Starting phenix.real_space_refine on Sat Mar 7 04:19:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7upw_26676/03_2026/7upw_26676_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7upw_26676/03_2026/7upw_26676.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7upw_26676/03_2026/7upw_26676.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7upw_26676/03_2026/7upw_26676.map" model { file = "/net/cci-nas-00/data/ceres_data/7upw_26676/03_2026/7upw_26676_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7upw_26676/03_2026/7upw_26676_neut.cif" } resolution = 2.7 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= 0.032 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 156 5.16 5 C 23952 2.51 5 N 6153 2.21 5 O 7632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 212 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37893 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 8766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1121, 8766 Classifications: {'peptide': 1121} Link IDs: {'PTRANS': 53, 'TRANS': 1067} Chain breaks: 3 Chain: "B" Number of atoms: 8766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1121, 8766 Classifications: {'peptide': 1121} Link IDs: {'PTRANS': 53, 'TRANS': 1067} Chain breaks: 3 Chain: "C" Number of atoms: 8766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1121, 8766 Classifications: {'peptide': 1121} Link IDs: {'PTRANS': 53, 'TRANS': 1067} Chain breaks: 3 Chain: "D" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1701 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 213} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1622 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 200} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "F" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1701 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 213} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1622 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 200} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1701 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 213} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1622 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 200} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 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: 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: "K" 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: 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: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 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: "P" 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: "Q" 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: "R" 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: "S" 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: "T" 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: "U" 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: "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: 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: "X" 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: "Y" 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: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 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: "b" 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: "c" 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: "d" 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: "e" 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: "f" 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: "g" 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: "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: 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: "j" 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: "k" 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: "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: 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: "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: 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: "p" 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: "q" 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: "r" 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: "s" 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: 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: 9.38, per 1000 atoms: 0.25 Number of scatterers: 37893 At special positions: 0 Unit cell: (166, 163.51, 248.17, 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 156 16.00 O 7632 8.00 N 6153 7.00 C 23952 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.01 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.05 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.05 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.01 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.05 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.01 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.01 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=2.05 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.05 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.01 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=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.01 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 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=2.05 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " 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=2.02 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.02 Simple disulfide: pdb=" SG CYS D 140 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 194 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 140 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 134 " - pdb=" SG CYS G 194 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM37167 O5 NAG h 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM37737 O5 NAG B1403 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-4 " NAG J 2 " - " MAN J 3 " " NAG K 2 " - " MAN K 3 " " NAG M 2 " - " MAN M 3 " " NAG O 2 " - " MAN O 3 " " NAG P 2 " - " MAN P 3 " " NAG R 2 " - " MAN R 3 " " NAG S 2 " - " MAN S 3 " " NAG U 2 " - " MAN U 3 " " NAG W 2 " - " MAN W 3 " " NAG X 2 " - " MAN X 3 " " NAG Y 2 " - " MAN Y 3 " " NAG a 2 " - " MAN a 3 " " NAG b 2 " - " MAN b 3 " " NAG d 2 " - " MAN d 3 " " NAG e 2 " - " MAN e 3 " " NAG g 2 " - " MAN g 3 " " NAG i 2 " - " MAN i 3 " " NAG j 2 " - " MAN j 3 " " NAG k 2 " - " MAN k 3 " " NAG m 2 " - " MAN m 3 " " NAG n 2 " - " MAN n 3 " " NAG p 2 " - " MAN p 3 " " NAG q 2 " - " MAN q 3 " " NAG s 2 " - " MAN s 3 " BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " BETA1-6 " NAG Q 1 " - " FUC Q 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG T 1 " - " FUC T 3 " " NAG c 1 " - " FUC c 3 " " NAG f 1 " - " FUC f 3 " " NAG o 1 " - " FUC o 3 " " NAG r 1 " - " FUC r 3 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 149 " " NAG A1403 " - " ASN A 331 " " 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 B1402 " - " ASN B 149 " " NAG B1403 " - " ASN B 331 " " 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 331 " " NAG C1404 " - " ASN C 603 " " NAG C1405 " - " ASN C 657 " " NAG C1406 " - " ASN C 709 " " NAG C1407 " - " ASN C1158 " " NAG I 1 " - " ASN A 17 " " NAG J 1 " - " ASN A 122 " " NAG K 1 " - " ASN A 234 " " NAG M 1 " - " ASN A 282 " " NAG N 1 " - " ASN A 616 " " NAG O 1 " - " ASN A 717 " " NAG P 1 " - " ASN A 801 " " NAG Q 1 " - " ASN A1074 " " NAG R 1 " - " ASN A1098 " " NAG S 1 " - " ASN A1134 " " NAG T 1 " - " ASN A 343 " " NAG U 1 " - " ASN A 165 " " NAG V 1 " - " ASN B 17 " " NAG W 1 " - " ASN B 122 " " NAG X 1 " - " ASN B 234 " " NAG Y 1 " - " ASN B 282 " " NAG Z 1 " - " ASN B 616 " " NAG a 1 " - " ASN B 717 " " NAG b 1 " - " ASN B 801 " " NAG c 1 " - " ASN B1074 " " NAG d 1 " - " ASN B1098 " " NAG e 1 " - " ASN B1134 " " NAG f 1 " - " ASN B 343 " " NAG g 1 " - " ASN B 165 " " NAG h 1 " - " ASN C 17 " " NAG i 1 " - " ASN C 122 " " NAG j 1 " - " ASN C 234 " " NAG k 1 " - " ASN C 282 " " NAG l 1 " - " ASN C 616 " " NAG m 1 " - " ASN C 717 " " NAG n 1 " - " ASN C 801 " " NAG o 1 " - " ASN C1074 " " NAG p 1 " - " ASN C1098 " " NAG q 1 " - " ASN C1134 " " NAG r 1 " - " ASN C 343 " " NAG s 1 " - " ASN C 165 " Time building additional restraints: 3.64 Conformation dependent library (CDL) restraints added in 1.4 seconds 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8712 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 81 sheets defined 22.2% alpha, 35.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.577A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.802A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.541A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 3.884A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 635 through 639 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: 3.833A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.753A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 847 removed outlier: 4.188A pdb=" N ALA A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ARG A 847 " --> pdb=" O ASP A 843 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 842 through 847' Processing helix chain 'A' and resid 849 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.569A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.053A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.868A 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 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.814A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1160 removed outlier: 4.075A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE A1148 " --> pdb=" O GLU A1144 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.059A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.432A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.427A 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 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: 3.931A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.560A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 847 removed outlier: 3.622A pdb=" N ALA B 846 " --> pdb=" O GLY B 842 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 855 removed outlier: 3.685A pdb=" N ALA B 852 " --> pdb=" O ASP B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.626A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.514A pdb=" N ASN B 919 " --> pdb=" O VAL B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.574A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.938A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA B1016 " --> pdb=" O LEU B1012 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1160 removed outlier: 3.940A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N PHE B1148 " --> pdb=" O GLU B1144 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N TYR B1155 " --> pdb=" O GLU B1151 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.821A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 removed outlier: 3.637A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.391A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 411 removed outlier: 4.320A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA C 411 " --> pdb=" O ARG C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 618 through 623 removed outlier: 4.030A pdb=" N VAL C 622 " --> pdb=" O THR C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 639 removed outlier: 3.718A 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 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.866A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.653A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 836 through 841 removed outlier: 5.876A pdb=" N LEU C 841 " --> pdb=" O GLY C 838 " (cutoff:3.500A) Processing helix chain 'C' and resid 842 through 847 removed outlier: 3.899A pdb=" N ALA C 846 " --> pdb=" O GLY C 842 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ARG C 847 " --> pdb=" O ASP C 843 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 842 through 847' Processing helix chain 'C' and resid 849 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.641A 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: 4.038A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.870A 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 984 removed outlier: 3.565A pdb=" N ARG C 983 " --> pdb=" O ASP C 979 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.845A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1159 removed outlier: 3.913A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N PHE C1148 " --> pdb=" O GLU C1144 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.991A pdb=" N THR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 64 Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'D' and resid 156 through 158 No H-bonds generated for 'chain 'D' and resid 156 through 158' Processing helix chain 'D' and resid 187 through 191 Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.706A pdb=" N ILE E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 128 Processing helix chain 'E' and resid 183 through 187 Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.838A pdb=" N THR F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'F' and resid 128 through 132 removed outlier: 3.595A pdb=" N SER F 132 " --> pdb=" O ARG F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 158 No H-bonds generated for 'chain 'F' and resid 156 through 158' Processing helix chain 'F' and resid 187 through 190 Processing helix chain 'F' and resid 201 through 204 Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.695A pdb=" N ILE G 83 " --> pdb=" O PRO G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 127 Processing helix chain 'G' and resid 183 through 187 Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.340A pdb=" N THR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 128 through 132 removed outlier: 3.616A pdb=" N SER H 132 " --> pdb=" O ARG H 129 " (cutoff:3.500A) Processing helix chain 'H' and resid 156 through 158 No H-bonds generated for 'chain 'H' and resid 156 through 158' Processing helix chain 'H' and resid 186 through 190 removed outlier: 4.464A pdb=" N GLY H 190 " --> pdb=" O SER H 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 186 through 190' Processing helix chain 'H' and resid 201 through 204 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.855A pdb=" N ILE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 126 Processing helix chain 'L' and resid 183 through 189 removed outlier: 3.537A pdb=" N HIS L 189 " --> pdb=" O ASP L 185 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.041A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.041A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ASN A 188 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ILE A 210 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N ARG A 190 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N THR A 208 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N PHE A 192 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N LYS A 206 " --> pdb=" O PHE A 192 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N PHE A 194 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N TYR A 204 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ASN A 196 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N LYS A 202 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.156A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.258A 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: 7.575A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.857A 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: 3.896A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER A 116 " --> pdb=" O CYS A 131 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 8.786A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 9.827A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.778A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 83 through 85 removed outlier: 13.124A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 12.162A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 9.523A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL A 143 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 8.786A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 9.827A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.778A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.127A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.068A 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: 4.344A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.642A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.749A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) 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 473 through 474 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.182A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.708A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.800A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.768A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.388A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.540A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.014A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.014A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.748A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 83 through 85 removed outlier: 13.210A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 12.173A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 9.465A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL B 143 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 9.784A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.709A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 83 through 85 removed outlier: 4.102A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.278A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.691A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 6.948A 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 358 removed outlier: 3.691A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (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 538 through 543 removed outlier: 5.217A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.166A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.903A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.800A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.440A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.499A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.097A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ASN C 188 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ILE C 210 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N ARG C 190 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N THR C 208 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N PHE C 192 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N LYS C 206 " --> pdb=" O PHE C 192 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N PHE C 194 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N TYR C 204 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ASN C 196 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N LYS C 202 " --> pdb=" O ASN C 196 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.770A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.900A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 10.080A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 10.438A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 12.762A pdb=" N PHE C 238 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 12.320A pdb=" N PHE C 135 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 12.879A pdb=" N THR C 240 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 10.448A pdb=" N ASN C 137 " --> pdb=" O THR C 240 " (cutoff:3.500A) removed outlier: 10.723A pdb=" N LEU C 242 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 10.080A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 10.438A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.168A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.184A 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 removed outlier: 3.661A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.909A 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: 6.155A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.535A 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: 3.913A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.491A 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: 5.764A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.635A 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: 4.320A 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: 4.428A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AF7, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.448A pdb=" N GLU D 10 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 120 through 124 removed outlier: 3.535A pdb=" N ASP D 144 " --> pdb=" O TYR D 176 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N TYR D 176 " --> pdb=" O ASP D 144 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 120 through 124 removed outlier: 3.535A pdb=" N ASP D 144 " --> pdb=" O TYR D 176 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N TYR D 176 " --> pdb=" O ASP D 144 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 150 through 154 removed outlier: 4.506A pdb=" N TYR D 194 " --> pdb=" O VAL D 211 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 4 through 6 removed outlier: 3.585A pdb=" N ASP E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.282A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLN E 37 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N LEU E 46 " --> pdb=" O GLN E 37 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.282A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 114 through 118 removed outlier: 3.640A pdb=" N VAL E 133 " --> pdb=" O PHE E 118 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N SER E 131 " --> pdb=" O LEU E 181 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LEU E 181 " --> pdb=" O SER E 131 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N VAL E 133 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LEU E 179 " --> pdb=" O VAL E 133 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N LEU E 135 " --> pdb=" O SER E 177 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N SER E 177 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ASN E 137 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LEU E 175 " --> pdb=" O ASN E 137 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 153 through 154 Processing sheet with id=AG7, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AG8, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.664A pdb=" N GLU F 10 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.664A pdb=" N GLU F 10 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL F 102 " --> pdb=" O ARG F 94 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'F' and resid 120 through 124 removed outlier: 6.180A pdb=" N TYR F 176 " --> pdb=" O ASP F 144 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'F' and resid 120 through 124 removed outlier: 6.180A pdb=" N TYR F 176 " --> pdb=" O ASP F 144 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'F' and resid 151 through 154 removed outlier: 4.131A pdb=" N TYR F 194 " --> pdb=" O VAL F 211 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'G' and resid 4 through 6 removed outlier: 3.699A pdb=" N ASP G 70 " --> pdb=" O SER G 67 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.259A pdb=" N GLN G 37 " --> pdb=" O LEU G 46 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N LEU G 46 " --> pdb=" O GLN G 37 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'G' and resid 10 through 13 Processing sheet with id=AH7, first strand: chain 'G' and resid 114 through 118 removed outlier: 4.905A pdb=" N SER G 131 " --> pdb=" O LEU G 181 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N LEU G 181 " --> pdb=" O SER G 131 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N VAL G 133 " --> pdb=" O LEU G 179 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LEU G 179 " --> pdb=" O VAL G 133 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N LEU G 135 " --> pdb=" O SER G 177 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N SER G 177 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N ASN G 137 " --> pdb=" O LEU G 175 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LEU G 175 " --> pdb=" O ASN G 137 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'G' and resid 153 through 155 removed outlier: 4.120A pdb=" N TRP G 148 " --> pdb=" O GLN G 155 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AI1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.696A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'H' and resid 120 through 124 removed outlier: 6.337A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'H' and resid 120 through 124 removed outlier: 6.337A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'H' and resid 151 through 154 removed outlier: 4.423A pdb=" N TYR H 194 " --> pdb=" O VAL H 211 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AI6, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.863A pdb=" N GLY L 84 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'L' and resid 114 through 118 removed outlier: 5.820A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N SER L 174 " --> pdb=" O THR L 164 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'L' and resid 145 through 150 Processing sheet with id=AI9, first strand: chain 'L' and resid 145 through 150 1573 hydrogen bonds defined for protein. 4182 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: 10.77 Time building geometry restraints manager: 4.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 6163 1.30 - 1.43: 10337 1.43 - 1.56: 22036 1.56 - 1.69: 5 1.69 - 1.82: 195 Bond restraints: 38736 Sorted by residual: bond pdb=" CA ARG D 38 " pdb=" C ARG D 38 " ideal model delta sigma weight residual 1.520 1.589 -0.069 1.20e-02 6.94e+03 3.27e+01 bond pdb=" C ARG B1019 " pdb=" O ARG B1019 " ideal model delta sigma weight residual 1.237 1.174 0.062 1.16e-02 7.43e+03 2.90e+01 bond pdb=" CA PRO E 119 " pdb=" C PRO E 119 " ideal model delta sigma weight residual 1.514 1.543 -0.029 5.50e-03 3.31e+04 2.81e+01 bond pdb=" C ARG C 905 " pdb=" O ARG C 905 " ideal model delta sigma weight residual 1.236 1.172 0.065 1.22e-02 6.72e+03 2.80e+01 bond pdb=" C ARG B1039 " pdb=" O ARG B1039 " ideal model delta sigma weight residual 1.235 1.174 0.061 1.20e-02 6.94e+03 2.61e+01 ... (remaining 38731 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 45030 2.70 - 5.40: 7314 5.40 - 8.10: 323 8.10 - 10.80: 37 10.80 - 13.50: 18 Bond angle restraints: 52722 Sorted by residual: angle pdb=" N ARG C 214 " pdb=" CA ARG C 214 " pdb=" C ARG C 214 " ideal model delta sigma weight residual 110.41 122.91 -12.50 1.18e+00 7.18e-01 1.12e+02 angle pdb=" C GLU H 148 " pdb=" N PRO H 149 " pdb=" CA PRO H 149 " ideal model delta sigma weight residual 119.84 133.02 -13.18 1.25e+00 6.40e-01 1.11e+02 angle pdb=" C GLU F 148 " pdb=" N PRO F 149 " pdb=" CA PRO F 149 " ideal model delta sigma weight residual 119.84 132.98 -13.14 1.25e+00 6.40e-01 1.11e+02 angle pdb=" C GLU D 148 " pdb=" N PRO D 149 " pdb=" CA PRO D 149 " ideal model delta sigma weight residual 119.84 132.95 -13.11 1.25e+00 6.40e-01 1.10e+02 angle pdb=" N ASN L 138 " pdb=" CA ASN L 138 " pdb=" C ASN L 138 " ideal model delta sigma weight residual 111.24 124.17 -12.93 1.38e+00 5.25e-01 8.78e+01 ... (remaining 52717 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.00: 23297 25.00 - 50.00: 956 50.00 - 75.00: 225 75.00 - 100.00: 65 100.00 - 125.00: 78 Dihedral angle restraints: 24621 sinusoidal: 11046 harmonic: 13575 Sorted by residual: dihedral pdb=" CB CYS B 840 " pdb=" SG CYS B 840 " pdb=" SG CYS B 851 " pdb=" CB CYS B 851 " ideal model delta sinusoidal sigma weight residual -86.00 -160.40 74.40 1 1.00e+01 1.00e-02 7.02e+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 -154.29 68.29 1 1.00e+01 1.00e-02 6.05e+01 dihedral pdb=" CB CYS C 840 " pdb=" SG CYS C 840 " pdb=" SG CYS C 851 " pdb=" CB CYS C 851 " ideal model delta sinusoidal sigma weight residual -86.00 -151.94 65.94 1 1.00e+01 1.00e-02 5.69e+01 ... (remaining 24618 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.310: 6258 0.310 - 0.619: 57 0.619 - 0.929: 3 0.929 - 1.239: 0 1.239 - 1.549: 3 Chirality restraints: 6321 Sorted by residual: chirality pdb=" C1 FUC f 3 " pdb=" O6 NAG f 1 " pdb=" C2 FUC f 3 " pdb=" O5 FUC f 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.57e+02 chirality pdb=" C1 NAG W 2 " pdb=" O4 NAG W 1 " pdb=" C2 NAG W 2 " pdb=" O5 NAG W 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.37e+01 chirality pdb=" C1 NAG b 2 " pdb=" O4 NAG b 1 " pdb=" C2 NAG b 2 " pdb=" O5 NAG b 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.63e+01 ... (remaining 6318 not shown) Planarity restraints: 6693 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 61 " -0.114 2.00e-02 2.50e+03 1.26e-01 1.99e+02 pdb=" CG ASN A 61 " 0.067 2.00e-02 2.50e+03 pdb=" OD1 ASN A 61 " -0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN A 61 " 0.200 2.00e-02 2.50e+03 pdb=" C1 NAG A1401 " -0.148 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C1158 " -0.089 2.00e-02 2.50e+03 1.19e-01 1.76e+02 pdb=" CG ASN C1158 " 0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN C1158 " -0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN C1158 " 0.205 2.00e-02 2.50e+03 pdb=" C1 NAG C1407 " -0.138 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 603 " -0.008 2.00e-02 2.50e+03 1.16e-01 1.67e+02 pdb=" CG ASN B 603 " 0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN B 603 " -0.097 2.00e-02 2.50e+03 pdb=" ND2 ASN B 603 " 0.199 2.00e-02 2.50e+03 pdb=" C1 NAG B1404 " -0.129 2.00e-02 2.50e+03 ... (remaining 6690 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 80 2.57 - 3.15: 27902 3.15 - 3.73: 56985 3.73 - 4.32: 85039 4.32 - 4.90: 137992 Nonbonded interactions: 307998 Sorted by model distance: nonbonded pdb=" NH1 ARG H 100A" pdb=" OH TYR L 91 " model vdw 1.984 3.120 nonbonded pdb=" OE1 GLU C 156 " pdb=" NH1 ARG C 158 " model vdw 2.094 3.120 nonbonded pdb=" CD1 TYR G 32 " pdb=" OH TYR G 91 " model vdw 2.102 3.340 nonbonded pdb=" OD1 ASP C 442 " pdb=" OG SER H 100B" model vdw 2.135 3.040 nonbonded pdb=" OG1 THR F 116 " pdb=" CG PRO F 147 " model vdw 2.179 3.440 ... (remaining 307993 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'N' selection = chain 'V' selection = chain 'Z' selection = chain 'h' selection = chain 'l' } ncs_group { reference = (chain 'J' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'M' and resid 1 through 2) selection = (chain 'O' and resid 1 through 2) selection = (chain 'P' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) selection = (chain 'R' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'Y' and resid 1 through 2) selection = (chain 'a' and resid 1 through 2) selection = (chain 'b' and resid 1 through 2) selection = (chain 'c' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) selection = (chain 'f' and resid 1 through 2) selection = (chain 'g' and resid 1 through 2) selection = (chain 'i' and resid 1 through 2) selection = (chain 'j' and resid 1 through 2) selection = (chain 'k' and resid 1 through 2) selection = (chain 'm' and resid 1 through 2) selection = (chain 'n' and resid 1 through 2) selection = (chain 'o' and resid 1 through 2) selection = (chain 'p' and resid 1 through 2) selection = (chain 'q' and resid 1 through 2) selection = (chain 'r' and resid 1 through 2) selection = (chain 's' 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: 7.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.650 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 37.830 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.110 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:6.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 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 : 0.014 0.090 38913 Z= 0.825 Angle : 1.948 34.811 53199 Z= 1.235 Chirality : 0.111 1.549 6321 Planarity : 0.012 0.120 6636 Dihedral : 16.960 124.998 15747 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 1.10 % Allowed : 5.86 % Favored : 93.04 % Rotamer: Outliers : 2.59 % Allowed : 5.83 % Favored : 91.58 % Cbeta Deviations : 0.53 % 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: -1.40 (0.11), residues: 4638 helix: -1.54 (0.15), residues: 831 sheet: 0.44 (0.14), residues: 1188 loop : -1.40 (0.11), residues: 2619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 346 TYR 0.120 0.020 TYR C 269 PHE 0.118 0.014 PHE A 718 TRP 0.129 0.020 TRP C 104 HIS 0.013 0.004 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.01446 (38736) covalent geometry : angle 1.86940 (52722) SS BOND : bond 0.01350 ( 54) SS BOND : angle 2.77266 ( 108) hydrogen bonds : bond 0.15836 ( 1479) hydrogen bonds : angle 8.51701 ( 4182) link_ALPHA1-4 : bond 0.02601 ( 24) link_ALPHA1-4 : angle 4.10606 ( 72) link_BETA1-4 : bond 0.02405 ( 36) link_BETA1-4 : angle 4.21572 ( 108) link_BETA1-6 : bond 0.03113 ( 6) link_BETA1-6 : angle 3.48308 ( 18) link_NAG-ASN : bond 0.01665 ( 57) link_NAG-ASN : angle 8.85266 ( 171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 4059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 441 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 780 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.7788 (mt-10) REVERT: A 854 LYS cc_start: 0.7710 (tttt) cc_final: 0.7466 (tmtt) REVERT: B 99 ASN cc_start: 0.7402 (m-40) cc_final: 0.7162 (m110) REVERT: B 345 THR cc_start: 0.8185 (m) cc_final: 0.7909 (m) REVERT: B 420 ASP cc_start: 0.6908 (t0) cc_final: 0.6674 (t0) REVERT: B 1038 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8537 (mmtm) REVERT: B 1045 LYS cc_start: 0.8676 (mmtm) cc_final: 0.8288 (tptt) REVERT: C 346 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7596 (ptp-110) REVERT: C 427 ASP cc_start: 0.7459 (m-30) cc_final: 0.7192 (m-30) REVERT: C 634 ARG cc_start: 0.6367 (OUTLIER) cc_final: 0.5850 (mtm180) REVERT: C 758 SER cc_start: 0.7824 (t) cc_final: 0.7473 (m) REVERT: C 1038 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8382 (mmtm) REVERT: F 48 MET cc_start: 0.5664 (mpp) cc_final: 0.5091 (mmm) REVERT: F 71 ARG cc_start: 0.5932 (OUTLIER) cc_final: 0.4085 (ptm-80) REVERT: H 71 ARG cc_start: 0.6313 (OUTLIER) cc_final: 0.4536 (ptm-80) REVERT: L 175 LEU cc_start: 0.1812 (OUTLIER) cc_final: 0.1543 (pt) outliers start: 105 outliers final: 28 residues processed: 529 average time/residue: 0.6622 time to fit residues: 426.6531 Evaluate side-chains 341 residues out of total 4059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 305 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 843 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 50 TRP Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain F residue 71 ARG Chi-restraints excluded: chain F residue 99 TYR Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 96 ARG Chi-restraints excluded: chain H residue 209 LYS Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 175 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 432 optimal weight: 0.9980 chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 5.9990 chunk 455 optimal weight: 6.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.5980 chunk 401 optimal weight: 9.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 422 ASN A 437 ASN A 762 GLN A 957 GLN B 188 ASN B 211 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B 914 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 422 ASN C 762 GLN C 907 ASN E 53 ASN ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.221093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.165232 restraints weight = 42625.509| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 2.47 r_work: 0.3214 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 38913 Z= 0.167 Angle : 0.795 16.108 53199 Z= 0.387 Chirality : 0.048 0.266 6321 Planarity : 0.005 0.070 6636 Dihedral : 13.833 113.279 7610 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.39 % Allowed : 3.47 % Favored : 96.14 % Rotamer: Outliers : 2.62 % Allowed : 9.80 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.46 (0.12), residues: 4638 helix: 0.51 (0.18), residues: 834 sheet: 0.33 (0.13), residues: 1407 loop : -0.98 (0.12), residues: 2397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 38 TYR 0.023 0.002 TYR E 91 PHE 0.033 0.002 PHE H 146 TRP 0.020 0.002 TRP D 154 HIS 0.006 0.001 HIS L 198 Details of bonding type rmsd covalent geometry : bond 0.00360 (38736) covalent geometry : angle 0.75487 (52722) SS BOND : bond 0.01402 ( 54) SS BOND : angle 1.43358 ( 108) hydrogen bonds : bond 0.04521 ( 1479) hydrogen bonds : angle 6.27289 ( 4182) link_ALPHA1-4 : bond 0.01208 ( 24) link_ALPHA1-4 : angle 2.89462 ( 72) link_BETA1-4 : bond 0.00455 ( 36) link_BETA1-4 : angle 1.89104 ( 108) link_BETA1-6 : bond 0.01258 ( 6) link_BETA1-6 : angle 1.62473 ( 18) link_NAG-ASN : bond 0.00674 ( 57) link_NAG-ASN : angle 3.71370 ( 171) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 4059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 384 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.7332 (OUTLIER) cc_final: 0.7071 (p90) REVERT: A 378 LYS cc_start: 0.7315 (tppt) cc_final: 0.6808 (tptp) REVERT: A 420 ASP cc_start: 0.6974 (m-30) cc_final: 0.6469 (m-30) REVERT: A 619 GLU cc_start: 0.6104 (mp0) cc_final: 0.5889 (mp0) REVERT: A 675 GLN cc_start: 0.7702 (mt0) cc_final: 0.7426 (mm-40) REVERT: A 780 GLU cc_start: 0.9066 (mm-30) cc_final: 0.8074 (pt0) REVERT: A 1005 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8599 (mt0) REVERT: B 21 ARG cc_start: 0.6500 (OUTLIER) cc_final: 0.5888 (ptm160) REVERT: B 309 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.7929 (mp0) REVERT: B 407 VAL cc_start: 0.8338 (OUTLIER) cc_final: 0.8069 (p) REVERT: B 420 ASP cc_start: 0.7252 (t0) cc_final: 0.7004 (t0) REVERT: B 529 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.7454 (mttp) REVERT: B 661 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8198 (tt0) REVERT: B 950 ASP cc_start: 0.8602 (m-30) cc_final: 0.8357 (m-30) REVERT: B 994 ASP cc_start: 0.8277 (OUTLIER) cc_final: 0.8028 (t70) REVERT: C 169 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7846 (mt-10) REVERT: C 427 ASP cc_start: 0.8018 (m-30) cc_final: 0.7619 (m-30) REVERT: C 675 GLN cc_start: 0.7583 (mt0) cc_final: 0.7259 (mm-40) REVERT: C 787 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.8230 (mt0) REVERT: C 950 ASP cc_start: 0.8586 (m-30) cc_final: 0.8251 (m-30) REVERT: C 1005 GLN cc_start: 0.8955 (mt0) cc_final: 0.8724 (mt0) REVERT: D 100 ARG cc_start: 0.5938 (ttm110) cc_final: 0.5656 (ttm110) REVERT: D 159 LEU cc_start: 0.2029 (pp) cc_final: 0.1713 (tm) REVERT: D 214 LYS cc_start: 0.1672 (pttt) cc_final: 0.0468 (ptpt) REVERT: F 48 MET cc_start: 0.6042 (mpp) cc_final: 0.4679 (mmm) REVERT: F 71 ARG cc_start: 0.5674 (OUTLIER) cc_final: 0.4135 (ptm-80) REVERT: F 100 ARG cc_start: 0.6245 (OUTLIER) cc_final: 0.5933 (ttm110) REVERT: G 4 MET cc_start: 0.4350 (mmp) cc_final: 0.4104 (mpp) REVERT: H 4 LEU cc_start: 0.4015 (OUTLIER) cc_final: 0.3413 (mp) REVERT: H 23 LYS cc_start: 0.5938 (mmmt) cc_final: 0.5651 (tptp) REVERT: H 48 MET cc_start: 0.5720 (OUTLIER) cc_final: 0.5510 (mmt) REVERT: H 71 ARG cc_start: 0.5444 (OUTLIER) cc_final: 0.5201 (ptm-80) REVERT: L 59 PRO cc_start: 0.4092 (Cg_exo) cc_final: 0.3822 (Cg_endo) REVERT: L 103 LYS cc_start: 0.4573 (tmmt) cc_final: 0.4142 (pptt) REVERT: L 124 GLN cc_start: 0.2210 (OUTLIER) cc_final: 0.1207 (tm-30) outliers start: 106 outliers final: 42 residues processed: 451 average time/residue: 0.6295 time to fit residues: 349.3098 Evaluate side-chains 365 residues out of total 4059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 308 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 71 ARG Chi-restraints excluded: chain F residue 99 TYR Chi-restraints excluded: chain F residue 100 ARG Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 172 SER Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 124 GLN Chi-restraints excluded: chain L residue 133 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 309 optimal weight: 0.5980 chunk 462 optimal weight: 30.0000 chunk 361 optimal weight: 6.9990 chunk 187 optimal weight: 0.4980 chunk 7 optimal weight: 3.9990 chunk 398 optimal weight: 10.0000 chunk 80 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 274 optimal weight: 4.9990 chunk 322 optimal weight: 0.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 GLN A 957 GLN B 99 ASN B 146 HIS B 211 ASN B 321 GLN B 422 ASN B 703 ASN B 907 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1113 GLN C 211 ASN C 314 GLN C 613 GLN C 703 ASN C 762 GLN E 53 ASN G 53 ASN ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.218572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.162559 restraints weight = 42233.199| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 2.50 r_work: 0.3172 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 38913 Z= 0.210 Angle : 0.778 14.346 53199 Z= 0.378 Chirality : 0.049 0.349 6321 Planarity : 0.005 0.057 6636 Dihedral : 13.032 112.906 7570 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.79 % Favored : 94.98 % Rotamer: Outliers : 3.53 % Allowed : 10.91 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 (0.12), residues: 4638 helix: 0.84 (0.19), residues: 834 sheet: 0.38 (0.13), residues: 1419 loop : -1.00 (0.12), residues: 2385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 634 TYR 0.023 0.002 TYR A1067 PHE 0.023 0.002 PHE B 592 TRP 0.015 0.002 TRP H 50 HIS 0.007 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00495 (38736) covalent geometry : angle 0.74261 (52722) SS BOND : bond 0.00479 ( 54) SS BOND : angle 1.50039 ( 108) hydrogen bonds : bond 0.04703 ( 1479) hydrogen bonds : angle 5.98782 ( 4182) link_ALPHA1-4 : bond 0.01637 ( 24) link_ALPHA1-4 : angle 3.04356 ( 72) link_BETA1-4 : bond 0.00422 ( 36) link_BETA1-4 : angle 1.66325 ( 108) link_BETA1-6 : bond 0.01379 ( 6) link_BETA1-6 : angle 1.74368 ( 18) link_NAG-ASN : bond 0.00395 ( 57) link_NAG-ASN : angle 3.32276 ( 171) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 4059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 312 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 LYS cc_start: 0.7467 (mmmm) cc_final: 0.7155 (mmmm) REVERT: A 309 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8308 (mp0) REVERT: A 310 LYS cc_start: 0.9155 (OUTLIER) cc_final: 0.8682 (ttpm) REVERT: A 368 LEU cc_start: 0.8142 (mp) cc_final: 0.7868 (mt) REVERT: A 378 LYS cc_start: 0.7364 (tppt) cc_final: 0.6888 (tptp) REVERT: A 403 ARG cc_start: 0.7090 (ptm-80) cc_final: 0.6798 (ptm-80) REVERT: A 675 GLN cc_start: 0.7837 (mt0) cc_final: 0.7465 (mm-40) REVERT: A 780 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8165 (pt0) REVERT: A 1005 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8586 (mt0) REVERT: B 52 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.8111 (tm130) REVERT: B 309 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.7961 (mp0) REVERT: B 358 ILE cc_start: 0.8663 (OUTLIER) cc_final: 0.8255 (mt) REVERT: B 407 VAL cc_start: 0.8265 (OUTLIER) cc_final: 0.7968 (p) REVERT: B 420 ASP cc_start: 0.7251 (t0) cc_final: 0.6852 (t0) REVERT: B 529 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.7634 (mttp) REVERT: B 661 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8243 (tt0) REVERT: B 916 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8653 (tt) REVERT: B 994 ASP cc_start: 0.8394 (OUTLIER) cc_final: 0.8129 (t70) REVERT: C 52 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.8080 (tm130) REVERT: C 427 ASP cc_start: 0.8154 (m-30) cc_final: 0.7797 (m-30) REVERT: C 465 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7752 (mt-10) REVERT: C 567 ARG cc_start: 0.8161 (mmt-90) cc_final: 0.7756 (mmt-90) REVERT: C 675 GLN cc_start: 0.7658 (mt0) cc_final: 0.7331 (mm-40) REVERT: C 780 GLU cc_start: 0.9037 (mm-30) cc_final: 0.8111 (pt0) REVERT: C 787 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.8244 (mt0) REVERT: C 790 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8264 (mmtt) REVERT: C 1141 LEU cc_start: 0.7500 (OUTLIER) cc_final: 0.7241 (tm) REVERT: D 159 LEU cc_start: 0.2433 (pp) cc_final: 0.1832 (tp) REVERT: D 214 LYS cc_start: 0.1613 (pttt) cc_final: 0.0455 (ptpt) REVERT: F 48 MET cc_start: 0.6299 (mpp) cc_final: 0.6086 (mpp) REVERT: G 4 MET cc_start: 0.4535 (mmp) cc_final: 0.4306 (mpp) REVERT: G 47 LEU cc_start: 0.7107 (mt) cc_final: 0.6777 (mm) REVERT: G 105 GLU cc_start: 0.4909 (OUTLIER) cc_final: 0.4335 (pm20) REVERT: H 4 LEU cc_start: 0.3939 (OUTLIER) cc_final: 0.3323 (mp) REVERT: H 159 LEU cc_start: 0.4230 (OUTLIER) cc_final: 0.3968 (pp) REVERT: L 103 LYS cc_start: 0.4708 (tmmt) cc_final: 0.4315 (pptt) REVERT: L 124 GLN cc_start: 0.2334 (OUTLIER) cc_final: 0.1463 (tm-30) REVERT: L 183 LYS cc_start: 0.3694 (ttmm) cc_final: 0.3192 (tttp) outliers start: 143 outliers final: 64 residues processed: 409 average time/residue: 0.6209 time to fit residues: 314.0407 Evaluate side-chains 376 residues out of total 4059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 292 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 19 LYS Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 99 TYR Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 105 GLU Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain H residue 161 SER Chi-restraints excluded: chain H residue 172 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 124 GLN Chi-restraints excluded: chain L residue 133 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 203 optimal weight: 3.9990 chunk 346 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 311 optimal weight: 0.6980 chunk 298 optimal weight: 0.6980 chunk 50 optimal weight: 7.9990 chunk 379 optimal weight: 30.0000 chunk 380 optimal weight: 20.0000 chunk 262 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 344 optimal weight: 20.0000 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN A 957 GLN B 99 ASN B 211 ASN B 804 GLN B 907 ASN B 935 GLN B 957 GLN C 211 ASN E 53 ASN G 53 ASN ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.218277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.161118 restraints weight = 42104.257| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 2.39 r_work: 0.3184 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 38913 Z= 0.206 Angle : 0.752 13.465 53199 Z= 0.359 Chirality : 0.048 0.376 6321 Planarity : 0.004 0.051 6636 Dihedral : 12.515 111.795 7551 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.69 % Favored : 96.12 % Rotamer: Outliers : 3.68 % Allowed : 12.10 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.33 (0.12), residues: 4638 helix: 0.96 (0.19), residues: 834 sheet: 0.37 (0.13), residues: 1434 loop : -1.02 (0.12), residues: 2370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 100A TYR 0.022 0.002 TYR B 265 PHE 0.030 0.002 PHE L 118 TRP 0.012 0.001 TRP D 50 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00486 (38736) covalent geometry : angle 0.71618 (52722) SS BOND : bond 0.00484 ( 54) SS BOND : angle 1.43064 ( 108) hydrogen bonds : bond 0.04378 ( 1479) hydrogen bonds : angle 5.83828 ( 4182) link_ALPHA1-4 : bond 0.01582 ( 24) link_ALPHA1-4 : angle 2.96487 ( 72) link_BETA1-4 : bond 0.00382 ( 36) link_BETA1-4 : angle 1.54361 ( 108) link_BETA1-6 : bond 0.01444 ( 6) link_BETA1-6 : angle 1.95057 ( 18) link_NAG-ASN : bond 0.00420 ( 57) link_NAG-ASN : angle 3.28831 ( 171) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 4059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 299 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.9039 (OUTLIER) cc_final: 0.8378 (tt0) REVERT: A 178 ASP cc_start: 0.6706 (m-30) cc_final: 0.6217 (p0) REVERT: A 187 LYS cc_start: 0.7484 (mmmm) cc_final: 0.7180 (mmmm) REVERT: A 309 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8179 (mp0) REVERT: A 310 LYS cc_start: 0.9173 (OUTLIER) cc_final: 0.8660 (ttpm) REVERT: A 368 LEU cc_start: 0.8109 (mp) cc_final: 0.7841 (mt) REVERT: A 378 LYS cc_start: 0.7316 (tppt) cc_final: 0.6789 (tptp) REVERT: A 567 ARG cc_start: 0.8152 (mtt90) cc_final: 0.7853 (mmt-90) REVERT: A 661 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8055 (tm-30) REVERT: A 675 GLN cc_start: 0.7817 (mt0) cc_final: 0.7455 (mm-40) REVERT: A 740 MET cc_start: 0.8961 (ttt) cc_final: 0.8744 (tpt) REVERT: A 780 GLU cc_start: 0.9009 (mm-30) cc_final: 0.8181 (pt0) REVERT: A 787 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.8184 (mt0) REVERT: A 1002 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.8377 (mp10) REVERT: A 1005 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8575 (mt0) REVERT: B 309 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.7955 (mp0) REVERT: B 358 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8231 (mt) REVERT: B 407 VAL cc_start: 0.8225 (OUTLIER) cc_final: 0.7963 (p) REVERT: B 420 ASP cc_start: 0.7157 (t0) cc_final: 0.6788 (t0) REVERT: B 529 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.7587 (mttp) REVERT: B 661 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8216 (tt0) REVERT: B 780 GLU cc_start: 0.8959 (mm-30) cc_final: 0.8063 (pt0) REVERT: B 916 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8634 (tt) REVERT: B 994 ASP cc_start: 0.8328 (OUTLIER) cc_final: 0.8061 (t70) REVERT: B 1045 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8722 (tppt) REVERT: C 52 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.8065 (tm130) REVERT: C 96 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.8096 (tp30) REVERT: C 420 ASP cc_start: 0.6976 (m-30) cc_final: 0.6743 (m-30) REVERT: C 427 ASP cc_start: 0.8157 (m-30) cc_final: 0.7813 (m-30) REVERT: C 567 ARG cc_start: 0.8131 (mmt-90) cc_final: 0.7715 (mmt-90) REVERT: C 661 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8086 (tm-30) REVERT: C 675 GLN cc_start: 0.7644 (mt0) cc_final: 0.7341 (mm-40) REVERT: C 780 GLU cc_start: 0.8974 (mm-30) cc_final: 0.8088 (pt0) REVERT: C 787 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.8198 (mt0) REVERT: D 71 ARG cc_start: 0.5809 (OUTLIER) cc_final: 0.4033 (ptm-80) REVERT: D 159 LEU cc_start: 0.2177 (OUTLIER) cc_final: 0.1598 (tp) REVERT: D 214 LYS cc_start: 0.1673 (pttt) cc_final: 0.0442 (ptpt) REVERT: E 31 ASP cc_start: 0.7233 (t0) cc_final: 0.6904 (m-30) REVERT: E 55 GLU cc_start: 0.6342 (tp30) cc_final: 0.5669 (tp30) REVERT: F 71 ARG cc_start: 0.5573 (OUTLIER) cc_final: 0.3957 (ptm-80) REVERT: F 100 ARG cc_start: 0.6280 (ttm110) cc_final: 0.5029 (ttm-80) REVERT: G 4 MET cc_start: 0.4602 (mmp) cc_final: 0.4347 (mpp) REVERT: G 24 GLN cc_start: 0.6545 (OUTLIER) cc_final: 0.6058 (tm-30) REVERT: G 47 LEU cc_start: 0.7123 (mt) cc_final: 0.6871 (mm) REVERT: G 105 GLU cc_start: 0.4754 (OUTLIER) cc_final: 0.4213 (pm20) REVERT: H 4 LEU cc_start: 0.3890 (OUTLIER) cc_final: 0.3218 (mp) REVERT: H 71 ARG cc_start: 0.5281 (OUTLIER) cc_final: 0.3435 (ptm-80) REVERT: H 159 LEU cc_start: 0.4327 (OUTLIER) cc_final: 0.4064 (pp) REVERT: H 201 LYS cc_start: 0.6018 (mmtt) cc_final: 0.5510 (mtmm) REVERT: L 42 LYS cc_start: 0.5622 (tptp) cc_final: 0.5083 (mppt) REVERT: L 124 GLN cc_start: 0.2398 (OUTLIER) cc_final: 0.1409 (tm-30) outliers start: 149 outliers final: 74 residues processed: 399 average time/residue: 0.6216 time to fit residues: 306.2219 Evaluate side-chains 384 residues out of total 4059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 282 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 71 ARG Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 71 ARG Chi-restraints excluded: chain F residue 99 TYR Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 105 GLU Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain H residue 161 SER Chi-restraints excluded: chain H residue 172 SER Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 124 GLN Chi-restraints excluded: chain L residue 133 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 183 optimal weight: 0.4980 chunk 226 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 204 optimal weight: 3.9990 chunk 217 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 112 optimal weight: 9.9990 chunk 125 optimal weight: 0.4980 chunk 123 optimal weight: 1.9990 chunk 188 optimal weight: 0.0670 chunk 341 optimal weight: 10.0000 overall best weight: 0.5720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN B 99 ASN B 388 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B 907 ASN C 99 ASN C 146 HIS C 211 ASN E 53 ASN G 53 ASN ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.220697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.170636 restraints weight = 42336.000| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 2.17 r_work: 0.3268 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 38913 Z= 0.125 Angle : 0.685 14.768 53199 Z= 0.323 Chirality : 0.045 0.346 6321 Planarity : 0.004 0.061 6636 Dihedral : 11.640 108.217 7551 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.51 % Favored : 96.31 % Rotamer: Outliers : 2.77 % Allowed : 13.98 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 (0.12), residues: 4638 helix: 1.32 (0.19), residues: 852 sheet: 0.48 (0.13), residues: 1407 loop : -0.94 (0.12), residues: 2379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 100A TYR 0.025 0.001 TYR C 508 PHE 0.028 0.001 PHE B 592 TRP 0.014 0.001 TRP D 50 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00268 (38736) covalent geometry : angle 0.65191 (52722) SS BOND : bond 0.00418 ( 54) SS BOND : angle 1.43401 ( 108) hydrogen bonds : bond 0.03567 ( 1479) hydrogen bonds : angle 5.57140 ( 4182) link_ALPHA1-4 : bond 0.01578 ( 24) link_ALPHA1-4 : angle 3.02494 ( 72) link_BETA1-4 : bond 0.00426 ( 36) link_BETA1-4 : angle 1.35118 ( 108) link_BETA1-6 : bond 0.01613 ( 6) link_BETA1-6 : angle 2.09344 ( 18) link_NAG-ASN : bond 0.00415 ( 57) link_NAG-ASN : angle 2.89321 ( 171) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 4059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 322 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ASN cc_start: 0.7601 (OUTLIER) cc_final: 0.7113 (p0) REVERT: A 187 LYS cc_start: 0.7477 (mmmm) cc_final: 0.7119 (mmmm) REVERT: A 240 THR cc_start: 0.8776 (t) cc_final: 0.8552 (m) REVERT: A 309 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8217 (mp0) REVERT: A 316 SER cc_start: 0.8298 (OUTLIER) cc_final: 0.7917 (p) REVERT: A 319 ARG cc_start: 0.7911 (ttm170) cc_final: 0.7247 (ttm110) REVERT: A 368 LEU cc_start: 0.8098 (mp) cc_final: 0.7824 (mt) REVERT: A 378 LYS cc_start: 0.7337 (tppt) cc_final: 0.6815 (tptm) REVERT: A 403 ARG cc_start: 0.7121 (ptm-80) cc_final: 0.6919 (ptm-80) REVERT: A 567 ARG cc_start: 0.8226 (mtt90) cc_final: 0.8023 (mmt-90) REVERT: A 572 THR cc_start: 0.8763 (p) cc_final: 0.8484 (t) REVERT: A 675 GLN cc_start: 0.7854 (mt0) cc_final: 0.7591 (mm-40) REVERT: A 780 GLU cc_start: 0.8941 (mm-30) cc_final: 0.8231 (pt0) REVERT: A 1005 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.8561 (mt0) REVERT: B 187 LYS cc_start: 0.7539 (mmmt) cc_final: 0.7079 (mmmt) REVERT: B 211 ASN cc_start: 0.7071 (t0) cc_final: 0.6424 (t0) REVERT: B 309 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.7975 (mp0) REVERT: B 319 ARG cc_start: 0.7820 (ttm170) cc_final: 0.7175 (ttm110) REVERT: B 358 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8276 (mt) REVERT: B 407 VAL cc_start: 0.8257 (t) cc_final: 0.8045 (p) REVERT: B 408 ARG cc_start: 0.7496 (ttp80) cc_final: 0.7248 (ptm-80) REVERT: B 420 ASP cc_start: 0.7149 (t0) cc_final: 0.6783 (t0) REVERT: B 442 ASP cc_start: 0.5986 (m-30) cc_final: 0.5616 (m-30) REVERT: B 780 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8149 (pt0) REVERT: B 916 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8593 (tt) REVERT: B 994 ASP cc_start: 0.8294 (OUTLIER) cc_final: 0.8014 (t70) REVERT: B 1045 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8704 (tppt) REVERT: C 408 ARG cc_start: 0.7091 (OUTLIER) cc_final: 0.6797 (tmm160) REVERT: C 420 ASP cc_start: 0.6975 (m-30) cc_final: 0.6678 (m-30) REVERT: C 427 ASP cc_start: 0.8175 (m-30) cc_final: 0.7835 (m-30) REVERT: C 529 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.7377 (mptp) REVERT: C 567 ARG cc_start: 0.8087 (mmt-90) cc_final: 0.7659 (mmt-90) REVERT: C 629 LEU cc_start: 0.3370 (OUTLIER) cc_final: 0.2951 (mp) REVERT: C 661 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8088 (tm-30) REVERT: C 675 GLN cc_start: 0.7637 (mt0) cc_final: 0.7379 (mm-40) REVERT: C 780 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8149 (pt0) REVERT: C 950 ASP cc_start: 0.8663 (m-30) cc_final: 0.8364 (m-30) REVERT: C 1141 LEU cc_start: 0.7539 (OUTLIER) cc_final: 0.7244 (tm) REVERT: D 99 TYR cc_start: 0.7146 (OUTLIER) cc_final: 0.5991 (m-80) REVERT: D 159 LEU cc_start: 0.2179 (OUTLIER) cc_final: 0.1628 (tp) REVERT: D 214 LYS cc_start: 0.1717 (pttt) cc_final: 0.0447 (ptpt) REVERT: E 31 ASP cc_start: 0.7269 (t0) cc_final: 0.7036 (m-30) REVERT: E 55 GLU cc_start: 0.6224 (tp30) cc_final: 0.5749 (tp30) REVERT: E 183 LYS cc_start: -0.0040 (mptt) cc_final: -0.1014 (ttmt) REVERT: G 47 LEU cc_start: 0.7145 (mt) cc_final: 0.6904 (mm) REVERT: G 105 GLU cc_start: 0.4676 (OUTLIER) cc_final: 0.4443 (pm20) REVERT: H 4 LEU cc_start: 0.3874 (OUTLIER) cc_final: 0.3214 (mp) REVERT: H 71 ARG cc_start: 0.5382 (OUTLIER) cc_final: 0.3605 (ptm-80) REVERT: H 159 LEU cc_start: 0.4309 (OUTLIER) cc_final: 0.4045 (pp) REVERT: H 201 LYS cc_start: 0.5897 (mmtt) cc_final: 0.5386 (mtmm) REVERT: L 42 LYS cc_start: 0.5624 (tptp) cc_final: 0.5208 (mppt) REVERT: L 124 GLN cc_start: 0.2418 (OUTLIER) cc_final: 0.1491 (tm-30) REVERT: L 145 LYS cc_start: 0.3501 (mttp) cc_final: 0.3100 (tptt) REVERT: L 163 VAL cc_start: 0.2181 (OUTLIER) cc_final: 0.1953 (m) outliers start: 112 outliers final: 55 residues processed: 400 average time/residue: 0.6528 time to fit residues: 319.7979 Evaluate side-chains 379 residues out of total 4059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 302 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain F residue 99 TYR Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 105 GLU Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain H residue 161 SER Chi-restraints excluded: chain H residue 172 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 124 GLN Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 163 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 188 optimal weight: 0.0870 chunk 320 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 chunk 231 optimal weight: 0.0040 chunk 218 optimal weight: 0.7980 chunk 158 optimal weight: 9.9990 chunk 332 optimal weight: 6.9990 chunk 407 optimal weight: 20.0000 chunk 281 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 196 optimal weight: 1.9990 overall best weight: 0.9774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN B 321 GLN B 804 GLN C 99 ASN C 239 GLN E 53 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.219954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.170496 restraints weight = 42352.155| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 2.17 r_work: 0.3244 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 38913 Z= 0.146 Angle : 0.694 12.856 53199 Z= 0.326 Chirality : 0.045 0.318 6321 Planarity : 0.004 0.058 6636 Dihedral : 11.112 106.117 7549 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.75 % Favored : 96.05 % Rotamer: Outliers : 3.46 % Allowed : 14.37 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.08 (0.12), residues: 4638 helix: 1.36 (0.19), residues: 855 sheet: 0.56 (0.14), residues: 1371 loop : -0.95 (0.12), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 100A TYR 0.027 0.002 TYR C 508 PHE 0.032 0.001 PHE B 592 TRP 0.011 0.001 TRP D 50 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00330 (38736) covalent geometry : angle 0.66009 (52722) SS BOND : bond 0.00374 ( 54) SS BOND : angle 1.37142 ( 108) hydrogen bonds : bond 0.03736 ( 1479) hydrogen bonds : angle 5.51751 ( 4182) link_ALPHA1-4 : bond 0.01621 ( 24) link_ALPHA1-4 : angle 3.12938 ( 72) link_BETA1-4 : bond 0.00411 ( 36) link_BETA1-4 : angle 1.33917 ( 108) link_BETA1-6 : bond 0.01660 ( 6) link_BETA1-6 : angle 2.22062 ( 18) link_NAG-ASN : bond 0.00450 ( 57) link_NAG-ASN : angle 2.89745 ( 171) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 4059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 313 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.9024 (OUTLIER) cc_final: 0.8386 (tt0) REVERT: A 87 ASN cc_start: 0.7682 (OUTLIER) cc_final: 0.7211 (p0) REVERT: A 187 LYS cc_start: 0.7466 (mmmm) cc_final: 0.7160 (mmmm) REVERT: A 190 ARG cc_start: 0.8841 (mtt90) cc_final: 0.8551 (mtt180) REVERT: A 240 THR cc_start: 0.8783 (OUTLIER) cc_final: 0.8543 (m) REVERT: A 309 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8229 (mp0) REVERT: A 310 LYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8684 (ttpm) REVERT: A 319 ARG cc_start: 0.7920 (ttm170) cc_final: 0.7264 (ttm110) REVERT: A 368 LEU cc_start: 0.8138 (mp) cc_final: 0.7862 (mt) REVERT: A 378 LYS cc_start: 0.7306 (tppt) cc_final: 0.6816 (tptm) REVERT: A 403 ARG cc_start: 0.7050 (ptm-80) cc_final: 0.6845 (ptm-80) REVERT: A 661 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8115 (tm-30) REVERT: A 675 GLN cc_start: 0.7864 (mt0) cc_final: 0.7578 (mm-40) REVERT: A 780 GLU cc_start: 0.8986 (mm-30) cc_final: 0.8288 (pt0) REVERT: A 1005 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.8508 (mt0) REVERT: A 1153 ASP cc_start: 0.1975 (OUTLIER) cc_final: 0.1664 (t0) REVERT: B 187 LYS cc_start: 0.7578 (mmmt) cc_final: 0.7070 (mmmt) REVERT: B 211 ASN cc_start: 0.7172 (t0) cc_final: 0.6397 (t0) REVERT: B 309 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8038 (mp0) REVERT: B 358 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8297 (mt) REVERT: B 408 ARG cc_start: 0.7467 (ttp80) cc_final: 0.7255 (ptm-80) REVERT: B 420 ASP cc_start: 0.7209 (t0) cc_final: 0.6843 (t0) REVERT: B 442 ASP cc_start: 0.6070 (m-30) cc_final: 0.5779 (m-30) REVERT: B 661 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8305 (tt0) REVERT: B 780 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8193 (pt0) REVERT: B 916 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8559 (tt) REVERT: B 994 ASP cc_start: 0.8313 (OUTLIER) cc_final: 0.8021 (t70) REVERT: B 1045 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8719 (tppt) REVERT: B 1149 LYS cc_start: 0.5038 (OUTLIER) cc_final: 0.4493 (ptmt) REVERT: C 52 GLN cc_start: 0.9010 (OUTLIER) cc_final: 0.8248 (tt0) REVERT: C 185 ASN cc_start: 0.5739 (p0) cc_final: 0.5512 (p0) REVERT: C 408 ARG cc_start: 0.7175 (OUTLIER) cc_final: 0.6838 (tmm160) REVERT: C 427 ASP cc_start: 0.8218 (m-30) cc_final: 0.7894 (m-30) REVERT: C 529 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.7494 (mptp) REVERT: C 629 LEU cc_start: 0.3396 (OUTLIER) cc_final: 0.2993 (mp) REVERT: C 661 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8100 (tm-30) REVERT: C 675 GLN cc_start: 0.7699 (mt0) cc_final: 0.7435 (mm110) REVERT: C 731 MET cc_start: 0.9218 (ptt) cc_final: 0.9008 (ptt) REVERT: C 780 GLU cc_start: 0.8898 (mm-30) cc_final: 0.8185 (pt0) REVERT: C 787 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.8126 (mt0) REVERT: C 1141 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7243 (tm) REVERT: D 71 ARG cc_start: 0.5869 (OUTLIER) cc_final: 0.4241 (ptm-80) REVERT: D 99 TYR cc_start: 0.7095 (OUTLIER) cc_final: 0.6092 (m-80) REVERT: D 159 LEU cc_start: 0.2193 (OUTLIER) cc_final: 0.1640 (tp) REVERT: E 55 GLU cc_start: 0.6244 (tp30) cc_final: 0.5802 (tp30) REVERT: E 183 LYS cc_start: 0.0087 (mptt) cc_final: -0.0929 (ttmt) REVERT: G 24 GLN cc_start: 0.6605 (OUTLIER) cc_final: 0.6237 (tm-30) REVERT: G 105 GLU cc_start: 0.4622 (OUTLIER) cc_final: 0.4086 (pm20) REVERT: H 4 LEU cc_start: 0.3839 (OUTLIER) cc_final: 0.3234 (mp) REVERT: H 71 ARG cc_start: 0.5516 (OUTLIER) cc_final: 0.3777 (ptm-80) REVERT: H 159 LEU cc_start: 0.4327 (OUTLIER) cc_final: 0.4019 (pp) REVERT: H 201 LYS cc_start: 0.5863 (mmtt) cc_final: 0.5332 (mtmm) REVERT: L 42 LYS cc_start: 0.5936 (tptp) cc_final: 0.5445 (mppt) REVERT: L 124 GLN cc_start: 0.2380 (OUTLIER) cc_final: 0.1573 (tm-30) REVERT: L 145 LYS cc_start: 0.3414 (mttp) cc_final: 0.3047 (tptt) REVERT: L 163 VAL cc_start: 0.2012 (OUTLIER) cc_final: 0.1792 (m) REVERT: L 175 LEU cc_start: 0.1252 (OUTLIER) cc_final: 0.1031 (pt) REVERT: L 183 LYS cc_start: 0.3748 (ttmm) cc_final: 0.3159 (tttp) outliers start: 140 outliers final: 72 residues processed: 413 average time/residue: 0.6419 time to fit residues: 324.5911 Evaluate side-chains 401 residues out of total 4059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 296 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1153 ASP Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1149 LYS Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 19 LYS Chi-restraints excluded: chain D residue 71 ARG Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 99 TYR Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 105 GLU Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain H residue 161 SER Chi-restraints excluded: chain H residue 172 SER Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 124 GLN Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 175 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 69 optimal weight: 2.9990 chunk 301 optimal weight: 0.4980 chunk 27 optimal weight: 3.9990 chunk 401 optimal weight: 6.9990 chunk 231 optimal weight: 5.9990 chunk 208 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 128 optimal weight: 0.0050 chunk 299 optimal weight: 0.0670 chunk 422 optimal weight: 20.0000 chunk 67 optimal weight: 0.5980 overall best weight: 0.3932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN B 321 GLN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN C 211 ASN E 53 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN G 90 GLN ** G 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.221614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.172036 restraints weight = 42563.827| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 2.15 r_work: 0.3288 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 38913 Z= 0.116 Angle : 0.667 12.749 53199 Z= 0.312 Chirality : 0.044 0.407 6321 Planarity : 0.004 0.051 6636 Dihedral : 10.521 103.820 7547 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.62 % Favored : 96.18 % Rotamer: Outliers : 2.62 % Allowed : 15.33 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.04 (0.12), residues: 4638 helix: 1.58 (0.19), residues: 843 sheet: 0.68 (0.14), residues: 1350 loop : -0.93 (0.12), residues: 2445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 100A TYR 0.024 0.001 TYR C 508 PHE 0.032 0.001 PHE B 592 TRP 0.013 0.001 TRP D 50 HIS 0.003 0.000 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00246 (38736) covalent geometry : angle 0.63218 (52722) SS BOND : bond 0.00529 ( 54) SS BOND : angle 1.61744 ( 108) hydrogen bonds : bond 0.03308 ( 1479) hydrogen bonds : angle 5.35489 ( 4182) link_ALPHA1-4 : bond 0.01631 ( 24) link_ALPHA1-4 : angle 3.08615 ( 72) link_BETA1-4 : bond 0.00407 ( 36) link_BETA1-4 : angle 1.34309 ( 108) link_BETA1-6 : bond 0.01745 ( 6) link_BETA1-6 : angle 2.25562 ( 18) link_NAG-ASN : bond 0.00583 ( 57) link_NAG-ASN : angle 2.82511 ( 171) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 4059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 336 time to evaluate : 1.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.8816 (mtt90) cc_final: 0.8516 (mtt180) REVERT: A 240 THR cc_start: 0.8744 (t) cc_final: 0.8514 (m) REVERT: A 309 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8175 (mp0) REVERT: A 316 SER cc_start: 0.8244 (OUTLIER) cc_final: 0.7855 (p) REVERT: A 319 ARG cc_start: 0.7810 (ttm170) cc_final: 0.7175 (ttm110) REVERT: A 368 LEU cc_start: 0.8108 (mp) cc_final: 0.7834 (mt) REVERT: A 378 LYS cc_start: 0.7298 (tppt) cc_final: 0.6888 (tptm) REVERT: A 403 ARG cc_start: 0.6932 (ptm-80) cc_final: 0.6610 (ptm-80) REVERT: A 572 THR cc_start: 0.8738 (p) cc_final: 0.8499 (t) REVERT: A 675 GLN cc_start: 0.7845 (mt0) cc_final: 0.7631 (mm110) REVERT: A 780 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8270 (pt0) REVERT: B 187 LYS cc_start: 0.7558 (mmmt) cc_final: 0.7040 (mmmt) REVERT: B 211 ASN cc_start: 0.7027 (t0) cc_final: 0.6309 (t0) REVERT: B 309 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.7961 (mp0) REVERT: B 358 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8299 (mt) REVERT: B 420 ASP cc_start: 0.7237 (t0) cc_final: 0.6878 (t70) REVERT: B 442 ASP cc_start: 0.5949 (m-30) cc_final: 0.5715 (m-30) REVERT: B 661 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8291 (tt0) REVERT: B 740 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.8071 (ttt) REVERT: B 780 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8226 (pt0) REVERT: B 916 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8495 (tt) REVERT: B 994 ASP cc_start: 0.8244 (OUTLIER) cc_final: 0.7971 (t70) REVERT: B 1045 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8687 (tppt) REVERT: C 185 ASN cc_start: 0.5675 (p0) cc_final: 0.5274 (p0) REVERT: C 408 ARG cc_start: 0.7061 (OUTLIER) cc_final: 0.6854 (ttp-110) REVERT: C 427 ASP cc_start: 0.8148 (m-30) cc_final: 0.7818 (m-30) REVERT: C 516 GLU cc_start: 0.7873 (pt0) cc_final: 0.7188 (pp20) REVERT: C 529 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.7429 (mptp) REVERT: C 629 LEU cc_start: 0.3293 (OUTLIER) cc_final: 0.2884 (mp) REVERT: C 661 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8079 (tm-30) REVERT: C 675 GLN cc_start: 0.7701 (mt0) cc_final: 0.7466 (mm110) REVERT: C 780 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8210 (pt0) REVERT: C 787 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.8100 (mt0) REVERT: C 950 ASP cc_start: 0.8648 (m-30) cc_final: 0.8333 (m-30) REVERT: C 1141 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7281 (tm) REVERT: D 71 ARG cc_start: 0.5916 (OUTLIER) cc_final: 0.4364 (ptm-80) REVERT: D 99 TYR cc_start: 0.7021 (OUTLIER) cc_final: 0.6264 (m-80) REVERT: D 159 LEU cc_start: 0.2160 (OUTLIER) cc_final: 0.1571 (tp) REVERT: D 214 LYS cc_start: 0.1753 (OUTLIER) cc_final: 0.1351 (pttt) REVERT: E 55 GLU cc_start: 0.6202 (tp30) cc_final: 0.5749 (tp30) REVERT: E 183 LYS cc_start: 0.0049 (mptt) cc_final: -0.0979 (ttpt) REVERT: F 80 MET cc_start: 0.4508 (ppp) cc_final: 0.4256 (ttp) REVERT: G 47 LEU cc_start: 0.7202 (mt) cc_final: 0.6969 (mm) REVERT: G 154 LEU cc_start: 0.2340 (OUTLIER) cc_final: 0.1804 (pp) REVERT: H 4 LEU cc_start: 0.3756 (OUTLIER) cc_final: 0.3150 (mp) REVERT: H 159 LEU cc_start: 0.4304 (OUTLIER) cc_final: 0.4003 (pp) REVERT: H 201 LYS cc_start: 0.5913 (mmtt) cc_final: 0.5392 (mtmm) REVERT: L 42 LYS cc_start: 0.5904 (tptp) cc_final: 0.5491 (mppt) REVERT: L 124 GLN cc_start: 0.2822 (OUTLIER) cc_final: 0.1927 (tm-30) REVERT: L 145 LYS cc_start: 0.3451 (mttp) cc_final: 0.3078 (tptt) REVERT: L 163 VAL cc_start: 0.2262 (OUTLIER) cc_final: 0.1985 (m) outliers start: 106 outliers final: 49 residues processed: 406 average time/residue: 0.6453 time to fit residues: 320.7252 Evaluate side-chains 386 residues out of total 4059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 313 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 19 LYS Chi-restraints excluded: chain D residue 71 ARG Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 214 LYS Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 99 TYR Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain H residue 172 SER Chi-restraints excluded: chain L residue 124 GLN Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 163 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 75 optimal weight: 0.0980 chunk 239 optimal weight: 0.8980 chunk 424 optimal weight: 8.9990 chunk 267 optimal weight: 5.9990 chunk 276 optimal weight: 7.9990 chunk 411 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 312 optimal weight: 2.9990 chunk 341 optimal weight: 0.9980 chunk 212 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN A1119 ASN E 53 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.219799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.170204 restraints weight = 42185.635| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 2.17 r_work: 0.3242 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 38913 Z= 0.159 Angle : 0.702 12.697 53199 Z= 0.329 Chirality : 0.045 0.353 6321 Planarity : 0.004 0.065 6636 Dihedral : 10.128 100.948 7546 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.64 % Favored : 96.14 % Rotamer: Outliers : 2.57 % Allowed : 16.25 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.12), residues: 4638 helix: 1.65 (0.19), residues: 822 sheet: 0.64 (0.14), residues: 1380 loop : -0.96 (0.12), residues: 2436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 100A TYR 0.022 0.002 TYR A1067 PHE 0.032 0.001 PHE B 592 TRP 0.009 0.001 TRP A 436 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00366 (38736) covalent geometry : angle 0.66739 (52722) SS BOND : bond 0.00427 ( 54) SS BOND : angle 1.46103 ( 108) hydrogen bonds : bond 0.03804 ( 1479) hydrogen bonds : angle 5.45030 ( 4182) link_ALPHA1-4 : bond 0.01709 ( 24) link_ALPHA1-4 : angle 3.15563 ( 72) link_BETA1-4 : bond 0.00418 ( 36) link_BETA1-4 : angle 1.32376 ( 108) link_BETA1-6 : bond 0.01759 ( 6) link_BETA1-6 : angle 2.37964 ( 18) link_NAG-ASN : bond 0.00488 ( 57) link_NAG-ASN : angle 2.92273 ( 171) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 4059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 317 time to evaluate : 1.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.9060 (OUTLIER) cc_final: 0.8450 (tt0) REVERT: A 178 ASP cc_start: 0.6978 (m-30) cc_final: 0.6457 (p0) REVERT: A 187 LYS cc_start: 0.7440 (mmmm) cc_final: 0.7127 (mmmm) REVERT: A 190 ARG cc_start: 0.8864 (mtt90) cc_final: 0.8557 (mtt180) REVERT: A 309 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8176 (mp0) REVERT: A 319 ARG cc_start: 0.7899 (ttm170) cc_final: 0.7279 (ttm110) REVERT: A 368 LEU cc_start: 0.8135 (mp) cc_final: 0.7846 (mt) REVERT: A 378 LYS cc_start: 0.7310 (tppt) cc_final: 0.6906 (tptm) REVERT: A 389 ASP cc_start: 0.7747 (m-30) cc_final: 0.7344 (m-30) REVERT: A 403 ARG cc_start: 0.6943 (ptm-80) cc_final: 0.6670 (ptm-80) REVERT: A 661 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8166 (tm-30) REVERT: A 675 GLN cc_start: 0.7909 (mt0) cc_final: 0.7618 (mm-40) REVERT: A 780 GLU cc_start: 0.9005 (mm-30) cc_final: 0.8329 (pt0) REVERT: B 187 LYS cc_start: 0.7581 (mmmt) cc_final: 0.7220 (mmmt) REVERT: B 200 TYR cc_start: 0.8371 (m-80) cc_final: 0.8147 (m-80) REVERT: B 309 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8011 (mp0) REVERT: B 358 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8312 (mt) REVERT: B 378 LYS cc_start: 0.7625 (tptp) cc_final: 0.7083 (tppt) REVERT: B 420 ASP cc_start: 0.7312 (t0) cc_final: 0.7081 (t70) REVERT: B 442 ASP cc_start: 0.6145 (m-30) cc_final: 0.5745 (m-30) REVERT: B 661 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8352 (tt0) REVERT: B 740 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8191 (ttt) REVERT: B 780 GLU cc_start: 0.8870 (mm-30) cc_final: 0.8275 (pt0) REVERT: B 994 ASP cc_start: 0.8344 (OUTLIER) cc_final: 0.8069 (t70) REVERT: B 1045 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8714 (tppt) REVERT: C 408 ARG cc_start: 0.7168 (OUTLIER) cc_final: 0.6912 (ttp-110) REVERT: C 427 ASP cc_start: 0.8267 (m-30) cc_final: 0.7940 (m-30) REVERT: C 529 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.7472 (mptp) REVERT: C 629 LEU cc_start: 0.3238 (OUTLIER) cc_final: 0.2865 (mp) REVERT: C 661 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8124 (tm-30) REVERT: C 675 GLN cc_start: 0.7730 (mt0) cc_final: 0.7498 (mm110) REVERT: C 780 GLU cc_start: 0.8936 (mm-30) cc_final: 0.8238 (pt0) REVERT: C 787 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.8160 (mt0) REVERT: C 1029 MET cc_start: 0.9345 (tpp) cc_final: 0.9141 (tpp) REVERT: C 1141 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7296 (tm) REVERT: D 71 ARG cc_start: 0.5965 (OUTLIER) cc_final: 0.4380 (ptm-80) REVERT: D 99 TYR cc_start: 0.7118 (OUTLIER) cc_final: 0.6389 (m-80) REVERT: D 159 LEU cc_start: 0.2104 (OUTLIER) cc_final: 0.1557 (tp) REVERT: E 55 GLU cc_start: 0.6264 (tp30) cc_final: 0.5835 (tp30) REVERT: E 183 LYS cc_start: 0.0052 (mptt) cc_final: -0.0959 (ttpt) REVERT: F 80 MET cc_start: 0.4742 (ppp) cc_final: 0.4515 (ttp) REVERT: F 209 LYS cc_start: 0.1615 (OUTLIER) cc_final: 0.1351 (pptt) REVERT: G 145 LYS cc_start: 0.4047 (tptt) cc_final: 0.3780 (tmtp) REVERT: G 154 LEU cc_start: 0.2351 (OUTLIER) cc_final: 0.1799 (pp) REVERT: H 4 LEU cc_start: 0.3770 (OUTLIER) cc_final: 0.3165 (mp) REVERT: H 159 LEU cc_start: 0.4177 (OUTLIER) cc_final: 0.3901 (pp) REVERT: H 201 LYS cc_start: 0.5844 (mmtt) cc_final: 0.5300 (mtmm) REVERT: L 42 LYS cc_start: 0.5944 (tptp) cc_final: 0.5550 (mppt) REVERT: L 124 GLN cc_start: 0.2694 (OUTLIER) cc_final: 0.1882 (tm130) REVERT: L 145 LYS cc_start: 0.3431 (mttp) cc_final: 0.3053 (tptt) REVERT: L 163 VAL cc_start: 0.2548 (OUTLIER) cc_final: 0.2289 (m) REVERT: L 175 LEU cc_start: 0.1463 (OUTLIER) cc_final: 0.1201 (pt) REVERT: L 183 LYS cc_start: 0.3645 (ttmm) cc_final: 0.3008 (tttp) outliers start: 104 outliers final: 63 residues processed: 393 average time/residue: 0.6395 time to fit residues: 308.8440 Evaluate side-chains 399 residues out of total 4059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 311 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 19 LYS Chi-restraints excluded: chain D residue 71 ARG Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 99 TYR Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain F residue 209 LYS Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 124 GLN Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 175 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 256 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 246 optimal weight: 3.9990 chunk 293 optimal weight: 3.9990 chunk 239 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 chunk 401 optimal weight: 0.2980 chunk 257 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN B 703 ASN C 185 ASN C 211 ASN E 53 ASN G 6 GLN G 53 ASN G 90 GLN ** G 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 58 ASN L 3 GLN ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.220536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.171766 restraints weight = 42447.868| |-----------------------------------------------------------------------------| r_work (start): 0.3949 rms_B_bonded: 2.19 r_work: 0.3257 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 38913 Z= 0.134 Angle : 0.691 15.526 53199 Z= 0.322 Chirality : 0.048 1.406 6321 Planarity : 0.004 0.062 6636 Dihedral : 9.715 108.328 7546 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.69 % Favored : 96.10 % Rotamer: Outliers : 2.81 % Allowed : 16.15 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.12), residues: 4638 helix: 1.71 (0.19), residues: 822 sheet: 0.69 (0.14), residues: 1356 loop : -0.95 (0.12), residues: 2460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 100A TYR 0.019 0.001 TYR B 265 PHE 0.026 0.001 PHE A1075 TRP 0.011 0.001 TRP D 50 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00296 (38736) covalent geometry : angle 0.65382 (52722) SS BOND : bond 0.00373 ( 54) SS BOND : angle 1.19977 ( 108) hydrogen bonds : bond 0.03546 ( 1479) hydrogen bonds : angle 5.36420 ( 4182) link_ALPHA1-4 : bond 0.01750 ( 24) link_ALPHA1-4 : angle 3.16293 ( 72) link_BETA1-4 : bond 0.00441 ( 36) link_BETA1-4 : angle 1.32710 ( 108) link_BETA1-6 : bond 0.01728 ( 6) link_BETA1-6 : angle 2.53185 ( 18) link_NAG-ASN : bond 0.00478 ( 57) link_NAG-ASN : angle 3.16414 ( 171) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 4059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 316 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ASP cc_start: 0.6935 (m-30) cc_final: 0.6427 (p0) REVERT: A 186 PHE cc_start: 0.7457 (m-10) cc_final: 0.6970 (m-10) REVERT: A 187 LYS cc_start: 0.7374 (mmmm) cc_final: 0.7033 (mmmm) REVERT: A 190 ARG cc_start: 0.8844 (mtt90) cc_final: 0.8527 (mtt180) REVERT: A 240 THR cc_start: 0.8752 (t) cc_final: 0.8491 (m) REVERT: A 309 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8190 (mp0) REVERT: A 319 ARG cc_start: 0.7829 (ttm170) cc_final: 0.7237 (ttm110) REVERT: A 368 LEU cc_start: 0.8134 (mp) cc_final: 0.7856 (mt) REVERT: A 378 LYS cc_start: 0.7283 (tppt) cc_final: 0.6885 (tptm) REVERT: A 403 ARG cc_start: 0.6835 (ptm-80) cc_final: 0.6486 (ptm-80) REVERT: A 572 THR cc_start: 0.8764 (p) cc_final: 0.8471 (t) REVERT: A 661 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8136 (tm-30) REVERT: A 675 GLN cc_start: 0.7900 (mt0) cc_final: 0.7614 (mm-40) REVERT: A 780 GLU cc_start: 0.8969 (mm-30) cc_final: 0.8310 (pt0) REVERT: B 187 LYS cc_start: 0.7573 (mmmt) cc_final: 0.7074 (mmmt) REVERT: B 200 TYR cc_start: 0.8348 (m-80) cc_final: 0.8097 (m-80) REVERT: B 309 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8010 (mp0) REVERT: B 358 ILE cc_start: 0.8701 (OUTLIER) cc_final: 0.8287 (mt) REVERT: B 378 LYS cc_start: 0.7618 (tptp) cc_final: 0.7094 (tppt) REVERT: B 420 ASP cc_start: 0.7270 (t0) cc_final: 0.7049 (t70) REVERT: B 442 ASP cc_start: 0.6086 (m-30) cc_final: 0.5661 (m-30) REVERT: B 568 ASP cc_start: 0.7624 (m-30) cc_final: 0.7362 (m-30) REVERT: B 661 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8332 (tt0) REVERT: B 740 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8163 (ttt) REVERT: B 780 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8251 (pt0) REVERT: B 916 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8497 (tt) REVERT: B 994 ASP cc_start: 0.8311 (OUTLIER) cc_final: 0.8038 (t70) REVERT: B 1045 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8706 (tppt) REVERT: B 1141 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7332 (tm) REVERT: C 427 ASP cc_start: 0.8192 (m-30) cc_final: 0.7857 (m-30) REVERT: C 516 GLU cc_start: 0.7940 (pt0) cc_final: 0.7303 (pp20) REVERT: C 629 LEU cc_start: 0.3241 (OUTLIER) cc_final: 0.2873 (mp) REVERT: C 661 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8110 (tm-30) REVERT: C 675 GLN cc_start: 0.7715 (mt0) cc_final: 0.7487 (mm110) REVERT: C 780 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8216 (pt0) REVERT: C 787 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.8124 (mt0) REVERT: C 1141 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7290 (tm) REVERT: D 71 ARG cc_start: 0.5953 (OUTLIER) cc_final: 0.4413 (ptm-80) REVERT: D 99 TYR cc_start: 0.7000 (OUTLIER) cc_final: 0.6553 (m-80) REVERT: D 159 LEU cc_start: 0.2091 (OUTLIER) cc_final: 0.1526 (tp) REVERT: E 55 GLU cc_start: 0.6246 (tp30) cc_final: 0.5810 (tp30) REVERT: E 145 LYS cc_start: 0.3561 (tptt) cc_final: 0.2678 (mptt) REVERT: E 183 LYS cc_start: 0.0232 (mptt) cc_final: -0.0834 (ttpt) REVERT: F 80 MET cc_start: 0.4749 (ppp) cc_final: 0.4448 (ttp) REVERT: F 197 ASN cc_start: 0.2674 (OUTLIER) cc_final: 0.2191 (m-40) REVERT: G 24 GLN cc_start: 0.6579 (OUTLIER) cc_final: 0.6197 (tm-30) REVERT: G 154 LEU cc_start: 0.2377 (OUTLIER) cc_final: 0.1843 (pp) REVERT: H 4 LEU cc_start: 0.3740 (OUTLIER) cc_final: 0.3127 (mp) REVERT: H 58 ASN cc_start: 0.5078 (t0) cc_final: 0.4732 (t0) REVERT: H 159 LEU cc_start: 0.4150 (OUTLIER) cc_final: 0.3915 (pp) REVERT: H 201 LYS cc_start: 0.5860 (mmtt) cc_final: 0.5351 (mtmm) REVERT: L 42 LYS cc_start: 0.5916 (tptp) cc_final: 0.5566 (mppt) REVERT: L 124 GLN cc_start: 0.2675 (OUTLIER) cc_final: 0.1881 (tm130) REVERT: L 145 LYS cc_start: 0.3336 (mttp) cc_final: 0.2970 (tptt) REVERT: L 163 VAL cc_start: 0.2640 (OUTLIER) cc_final: 0.2383 (m) REVERT: L 175 LEU cc_start: 0.1475 (OUTLIER) cc_final: 0.1226 (pt) REVERT: L 183 LYS cc_start: 0.3540 (ttmm) cc_final: 0.2891 (tttp) REVERT: L 207 LYS cc_start: 0.3126 (ptmt) cc_final: 0.2826 (mtmt) outliers start: 114 outliers final: 67 residues processed: 400 average time/residue: 0.6553 time to fit residues: 320.4676 Evaluate side-chains 397 residues out of total 4059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 305 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 19 LYS Chi-restraints excluded: chain D residue 71 ARG Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 99 TYR Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 124 GLN Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 175 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 120 optimal weight: 0.5980 chunk 129 optimal weight: 2.9990 chunk 351 optimal weight: 7.9990 chunk 286 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 371 optimal weight: 8.9990 chunk 43 optimal weight: 0.8980 chunk 294 optimal weight: 2.9990 chunk 424 optimal weight: 9.9990 chunk 173 optimal weight: 0.8980 chunk 142 optimal weight: 0.0670 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN A1119 ASN C 99 ASN E 53 ASN G 6 GLN G 53 ASN G 90 GLN ** G 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.220496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.171167 restraints weight = 42132.730| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 2.17 r_work: 0.3255 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 38913 Z= 0.140 Angle : 0.689 13.874 53199 Z= 0.323 Chirality : 0.046 0.913 6321 Planarity : 0.004 0.062 6636 Dihedral : 8.901 99.118 7546 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.77 % Favored : 96.01 % Rotamer: Outliers : 2.52 % Allowed : 16.44 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.12), residues: 4638 helix: 1.72 (0.19), residues: 822 sheet: 0.67 (0.14), residues: 1371 loop : -0.94 (0.12), residues: 2445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 567 TYR 0.020 0.001 TYR L 49 PHE 0.020 0.001 PHE C 400 TRP 0.010 0.001 TRP H 50 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00313 (38736) covalent geometry : angle 0.65184 (52722) SS BOND : bond 0.00352 ( 54) SS BOND : angle 1.17287 ( 108) hydrogen bonds : bond 0.03579 ( 1479) hydrogen bonds : angle 5.33082 ( 4182) link_ALPHA1-4 : bond 0.01833 ( 24) link_ALPHA1-4 : angle 3.36552 ( 72) link_BETA1-4 : bond 0.00430 ( 36) link_BETA1-4 : angle 1.24471 ( 108) link_BETA1-6 : bond 0.01946 ( 6) link_BETA1-6 : angle 2.44089 ( 18) link_NAG-ASN : bond 0.00487 ( 57) link_NAG-ASN : angle 3.07814 ( 171) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 4059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 323 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ASP cc_start: 0.6984 (m-30) cc_final: 0.6314 (p0) REVERT: A 186 PHE cc_start: 0.7519 (m-10) cc_final: 0.7026 (m-10) REVERT: A 187 LYS cc_start: 0.7246 (mmmm) cc_final: 0.6901 (mmmm) REVERT: A 190 ARG cc_start: 0.8824 (mtt90) cc_final: 0.8576 (mtt180) REVERT: A 309 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8160 (mp0) REVERT: A 316 SER cc_start: 0.8299 (OUTLIER) cc_final: 0.7900 (p) REVERT: A 319 ARG cc_start: 0.7814 (ttm170) cc_final: 0.7210 (ttm110) REVERT: A 368 LEU cc_start: 0.8122 (mp) cc_final: 0.7849 (mt) REVERT: A 378 LYS cc_start: 0.7274 (tppt) cc_final: 0.6865 (tptm) REVERT: A 403 ARG cc_start: 0.6692 (ptm-80) cc_final: 0.6362 (ptm-80) REVERT: A 572 THR cc_start: 0.8744 (p) cc_final: 0.8452 (t) REVERT: A 661 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8127 (tm-30) REVERT: A 675 GLN cc_start: 0.7908 (mt0) cc_final: 0.7616 (mm-40) REVERT: A 780 GLU cc_start: 0.8960 (mm-30) cc_final: 0.8286 (pt0) REVERT: B 187 LYS cc_start: 0.7581 (mmmt) cc_final: 0.7087 (mmmt) REVERT: B 200 TYR cc_start: 0.8297 (m-80) cc_final: 0.8048 (m-80) REVERT: B 309 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8020 (mp0) REVERT: B 340 GLU cc_start: 0.7571 (mp0) cc_final: 0.7327 (mt-10) REVERT: B 358 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8291 (mt) REVERT: B 378 LYS cc_start: 0.7601 (tptp) cc_final: 0.7057 (tppt) REVERT: B 420 ASP cc_start: 0.7211 (t0) cc_final: 0.6961 (t70) REVERT: B 442 ASP cc_start: 0.6070 (m-30) cc_final: 0.5674 (m-30) REVERT: B 568 ASP cc_start: 0.7619 (m-30) cc_final: 0.7344 (m-30) REVERT: B 661 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8299 (tt0) REVERT: B 740 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.8169 (ttt) REVERT: B 780 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8242 (pt0) REVERT: B 916 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8495 (tt) REVERT: B 994 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.8015 (t70) REVERT: B 1045 LYS cc_start: 0.8973 (OUTLIER) cc_final: 0.8708 (tppt) REVERT: C 208 THR cc_start: 0.8101 (OUTLIER) cc_final: 0.7756 (p) REVERT: C 427 ASP cc_start: 0.8220 (m-30) cc_final: 0.7870 (m-30) REVERT: C 516 GLU cc_start: 0.7943 (pt0) cc_final: 0.7246 (pp20) REVERT: C 629 LEU cc_start: 0.3317 (OUTLIER) cc_final: 0.2944 (mp) REVERT: C 661 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8121 (tm-30) REVERT: C 675 GLN cc_start: 0.7733 (mt0) cc_final: 0.7494 (mm110) REVERT: C 740 MET cc_start: 0.8982 (tpt) cc_final: 0.8689 (tpt) REVERT: C 780 GLU cc_start: 0.8896 (mm-30) cc_final: 0.8211 (pt0) REVERT: C 787 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.8147 (mt0) REVERT: C 1141 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.7218 (tm) REVERT: D 13 LYS cc_start: 0.6361 (ptpp) cc_final: 0.5759 (mmmm) REVERT: D 71 ARG cc_start: 0.5944 (OUTLIER) cc_final: 0.4402 (ptm-80) REVERT: D 99 TYR cc_start: 0.6949 (OUTLIER) cc_final: 0.6548 (m-80) REVERT: D 159 LEU cc_start: 0.2149 (OUTLIER) cc_final: 0.1577 (tp) REVERT: E 55 GLU cc_start: 0.6246 (tp30) cc_final: 0.5812 (tp30) REVERT: E 145 LYS cc_start: 0.3591 (tptt) cc_final: 0.2821 (mptt) REVERT: E 183 LYS cc_start: 0.0338 (mptt) cc_final: -0.0777 (ttpt) REVERT: F 80 MET cc_start: 0.4767 (ppp) cc_final: 0.4480 (ttp) REVERT: F 100 ARG cc_start: 0.6356 (ttm110) cc_final: 0.5010 (ttm-80) REVERT: F 197 ASN cc_start: 0.3041 (OUTLIER) cc_final: 0.2494 (m-40) REVERT: G 6 GLN cc_start: 0.3941 (OUTLIER) cc_final: 0.3647 (mp10) REVERT: G 24 GLN cc_start: 0.6641 (OUTLIER) cc_final: 0.6252 (tm-30) REVERT: G 28 ASP cc_start: 0.5126 (OUTLIER) cc_final: 0.4888 (m-30) REVERT: G 145 LYS cc_start: 0.4109 (tptt) cc_final: 0.3526 (mptt) REVERT: H 4 LEU cc_start: 0.3685 (OUTLIER) cc_final: 0.3093 (mp) REVERT: H 58 ASN cc_start: 0.5028 (t0) cc_final: 0.4708 (t0) REVERT: H 159 LEU cc_start: 0.4227 (OUTLIER) cc_final: 0.3949 (pp) REVERT: L 42 LYS cc_start: 0.5939 (tptp) cc_final: 0.5614 (mppt) REVERT: L 124 GLN cc_start: 0.2497 (OUTLIER) cc_final: 0.1751 (tm130) REVERT: L 145 LYS cc_start: 0.3323 (mttp) cc_final: 0.2979 (tptt) REVERT: L 183 LYS cc_start: 0.3509 (ttmm) cc_final: 0.2898 (tttp) REVERT: L 207 LYS cc_start: 0.2982 (ptmt) cc_final: 0.2720 (mtmt) outliers start: 102 outliers final: 64 residues processed: 401 average time/residue: 0.6245 time to fit residues: 309.1536 Evaluate side-chains 400 residues out of total 4059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 311 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 19 LYS Chi-restraints excluded: chain D residue 71 ARG Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 99 TYR Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 124 GLN Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 163 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 75 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 337 optimal weight: 8.9990 chunk 94 optimal weight: 0.6980 chunk 256 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 132 optimal weight: 0.5980 chunk 99 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 353 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN B 99 ASN B 321 GLN B 703 ASN C 99 ASN G 53 ASN ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.220121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.163733 restraints weight = 42254.939| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 2.33 r_work: 0.3229 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 38913 Z= 0.151 Angle : 0.700 13.093 53199 Z= 0.328 Chirality : 0.046 0.877 6321 Planarity : 0.004 0.060 6636 Dihedral : 8.514 98.374 7546 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.75 % Favored : 96.05 % Rotamer: Outliers : 2.40 % Allowed : 16.77 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.12), residues: 4638 helix: 1.70 (0.19), residues: 822 sheet: 0.68 (0.14), residues: 1359 loop : -0.93 (0.12), residues: 2457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 100A TYR 0.024 0.001 TYR D 100F PHE 0.020 0.001 PHE C 400 TRP 0.009 0.001 TRP D 50 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00344 (38736) covalent geometry : angle 0.66301 (52722) SS BOND : bond 0.00365 ( 54) SS BOND : angle 1.29974 ( 108) hydrogen bonds : bond 0.03657 ( 1479) hydrogen bonds : angle 5.34647 ( 4182) link_ALPHA1-4 : bond 0.01831 ( 24) link_ALPHA1-4 : angle 3.37012 ( 72) link_BETA1-4 : bond 0.00449 ( 36) link_BETA1-4 : angle 1.25763 ( 108) link_BETA1-6 : bond 0.01933 ( 6) link_BETA1-6 : angle 2.43439 ( 18) link_NAG-ASN : bond 0.00476 ( 57) link_NAG-ASN : angle 3.05171 ( 171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18027.23 seconds wall clock time: 306 minutes 8.52 seconds (18368.52 seconds total)