Starting phenix.real_space_refine on Sun Aug 9 18:16:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vwj_65398/08_2026/9vwj_65398.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vwj_65398/08_2026/9vwj_65398.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vwj_65398/08_2026/9vwj_65398.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vwj_65398/08_2026/9vwj_65398.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vwj_65398/08_2026/9vwj_65398.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vwj_65398/08_2026/9vwj_65398.map" } resolution = 1.89 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= 0.012 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 384 5.16 5 C 22080 2.51 5 N 6336 2.21 5 O 7704 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 95 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 36504 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 1487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1487 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain: "B" Number of atoms: 1487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1487 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain: "C" Number of atoms: 1487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1487 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain: "D" Number of atoms: 1487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1487 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain: "E" Number of atoms: 1487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1487 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain: "F" Number of atoms: 1487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1487 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain: "G" Number of atoms: 1487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1487 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain: "H" Number of atoms: 1487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1487 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain: "I" Number of atoms: 1487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1487 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain: "J" Number of atoms: 1487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1487 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain: "K" Number of atoms: 1487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1487 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain: "L" Number of atoms: 1487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1487 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain: "M" Number of atoms: 1487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1487 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain: "N" Number of atoms: 1487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1487 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain: "O" Number of atoms: 1487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1487 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain: "P" Number of atoms: 1487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1487 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain: "Q" Number of atoms: 1487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1487 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain: "R" Number of atoms: 1487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1487 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain: "S" Number of atoms: 1487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1487 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain: "T" Number of atoms: 1487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1487 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain: "U" Number of atoms: 1487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1487 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain: "V" Number of atoms: 1487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1487 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain: "W" Number of atoms: 1487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1487 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain: "X" Number of atoms: 1487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1487 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain: "Y" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {'BGC': 1, 'GAL': 1, 'GLA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {'BGC': 1, 'GAL': 1, 'GLA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {'BGC': 1, 'GAL': 1, 'GLA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {'BGC': 1, 'GAL': 1, 'GLA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {'BGC': 1, 'GAL': 1, 'GLA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {'BGC': 1, 'GAL': 1, 'GLA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {'BGC': 1, 'GAL': 1, 'GLA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {'BGC': 1, 'GAL': 1, 'GLA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {'BGC': 1, 'GAL': 1, 'GLA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {'BGC': 1, 'GAL': 1, 'GLA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {'BGC': 1, 'GAL': 1, 'GLA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {'BGC': 1, 'GAL': 1, 'GLA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {'BGC': 1, 'GAL': 1, 'GLA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {'BGC': 1, 'GAL': 1, 'GLA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {'BGC': 1, 'GAL': 1, 'GLA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {'BGC': 1, 'GAL': 1, 'GLA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {'BGC': 1, 'GAL': 1, 'GLA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {'BGC': 1, 'GAL': 1, 'GLA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {'BGC': 1, 'GAL': 1, 'GLA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {'BGC': 1, 'GAL': 1, 'GLA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {'BGC': 1, 'GAL': 1, 'GLA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {'BGC': 1, 'GAL': 1, 'GLA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {'BGC': 1, 'GAL': 1, 'GLA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {'BGC': 1, 'GAL': 1, 'GLA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.40, per 1000 atoms: 0.18 Number of scatterers: 36504 At special positions: 0 Unit cell: (139.476, 139.476, 139.476, 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 384 16.00 O 7704 8.00 N 6336 7.00 C 22080 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=192, symmetry=0 Simple disulfide: pdb=" SG CYS A 6 " - pdb=" SG CYS A 37 " distance=2.03 Simple disulfide: pdb=" SG CYS A 17 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 51 " - pdb=" SG CYS A 83 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 70 " distance=2.03 Simple disulfide: pdb=" SG CYS A 105 " - pdb=" SG CYS A 134 " distance=2.03 Simple disulfide: pdb=" SG CYS A 114 " - pdb=" SG CYS A 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 148 " - pdb=" SG CYS A 181 " distance=2.03 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 168 " distance=2.04 Simple disulfide: pdb=" SG CYS B 6 " - pdb=" SG CYS B 37 " distance=2.03 Simple disulfide: pdb=" SG CYS B 17 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 51 " - pdb=" SG CYS B 83 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 70 " distance=2.03 Simple disulfide: pdb=" SG CYS B 105 " - pdb=" SG CYS B 134 " distance=2.03 Simple disulfide: pdb=" SG CYS B 114 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS B 148 " - pdb=" SG CYS B 181 " distance=2.03 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 168 " distance=2.07 Simple disulfide: pdb=" SG CYS C 6 " - pdb=" SG CYS C 37 " distance=2.03 Simple disulfide: pdb=" SG CYS C 17 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 51 " - pdb=" SG CYS C 83 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 70 " distance=2.03 Simple disulfide: pdb=" SG CYS C 105 " - pdb=" SG CYS C 134 " distance=2.03 Simple disulfide: pdb=" SG CYS C 114 " - pdb=" SG CYS C 194 " distance=2.03 Simple disulfide: pdb=" SG CYS C 148 " - pdb=" SG CYS C 181 " distance=2.03 Simple disulfide: pdb=" SG CYS C 162 " - pdb=" SG CYS C 168 " distance=2.07 Simple disulfide: pdb=" SG CYS D 6 " - pdb=" SG CYS D 37 " distance=2.03 Simple disulfide: pdb=" SG CYS D 17 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 51 " - pdb=" SG CYS D 83 " distance=2.03 Simple disulfide: pdb=" SG CYS D 64 " - pdb=" SG CYS D 70 " distance=2.03 Simple disulfide: pdb=" SG CYS D 105 " - pdb=" SG CYS D 134 " distance=2.03 Simple disulfide: pdb=" SG CYS D 114 " - pdb=" SG CYS D 194 " distance=2.03 Simple disulfide: pdb=" SG CYS D 148 " - pdb=" SG CYS D 181 " distance=2.03 Simple disulfide: pdb=" SG CYS D 162 " - pdb=" SG CYS D 168 " distance=2.04 Simple disulfide: pdb=" SG CYS E 6 " - pdb=" SG CYS E 37 " distance=2.03 Simple disulfide: pdb=" SG CYS E 17 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 51 " - pdb=" SG CYS E 83 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 70 " distance=2.03 Simple disulfide: pdb=" SG CYS E 105 " - pdb=" SG CYS E 134 " distance=2.03 Simple disulfide: pdb=" SG CYS E 114 " - pdb=" SG CYS E 194 " distance=2.03 Simple disulfide: pdb=" SG CYS E 148 " - pdb=" SG CYS E 181 " distance=2.03 Simple disulfide: pdb=" SG CYS E 162 " - pdb=" SG CYS E 168 " distance=2.04 Simple disulfide: pdb=" SG CYS F 6 " - pdb=" SG CYS F 37 " distance=2.03 Simple disulfide: pdb=" SG CYS F 17 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 51 " - pdb=" SG CYS F 83 " distance=2.03 Simple disulfide: pdb=" SG CYS F 64 " - pdb=" SG CYS F 70 " distance=2.03 Simple disulfide: pdb=" SG CYS F 105 " - pdb=" SG CYS F 134 " distance=2.03 Simple disulfide: pdb=" SG CYS F 114 " - pdb=" SG CYS F 194 " distance=2.03 Simple disulfide: pdb=" SG CYS F 148 " - pdb=" SG CYS F 181 " distance=2.03 Simple disulfide: pdb=" SG CYS F 162 " - pdb=" SG CYS F 168 " distance=2.08 Simple disulfide: pdb=" SG CYS G 6 " - pdb=" SG CYS G 37 " distance=2.03 Simple disulfide: pdb=" SG CYS G 17 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 51 " - pdb=" SG CYS G 83 " distance=2.03 Simple disulfide: pdb=" SG CYS G 64 " - pdb=" SG CYS G 70 " distance=2.03 Simple disulfide: pdb=" SG CYS G 105 " - pdb=" SG CYS G 134 " distance=2.03 Simple disulfide: pdb=" SG CYS G 114 " - pdb=" SG CYS G 194 " distance=2.03 Simple disulfide: pdb=" SG CYS G 148 " - pdb=" SG CYS G 181 " distance=2.03 Simple disulfide: pdb=" SG CYS G 162 " - pdb=" SG CYS G 168 " distance=2.07 Simple disulfide: pdb=" SG CYS H 6 " - pdb=" SG CYS H 37 " distance=2.03 Simple disulfide: pdb=" SG CYS H 17 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 51 " - pdb=" SG CYS H 83 " distance=2.03 Simple disulfide: pdb=" SG CYS H 64 " - pdb=" SG CYS H 70 " distance=2.03 Simple disulfide: pdb=" SG CYS H 105 " - pdb=" SG CYS H 134 " distance=2.03 Simple disulfide: pdb=" SG CYS H 114 " - pdb=" SG CYS H 194 " distance=2.03 Simple disulfide: pdb=" SG CYS H 148 " - pdb=" SG CYS H 181 " distance=2.03 Simple disulfide: pdb=" SG CYS H 162 " - pdb=" SG CYS H 168 " distance=2.08 Simple disulfide: pdb=" SG CYS I 6 " - pdb=" SG CYS I 37 " distance=2.03 Simple disulfide: pdb=" SG CYS I 17 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 51 " - pdb=" SG CYS I 83 " distance=2.03 Simple disulfide: pdb=" SG CYS I 64 " - pdb=" SG CYS I 70 " distance=2.03 Simple disulfide: pdb=" SG CYS I 105 " - pdb=" SG CYS I 134 " distance=2.03 Simple disulfide: pdb=" SG CYS I 114 " - pdb=" SG CYS I 194 " distance=2.03 Simple disulfide: pdb=" SG CYS I 148 " - pdb=" SG CYS I 181 " distance=2.03 Simple disulfide: pdb=" SG CYS I 162 " - pdb=" SG CYS I 168 " distance=2.08 Simple disulfide: pdb=" SG CYS J 6 " - pdb=" SG CYS J 37 " distance=2.03 Simple disulfide: pdb=" SG CYS J 17 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 51 " - pdb=" SG CYS J 83 " distance=2.03 Simple disulfide: pdb=" SG CYS J 64 " - pdb=" SG CYS J 70 " distance=2.03 Simple disulfide: pdb=" SG CYS J 105 " - pdb=" SG CYS J 134 " distance=2.03 Simple disulfide: pdb=" SG CYS J 114 " - pdb=" SG CYS J 194 " distance=2.03 Simple disulfide: pdb=" SG CYS J 148 " - pdb=" SG CYS J 181 " distance=2.03 Simple disulfide: pdb=" SG CYS J 162 " - pdb=" SG CYS J 168 " distance=2.04 Simple disulfide: pdb=" SG CYS K 6 " - pdb=" SG CYS K 37 " distance=2.03 Simple disulfide: pdb=" SG CYS K 17 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 51 " - pdb=" SG CYS K 83 " distance=2.03 Simple disulfide: pdb=" SG CYS K 64 " - pdb=" SG CYS K 70 " distance=2.03 Simple disulfide: pdb=" SG CYS K 105 " - pdb=" SG CYS K 134 " distance=2.03 Simple disulfide: pdb=" SG CYS K 114 " - pdb=" SG CYS K 194 " distance=2.03 Simple disulfide: pdb=" SG CYS K 148 " - pdb=" SG CYS K 181 " distance=2.02 Simple disulfide: pdb=" SG CYS K 162 " - pdb=" SG CYS K 168 " distance=2.07 Simple disulfide: pdb=" SG CYS L 6 " - pdb=" SG CYS L 37 " distance=2.03 Simple disulfide: pdb=" SG CYS L 17 " - pdb=" SG CYS L 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 51 " - pdb=" SG CYS L 83 " distance=2.03 Simple disulfide: pdb=" SG CYS L 64 " - pdb=" SG CYS L 70 " distance=2.03 Simple disulfide: pdb=" SG CYS L 105 " - pdb=" SG CYS L 134 " distance=2.03 Simple disulfide: pdb=" SG CYS L 114 " - pdb=" SG CYS L 194 " distance=2.03 Simple disulfide: pdb=" SG CYS L 148 " - pdb=" SG CYS L 181 " distance=2.03 Simple disulfide: pdb=" SG CYS L 162 " - pdb=" SG CYS L 168 " distance=2.04 Simple disulfide: pdb=" SG CYS M 6 " - pdb=" SG CYS M 37 " distance=2.03 Simple disulfide: pdb=" SG CYS M 17 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS M 51 " - pdb=" SG CYS M 83 " distance=2.03 Simple disulfide: pdb=" SG CYS M 64 " - pdb=" SG CYS M 70 " distance=2.03 Simple disulfide: pdb=" SG CYS M 105 " - pdb=" SG CYS M 134 " distance=2.03 Simple disulfide: pdb=" SG CYS M 114 " - pdb=" SG CYS M 194 " distance=2.03 Simple disulfide: pdb=" SG CYS M 148 " - pdb=" SG CYS M 181 " distance=2.03 Simple disulfide: pdb=" SG CYS M 162 " - pdb=" SG CYS M 168 " distance=2.07 Simple disulfide: pdb=" SG CYS N 6 " - pdb=" SG CYS N 37 " distance=2.03 Simple disulfide: pdb=" SG CYS N 17 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 51 " - pdb=" SG CYS N 83 " distance=2.03 Simple disulfide: pdb=" SG CYS N 64 " - pdb=" SG CYS N 70 " distance=2.03 Simple disulfide: pdb=" SG CYS N 105 " - pdb=" SG CYS N 134 " distance=2.03 Simple disulfide: pdb=" SG CYS N 114 " - pdb=" SG CYS N 194 " distance=2.03 Simple disulfide: pdb=" SG CYS N 148 " - pdb=" SG CYS N 181 " distance=2.03 Simple disulfide: pdb=" SG CYS N 162 " - pdb=" SG CYS N 168 " distance=2.07 Simple disulfide: pdb=" SG CYS O 6 " - pdb=" SG CYS O 37 " distance=2.03 Simple disulfide: pdb=" SG CYS O 17 " - pdb=" SG CYS O 96 " distance=2.03 Simple disulfide: pdb=" SG CYS O 51 " - pdb=" SG CYS O 83 " distance=2.03 Simple disulfide: pdb=" SG CYS O 64 " - pdb=" SG CYS O 70 " distance=2.03 Simple disulfide: pdb=" SG CYS O 105 " - pdb=" SG CYS O 134 " distance=2.03 Simple disulfide: pdb=" SG CYS O 114 " - pdb=" SG CYS O 194 " distance=2.03 Simple disulfide: pdb=" SG CYS O 148 " - pdb=" SG CYS O 181 " distance=2.03 Simple disulfide: pdb=" SG CYS O 162 " - pdb=" SG CYS O 168 " distance=2.07 Simple disulfide: pdb=" SG CYS P 6 " - pdb=" SG CYS P 37 " distance=2.03 Simple disulfide: pdb=" SG CYS P 17 " - pdb=" SG CYS P 96 " distance=2.03 Simple disulfide: pdb=" SG CYS P 51 " - pdb=" SG CYS P 83 " distance=2.03 Simple disulfide: pdb=" SG CYS P 64 " - pdb=" SG CYS P 70 " distance=2.03 Simple disulfide: pdb=" SG CYS P 105 " - pdb=" SG CYS P 134 " distance=2.03 Simple disulfide: pdb=" SG CYS P 114 " - pdb=" SG CYS P 194 " distance=2.03 Simple disulfide: pdb=" SG CYS P 148 " - pdb=" SG CYS P 181 " distance=2.03 Simple disulfide: pdb=" SG CYS P 162 " - pdb=" SG CYS P 168 " distance=2.07 Simple disulfide: pdb=" SG CYS Q 6 " - pdb=" SG CYS Q 37 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 17 " - pdb=" SG CYS Q 96 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 51 " - pdb=" SG CYS Q 83 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 64 " - pdb=" SG CYS Q 70 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 105 " - pdb=" SG CYS Q 134 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 114 " - pdb=" SG CYS Q 194 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 148 " - pdb=" SG CYS Q 181 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 162 " - pdb=" SG CYS Q 168 " distance=2.04 Simple disulfide: pdb=" SG CYS R 6 " - pdb=" SG CYS R 37 " distance=2.03 Simple disulfide: pdb=" SG CYS R 17 " - pdb=" SG CYS R 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 51 " - pdb=" SG CYS R 83 " distance=2.03 Simple disulfide: pdb=" SG CYS R 64 " - pdb=" SG CYS R 70 " distance=2.03 Simple disulfide: pdb=" SG CYS R 105 " - pdb=" SG CYS R 134 " distance=2.03 Simple disulfide: pdb=" SG CYS R 114 " - pdb=" SG CYS R 194 " distance=2.03 Simple disulfide: pdb=" SG CYS R 148 " - pdb=" SG CYS R 181 " distance=2.03 Simple disulfide: pdb=" SG CYS R 162 " - pdb=" SG CYS R 168 " distance=2.07 Simple disulfide: pdb=" SG CYS S 6 " - pdb=" SG CYS S 37 " distance=2.03 Simple disulfide: pdb=" SG CYS S 17 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 51 " - pdb=" SG CYS S 83 " distance=2.03 Simple disulfide: pdb=" SG CYS S 64 " - pdb=" SG CYS S 70 " distance=2.03 Simple disulfide: pdb=" SG CYS S 105 " - pdb=" SG CYS S 134 " distance=2.03 Simple disulfide: pdb=" SG CYS S 114 " - pdb=" SG CYS S 194 " distance=2.03 Simple disulfide: pdb=" SG CYS S 148 " - pdb=" SG CYS S 181 " distance=2.03 Simple disulfide: pdb=" SG CYS S 162 " - pdb=" SG CYS S 168 " distance=2.06 Simple disulfide: pdb=" SG CYS T 6 " - pdb=" SG CYS T 37 " distance=2.03 Simple disulfide: pdb=" SG CYS T 17 " - pdb=" SG CYS T 96 " distance=2.03 Simple disulfide: pdb=" SG CYS T 51 " - pdb=" SG CYS T 83 " distance=2.03 Simple disulfide: pdb=" SG CYS T 64 " - pdb=" SG CYS T 70 " distance=2.03 Simple disulfide: pdb=" SG CYS T 105 " - pdb=" SG CYS T 134 " distance=2.03 Simple disulfide: pdb=" SG CYS T 114 " - pdb=" SG CYS T 194 " distance=2.03 Simple disulfide: pdb=" SG CYS T 148 " - pdb=" SG CYS T 181 " distance=2.03 Simple disulfide: pdb=" SG CYS T 162 " - pdb=" SG CYS T 168 " distance=2.04 Simple disulfide: pdb=" SG CYS U 6 " - pdb=" SG CYS U 37 " distance=2.03 Simple disulfide: pdb=" SG CYS U 17 " - pdb=" SG CYS U 96 " distance=2.03 Simple disulfide: pdb=" SG CYS U 51 " - pdb=" SG CYS U 83 " distance=2.03 Simple disulfide: pdb=" SG CYS U 64 " - pdb=" SG CYS U 70 " distance=2.03 Simple disulfide: pdb=" SG CYS U 105 " - pdb=" SG CYS U 134 " distance=2.03 Simple disulfide: pdb=" SG CYS U 114 " - pdb=" SG CYS U 194 " distance=2.03 Simple disulfide: pdb=" SG CYS U 148 " - pdb=" SG CYS U 181 " distance=2.03 Simple disulfide: pdb=" SG CYS U 162 " - pdb=" SG CYS U 168 " distance=2.06 Simple disulfide: pdb=" SG CYS V 6 " - pdb=" SG CYS V 37 " distance=2.03 Simple disulfide: pdb=" SG CYS V 17 " - pdb=" SG CYS V 96 " distance=2.03 Simple disulfide: pdb=" SG CYS V 51 " - pdb=" SG CYS V 83 " distance=2.03 Simple disulfide: pdb=" SG CYS V 64 " - pdb=" SG CYS V 70 " distance=2.03 Simple disulfide: pdb=" SG CYS V 105 " - pdb=" SG CYS V 134 " distance=2.03 Simple disulfide: pdb=" SG CYS V 114 " - pdb=" SG CYS V 194 " distance=2.02 Simple disulfide: pdb=" SG CYS V 148 " - pdb=" SG CYS V 181 " distance=2.03 Simple disulfide: pdb=" SG CYS V 162 " - pdb=" SG CYS V 168 " distance=2.04 Simple disulfide: pdb=" SG CYS W 6 " - pdb=" SG CYS W 37 " distance=2.03 Simple disulfide: pdb=" SG CYS W 17 " - pdb=" SG CYS W 96 " distance=2.03 Simple disulfide: pdb=" SG CYS W 51 " - pdb=" SG CYS W 83 " distance=2.03 Simple disulfide: pdb=" SG CYS W 64 " - pdb=" SG CYS W 70 " distance=2.03 Simple disulfide: pdb=" SG CYS W 105 " - pdb=" SG CYS W 134 " distance=2.03 Simple disulfide: pdb=" SG CYS W 114 " - pdb=" SG CYS W 194 " distance=2.03 Simple disulfide: pdb=" SG CYS W 148 " - pdb=" SG CYS W 181 " distance=2.03 Simple disulfide: pdb=" SG CYS W 162 " - pdb=" SG CYS W 168 " distance=2.07 Simple disulfide: pdb=" SG CYS X 6 " - pdb=" SG CYS X 37 " distance=2.03 Simple disulfide: pdb=" SG CYS X 17 " - pdb=" SG CYS X 96 " distance=2.03 Simple disulfide: pdb=" SG CYS X 51 " - pdb=" SG CYS X 83 " distance=2.03 Simple disulfide: pdb=" SG CYS X 64 " - pdb=" SG CYS X 70 " distance=2.03 Simple disulfide: pdb=" SG CYS X 105 " - pdb=" SG CYS X 134 " distance=2.03 Simple disulfide: pdb=" SG CYS X 114 " - pdb=" SG CYS X 194 " distance=2.02 Simple disulfide: pdb=" SG CYS X 148 " - pdb=" SG CYS X 181 " distance=2.03 Simple disulfide: pdb=" SG CYS X 162 " - pdb=" SG CYS X 168 " distance=2.07 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-4 " GAL Y 2 " - " GLA Y 3 " " GAL Z 2 " - " GLA Z 3 " " GAL a 2 " - " GLA a 3 " " GAL b 2 " - " GLA b 3 " " GAL c 2 " - " GLA c 3 " " GAL d 2 " - " GLA d 3 " " GAL e 2 " - " GLA e 3 " " GAL f 2 " - " GLA f 3 " " GAL g 2 " - " GLA g 3 " " GAL h 2 " - " GLA h 3 " " GAL i 2 " - " GLA i 3 " " GAL j 2 " - " GLA j 3 " " GAL k 2 " - " GLA k 3 " " GAL l 2 " - " GLA l 3 " " GAL m 2 " - " GLA m 3 " " GAL n 2 " - " GLA n 3 " " GAL o 2 " - " GLA o 3 " " GAL p 2 " - " GLA p 3 " " GAL q 2 " - " GLA q 3 " " GAL r 2 " - " GLA r 3 " " GAL s 2 " - " GLA s 3 " " GAL t 2 " - " GLA t 3 " " GAL u 2 " - " GLA u 3 " " GAL v 2 " - " GLA v 3 " BETA1-4 " BGC Y 1 " - " GAL Y 2 " " BGC Z 1 " - " GAL Z 2 " " BGC a 1 " - " GAL a 2 " " BGC b 1 " - " GAL b 2 " " BGC c 1 " - " GAL c 2 " " BGC d 1 " - " GAL d 2 " " BGC e 1 " - " GAL e 2 " " BGC f 1 " - " GAL f 2 " " BGC g 1 " - " GAL g 2 " " BGC h 1 " - " GAL h 2 " " BGC i 1 " - " GAL i 2 " " BGC j 1 " - " GAL j 2 " " BGC k 1 " - " GAL k 2 " " BGC l 1 " - " GAL l 2 " " BGC m 1 " - " GAL m 2 " " BGC n 1 " - " GAL n 2 " " BGC o 1 " - " GAL o 2 " " BGC p 1 " - " GAL p 2 " " BGC q 1 " - " GAL q 2 " " BGC r 1 " - " GAL r 2 " " BGC s 1 " - " GAL s 2 " " BGC t 1 " - " GAL t 2 " " BGC u 1 " - " GAL u 2 " " BGC v 1 " - " GAL v 2 " Time building additional restraints: 2.41 Conformation dependent library (CDL) restraints added in 1.1 seconds 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8688 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 72 sheets defined 23.1% alpha, 31.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 42 through 46 Processing helix chain 'A' and resid 55 through 65 Processing helix chain 'A' and resid 75 through 78 Processing helix chain 'A' and resid 139 through 143 Processing helix chain 'A' and resid 150 through 163 Processing helix chain 'A' and resid 173 through 178 removed outlier: 3.552A pdb=" N TYR A 177 " --> pdb=" O SER A 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 46 Processing helix chain 'B' and resid 55 through 65 Processing helix chain 'B' and resid 75 through 78 Processing helix chain 'B' and resid 139 through 143 Processing helix chain 'B' and resid 150 through 163 Processing helix chain 'B' and resid 173 through 178 removed outlier: 3.553A pdb=" N TYR B 177 " --> pdb=" O SER B 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 46 Processing helix chain 'C' and resid 55 through 65 Processing helix chain 'C' and resid 75 through 78 Processing helix chain 'C' and resid 139 through 143 Processing helix chain 'C' and resid 150 through 163 Processing helix chain 'C' and resid 173 through 178 removed outlier: 3.552A pdb=" N TYR C 177 " --> pdb=" O SER C 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 46 Processing helix chain 'D' and resid 55 through 65 Processing helix chain 'D' and resid 75 through 78 Processing helix chain 'D' and resid 139 through 143 Processing helix chain 'D' and resid 150 through 163 Processing helix chain 'D' and resid 173 through 178 removed outlier: 3.552A pdb=" N TYR D 177 " --> pdb=" O SER D 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 46 Processing helix chain 'E' and resid 55 through 65 Processing helix chain 'E' and resid 75 through 78 Processing helix chain 'E' and resid 139 through 143 Processing helix chain 'E' and resid 150 through 163 Processing helix chain 'E' and resid 173 through 178 removed outlier: 3.552A pdb=" N TYR E 177 " --> pdb=" O SER E 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 46 Processing helix chain 'F' and resid 55 through 65 Processing helix chain 'F' and resid 75 through 78 Processing helix chain 'F' and resid 139 through 143 Processing helix chain 'F' and resid 150 through 163 Processing helix chain 'F' and resid 173 through 178 removed outlier: 3.552A pdb=" N TYR F 177 " --> pdb=" O SER F 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 46 Processing helix chain 'G' and resid 55 through 65 Processing helix chain 'G' and resid 75 through 78 Processing helix chain 'G' and resid 139 through 143 Processing helix chain 'G' and resid 150 through 163 Processing helix chain 'G' and resid 173 through 178 removed outlier: 3.552A pdb=" N TYR G 177 " --> pdb=" O SER G 173 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 46 Processing helix chain 'H' and resid 55 through 65 Processing helix chain 'H' and resid 75 through 78 Processing helix chain 'H' and resid 139 through 143 Processing helix chain 'H' and resid 150 through 163 Processing helix chain 'H' and resid 173 through 178 removed outlier: 3.552A pdb=" N TYR H 177 " --> pdb=" O SER H 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 46 Processing helix chain 'I' and resid 55 through 65 Processing helix chain 'I' and resid 75 through 78 Processing helix chain 'I' and resid 139 through 143 Processing helix chain 'I' and resid 150 through 163 Processing helix chain 'I' and resid 173 through 178 removed outlier: 3.552A pdb=" N TYR I 177 " --> pdb=" O SER I 173 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 46 Processing helix chain 'J' and resid 55 through 65 Processing helix chain 'J' and resid 75 through 78 Processing helix chain 'J' and resid 139 through 143 Processing helix chain 'J' and resid 150 through 163 Processing helix chain 'J' and resid 173 through 178 removed outlier: 3.552A pdb=" N TYR J 177 " --> pdb=" O SER J 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 42 through 46 Processing helix chain 'K' and resid 55 through 65 Processing helix chain 'K' and resid 75 through 78 Processing helix chain 'K' and resid 139 through 143 Processing helix chain 'K' and resid 150 through 163 Processing helix chain 'K' and resid 173 through 178 removed outlier: 3.552A pdb=" N TYR K 177 " --> pdb=" O SER K 173 " (cutoff:3.500A) Processing helix chain 'L' and resid 42 through 46 Processing helix chain 'L' and resid 55 through 65 Processing helix chain 'L' and resid 75 through 78 Processing helix chain 'L' and resid 139 through 143 Processing helix chain 'L' and resid 150 through 163 Processing helix chain 'L' and resid 173 through 178 removed outlier: 3.553A pdb=" N TYR L 177 " --> pdb=" O SER L 173 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 46 Processing helix chain 'M' and resid 55 through 65 Processing helix chain 'M' and resid 75 through 78 Processing helix chain 'M' and resid 139 through 143 Processing helix chain 'M' and resid 150 through 163 Processing helix chain 'M' and resid 173 through 178 removed outlier: 3.552A pdb=" N TYR M 177 " --> pdb=" O SER M 173 " (cutoff:3.500A) Processing helix chain 'N' and resid 42 through 46 Processing helix chain 'N' and resid 55 through 65 Processing helix chain 'N' and resid 75 through 78 Processing helix chain 'N' and resid 139 through 143 Processing helix chain 'N' and resid 150 through 163 Processing helix chain 'N' and resid 173 through 178 removed outlier: 3.552A pdb=" N TYR N 177 " --> pdb=" O SER N 173 " (cutoff:3.500A) Processing helix chain 'O' and resid 42 through 46 Processing helix chain 'O' and resid 55 through 65 Processing helix chain 'O' and resid 75 through 78 Processing helix chain 'O' and resid 139 through 143 Processing helix chain 'O' and resid 150 through 163 Processing helix chain 'O' and resid 173 through 178 removed outlier: 3.552A pdb=" N TYR O 177 " --> pdb=" O SER O 173 " (cutoff:3.500A) Processing helix chain 'P' and resid 42 through 46 Processing helix chain 'P' and resid 55 through 65 Processing helix chain 'P' and resid 75 through 78 Processing helix chain 'P' and resid 139 through 143 Processing helix chain 'P' and resid 150 through 163 Processing helix chain 'P' and resid 173 through 178 removed outlier: 3.552A pdb=" N TYR P 177 " --> pdb=" O SER P 173 " (cutoff:3.500A) Processing helix chain 'Q' and resid 42 through 46 Processing helix chain 'Q' and resid 55 through 65 Processing helix chain 'Q' and resid 75 through 78 Processing helix chain 'Q' and resid 139 through 143 Processing helix chain 'Q' and resid 150 through 163 Processing helix chain 'Q' and resid 173 through 178 removed outlier: 3.552A pdb=" N TYR Q 177 " --> pdb=" O SER Q 173 " (cutoff:3.500A) Processing helix chain 'R' and resid 42 through 46 Processing helix chain 'R' and resid 55 through 65 Processing helix chain 'R' and resid 75 through 78 Processing helix chain 'R' and resid 139 through 143 Processing helix chain 'R' and resid 150 through 163 Processing helix chain 'R' and resid 173 through 178 removed outlier: 3.552A pdb=" N TYR R 177 " --> pdb=" O SER R 173 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 46 Processing helix chain 'S' and resid 55 through 65 Processing helix chain 'S' and resid 75 through 78 Processing helix chain 'S' and resid 139 through 143 Processing helix chain 'S' and resid 150 through 163 Processing helix chain 'S' and resid 173 through 178 removed outlier: 3.552A pdb=" N TYR S 177 " --> pdb=" O SER S 173 " (cutoff:3.500A) Processing helix chain 'T' and resid 42 through 46 Processing helix chain 'T' and resid 55 through 65 Processing helix chain 'T' and resid 75 through 78 Processing helix chain 'T' and resid 139 through 143 Processing helix chain 'T' and resid 150 through 163 Processing helix chain 'T' and resid 173 through 178 removed outlier: 3.552A pdb=" N TYR T 177 " --> pdb=" O SER T 173 " (cutoff:3.500A) Processing helix chain 'U' and resid 42 through 46 Processing helix chain 'U' and resid 55 through 65 Processing helix chain 'U' and resid 75 through 78 Processing helix chain 'U' and resid 139 through 143 Processing helix chain 'U' and resid 150 through 163 Processing helix chain 'U' and resid 173 through 178 removed outlier: 3.552A pdb=" N TYR U 177 " --> pdb=" O SER U 173 " (cutoff:3.500A) Processing helix chain 'V' and resid 42 through 46 Processing helix chain 'V' and resid 55 through 65 Processing helix chain 'V' and resid 75 through 78 Processing helix chain 'V' and resid 139 through 143 Processing helix chain 'V' and resid 150 through 163 Processing helix chain 'V' and resid 173 through 178 removed outlier: 3.552A pdb=" N TYR V 177 " --> pdb=" O SER V 173 " (cutoff:3.500A) Processing helix chain 'W' and resid 42 through 46 Processing helix chain 'W' and resid 55 through 65 Processing helix chain 'W' and resid 75 through 78 Processing helix chain 'W' and resid 139 through 143 Processing helix chain 'W' and resid 150 through 163 Processing helix chain 'W' and resid 173 through 178 removed outlier: 3.552A pdb=" N TYR W 177 " --> pdb=" O SER W 173 " (cutoff:3.500A) Processing helix chain 'X' and resid 42 through 46 Processing helix chain 'X' and resid 55 through 65 Processing helix chain 'X' and resid 75 through 78 Processing helix chain 'X' and resid 139 through 143 Processing helix chain 'X' and resid 150 through 163 Processing helix chain 'X' and resid 173 through 178 removed outlier: 3.552A pdb=" N TYR X 177 " --> pdb=" O SER X 173 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 52 removed outlier: 5.617A pdb=" N ILE A 22 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N LEU A 97 " --> pdb=" O ILE A 22 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ILE A 24 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N THR A 95 " --> pdb=" O ILE A 24 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ARG A 2 " --> pdb=" O LEU N 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 12 through 16 Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 105 removed outlier: 6.153A pdb=" N TYR A 187 " --> pdb=" O TYR A 126 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N TYR A 126 " --> pdb=" O TYR A 187 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASP A 189 " --> pdb=" O ALA A 124 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA A 124 " --> pdb=" O ASP A 189 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ALA A 191 " --> pdb=" O HIS A 122 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 167 through 171 removed outlier: 5.016A pdb=" N ARG P 2 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N THR P 95 " --> pdb=" O ILE P 24 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ILE P 24 " --> pdb=" O THR P 95 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N LEU P 97 " --> pdb=" O ILE P 22 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ILE P 22 " --> pdb=" O LEU P 97 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 51 through 52 removed outlier: 5.617A pdb=" N ILE B 22 " --> pdb=" O LEU B 97 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N LEU B 97 " --> pdb=" O ILE B 22 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ILE B 24 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N THR B 95 " --> pdb=" O ILE B 24 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ARG B 2 " --> pdb=" O LEU Q 111 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 12 through 16 Processing sheet with id=AA7, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.442A pdb=" N THR B 193 " --> pdb=" O ILE B 121 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N ILE B 121 " --> pdb=" O THR B 193 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLY B 195 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N ILE B 119 " --> pdb=" O GLY B 195 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 167 through 171 removed outlier: 5.048A pdb=" N ARG X 2 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N THR X 95 " --> pdb=" O ILE X 24 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ILE X 24 " --> pdb=" O THR X 95 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N LEU X 97 " --> pdb=" O ILE X 22 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ILE X 22 " --> pdb=" O LEU X 97 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 51 through 52 removed outlier: 5.617A pdb=" N ILE C 22 " --> pdb=" O LEU C 97 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N LEU C 97 " --> pdb=" O ILE C 22 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ILE C 24 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N THR C 95 " --> pdb=" O ILE C 24 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ARG C 2 " --> pdb=" O LEU O 111 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 12 through 16 Processing sheet with id=AB2, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.441A pdb=" N THR C 193 " --> pdb=" O ILE C 121 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ILE C 121 " --> pdb=" O THR C 193 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLY C 195 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N ILE C 119 " --> pdb=" O GLY C 195 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 167 through 171 removed outlier: 5.022A pdb=" N ARG G 2 " --> pdb=" O LEU C 111 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N THR G 95 " --> pdb=" O ILE G 24 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ILE G 24 " --> pdb=" O THR G 95 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N LEU G 97 " --> pdb=" O ILE G 22 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ILE G 22 " --> pdb=" O LEU G 97 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 51 through 52 removed outlier: 5.617A pdb=" N ILE D 22 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N LEU D 97 " --> pdb=" O ILE D 22 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ILE D 24 " --> pdb=" O THR D 95 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR D 95 " --> pdb=" O ILE D 24 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ARG D 2 " --> pdb=" O LEU U 111 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 12 through 16 Processing sheet with id=AB6, first strand: chain 'D' and resid 100 through 105 removed outlier: 6.154A pdb=" N TYR D 187 " --> pdb=" O TYR D 126 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N TYR D 126 " --> pdb=" O TYR D 187 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASP D 189 " --> pdb=" O ALA D 124 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA D 124 " --> pdb=" O ASP D 189 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA D 191 " --> pdb=" O HIS D 122 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 167 through 171 removed outlier: 5.149A pdb=" N ARG R 2 " --> pdb=" O LEU D 111 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR R 95 " --> pdb=" O ILE R 24 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ILE R 24 " --> pdb=" O THR R 95 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N LEU R 97 " --> pdb=" O ILE R 22 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ILE R 22 " --> pdb=" O LEU R 97 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 51 through 52 removed outlier: 5.617A pdb=" N ILE E 22 " --> pdb=" O LEU E 97 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N LEU E 97 " --> pdb=" O ILE E 22 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ILE E 24 " --> pdb=" O THR E 95 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR E 95 " --> pdb=" O ILE E 24 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ARG E 2 " --> pdb=" O LEU V 111 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 12 through 16 Processing sheet with id=AC1, first strand: chain 'E' and resid 100 through 105 removed outlier: 6.441A pdb=" N THR E 193 " --> pdb=" O ILE E 121 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ILE E 121 " --> pdb=" O THR E 193 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N GLY E 195 " --> pdb=" O ILE E 119 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N ILE E 119 " --> pdb=" O GLY E 195 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 167 through 171 removed outlier: 4.977A pdb=" N ARG J 2 " --> pdb=" O LEU E 111 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR J 95 " --> pdb=" O ILE J 24 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ILE J 24 " --> pdb=" O THR J 95 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LEU J 97 " --> pdb=" O ILE J 22 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ILE J 22 " --> pdb=" O LEU J 97 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 51 through 52 removed outlier: 5.617A pdb=" N ILE F 22 " --> pdb=" O LEU F 97 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LEU F 97 " --> pdb=" O ILE F 22 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ILE F 24 " --> pdb=" O THR F 95 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR F 95 " --> pdb=" O ILE F 24 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N ARG F 2 " --> pdb=" O LEU K 111 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 12 through 16 Processing sheet with id=AC5, first strand: chain 'F' and resid 100 through 105 removed outlier: 6.153A pdb=" N TYR F 187 " --> pdb=" O TYR F 126 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N TYR F 126 " --> pdb=" O TYR F 187 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ASP F 189 " --> pdb=" O ALA F 124 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA F 124 " --> pdb=" O ASP F 189 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA F 191 " --> pdb=" O HIS F 122 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 167 through 171 removed outlier: 5.056A pdb=" N ARG S 2 " --> pdb=" O LEU F 111 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N THR S 95 " --> pdb=" O ILE S 24 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ILE S 24 " --> pdb=" O THR S 95 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N LEU S 97 " --> pdb=" O ILE S 22 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ILE S 22 " --> pdb=" O LEU S 97 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 12 through 16 Processing sheet with id=AC8, first strand: chain 'G' and resid 100 through 105 removed outlier: 6.443A pdb=" N THR G 193 " --> pdb=" O ILE G 121 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N ILE G 121 " --> pdb=" O THR G 193 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLY G 195 " --> pdb=" O ILE G 119 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N ILE G 119 " --> pdb=" O GLY G 195 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 167 through 171 removed outlier: 5.183A pdb=" N ARG O 2 " --> pdb=" O LEU G 111 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N THR O 95 " --> pdb=" O ILE O 24 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ILE O 24 " --> pdb=" O THR O 95 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LEU O 97 " --> pdb=" O ILE O 22 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ILE O 22 " --> pdb=" O LEU O 97 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 51 through 52 removed outlier: 5.616A pdb=" N ILE H 22 " --> pdb=" O LEU H 97 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N LEU H 97 " --> pdb=" O ILE H 22 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ILE H 24 " --> pdb=" O THR H 95 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR H 95 " --> pdb=" O ILE H 24 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ARG H 2 " --> pdb=" O LEU W 111 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 12 through 16 Processing sheet with id=AD3, first strand: chain 'H' and resid 100 through 105 removed outlier: 6.443A pdb=" N THR H 193 " --> pdb=" O ILE H 121 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N ILE H 121 " --> pdb=" O THR H 193 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N GLY H 195 " --> pdb=" O ILE H 119 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ILE H 119 " --> pdb=" O GLY H 195 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 167 through 171 removed outlier: 5.019A pdb=" N ARG M 2 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR M 95 " --> pdb=" O ILE M 24 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ILE M 24 " --> pdb=" O THR M 95 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N LEU M 97 " --> pdb=" O ILE M 22 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ILE M 22 " --> pdb=" O LEU M 97 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 51 through 52 removed outlier: 5.617A pdb=" N ILE I 22 " --> pdb=" O LEU I 97 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N LEU I 97 " --> pdb=" O ILE I 22 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ILE I 24 " --> pdb=" O THR I 95 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N THR I 95 " --> pdb=" O ILE I 24 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ARG I 2 " --> pdb=" O LEU L 111 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 12 through 16 Processing sheet with id=AD7, first strand: chain 'I' and resid 100 through 105 removed outlier: 6.443A pdb=" N THR I 193 " --> pdb=" O ILE I 121 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ILE I 121 " --> pdb=" O THR I 193 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N GLY I 195 " --> pdb=" O ILE I 119 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ILE I 119 " --> pdb=" O GLY I 195 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 167 through 171 removed outlier: 4.980A pdb=" N ARG T 2 " --> pdb=" O LEU I 111 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N THR T 95 " --> pdb=" O ILE T 24 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ILE T 24 " --> pdb=" O THR T 95 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N LEU T 97 " --> pdb=" O ILE T 22 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ILE T 22 " --> pdb=" O LEU T 97 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 12 through 16 Processing sheet with id=AE1, first strand: chain 'J' and resid 100 through 105 removed outlier: 6.443A pdb=" N THR J 193 " --> pdb=" O ILE J 121 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N ILE J 121 " --> pdb=" O THR J 193 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N GLY J 195 " --> pdb=" O ILE J 119 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N ILE J 119 " --> pdb=" O GLY J 195 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 167 through 171 removed outlier: 5.050A pdb=" N ARG V 2 " --> pdb=" O LEU J 111 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N THR V 95 " --> pdb=" O ILE V 24 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ILE V 24 " --> pdb=" O THR V 95 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LEU V 97 " --> pdb=" O ILE V 22 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ILE V 22 " --> pdb=" O LEU V 97 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 51 through 52 removed outlier: 5.617A pdb=" N ILE K 22 " --> pdb=" O LEU K 97 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LEU K 97 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ILE K 24 " --> pdb=" O THR K 95 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR K 95 " --> pdb=" O ILE K 24 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ARG K 2 " --> pdb=" O LEU S 111 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 12 through 16 Processing sheet with id=AE5, first strand: chain 'K' and resid 100 through 105 removed outlier: 6.441A pdb=" N THR K 193 " --> pdb=" O ILE K 121 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ILE K 121 " --> pdb=" O THR K 193 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLY K 195 " --> pdb=" O ILE K 119 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ILE K 119 " --> pdb=" O GLY K 195 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 51 through 52 removed outlier: 5.618A pdb=" N ILE L 22 " --> pdb=" O LEU L 97 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N LEU L 97 " --> pdb=" O ILE L 22 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N ILE L 24 " --> pdb=" O THR L 95 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N THR L 95 " --> pdb=" O ILE L 24 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ARG L 2 " --> pdb=" O LEU T 111 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 12 through 16 Processing sheet with id=AE8, first strand: chain 'L' and resid 100 through 105 removed outlier: 6.444A pdb=" N THR L 193 " --> pdb=" O ILE L 121 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ILE L 121 " --> pdb=" O THR L 193 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N GLY L 195 " --> pdb=" O ILE L 119 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N ILE L 119 " --> pdb=" O GLY L 195 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 12 through 16 Processing sheet with id=AF1, first strand: chain 'M' and resid 100 through 105 removed outlier: 6.443A pdb=" N THR M 193 " --> pdb=" O ILE M 121 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N ILE M 121 " --> pdb=" O THR M 193 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLY M 195 " --> pdb=" O ILE M 119 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ILE M 119 " --> pdb=" O GLY M 195 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 167 through 171 removed outlier: 5.063A pdb=" N ARG W 2 " --> pdb=" O LEU M 111 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR W 95 " --> pdb=" O ILE W 24 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ILE W 24 " --> pdb=" O THR W 95 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LEU W 97 " --> pdb=" O ILE W 22 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ILE W 22 " --> pdb=" O LEU W 97 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'N' and resid 51 through 52 removed outlier: 5.617A pdb=" N ILE N 22 " --> pdb=" O LEU N 97 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LEU N 97 " --> pdb=" O ILE N 22 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N ILE N 24 " --> pdb=" O THR N 95 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR N 95 " --> pdb=" O ILE N 24 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ARG N 2 " --> pdb=" O LEU P 111 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'N' and resid 12 through 16 Processing sheet with id=AF5, first strand: chain 'N' and resid 100 through 105 removed outlier: 6.444A pdb=" N THR N 193 " --> pdb=" O ILE N 121 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N ILE N 121 " --> pdb=" O THR N 193 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N GLY N 195 " --> pdb=" O ILE N 119 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ILE N 119 " --> pdb=" O GLY N 195 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'O' and resid 12 through 16 Processing sheet with id=AF7, first strand: chain 'O' and resid 100 through 105 removed outlier: 6.443A pdb=" N THR O 193 " --> pdb=" O ILE O 121 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N ILE O 121 " --> pdb=" O THR O 193 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLY O 195 " --> pdb=" O ILE O 119 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N ILE O 119 " --> pdb=" O GLY O 195 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'P' and resid 12 through 16 Processing sheet with id=AF9, first strand: chain 'P' and resid 100 through 105 removed outlier: 6.153A pdb=" N TYR P 187 " --> pdb=" O TYR P 126 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N TYR P 126 " --> pdb=" O TYR P 187 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASP P 189 " --> pdb=" O ALA P 124 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA P 124 " --> pdb=" O ASP P 189 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ALA P 191 " --> pdb=" O HIS P 122 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'Q' and resid 51 through 52 removed outlier: 5.617A pdb=" N ILE Q 22 " --> pdb=" O LEU Q 97 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N LEU Q 97 " --> pdb=" O ILE Q 22 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ILE Q 24 " --> pdb=" O THR Q 95 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR Q 95 " --> pdb=" O ILE Q 24 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ARG Q 2 " --> pdb=" O LEU X 111 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'Q' and resid 12 through 16 Processing sheet with id=AG3, first strand: chain 'Q' and resid 100 through 105 removed outlier: 6.152A pdb=" N TYR Q 187 " --> pdb=" O TYR Q 126 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N TYR Q 126 " --> pdb=" O TYR Q 187 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASP Q 189 " --> pdb=" O ALA Q 124 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA Q 124 " --> pdb=" O ASP Q 189 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ALA Q 191 " --> pdb=" O HIS Q 122 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'R' and resid 12 through 16 Processing sheet with id=AG5, first strand: chain 'R' and resid 100 through 105 removed outlier: 6.442A pdb=" N THR R 193 " --> pdb=" O ILE R 121 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ILE R 121 " --> pdb=" O THR R 193 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLY R 195 " --> pdb=" O ILE R 119 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ILE R 119 " --> pdb=" O GLY R 195 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'R' and resid 167 through 171 removed outlier: 5.050A pdb=" N ARG U 2 " --> pdb=" O LEU R 111 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR U 95 " --> pdb=" O ILE U 24 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ILE U 24 " --> pdb=" O THR U 95 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N LEU U 97 " --> pdb=" O ILE U 22 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ILE U 22 " --> pdb=" O LEU U 97 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'S' and resid 12 through 16 Processing sheet with id=AG8, first strand: chain 'S' and resid 100 through 105 removed outlier: 6.442A pdb=" N THR S 193 " --> pdb=" O ILE S 121 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ILE S 121 " --> pdb=" O THR S 193 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N GLY S 195 " --> pdb=" O ILE S 119 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N ILE S 119 " --> pdb=" O GLY S 195 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'T' and resid 12 through 16 Processing sheet with id=AH1, first strand: chain 'T' and resid 100 through 105 removed outlier: 6.153A pdb=" N TYR T 187 " --> pdb=" O TYR T 126 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N TYR T 126 " --> pdb=" O TYR T 187 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASP T 189 " --> pdb=" O ALA T 124 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA T 124 " --> pdb=" O ASP T 189 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ALA T 191 " --> pdb=" O HIS T 122 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'U' and resid 12 through 16 Processing sheet with id=AH3, first strand: chain 'U' and resid 100 through 105 removed outlier: 6.441A pdb=" N THR U 193 " --> pdb=" O ILE U 121 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ILE U 121 " --> pdb=" O THR U 193 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLY U 195 " --> pdb=" O ILE U 119 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ILE U 119 " --> pdb=" O GLY U 195 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'V' and resid 12 through 16 Processing sheet with id=AH5, first strand: chain 'V' and resid 100 through 105 removed outlier: 6.153A pdb=" N TYR V 187 " --> pdb=" O TYR V 126 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N TYR V 126 " --> pdb=" O TYR V 187 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASP V 189 " --> pdb=" O ALA V 124 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA V 124 " --> pdb=" O ASP V 189 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ALA V 191 " --> pdb=" O HIS V 122 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'W' and resid 12 through 16 Processing sheet with id=AH7, first strand: chain 'W' and resid 100 through 105 removed outlier: 6.443A pdb=" N THR W 193 " --> pdb=" O ILE W 121 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ILE W 121 " --> pdb=" O THR W 193 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N GLY W 195 " --> pdb=" O ILE W 119 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ILE W 119 " --> pdb=" O GLY W 195 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'X' and resid 12 through 16 Processing sheet with id=AH9, first strand: chain 'X' and resid 100 through 105 removed outlier: 6.153A pdb=" N TYR X 187 " --> pdb=" O TYR X 126 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N TYR X 126 " --> pdb=" O TYR X 187 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ASP X 189 " --> pdb=" O ALA X 124 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA X 124 " --> pdb=" O ASP X 189 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ALA X 191 " --> pdb=" O HIS X 122 " (cutoff:3.500A) 1384 hydrogen bonds defined for protein. 3504 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: 6.32 Time building geometry restraints manager: 3.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 7232 1.32 - 1.45: 8624 1.45 - 1.57: 20744 1.57 - 1.69: 0 1.69 - 1.81: 384 Bond restraints: 36984 Sorted by residual: bond pdb=" C3 BGC e 1 " pdb=" O3 BGC e 1 " ideal model delta sigma weight residual 1.408 1.510 -0.102 2.00e-02 2.50e+03 2.60e+01 bond pdb=" C3 BGC j 1 " pdb=" O3 BGC j 1 " ideal model delta sigma weight residual 1.408 1.510 -0.102 2.00e-02 2.50e+03 2.60e+01 bond pdb=" C3 BGC n 1 " pdb=" O3 BGC n 1 " ideal model delta sigma weight residual 1.408 1.510 -0.102 2.00e-02 2.50e+03 2.60e+01 bond pdb=" C3 BGC k 1 " pdb=" O3 BGC k 1 " ideal model delta sigma weight residual 1.408 1.510 -0.102 2.00e-02 2.50e+03 2.60e+01 bond pdb=" C3 BGC v 1 " pdb=" O3 BGC v 1 " ideal model delta sigma weight residual 1.408 1.510 -0.102 2.00e-02 2.50e+03 2.58e+01 ... (remaining 36979 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 46687 1.67 - 3.34: 2988 3.34 - 5.01: 476 5.01 - 6.67: 79 6.67 - 8.34: 2 Bond angle restraints: 50232 Sorted by residual: angle pdb=" N LEU J 112 " pdb=" CA LEU J 112 " pdb=" C LEU J 112 " ideal model delta sigma weight residual 110.20 103.94 6.26 1.58e+00 4.01e-01 1.57e+01 angle pdb=" N LEU F 112 " pdb=" CA LEU F 112 " pdb=" C LEU F 112 " ideal model delta sigma weight residual 110.20 103.96 6.24 1.58e+00 4.01e-01 1.56e+01 angle pdb=" CA THR L 118 " pdb=" CB THR L 118 " pdb=" OG1 THR L 118 " ideal model delta sigma weight residual 109.60 103.68 5.92 1.50e+00 4.44e-01 1.56e+01 angle pdb=" N LEU M 112 " pdb=" CA LEU M 112 " pdb=" C LEU M 112 " ideal model delta sigma weight residual 110.20 103.98 6.22 1.58e+00 4.01e-01 1.55e+01 angle pdb=" N LEU X 112 " pdb=" CA LEU X 112 " pdb=" C LEU X 112 " ideal model delta sigma weight residual 110.20 103.98 6.22 1.58e+00 4.01e-01 1.55e+01 ... (remaining 50227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.09: 21344 17.09 - 34.17: 1921 34.17 - 51.26: 427 51.26 - 68.34: 283 68.34 - 85.43: 25 Dihedral angle restraints: 24000 sinusoidal: 10440 harmonic: 13560 Sorted by residual: dihedral pdb=" CB CYS V 17 " pdb=" SG CYS V 17 " pdb=" SG CYS V 96 " pdb=" CB CYS V 96 " ideal model delta sinusoidal sigma weight residual -86.00 -115.82 29.82 1 1.00e+01 1.00e-02 1.27e+01 dihedral pdb=" CB CYS C 17 " pdb=" SG CYS C 17 " pdb=" SG CYS C 96 " pdb=" CB CYS C 96 " ideal model delta sinusoidal sigma weight residual -86.00 -115.81 29.81 1 1.00e+01 1.00e-02 1.27e+01 dihedral pdb=" CB CYS A 17 " pdb=" SG CYS A 17 " pdb=" SG CYS A 96 " pdb=" CB CYS A 96 " ideal model delta sinusoidal sigma weight residual -86.00 -115.80 29.80 1 1.00e+01 1.00e-02 1.27e+01 ... (remaining 23997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 4185 0.043 - 0.087: 1215 0.087 - 0.130: 461 0.130 - 0.173: 167 0.173 - 0.217: 68 Chirality restraints: 6096 Sorted by residual: chirality pdb=" C1 GAL Y 2 " pdb=" O4 BGC Y 1 " pdb=" C2 GAL Y 2 " pdb=" O5 GAL Y 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.33 -0.07 2.00e-02 2.50e+03 1.39e+01 chirality pdb=" C1 GAL q 2 " pdb=" O4 BGC q 1 " pdb=" C2 GAL q 2 " pdb=" O5 GAL q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.33 -0.07 2.00e-02 2.50e+03 1.39e+01 chirality pdb=" C1 GAL f 2 " pdb=" O4 BGC f 1 " pdb=" C2 GAL f 2 " pdb=" O5 GAL f 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.33 -0.07 2.00e-02 2.50e+03 1.37e+01 ... (remaining 6093 not shown) Planarity restraints: 6504 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR U 1 " 0.016 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C THR U 1 " -0.056 2.00e-02 2.50e+03 pdb=" O THR U 1 " 0.021 2.00e-02 2.50e+03 pdb=" N ARG U 2 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 2 " -0.281 9.50e-02 1.11e+02 1.26e-01 9.72e+00 pdb=" NE ARG J 2 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG J 2 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG J 2 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG J 2 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG N 164 " -0.279 9.50e-02 1.11e+02 1.25e-01 9.62e+00 pdb=" NE ARG N 164 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG N 164 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG N 164 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG N 164 " -0.009 2.00e-02 2.50e+03 ... (remaining 6501 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 10471 2.81 - 3.33: 32615 3.33 - 3.85: 67298 3.85 - 4.38: 81670 4.38 - 4.90: 133500 Nonbonded interactions: 325554 Sorted by model distance: nonbonded pdb=" OD2 ASP C 7 " pdb=" OH TYR C 29 " model vdw 2.282 3.040 nonbonded pdb=" OD2 ASP V 7 " pdb=" OH TYR V 29 " model vdw 2.282 3.040 nonbonded pdb=" OD2 ASP K 7 " pdb=" OH TYR K 29 " model vdw 2.283 3.040 nonbonded pdb=" OD2 ASP H 7 " pdb=" OH TYR H 29 " model vdw 2.283 3.040 nonbonded pdb=" OD2 ASP X 7 " pdb=" OH TYR X 29 " model vdw 2.283 3.040 ... (remaining 325549 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } ncs_group { reference = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.690 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 27.030 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.160 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:5.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9280 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 : 0.010 0.102 37224 Z= 0.571 Angle : 0.862 8.342 50760 Z= 0.542 Chirality : 0.054 0.217 6096 Planarity : 0.008 0.126 6504 Dihedral : 15.131 85.430 14736 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Rotamer: Outliers : 0.10 % Allowed : 19.40 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.12), residues: 4632 helix: 0.13 (0.21), residues: 648 sheet: 0.61 (0.14), residues: 1368 loop : -0.15 (0.12), residues: 2616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 26 TYR 0.014 0.001 TYR J 89 PHE 0.008 0.002 PHE U 77 HIS 0.002 0.001 HIS A 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00957 / 0.56 (36984) covalent geometry : angle 0.85005 / 0.54 (50232) SS BOND : bond 0.01221 / 0.84 ( 192) SS BOND : angle 0.58231 / 0.39 ( 384) hydrogen bonds : bond 0.12431 / 8.58 ( 1384) hydrogen bonds : angle 7.15684 / 4.90 ( 3504) link_ALPHA1-4 : bond 0.06653 / 4.57 ( 24) link_ALPHA1-4 : angle 3.62700 / 2.57 ( 72) link_BETA1-4 : bond 0.06406 / 4.40 ( 24) link_BETA1-4 : angle 2.28362 / 1.60 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 875 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 871 time to evaluate : 1.225 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 116 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7695 (mp0) REVERT: E 113 GLU cc_start: 0.8372 (tt0) cc_final: 0.8095 (tp30) REVERT: F 113 GLU cc_start: 0.8745 (tt0) cc_final: 0.8350 (tt0) REVERT: G 113 GLU cc_start: 0.8427 (tt0) cc_final: 0.8223 (tt0) REVERT: H 138 ARG cc_start: 0.8868 (mmp80) cc_final: 0.8597 (mmp-170) REVERT: J 113 GLU cc_start: 0.8677 (tt0) cc_final: 0.8293 (tt0) REVERT: O 113 GLU cc_start: 0.8541 (tt0) cc_final: 0.8318 (tt0) outliers start: 4 outliers final: 0 residues processed: 872 average time/residue: 0.7094 time to fit residues: 732.5293 Evaluate side-chains 819 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 819 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 432 optimal weight: 0.9980 chunk 197 optimal weight: 9.9990 chunk 388 optimal weight: 4.9990 chunk 455 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.9980 chunk 401 optimal weight: 7.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 GLN A 151 GLN A 167 GLN B 120 GLN B 151 GLN B 167 GLN C 120 GLN C 151 GLN D 120 GLN D 151 GLN E 120 GLN E 151 GLN F 151 GLN F 163 ASN F 167 GLN G 120 GLN G 151 GLN G 167 GLN H 120 GLN H 151 GLN H 163 ASN I 120 GLN I 151 GLN J 120 GLN J 151 GLN J 167 GLN K 120 GLN K 151 GLN L 120 GLN L 151 GLN M 120 GLN M 151 GLN M 167 GLN N 151 GLN O 120 GLN O 151 GLN ** O 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 120 GLN P 151 GLN Q 151 GLN Q 167 GLN R 120 GLN R 151 GLN S 120 GLN S 151 GLN S 167 GLN T 120 GLN T 151 GLN T 167 GLN U 120 GLN U 151 GLN V 120 GLN V 151 GLN V 167 GLN W 120 GLN W 151 GLN X 120 GLN X 151 GLN X 167 GLN Total number of N/Q/H flips: 58 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.104466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.085458 restraints weight = 37384.081| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.72 r_work: 0.2884 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9324 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 37224 Z= 0.128 Angle : 0.461 4.103 50760 Z= 0.251 Chirality : 0.043 0.138 6096 Planarity : 0.004 0.031 6504 Dihedral : 4.403 16.221 6600 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.04 % Favored : 99.96 % Rotamer: Outliers : 2.22 % Allowed : 15.28 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.12), residues: 4632 helix: 0.69 (0.21), residues: 648 sheet: 0.74 (0.14), residues: 1368 loop : -0.15 (0.12), residues: 2616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 164 TYR 0.006 0.001 TYR J 89 PHE 0.009 0.002 PHE P 14 HIS 0.002 0.001 HIS I 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.13 (36984) covalent geometry : angle 0.45154 / 0.25 (50232) SS BOND : bond 0.00174 / 0.12 ( 192) SS BOND : angle 0.43101 / 0.30 ( 384) hydrogen bonds : bond 0.03824 / 2.59 ( 1384) hydrogen bonds : angle 6.14243 / 4.22 ( 3504) link_ALPHA1-4 : bond 0.00109 / 0.08 ( 24) link_ALPHA1-4 : angle 1.93300 / 1.37 ( 72) link_BETA1-4 : bond 0.00473 / 0.32 ( 24) link_BETA1-4 : angle 1.70983 / 1.19 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 929 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 838 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7920 (mp0) REVERT: E 113 GLU cc_start: 0.8256 (tt0) cc_final: 0.7890 (tt0) REVERT: F 113 GLU cc_start: 0.8695 (tt0) cc_final: 0.8332 (tt0) REVERT: H 138 ARG cc_start: 0.8860 (mmp80) cc_final: 0.8655 (mmp-170) REVERT: I 113 GLU cc_start: 0.8118 (tp30) cc_final: 0.7807 (mt-10) REVERT: J 113 GLU cc_start: 0.8721 (tt0) cc_final: 0.8327 (tt0) REVERT: O 113 GLU cc_start: 0.8589 (tt0) cc_final: 0.8263 (tt0) REVERT: P 151 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.8461 (tt0) REVERT: U 113 GLU cc_start: 0.8569 (tt0) cc_final: 0.8340 (tt0) REVERT: W 151 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.8462 (tt0) outliers start: 91 outliers final: 0 residues processed: 873 average time/residue: 0.6834 time to fit residues: 712.1206 Evaluate side-chains 826 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 824 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 151 GLN Chi-restraints excluded: chain W residue 151 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 440 optimal weight: 8.9990 chunk 198 optimal weight: 0.7980 chunk 166 optimal weight: 10.0000 chunk 446 optimal weight: 5.9990 chunk 453 optimal weight: 6.9990 chunk 235 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 chunk 329 optimal weight: 3.9990 chunk 223 optimal weight: 5.9990 chunk 354 optimal weight: 8.9990 chunk 13 optimal weight: 9.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 GLN A 141 ASN A 151 GLN B 120 GLN B 151 GLN C 120 GLN D 120 GLN D 151 GLN E 120 GLN E 151 GLN F 120 GLN F 151 GLN G 120 GLN H 151 GLN I 120 GLN J 120 GLN J 141 ASN J 151 GLN K 120 GLN K 151 GLN M 120 GLN N 141 ASN N 151 GLN O 120 GLN P 120 GLN P 151 GLN Q 120 GLN Q 151 GLN R 120 GLN R 151 GLN S 120 GLN S 141 ASN T 120 GLN U 120 GLN V 120 GLN V 141 ASN V 151 GLN V 167 GLN W 120 GLN W 151 GLN X 120 GLN X 151 GLN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.099285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.079726 restraints weight = 36891.123| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 1.71 r_work: 0.2758 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2600 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9395 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.049 37224 Z= 0.359 Angle : 0.582 9.436 50760 Z= 0.320 Chirality : 0.049 0.224 6096 Planarity : 0.004 0.044 6504 Dihedral : 5.011 16.572 6600 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.92 % Allowed : 13.74 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.12), residues: 4632 helix: 0.63 (0.20), residues: 648 sheet: 0.85 (0.14), residues: 1368 loop : -0.27 (0.11), residues: 2616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 164 TYR 0.006 0.001 TYR T 94 PHE 0.016 0.003 PHE B 77 HIS 0.007 0.002 HIS T 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00755 / 0.36 (36984) covalent geometry : angle 0.57125 / 0.32 (50232) SS BOND : bond 0.00465 / 0.31 ( 192) SS BOND : angle 0.66027 / 0.46 ( 384) hydrogen bonds : bond 0.05640 / 3.82 ( 1384) hydrogen bonds : angle 6.29416 / 4.34 ( 3504) link_ALPHA1-4 : bond 0.00467 / 0.32 ( 24) link_ALPHA1-4 : angle 2.00287 / 1.41 ( 72) link_BETA1-4 : bond 0.00030 / 0.02 ( 24) link_BETA1-4 : angle 2.20717 / 1.53 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 868 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 789 time to evaluate : 1.281 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 116 GLU cc_start: 0.8207 (mt-10) cc_final: 0.8002 (mp0) REVERT: E 113 GLU cc_start: 0.8150 (tt0) cc_final: 0.7747 (tt0) REVERT: J 113 GLU cc_start: 0.8751 (tt0) cc_final: 0.8369 (tt0) REVERT: O 113 GLU cc_start: 0.8543 (tt0) cc_final: 0.8287 (tt0) REVERT: O 167 GLN cc_start: 0.8136 (mt0) cc_final: 0.7833 (mt0) REVERT: U 113 GLU cc_start: 0.8605 (tt0) cc_final: 0.8397 (tt0) outliers start: 79 outliers final: 1 residues processed: 793 average time/residue: 0.7803 time to fit residues: 727.1791 Evaluate side-chains 769 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 768 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 164 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 190 optimal weight: 2.9990 chunk 449 optimal weight: 7.9990 chunk 370 optimal weight: 6.9990 chunk 316 optimal weight: 6.9990 chunk 59 optimal weight: 0.8980 chunk 234 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 197 optimal weight: 2.9990 chunk 247 optimal weight: 0.6980 chunk 187 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 GLN A 167 GLN B 120 GLN C 120 GLN D 120 GLN E 120 GLN ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 GLN G 120 GLN H 120 GLN I 120 GLN I 151 GLN I 167 GLN J 120 GLN J 167 GLN M 120 GLN M 167 GLN N 120 GLN N 167 GLN O 120 GLN O 151 GLN P 120 GLN Q 120 GLN R 120 GLN S 120 GLN T 120 GLN V 120 GLN W 120 GLN X 120 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.102854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.083544 restraints weight = 36979.419| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 1.71 r_work: 0.2836 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9349 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 37224 Z= 0.135 Angle : 0.464 6.705 50760 Z= 0.253 Chirality : 0.042 0.133 6096 Planarity : 0.003 0.032 6504 Dihedral : 4.541 17.839 6600 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.04 % Favored : 99.96 % Rotamer: Outliers : 1.51 % Allowed : 15.38 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.12), residues: 4632 helix: 0.86 (0.20), residues: 648 sheet: 0.76 (0.14), residues: 1368 loop : -0.21 (0.11), residues: 2616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 164 TYR 0.006 0.001 TYR F 126 PHE 0.009 0.002 PHE J 77 HIS 0.001 0.000 HIS V 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.14 (36984) covalent geometry : angle 0.45446 / 0.25 (50232) SS BOND : bond 0.00165 / 0.11 ( 192) SS BOND : angle 0.39019 / 0.27 ( 384) hydrogen bonds : bond 0.03994 / 2.69 ( 1384) hydrogen bonds : angle 6.07662 / 4.19 ( 3504) link_ALPHA1-4 : bond 0.00021 / 0.01 ( 24) link_ALPHA1-4 : angle 1.81820 / 1.29 ( 72) link_BETA1-4 : bond 0.00432 / 0.29 ( 24) link_BETA1-4 : angle 1.81813 / 1.26 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 909 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 847 time to evaluate : 1.274 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 116 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7930 (mp0) REVERT: D 167 GLN cc_start: 0.8817 (pt0) cc_final: 0.8607 (pt0) REVERT: E 113 GLU cc_start: 0.8098 (tt0) cc_final: 0.7886 (tp30) REVERT: I 113 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7898 (tt0) REVERT: Q 113 GLU cc_start: 0.8425 (tt0) cc_final: 0.8117 (tp30) outliers start: 62 outliers final: 0 residues processed: 879 average time/residue: 0.6755 time to fit residues: 707.9912 Evaluate side-chains 818 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 817 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 113 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 16 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 367 optimal weight: 4.9990 chunk 177 optimal weight: 3.9990 chunk 233 optimal weight: 10.0000 chunk 281 optimal weight: 4.9990 chunk 440 optimal weight: 6.9990 chunk 364 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 69 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 GLN A 151 GLN B 120 GLN B 151 GLN D 120 GLN D 151 GLN E 120 GLN E 151 GLN F 120 GLN F 151 GLN G 120 GLN H 151 GLN I 120 GLN I 151 GLN J 120 GLN J 151 GLN K 151 GLN K 167 GLN L 151 GLN M 120 GLN M 151 GLN N 120 GLN N 151 GLN O 151 GLN P 120 GLN Q 120 GLN Q 151 GLN R 120 GLN R 151 GLN ** R 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 120 GLN S 151 GLN T 120 GLN U 151 GLN V 120 GLN X 120 GLN X 151 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.099553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.079819 restraints weight = 36751.703| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 1.71 r_work: 0.2758 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9393 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 37224 Z= 0.332 Angle : 0.557 6.475 50760 Z= 0.307 Chirality : 0.047 0.144 6096 Planarity : 0.004 0.039 6504 Dihedral : 4.941 20.488 6600 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.78 % Allowed : 15.11 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.12), residues: 4632 helix: 0.69 (0.20), residues: 648 sheet: 0.84 (0.14), residues: 1368 loop : -0.27 (0.11), residues: 2616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 164 TYR 0.006 0.001 TYR H 94 PHE 0.015 0.003 PHE E 77 HIS 0.006 0.002 HIS X 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00697 / 0.33 (36984) covalent geometry : angle 0.54692 / 0.31 (50232) SS BOND : bond 0.00414 / 0.27 ( 192) SS BOND : angle 0.56510 / 0.39 ( 384) hydrogen bonds : bond 0.05476 / 3.70 ( 1384) hydrogen bonds : angle 6.25304 / 4.31 ( 3504) link_ALPHA1-4 : bond 0.00432 / 0.30 ( 24) link_ALPHA1-4 : angle 1.99081 / 1.40 ( 72) link_BETA1-4 : bond 0.00056 / 0.04 ( 24) link_BETA1-4 : angle 2.08559 / 1.44 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 854 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 781 time to evaluate : 1.210 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: E 113 GLU cc_start: 0.8214 (tt0) cc_final: 0.7873 (tp30) REVERT: I 113 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7886 (tt0) outliers start: 73 outliers final: 0 residues processed: 793 average time/residue: 0.7351 time to fit residues: 684.7850 Evaluate side-chains 767 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 766 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 113 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 443 optimal weight: 0.9980 chunk 333 optimal weight: 3.9990 chunk 280 optimal weight: 4.9990 chunk 187 optimal weight: 4.9990 chunk 276 optimal weight: 1.9990 chunk 401 optimal weight: 7.9990 chunk 297 optimal weight: 7.9990 chunk 73 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 GLN A 151 GLN A 167 GLN B 120 GLN B 151 GLN C 120 GLN D 120 GLN E 120 GLN E 151 GLN ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 GLN G 120 GLN G 151 GLN H 120 GLN H 151 GLN I 120 GLN I 151 GLN J 120 GLN J 151 GLN J 167 GLN K 151 GLN L 151 GLN M 120 GLN M 151 GLN M 167 GLN N 120 GLN N 151 GLN O 151 GLN P 120 GLN Q 120 GLN R 120 GLN R 151 GLN S 120 GLN S 151 GLN T 120 GLN T 151 GLN T 167 GLN U 151 GLN V 120 GLN V 151 GLN W 151 GLN X 120 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.100820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.081203 restraints weight = 37007.531| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 1.72 r_work: 0.2785 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9379 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 37224 Z= 0.224 Angle : 0.507 6.179 50760 Z= 0.280 Chirality : 0.044 0.138 6096 Planarity : 0.003 0.030 6504 Dihedral : 4.795 20.562 6600 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.44 % Allowed : 15.55 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.12), residues: 4632 helix: 0.79 (0.20), residues: 648 sheet: 0.79 (0.14), residues: 1368 loop : -0.26 (0.11), residues: 2616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 164 TYR 0.005 0.001 TYR F 126 PHE 0.012 0.002 PHE U 77 HIS 0.003 0.001 HIS X 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.22 (36984) covalent geometry : angle 0.49817 / 0.28 (50232) SS BOND : bond 0.00283 / 0.19 ( 192) SS BOND : angle 0.45133 / 0.32 ( 384) hydrogen bonds : bond 0.04788 / 3.23 ( 1384) hydrogen bonds : angle 6.16915 / 4.25 ( 3504) link_ALPHA1-4 : bond 0.00186 / 0.13 ( 24) link_ALPHA1-4 : angle 1.88036 / 1.33 ( 72) link_BETA1-4 : bond 0.00260 / 0.18 ( 24) link_BETA1-4 : angle 1.93286 / 1.34 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 858 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 799 time to evaluate : 1.018 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: E 113 GLU cc_start: 0.8197 (tt0) cc_final: 0.7953 (tp30) REVERT: I 113 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7957 (tt0) outliers start: 59 outliers final: 10 residues processed: 807 average time/residue: 0.7412 time to fit residues: 703.5422 Evaluate side-chains 788 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 777 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain I residue 113 GLU Chi-restraints excluded: chain K residue 132 LEU Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain M residue 132 LEU Chi-restraints excluded: chain P residue 132 LEU Chi-restraints excluded: chain S residue 132 LEU Chi-restraints excluded: chain U residue 132 LEU Chi-restraints excluded: chain X residue 132 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 383 optimal weight: 7.9990 chunk 155 optimal weight: 0.0060 chunk 433 optimal weight: 2.9990 chunk 283 optimal weight: 5.9990 chunk 334 optimal weight: 0.9990 chunk 253 optimal weight: 0.7980 chunk 401 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 422 optimal weight: 6.9990 chunk 268 optimal weight: 10.0000 chunk 233 optimal weight: 9.9990 overall best weight: 1.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 GLN A 151 GLN A 167 GLN B 120 GLN B 151 GLN C 120 GLN D 120 GLN D 167 GLN E 120 GLN E 151 GLN ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 GLN G 120 GLN G 151 GLN H 120 GLN H 151 GLN I 120 GLN I 151 GLN J 120 GLN J 151 GLN K 151 GLN L 151 GLN L 167 GLN M 120 GLN M 151 GLN N 120 GLN N 151 GLN O 120 GLN O 151 GLN O 167 GLN P 120 GLN Q 120 GLN R 120 GLN R 151 GLN S 120 GLN S 151 GLN T 120 GLN T 151 GLN U 151 GLN V 120 GLN V 151 GLN V 167 GLN W 120 GLN W 151 GLN X 120 GLN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.101944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.082409 restraints weight = 37136.052| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.72 r_work: 0.2812 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9362 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 37224 Z= 0.167 Angle : 0.483 6.305 50760 Z= 0.266 Chirality : 0.043 0.135 6096 Planarity : 0.003 0.025 6504 Dihedral : 4.638 19.956 6600 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 0.37 % Allowed : 16.98 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.12), residues: 4632 helix: 0.81 (0.20), residues: 648 sheet: 0.74 (0.14), residues: 1368 loop : -0.24 (0.11), residues: 2616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG S 164 TYR 0.005 0.001 TYR D 126 PHE 0.010 0.002 PHE B 14 HIS 0.002 0.001 HIS S 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.17 (36984) covalent geometry : angle 0.47401 / 0.26 (50232) SS BOND : bond 0.00195 / 0.13 ( 192) SS BOND : angle 0.40988 / 0.29 ( 384) hydrogen bonds : bond 0.04305 / 2.90 ( 1384) hydrogen bonds : angle 6.12433 / 4.21 ( 3504) link_ALPHA1-4 : bond 0.00085 / 0.06 ( 24) link_ALPHA1-4 : angle 1.81644 / 1.28 ( 72) link_BETA1-4 : bond 0.00331 / 0.23 ( 24) link_BETA1-4 : angle 1.84851 / 1.28 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 785 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 770 time to evaluate : 1.381 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 113 GLU cc_start: 0.8315 (tp30) cc_final: 0.8047 (tp30) REVERT: A 167 GLN cc_start: 0.8595 (pt0) cc_final: 0.8160 (mt0) outliers start: 15 outliers final: 10 residues processed: 771 average time/residue: 0.7527 time to fit residues: 682.4824 Evaluate side-chains 755 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 745 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain K residue 132 LEU Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain M residue 132 LEU Chi-restraints excluded: chain P residue 132 LEU Chi-restraints excluded: chain S residue 132 LEU Chi-restraints excluded: chain U residue 132 LEU Chi-restraints excluded: chain X residue 132 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 130 optimal weight: 8.9990 chunk 290 optimal weight: 5.9990 chunk 155 optimal weight: 10.0000 chunk 182 optimal weight: 5.9990 chunk 446 optimal weight: 4.9990 chunk 304 optimal weight: 4.9990 chunk 420 optimal weight: 0.0370 chunk 373 optimal weight: 9.9990 chunk 284 optimal weight: 3.9990 chunk 321 optimal weight: 0.4980 chunk 74 optimal weight: 0.0670 overall best weight: 1.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 GLN B 120 GLN D 120 GLN E 120 GLN ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 GLN G 120 GLN H 120 GLN I 120 GLN J 120 GLN J 167 GLN M 120 GLN M 167 GLN O 120 GLN P 120 GLN Q 120 GLN R 120 GLN S 120 GLN T 120 GLN V 120 GLN W 120 GLN W 151 GLN X 120 GLN X 151 GLN X 167 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.101601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.082041 restraints weight = 36891.809| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 1.72 r_work: 0.2804 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9367 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 37224 Z= 0.191 Angle : 0.493 6.308 50760 Z= 0.273 Chirality : 0.044 0.135 6096 Planarity : 0.003 0.028 6504 Dihedral : 4.656 20.972 6600 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Rotamer: Outliers : 0.32 % Allowed : 18.03 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.12), residues: 4632 helix: 0.76 (0.20), residues: 648 sheet: 0.73 (0.14), residues: 1368 loop : -0.26 (0.11), residues: 2616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 164 TYR 0.006 0.001 TYR D 126 PHE 0.011 0.002 PHE G 14 HIS 0.003 0.001 HIS Q 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.19 (36984) covalent geometry : angle 0.48407 / 0.27 (50232) SS BOND : bond 0.00225 / 0.15 ( 192) SS BOND : angle 0.40758 / 0.29 ( 384) hydrogen bonds : bond 0.04535 / 3.06 ( 1384) hydrogen bonds : angle 6.10188 / 4.20 ( 3504) link_ALPHA1-4 : bond 0.00137 / 0.10 ( 24) link_ALPHA1-4 : angle 1.82915 / 1.29 ( 72) link_BETA1-4 : bond 0.00289 / 0.20 ( 24) link_BETA1-4 : angle 1.87546 / 1.30 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 793 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 780 time to evaluate : 1.178 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: R 167 GLN cc_start: 0.8278 (pt0) cc_final: 0.7975 (pm20) outliers start: 13 outliers final: 7 residues processed: 781 average time/residue: 0.7658 time to fit residues: 702.7057 Evaluate side-chains 768 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 761 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain K residue 132 LEU Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain M residue 132 LEU Chi-restraints excluded: chain S residue 132 LEU Chi-restraints excluded: chain U residue 132 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 214 optimal weight: 0.5980 chunk 308 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 348 optimal weight: 0.9990 chunk 300 optimal weight: 4.9990 chunk 246 optimal weight: 4.9990 chunk 357 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 chunk 243 optimal weight: 0.9980 chunk 335 optimal weight: 9.9990 chunk 221 optimal weight: 9.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 GLN B 120 GLN D 120 GLN D 167 GLN E 120 GLN ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 GLN F 151 GLN G 120 GLN H 120 GLN I 120 GLN I 151 GLN J 120 GLN M 120 GLN O 120 GLN O 151 GLN P 120 GLN Q 120 GLN Q 151 GLN R 120 GLN S 120 GLN T 120 GLN V 120 GLN W 120 GLN X 120 GLN X 167 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.101837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.082295 restraints weight = 37129.936| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.72 r_work: 0.2812 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9363 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 37224 Z= 0.176 Angle : 0.486 6.196 50760 Z= 0.268 Chirality : 0.043 0.133 6096 Planarity : 0.003 0.025 6504 Dihedral : 4.609 21.324 6600 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 0.39 % Allowed : 17.98 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.12), residues: 4632 helix: 0.78 (0.20), residues: 648 sheet: 0.68 (0.14), residues: 1368 loop : -0.25 (0.11), residues: 2616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 164 TYR 0.006 0.001 TYR Q 126 PHE 0.010 0.002 PHE G 14 HIS 0.002 0.001 HIS Q 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.18 (36984) covalent geometry : angle 0.47725 / 0.27 (50232) SS BOND : bond 0.00206 / 0.14 ( 192) SS BOND : angle 0.39354 / 0.28 ( 384) hydrogen bonds : bond 0.04391 / 2.96 ( 1384) hydrogen bonds : angle 6.07230 / 4.18 ( 3504) link_ALPHA1-4 : bond 0.00123 / 0.08 ( 24) link_ALPHA1-4 : angle 1.81071 / 1.28 ( 72) link_BETA1-4 : bond 0.00322 / 0.22 ( 24) link_BETA1-4 : angle 1.83545 / 1.27 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 743 time to evaluate : 1.287 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: D 113 GLU cc_start: 0.8086 (tp30) cc_final: 0.7868 (tp30) outliers start: 16 outliers final: 9 residues processed: 744 average time/residue: 0.7651 time to fit residues: 670.4028 Evaluate side-chains 750 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 741 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain K residue 132 LEU Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain M residue 132 LEU Chi-restraints excluded: chain S residue 132 LEU Chi-restraints excluded: chain U residue 132 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 110 optimal weight: 6.9990 chunk 104 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 chunk 335 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 79 optimal weight: 9.9990 chunk 426 optimal weight: 0.0980 chunk 246 optimal weight: 5.9990 chunk 88 optimal weight: 9.9990 chunk 363 optimal weight: 0.0770 chunk 153 optimal weight: 6.9990 overall best weight: 3.0344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 GLN B 120 GLN B 167 GLN D 120 GLN E 120 GLN ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 GLN F 167 GLN G 120 GLN H 120 GLN H 167 GLN I 120 GLN J 120 GLN J 151 GLN M 120 GLN O 120 GLN P 120 GLN Q 120 GLN R 120 GLN S 120 GLN T 120 GLN V 120 GLN W 120 GLN W 151 GLN X 120 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.100468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.080766 restraints weight = 37024.595| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 1.72 r_work: 0.2778 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9382 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 37224 Z= 0.267 Angle : 0.536 6.347 50760 Z= 0.297 Chirality : 0.046 0.136 6096 Planarity : 0.003 0.033 6504 Dihedral : 4.812 21.868 6600 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.56 % Allowed : 17.62 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.12), residues: 4632 helix: 0.72 (0.20), residues: 648 sheet: 0.68 (0.14), residues: 1368 loop : -0.25 (0.11), residues: 2616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG U 164 TYR 0.006 0.001 TYR D 126 PHE 0.012 0.003 PHE P 77 HIS 0.004 0.001 HIS A 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.27 (36984) covalent geometry : angle 0.52763 / 0.30 (50232) SS BOND : bond 0.00325 / 0.22 ( 192) SS BOND : angle 0.47466 / 0.33 ( 384) hydrogen bonds : bond 0.05100 / 3.45 ( 1384) hydrogen bonds : angle 6.18758 / 4.26 ( 3504) link_ALPHA1-4 : bond 0.00279 / 0.19 ( 24) link_ALPHA1-4 : angle 1.89673 / 1.34 ( 72) link_BETA1-4 : bond 0.00212 / 0.14 ( 24) link_BETA1-4 : angle 1.95410 / 1.35 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 785 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 762 time to evaluate : 1.165 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: R 167 GLN cc_start: 0.8282 (pt0) cc_final: 0.7902 (pm20) outliers start: 23 outliers final: 2 residues processed: 765 average time/residue: 0.7636 time to fit residues: 684.6106 Evaluate side-chains 762 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 760 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain K residue 132 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 343 optimal weight: 7.9990 chunk 399 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 chunk 104 optimal weight: 6.9990 chunk 252 optimal weight: 5.9990 chunk 429 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 296 optimal weight: 10.0000 chunk 350 optimal weight: 0.0980 chunk 43 optimal weight: 0.9990 chunk 311 optimal weight: 0.9980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 GLN A 151 GLN B 120 GLN D 120 GLN E 120 GLN E 167 GLN F 120 GLN G 120 GLN G 167 GLN H 120 GLN I 120 GLN I 167 GLN J 120 GLN M 120 GLN N 167 GLN O 120 GLN P 120 GLN P 151 GLN Q 120 GLN R 120 GLN R 151 GLN S 120 GLN T 120 GLN V 120 GLN V 167 GLN W 120 GLN W 151 GLN X 120 GLN X 167 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.102746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.083370 restraints weight = 36880.554| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 1.71 r_work: 0.2833 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9350 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 37224 Z= 0.144 Angle : 0.479 8.522 50760 Z= 0.264 Chirality : 0.043 0.160 6096 Planarity : 0.003 0.025 6504 Dihedral : 4.563 22.860 6600 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % Rotamer: Outliers : 0.29 % Allowed : 18.01 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.12), residues: 4632 helix: 0.85 (0.20), residues: 648 sheet: 0.58 (0.14), residues: 1368 loop : -0.26 (0.11), residues: 2616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG U 164 TYR 0.005 0.001 TYR K 126 PHE 0.010 0.002 PHE G 14 HIS 0.002 0.001 HIS T 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (36984) covalent geometry : angle 0.47066 / 0.26 (50232) SS BOND : bond 0.00151 / 0.10 ( 192) SS BOND : angle 0.38418 / 0.27 ( 384) hydrogen bonds : bond 0.04070 / 2.74 ( 1384) hydrogen bonds : angle 6.06903 / 4.17 ( 3504) link_ALPHA1-4 : bond 0.00033 / 0.02 ( 24) link_ALPHA1-4 : angle 1.76820 / 1.25 ( 72) link_BETA1-4 : bond 0.00376 / 0.26 ( 24) link_BETA1-4 : angle 1.74767 / 1.21 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16978.86 seconds wall clock time: 289 minutes 27.19 seconds (17367.19 seconds total)