.044 0.470 4573 Planarity : 0.004 0.054 4775 Dihedral : 6.948 96.220 5621 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.92 % Favored : 97.05 % Rotamer: Outliers : 2.35 % Allowed : 13.01 % Favored : 84.64 % 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: -0.06 (0.14), residues: 3284 helix: 1.72 (0.19), residues: 754 sheet: 0.30 (0.18), residues: 710 loop : -0.95 (0.14), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 646 TYR 0.020 0.001 TYR C1067 PHE 0.030 0.001 PHE B 135 TRP 0.010 0.001 TRP B 436 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00287 (27897) covalent geometry : angle 0.57453 (37945) SS BOND : bond 0.00168 ( 43) SS BOND : angle 1.44371 ( 86) hydrogen bonds : bond 0.03574 ( 1101) hydrogen bonds : angle 5.60206 ( 3093) link_ALPHA1-4 : bond 0.01632 ( 3) link_ALPHA1-4 : angle 3.04907 ( 9) link_BETA1-4 : bond 0.00410 ( 36) link_BETA1-4 : angle 1.34747 ( 108) link_BETA1-6 : bond 0.02075 ( 3) link_BETA1-6 : angle 2.40709 ( 9) link_NAG-ASN : bond 0.00369 ( 54) link_NAG-ASN : angle 2.62326 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6568 Ramachandran restraints generated. 3284 Oldfield, 0 Emsley, 3284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6568 Ramachandran restraints generated. 3284 Oldfield, 0 Emsley, 3284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 217 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.6789 (m-90) cc_final: 0.6419 (m-90) REVERT: A 206 LYS cc_start: 0.7703 (OUTLIER) cc_final: 0.7463 (tmtt) REVERT: A 392 PHE cc_start: -0.3411 (OUTLIER) cc_final: -0.3629 (m-80) REVERT: A 646 ARG cc_start: 0.8132 (mmt-90) cc_final: 0.7840 (mtt90) REVERT: A 977 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8183 (mp) REVERT: A 1002 GLN cc_start: 0.8692 (tp-100) cc_final: 0.8467 (tp-100) REVERT: B 190 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.7421 (tpp80) REVERT: B 237 ARG cc_start: 0.7622 (mtt180) cc_final: 0.7269 (mpp80) REVERT: B 473 TYR cc_start: 0.7497 (t80) cc_final: 0.7093 (t80) REVERT: B 776 LYS cc_start: 0.9079 (tttt) cc_final: 0.8779 (tttm) REVERT: B 950 ASP cc_start: 0.7972 (t0) cc_final: 0.7596 (t0) REVERT: B 977 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8563 (mp) REVERT: B 979 ASP cc_start: 0.7593 (t70) cc_final: 0.7248 (t70) REVERT: C 242 LEU cc_start: 0.8785 (mt) cc_final: 0.8565 (mt) REVERT: C 342 PHE cc_start: 0.7068 (m-80) cc_final: 0.6742 (m-80) REVERT: C 370 ASN cc_start: 0.7554 (m-40) cc_final: 0.7337 (t0) REVERT: C 775 ASP cc_start: 0.8688 (m-30) cc_final: 0.8444 (m-30) REVERT: C 811 LYS cc_start: 0.6875 (OUTLIER) cc_final: 0.6530 (ttmt) REVERT: C 850 ILE cc_start: 0.5929 (mp) cc_final: 0.5635 (tp) REVERT: C 977 LEU cc_start: 0.8889 (tp) cc_final: 0.8471 (mp) REVERT: C 994 ASP cc_start: 0.8336 (t70) cc_final: 0.8078 (m-30) REVERT: C 1142 GLN cc_start: 0.8373 (tp40) cc_final: 0.7953 (mm-40) outliers start: 68 outliers final: 48 residues processed: 268 average time/residue: 0.1868 time to fit residues: 80.7602 Evaluate side-chains 251 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 197 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1148 PHE Chi-restraints excluded: chain B residue 1155 TYR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 811 LYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1118 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 328 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 chunk 74 optimal weight: 0.5980 chunk 117 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 123 optimal weight: 9.9990 chunk 194 optimal weight: 0.9980 chunk 204 optimal weight: 2.9990 chunk 279 optimal weight: 9.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN C 218 GLN C 493 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.170503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.116420 restraints weight = 43202.519| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.84 r_work: 0.3240 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 28036 Z= 0.134 Angle : 0.611 12.122 38319 Z= 0.293 Chirality : 0.044 0.456 4573 Planarity : 0.003 0.053 4775 Dihedral : 6.644 94.807 5621 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.14 % Favored : 96.83 % Rotamer: Outliers : 2.56 % Allowed : 13.35 % Favored : 84.09 % 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: -0.03 (0.14), residues: 3284 helix: 1.68 (0.19), residues: 761 sheet: 0.23 (0.18), residues: 727 loop : -0.89 (0.14), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 646 TYR 0.020 0.001 TYR C1067 PHE 0.024 0.001 PHE B 135 TRP 0.015 0.001 TRP C 152 HIS 0.005 0.001 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00309 (27897) covalent geometry : angle 0.57810 (37945) SS BOND : bond 0.00247 ( 43) SS BOND : angle 1.55887 ( 86) hydrogen bonds : bond 0.03544 ( 1101) hydrogen bonds : angle 5.56647 ( 3093) link_ALPHA1-4 : bond 0.01596 ( 3) link_ALPHA1-4 : angle 2.99382 ( 9) link_BETA1-4 : bond 0.00447 ( 36) link_BETA1-4 : angle 1.33282 ( 108) link_BETA1-6 : bond 0.02210 ( 3) link_BETA1-6 : angle 2.18738 ( 9) link_NAG-ASN : bond 0.00389 ( 54) link_NAG-ASN : angle 2.58850 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6568 Ramachandran restraints generated. 3284 Oldfield, 0 Emsley, 3284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6568 Ramachandran restraints generated. 3284 Oldfield, 0 Emsley, 3284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 216 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.6939 (m-90) cc_final: 0.6638 (m-90) REVERT: A 206 LYS cc_start: 0.7785 (OUTLIER) cc_final: 0.7541 (tmtt) REVERT: A 392 PHE cc_start: -0.3231 (OUTLIER) cc_final: -0.3481 (m-80) REVERT: A 646 ARG cc_start: 0.8275 (mmt-90) cc_final: 0.7856 (mtt90) REVERT: B 190 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.7526 (tpp80) REVERT: B 237 ARG cc_start: 0.7685 (mtt180) cc_final: 0.7267 (mpp80) REVERT: B 473 TYR cc_start: 0.7540 (t80) cc_final: 0.7170 (t80) REVERT: B 776 LYS cc_start: 0.9194 (tttt) cc_final: 0.8844 (tttm) REVERT: B 950 ASP cc_start: 0.8324 (t0) cc_final: 0.7944 (t0) REVERT: B 977 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8584 (mp) REVERT: B 979 ASP cc_start: 0.7724 (t70) cc_final: 0.7376 (t70) REVERT: C 66 HIS cc_start: 0.6972 (OUTLIER) cc_final: 0.6280 (t-90) REVERT: C 188 ASN cc_start: 0.7824 (m110) cc_final: 0.7321 (p0) REVERT: C 242 LEU cc_start: 0.8821 (mt) cc_final: 0.8593 (mt) REVERT: C 342 PHE cc_start: 0.7065 (m-80) cc_final: 0.6700 (m-80) REVERT: C 370 ASN cc_start: 0.7659 (m-40) cc_final: 0.7385 (t0) REVERT: C 396 TYR cc_start: 0.7661 (m-80) cc_final: 0.7436 (m-10) REVERT: C 775 ASP cc_start: 0.8858 (m-30) cc_final: 0.8562 (m-30) REVERT: C 811 LYS cc_start: 0.6936 (OUTLIER) cc_final: 0.6511 (ttmt) REVERT: C 850 ILE cc_start: 0.5823 (mp) cc_final: 0.5486 (tp) REVERT: C 977 LEU cc_start: 0.8964 (tp) cc_final: 0.8560 (mp) REVERT: C 994 ASP cc_start: 0.8582 (t70) cc_final: 0.8265 (m-30) REVERT: C 1142 GLN cc_start: 0.8345 (tp40) cc_final: 0.8000 (mm-40) outliers start: 74 outliers final: 56 residues processed: 270 average time/residue: 0.1901 time to fit residues: 81.8596 Evaluate side-chains 266 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 204 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1148 PHE Chi-restraints excluded: chain B residue 1155 TYR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 811 LYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 322 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 312 optimal weight: 0.9990 chunk 293 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 278 optimal weight: 4.9990 chunk 143 optimal weight: 0.3980 chunk 67 optimal weight: 0.3980 chunk 160 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN ** C 804 GLN ** 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 = 0.4208 r_free = 0.4208 target = 0.171137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.115817 restraints weight = 43504.930| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.89 r_work: 0.3219 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.4129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 28036 Z= 0.152 Angle : 0.613 12.018 38319 Z= 0.294 Chirality : 0.044 0.448 4573 Planarity : 0.004 0.052 4775 Dihedral : 6.501 93.068 5621 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.11 % Favored : 96.86 % Rotamer: Outliers : 2.46 % Allowed : 13.56 % Favored : 83.98 % 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: -0.03 (0.14), residues: 3284 helix: 1.70 (0.20), residues: 754 sheet: 0.24 (0.18), residues: 710 loop : -0.89 (0.14), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 567 TYR 0.020 0.001 TYR C1067 PHE 0.021 0.001 PHE B1148 TRP 0.016 0.001 TRP C 152 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00358 (27897) covalent geometry : angle 0.58076 (37945) SS BOND : bond 0.00190 ( 43) SS BOND : angle 1.50308 ( 86) hydrogen bonds : bond 0.03629 ( 1101) hydrogen bonds : angle 5.59347 ( 3093) link_ALPHA1-4 : bond 0.01584 ( 3) link_ALPHA1-4 : angle 2.94476 ( 9) link_BETA1-4 : bond 0.00391 ( 36) link_BETA1-4 : angle 1.33504 ( 108) link_BETA1-6 : bond 0.02343 ( 3) link_BETA1-6 : angle 2.06603 ( 9) link_NAG-ASN : bond 0.00368 ( 54) link_NAG-ASN : angle 2.57533 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6568 Ramachandran restraints generated. 3284 Oldfield, 0 Emsley, 3284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6568 Ramachandran restraints generated. 3284 Oldfield, 0 Emsley, 3284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 207 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.6930 (m-90) cc_final: 0.6653 (m-90) REVERT: A 206 LYS cc_start: 0.7809 (OUTLIER) cc_final: 0.7559 (tmtt) REVERT: A 646 ARG cc_start: 0.8274 (mmt-90) cc_final: 0.7878 (mtt90) REVERT: B 190 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.7541 (tpp80) REVERT: B 237 ARG cc_start: 0.7591 (mtt180) cc_final: 0.7201 (mpp80) REVERT: B 473 TYR cc_start: 0.7569 (t80) cc_final: 0.6962 (t80) REVERT: B 619 GLU cc_start: 0.7137 (mm-30) cc_final: 0.6933 (tp30) REVERT: B 776 LYS cc_start: 0.9195 (tttt) cc_final: 0.8822 (tttm) REVERT: B 950 ASP cc_start: 0.8381 (t0) cc_final: 0.8011 (t0) REVERT: B 977 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8592 (mp) REVERT: B 979 ASP cc_start: 0.7735 (t70) cc_final: 0.7374 (t70) REVERT: C 66 HIS cc_start: 0.7012 (OUTLIER) cc_final: 0.6328 (t-90) REVERT: C 188 ASN cc_start: 0.7805 (m110) cc_final: 0.7313 (p0) REVERT: C 342 PHE cc_start: 0.7039 (m-80) cc_final: 0.6697 (m-80) REVERT: C 370 ASN cc_start: 0.7686 (m-40) cc_final: 0.7423 (t0) REVERT: C 403 ARG cc_start: 0.6358 (mtp85) cc_final: 0.6043 (mtp180) REVERT: C 811 LYS cc_start: 0.6900 (OUTLIER) cc_final: 0.6533 (ttmt) REVERT: C 850 ILE cc_start: 0.5863 (mp) cc_final: 0.5512 (tp) REVERT: C 977 LEU cc_start: 0.8987 (tp) cc_final: 0.8606 (mp) REVERT: C 994 ASP cc_start: 0.8610 (t70) cc_final: 0.8293 (m-30) REVERT: C 1142 GLN cc_start: 0.8323 (tp40) cc_final: 0.7869 (mm-40) outliers start: 71 outliers final: 57 residues processed: 260 average time/residue: 0.1760 time to fit residues: 73.8618 Evaluate side-chains 261 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 199 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1148 PHE Chi-restraints excluded: chain B residue 1155 TYR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 811 LYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 67 optimal weight: 1.9990 chunk 265 optimal weight: 6.9990 chunk 72 optimal weight: 0.7980 chunk 24 optimal weight: 7.9990 chunk 78 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 266 optimal weight: 7.9990 chunk 209 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 200 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.167733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.114663 restraints weight = 43442.024| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.92 r_work: 0.3215 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 28036 Z= 0.183 Angle : 0.642 11.978 38319 Z= 0.309 Chirality : 0.045 0.461 4573 Planarity : 0.004 0.051 4775 Dihedral : 6.539 90.426 5621 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.65 % Favored : 96.32 % Rotamer: Outliers : 2.56 % Allowed : 13.77 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.14), residues: 3284 helix: 1.65 (0.20), residues: 746 sheet: 0.18 (0.18), residues: 724 loop : -0.93 (0.14), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 567 TYR 0.020 0.001 TYR C1067 PHE 0.022 0.002 PHE B1148 TRP 0.012 0.001 TRP C 152 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00433 (27897) covalent geometry : angle 0.61099 (37945) SS BOND : bond 0.00220 ( 43) SS BOND : angle 1.45335 ( 86) hydrogen bonds : bond 0.03832 ( 1101) hydrogen bonds : angle 5.66015 ( 3093) link_ALPHA1-4 : bond 0.01719 ( 3) link_ALPHA1-4 : angle 2.95807 ( 9) link_BETA1-4 : bond 0.00396 ( 36) link_BETA1-4 : angle 1.37016 ( 108) link_BETA1-6 : bond 0.01936 ( 3) link_BETA1-6 : angle 2.13653 ( 9) link_NAG-ASN : bond 0.00380 ( 54) link_NAG-ASN : angle 2.61611 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6568 Ramachandran restraints generated. 3284 Oldfield, 0 Emsley, 3284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6568 Ramachandran restraints generated. 3284 Oldfield, 0 Emsley, 3284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 206 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.8008 (tm-30) REVERT: A 392 PHE cc_start: -0.2936 (OUTLIER) cc_final: -0.3153 (m-80) REVERT: A 646 ARG cc_start: 0.8245 (mmt-90) cc_final: 0.7931 (mtt90) REVERT: B 145 TYR cc_start: 0.4661 (OUTLIER) cc_final: 0.3567 (p90) REVERT: B 237 ARG cc_start: 0.7585 (mtt180) cc_final: 0.7253 (mpp80) REVERT: B 269 TYR cc_start: 0.7707 (m-80) cc_final: 0.7204 (m-80) REVERT: B 776 LYS cc_start: 0.9145 (tttt) cc_final: 0.8816 (tttm) REVERT: B 950 ASP cc_start: 0.8399 (t0) cc_final: 0.8048 (t0) REVERT: B 977 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8633 (mp) REVERT: B 979 ASP cc_start: 0.7791 (t70) cc_final: 0.7404 (t70) REVERT: C 66 HIS cc_start: 0.7091 (OUTLIER) cc_final: 0.6369 (t-90) REVERT: C 100 ILE cc_start: 0.8043 (OUTLIER) cc_final: 0.7811 (mm) REVERT: C 188 ASN cc_start: 0.7786 (m110) cc_final: 0.7346 (p0) REVERT: C 342 PHE cc_start: 0.7057 (m-80) cc_final: 0.6712 (m-80) REVERT: C 370 ASN cc_start: 0.7747 (m-40) cc_final: 0.7523 (t0) REVERT: C 403 ARG cc_start: 0.6307 (mtp85) cc_final: 0.5935 (mtp180) REVERT: C 811 LYS cc_start: 0.6871 (OUTLIER) cc_final: 0.6509 (ttmt) REVERT: C 850 ILE cc_start: 0.5919 (mp) cc_final: 0.5577 (tp) REVERT: C 977 LEU cc_start: 0.8947 (tp) cc_final: 0.8559 (mp) REVERT: C 994 ASP cc_start: 0.8535 (t70) cc_final: 0.8279 (m-30) REVERT: C 1142 GLN cc_start: 0.8267 (tp40) cc_final: 0.7890 (mm-40) outliers start: 74 outliers final: 58 residues processed: 259 average time/residue: 0.1688 time to fit residues: 69.9448 Evaluate side-chains 253 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 188 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1148 PHE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 811 LYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 324 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 194 optimal weight: 2.9990 chunk 118 optimal weight: 10.0000 chunk 295 optimal weight: 0.1980 chunk 272 optimal weight: 0.5980 chunk 156 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 36 optimal weight: 20.0000 chunk 286 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** C 804 GLN ** 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 = 0.4180 r_free = 0.4180 target = 0.168253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.114211 restraints weight = 43402.460| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.85 r_work: 0.3187 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 28036 Z= 0.156 Angle : 0.634 12.653 38319 Z= 0.306 Chirality : 0.045 0.458 4573 Planarity : 0.004 0.051 4775 Dihedral : 6.421 89.841 5621 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.32 % Favored : 96.65 % Rotamer: Outliers : 2.14 % Allowed : 14.32 % Favored : 83.54 % 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: -0.11 (0.14), residues: 3284 helix: 1.61 (0.20), residues: 752 sheet: 0.22 (0.18), residues: 718 loop : -0.94 (0.14), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 567 TYR 0.020 0.001 TYR C1067 PHE 0.021 0.001 PHE B1148 TRP 0.012 0.001 TRP C 152 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00370 (27897) covalent geometry : angle 0.60171 (37945) SS BOND : bond 0.00265 ( 43) SS BOND : angle 1.80225 ( 86) hydrogen bonds : bond 0.03715 ( 1101) hydrogen bonds : angle 5.64505 ( 3093) link_ALPHA1-4 : bond 0.01741 ( 3) link_ALPHA1-4 : angle 3.01539 ( 9) link_BETA1-4 : bond 0.00388 ( 36) link_BETA1-4 : angle 1.34956 ( 108) link_BETA1-6 : bond 0.01838 ( 3) link_BETA1-6 : angle 2.10137 ( 9) link_NAG-ASN : bond 0.00348 ( 54) link_NAG-ASN : angle 2.53943 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6568 Ramachandran restraints generated. 3284 Oldfield, 0 Emsley, 3284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6568 Ramachandran restraints generated. 3284 Oldfield, 0 Emsley, 3284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 198 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 PHE cc_start: -0.2982 (OUTLIER) cc_final: -0.3253 (m-80) REVERT: A 646 ARG cc_start: 0.8268 (mmt-90) cc_final: 0.7917 (mtt90) REVERT: B 237 ARG cc_start: 0.7552 (mtt180) cc_final: 0.7216 (mpp80) REVERT: B 269 TYR cc_start: 0.7604 (m-80) cc_final: 0.7116 (m-80) REVERT: B 776 LYS cc_start: 0.9146 (tttt) cc_final: 0.8816 (tttm) REVERT: B 950 ASP cc_start: 0.8436 (t0) cc_final: 0.8075 (t0) REVERT: B 977 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8609 (mp) REVERT: B 979 ASP cc_start: 0.7769 (t70) cc_final: 0.7404 (t70) REVERT: C 66 HIS cc_start: 0.7083 (OUTLIER) cc_final: 0.6347 (t-90) REVERT: C 188 ASN cc_start: 0.7757 (m110) cc_final: 0.7319 (p0) REVERT: C 342 PHE cc_start: 0.7115 (m-80) cc_final: 0.6740 (m-80) REVERT: C 370 ASN cc_start: 0.7727 (m-40) cc_final: 0.7504 (t0) REVERT: C 403 ARG cc_start: 0.6322 (mtp85) cc_final: 0.5918 (mtp180) REVERT: C 811 LYS cc_start: 0.6805 (OUTLIER) cc_final: 0.6494 (ttmt) REVERT: C 850 ILE cc_start: 0.5869 (mp) cc_final: 0.5516 (tp) REVERT: C 977 LEU cc_start: 0.8953 (tp) cc_final: 0.8595 (mp) REVERT: C 994 ASP cc_start: 0.8579 (t70) cc_final: 0.8308 (m-30) REVERT: C 1142 GLN cc_start: 0.8282 (tp40) cc_final: 0.7897 (mm-40) outliers start: 62 outliers final: 55 residues processed: 241 average time/residue: 0.1858 time to fit residues: 71.6887 Evaluate side-chains 243 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 184 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1148 PHE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 811 LYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 215 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 42 optimal weight: 10.0000 chunk 222 optimal weight: 5.9990 chunk 113 optimal weight: 10.0000 chunk 130 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 89 optimal weight: 0.1980 chunk 286 optimal weight: 0.9980 chunk 177 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.168537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.112428 restraints weight = 43354.121| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.85 r_work: 0.3170 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 28036 Z= 0.175 Angle : 0.658 18.187 38319 Z= 0.317 Chirality : 0.046 0.461 4573 Planarity : 0.004 0.061 4775 Dihedral : 6.354 88.017 5619 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.68 % Favored : 96.29 % Rotamer: Outliers : 2.18 % Allowed : 14.35 % Favored : 83.47 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.16 (0.14), residues: 3284 helix: 1.52 (0.19), residues: 758 sheet: 0.16 (0.18), residues: 716 loop : -0.94 (0.14), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 567 TYR 0.020 0.001 TYR C1067 PHE 0.021 0.001 PHE B1148 TRP 0.012 0.001 TRP A 64 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00414 (27897) covalent geometry : angle 0.61794 (37945) SS BOND : bond 0.00215 ( 43) SS BOND : angle 1.66323 ( 86) hydrogen bonds : bond 0.03756 ( 1101) hydrogen bonds : angle 5.68766 ( 3093) link_ALPHA1-4 : bond 0.01795 ( 3) link_ALPHA1-4 : angle 3.06260 ( 9) link_BETA1-4 : bond 0.00356 ( 36) link_BETA1-4 : angle 1.36403 ( 108) link_BETA1-6 : bond 0.01795 ( 3) link_BETA1-6 : angle 2.09474 ( 9) link_NAG-ASN : bond 0.00399 ( 54) link_NAG-ASN : angle 3.08322 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9469.45 seconds wall clock time: 162 minutes 18.42 seconds (9738.42 seconds total)