Starting phenix.real_space_refine on Wed May 28 10:00:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bj3_44628/05_2025/9bj3_44628_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bj3_44628/05_2025/9bj3_44628.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bj3_44628/05_2025/9bj3_44628.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bj3_44628/05_2025/9bj3_44628.map" model { file = "/net/cci-nas-00/data/ceres_data/9bj3_44628/05_2025/9bj3_44628_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bj3_44628/05_2025/9bj3_44628_neut.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.031 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 126 5.16 5 C 19416 2.51 5 N 5001 2.21 5 O 6078 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 1.52s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 30621 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 8022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1037, 8022 Classifications: {'peptide': 1037} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 56, 'TRANS': 980} Chain breaks: 8 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 64 Chain: "B" Number of atoms: 8022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1037, 8022 Classifications: {'peptide': 1037} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 56, 'TRANS': 980} Chain breaks: 8 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 64 Chain: "C" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 970 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "D" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 807 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 100} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 970 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "F" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 807 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 100} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "H" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 970 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "L" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 807 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 100} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "S" Number of atoms: 8022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1037, 8022 Classifications: {'peptide': 1037} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 56, 'TRANS': 980} Chain breaks: 8 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 64 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "S" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 19.50, per 1000 atoms: 0.64 Number of scatterers: 30621 At special positions: 0 Unit cell: (155.082, 153.378, 188.314, 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 126 16.00 O 6078 8.00 N 5001 7.00 C 19416 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS S 15 " - pdb=" SG CYS S 136 " distance=2.03 Simple disulfide: pdb=" SG CYS S 131 " - pdb=" SG CYS S 166 " distance=2.04 Simple disulfide: pdb=" SG CYS S 291 " - pdb=" SG CYS S 301 " distance=2.03 Simple disulfide: pdb=" SG CYS S 336 " - pdb=" SG CYS S 361 " distance=2.03 Simple disulfide: pdb=" SG CYS S 379 " - pdb=" SG CYS S 432 " distance=2.04 Simple disulfide: pdb=" SG CYS S 391 " - pdb=" SG CYS S 525 " distance=2.03 Simple disulfide: pdb=" SG CYS S 538 " - pdb=" SG CYS S 590 " distance=2.04 Simple disulfide: pdb=" SG CYS S 617 " - pdb=" SG CYS S 649 " distance=2.03 Simple disulfide: pdb=" SG CYS S 662 " - pdb=" SG CYS S 671 " distance=2.03 Simple disulfide: pdb=" SG CYS S 738 " - pdb=" SG CYS S 760 " distance=2.03 Simple disulfide: pdb=" SG CYS S 743 " - pdb=" SG CYS S 749 " distance=2.03 Simple disulfide: pdb=" SG CYS S1032 " - pdb=" SG CYS S1043 " distance=2.03 Simple disulfide: pdb=" SG CYS S1082 " - pdb=" SG CYS S1126 " distance=2.04 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 ALPHA1-3 " BMA I 3 " - " MAN I 4 " " BMA U 3 " - " MAN U 4 " " BMA e 3 " - " MAN e 4 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B1074 " " NAG G 1 " - " ASN A 122 " " NAG I 1 " - " ASN A 234 " " NAG J 1 " - " ASN A 282 " " NAG K 1 " - " ASN A 331 " " NAG M 1 " - " ASN A 343 " " NAG N 1 " - " ASN A 709 " " NAG O 1 " - " ASN A 717 " " NAG P 1 " - " ASN A 801 " " NAG Q 1 " - " ASN A1098 " " NAG R 1 " - " ASN A1134 " " NAG S1301 " - " ASN S 61 " " NAG S1302 " - " ASN S 165 " " NAG S1303 " - " ASN S 603 " " NAG S1304 " - " ASN S 616 " " NAG S1305 " - " ASN S 657 " " NAG S1306 " - " ASN S1074 " " NAG T 1 " - " ASN B 122 " " NAG U 1 " - " ASN B 234 " " NAG V 1 " - " ASN B 282 " " NAG W 1 " - " ASN B 331 " " NAG X 1 " - " ASN B 343 " " NAG Y 1 " - " ASN B 709 " " NAG Z 1 " - " ASN B 717 " " NAG a 1 " - " ASN B 801 " " NAG b 1 " - " ASN B1098 " " NAG c 1 " - " ASN B1134 " " NAG d 1 " - " ASN S 122 " " NAG e 1 " - " ASN S 234 " " NAG f 1 " - " ASN S 282 " " NAG g 1 " - " ASN S 331 " " NAG h 1 " - " ASN S 343 " " NAG i 1 " - " ASN S 709 " " NAG j 1 " - " ASN S 717 " " NAG k 1 " - " ASN S 801 " " NAG l 1 " - " ASN S1098 " " NAG m 1 " - " ASN S1134 " Time building additional restraints: 8.26 Conformation dependent library (CDL) restraints added in 4.0 seconds 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7092 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 75 sheets defined 19.8% alpha, 27.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.78 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.829A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.691A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 390 removed outlier: 3.785A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.221A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.893A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 removed outlier: 3.520A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.568A pdb=" N ILE A 870 " --> pdb=" O THR A 866 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.727A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 886 through 890' Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.879A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 913 through 918' Processing helix chain 'A' and resid 919 through 932 Processing helix chain 'A' and resid 933 through 941 removed outlier: 3.596A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 946 removed outlier: 4.370A pdb=" N LEU A 945 " --> pdb=" O PRO A 942 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY A 946 " --> pdb=" O SER A 943 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 942 through 946' Processing helix chain 'A' and resid 947 through 949 No H-bonds generated for 'chain 'A' and resid 947 through 949' Processing helix chain 'A' and resid 950 through 964 removed outlier: 3.822A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 967 No H-bonds generated for 'chain 'A' and resid 965 through 967' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.943A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE A 993 " --> pdb=" O ALA A 989 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE A1018 " --> pdb=" O ARG A1014 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG A1019 " --> pdb=" O ALA A1015 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR A1027 " --> pdb=" O ASN A1023 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.807A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.704A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 390 removed outlier: 3.664A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.206A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.504A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.902A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 removed outlier: 3.537A pdb=" N LEU B 821 " --> pdb=" O PRO B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.562A pdb=" N ILE B 870 " --> pdb=" O THR B 866 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.714A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 886 through 890' Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.860A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 913 through 918' Processing helix chain 'B' and resid 919 through 932 Processing helix chain 'B' and resid 933 through 941 removed outlier: 3.603A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 946 removed outlier: 4.370A pdb=" N LEU B 945 " --> pdb=" O PRO B 942 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY B 946 " --> pdb=" O SER B 943 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 942 through 946' Processing helix chain 'B' and resid 947 through 949 No H-bonds generated for 'chain 'B' and resid 947 through 949' Processing helix chain 'B' and resid 950 through 964 removed outlier: 3.501A pdb=" N GLN B 954 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 967 No H-bonds generated for 'chain 'B' and resid 965 through 967' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.926A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE B 993 " --> pdb=" O ALA B 989 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE B1018 " --> pdb=" O ARG B1014 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG B1019 " --> pdb=" O ALA B1015 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ALA B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR B1027 " --> pdb=" O ASN B1023 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 31 removed outlier: 3.601A pdb=" N SER D 31 " --> pdb=" O VAL D 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 28 through 31' Processing helix chain 'D' and resid 79 through 83 removed outlier: 4.133A pdb=" N PHE D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 31 removed outlier: 3.576A pdb=" N SER F 31 " --> pdb=" O VAL F 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 28 through 31' Processing helix chain 'F' and resid 79 through 83 removed outlier: 4.115A pdb=" N PHE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 28 through 31 removed outlier: 3.577A pdb=" N SER L 31 " --> pdb=" O VAL L 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 28 through 31' Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.117A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'S' and resid 294 through 304 Processing helix chain 'S' and resid 338 through 343 removed outlier: 3.821A pdb=" N PHE S 342 " --> pdb=" O PHE S 338 " (cutoff:3.500A) Processing helix chain 'S' and resid 365 through 370 removed outlier: 3.715A pdb=" N TYR S 369 " --> pdb=" O TYR S 365 " (cutoff:3.500A) Processing helix chain 'S' and resid 385 through 390 removed outlier: 3.794A pdb=" N ASN S 388 " --> pdb=" O THR S 385 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU S 390 " --> pdb=" O LEU S 387 " (cutoff:3.500A) Processing helix chain 'S' and resid 405 through 410 removed outlier: 4.218A pdb=" N ARG S 408 " --> pdb=" O ASP S 405 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE S 410 " --> pdb=" O VAL S 407 " (cutoff:3.500A) Processing helix chain 'S' and resid 416 through 422 Processing helix chain 'S' and resid 737 through 743 Processing helix chain 'S' and resid 746 through 754 Processing helix chain 'S' and resid 755 through 757 No H-bonds generated for 'chain 'S' and resid 755 through 757' Processing helix chain 'S' and resid 758 through 783 removed outlier: 3.888A pdb=" N GLN S 762 " --> pdb=" O SER S 758 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU S 763 " --> pdb=" O PHE S 759 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASP S 775 " --> pdb=" O ALA S 771 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS S 776 " --> pdb=" O VAL S 772 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR S 778 " --> pdb=" O GLN S 774 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL S 781 " --> pdb=" O ASN S 777 " (cutoff:3.500A) Processing helix chain 'S' and resid 816 through 824 removed outlier: 3.556A pdb=" N LEU S 821 " --> pdb=" O PRO S 817 " (cutoff:3.500A) Processing helix chain 'S' and resid 866 through 884 removed outlier: 3.576A pdb=" N ILE S 870 " --> pdb=" O THR S 866 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA S 871 " --> pdb=" O ASP S 867 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN S 872 " --> pdb=" O GLU S 868 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR S 883 " --> pdb=" O ALA S 879 " (cutoff:3.500A) Processing helix chain 'S' and resid 886 through 890 removed outlier: 3.740A pdb=" N GLY S 889 " --> pdb=" O TRP S 886 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA S 890 " --> pdb=" O THR S 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 886 through 890' Processing helix chain 'S' and resid 897 through 908 Processing helix chain 'S' and resid 913 through 918 removed outlier: 3.850A pdb=" N TYR S 917 " --> pdb=" O GLN S 913 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU S 918 " --> pdb=" O ASN S 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 913 through 918' Processing helix chain 'S' and resid 919 through 932 Processing helix chain 'S' and resid 933 through 941 removed outlier: 3.588A pdb=" N THR S 941 " --> pdb=" O SER S 937 " (cutoff:3.500A) Processing helix chain 'S' and resid 942 through 946 removed outlier: 4.385A pdb=" N LEU S 945 " --> pdb=" O PRO S 942 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY S 946 " --> pdb=" O SER S 943 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 942 through 946' Processing helix chain 'S' and resid 947 through 949 No H-bonds generated for 'chain 'S' and resid 947 through 949' Processing helix chain 'S' and resid 950 through 964 removed outlier: 3.510A pdb=" N GLN S 954 " --> pdb=" O ASP S 950 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU S 962 " --> pdb=" O ALA S 958 " (cutoff:3.500A) Processing helix chain 'S' and resid 965 through 967 No H-bonds generated for 'chain 'S' and resid 965 through 967' Processing helix chain 'S' and resid 976 through 982 Processing helix chain 'S' and resid 985 through 1032 removed outlier: 4.947A pdb=" N VAL S 991 " --> pdb=" O PRO S 987 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLN S 992 " --> pdb=" O GLU S 988 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE S 993 " --> pdb=" O ALA S 989 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ASP S 994 " --> pdb=" O GLU S 990 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ARG S 995 " --> pdb=" O VAL S 991 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU S 996 " --> pdb=" O GLN S 992 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR S1007 " --> pdb=" O SER S1003 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLU S1017 " --> pdb=" O ILE S1013 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE S1018 " --> pdb=" O ARG S1014 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG S1019 " --> pdb=" O ALA S1015 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ALA S1020 " --> pdb=" O ALA S1016 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR S1027 " --> pdb=" O ASN S1023 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.837A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.894A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.503A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE A 106 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU A 132 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASN A 164 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN A 134 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.503A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE A 106 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 141 through 143 removed outlier: 3.801A pdb=" N GLY A 142 " --> pdb=" O GLU A 156 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.460A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.577A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 356 through 358 Processing sheet with id=AB2, first strand: chain 'A' and resid 400 through 403 Processing sheet with id=AB3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB4, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.083A pdb=" N PHE A 565 " --> pdb=" O PHE S 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.293A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY A 667 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.060A pdb=" N ALA A 701 " --> pdb=" O ILE S 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 712 Processing sheet with id=AB8, first strand: chain 'A' and resid 717 through 728 removed outlier: 6.169A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AC1, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AC2, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC3, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC4, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.982A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA B 263 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 27 through 30 Processing sheet with id=AC6, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AC7, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.901A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.467A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE B 106 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASN B 164 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN B 134 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.467A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE B 106 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 141 through 143 removed outlier: 3.803A pdb=" N GLY B 142 " --> pdb=" O GLU B 156 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.443A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.568A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 356 through 358 Processing sheet with id=AD5, first strand: chain 'B' and resid 400 through 403 Processing sheet with id=AD6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.398A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.899A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY B 667 " --> pdb=" O ILE B 670 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 711 through 712 Processing sheet with id=AD9, first strand: chain 'B' and resid 717 through 728 removed outlier: 6.176A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AE2, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AE3, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE4, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE5, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AE6, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.655A pdb=" N GLU C 10 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA C 88 " --> pdb=" O VAL C 109 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 98 through 99 Processing sheet with id=AE8, first strand: chain 'D' and resid 4 through 5 removed outlier: 3.839A pdb=" N ILE D 75 " --> pdb=" O ALA D 19 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE D 71 " --> pdb=" O CYS D 23 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 10 through 11 Processing sheet with id=AF1, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.686A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR D 97 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AF3, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.664A pdb=" N GLU E 10 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA E 88 " --> pdb=" O VAL E 109 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLY E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 98 through 99 Processing sheet with id=AF5, first strand: chain 'F' and resid 4 through 5 removed outlier: 3.849A pdb=" N ILE F 75 " --> pdb=" O ALA F 19 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE F 71 " --> pdb=" O CYS F 23 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 10 through 11 Processing sheet with id=AF7, first strand: chain 'F' and resid 53 through 54 removed outlier: 6.682A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR F 97 " --> pdb=" O GLN F 90 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AF9, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.659A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA H 88 " --> pdb=" O VAL H 109 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 98 through 99 Processing sheet with id=AG2, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.873A pdb=" N ILE L 75 " --> pdb=" O ALA L 19 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 10 through 11 Processing sheet with id=AG4, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.688A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'S' and resid 27 through 30 removed outlier: 3.504A pdb=" N ALA S 27 " --> pdb=" O TRP S 64 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N ASN S 61 " --> pdb=" O TYR S 269 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N TYR S 269 " --> pdb=" O ASN S 61 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ALA S 263 " --> pdb=" O ALA S 67 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N PHE S 201 " --> pdb=" O ASP S 228 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASP S 228 " --> pdb=" O PHE S 201 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE S 203 " --> pdb=" O LEU S 226 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N HIS S 207 " --> pdb=" O ALA S 222 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N ALA S 222 " --> pdb=" O HIS S 207 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N VAL S 36 " --> pdb=" O LEU S 223 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'S' and resid 27 through 30 removed outlier: 3.504A pdb=" N ALA S 27 " --> pdb=" O TRP S 64 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'S' and resid 47 through 55 removed outlier: 3.885A pdb=" N ASP S 287 " --> pdb=" O LYS S 278 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'S' and resid 84 through 85 removed outlier: 4.505A pdb=" N GLY S 103 " --> pdb=" O LEU S 241 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ARG S 102 " --> pdb=" O ASN S 121 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASN S 121 " --> pdb=" O ARG S 102 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE S 106 " --> pdb=" O LEU S 117 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU S 132 " --> pdb=" O ASN S 164 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASN S 164 " --> pdb=" O GLU S 132 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN S 134 " --> pdb=" O SER S 162 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N SER S 162 " --> pdb=" O GLN S 134 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'S' and resid 84 through 85 removed outlier: 4.505A pdb=" N GLY S 103 " --> pdb=" O LEU S 241 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ARG S 102 " --> pdb=" O ASN S 121 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASN S 121 " --> pdb=" O ARG S 102 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE S 106 " --> pdb=" O LEU S 117 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'S' and resid 141 through 143 removed outlier: 3.762A pdb=" N GLY S 142 " --> pdb=" O GLU S 156 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'S' and resid 311 through 319 removed outlier: 5.542A pdb=" N ILE S 312 " --> pdb=" O THR S 599 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N THR S 599 " --> pdb=" O ILE S 312 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N GLN S 314 " --> pdb=" O VAL S 597 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL S 597 " --> pdb=" O GLN S 314 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER S 316 " --> pdb=" O VAL S 595 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLY S 594 " --> pdb=" O GLN S 613 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY S 648 " --> pdb=" O THR S 645 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'S' and resid 325 through 328 removed outlier: 3.756A pdb=" N THR S 553 " --> pdb=" O ASP S 586 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'S' and resid 356 through 358 Processing sheet with id=AH5, first strand: chain 'S' and resid 400 through 403 Processing sheet with id=AH6, first strand: chain 'S' and resid 452 through 454 Processing sheet with id=AH7, first strand: chain 'S' and resid 654 through 655 removed outlier: 6.272A pdb=" N GLU S 654 " --> pdb=" O ALA S 694 " (cutoff:3.500A) removed outlier: 8.795A pdb=" N THR S 696 " --> pdb=" O GLU S 654 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY S 667 " --> pdb=" O ILE S 670 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ALA S 672 " --> pdb=" O PRO S 665 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'S' and resid 711 through 712 Processing sheet with id=AH9, first strand: chain 'S' and resid 717 through 728 removed outlier: 6.164A pdb=" N TYR S1067 " --> pdb=" O HIS S1048 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N HIS S1048 " --> pdb=" O TYR S1067 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'S' and resid 734 through 736 Processing sheet with id=AI2, first strand: chain 'S' and resid 1120 through 1122 Processing sheet with id=AI3, first strand: chain 'S' and resid 1094 through 1097 1050 hydrogen bonds defined for protein. 2766 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: 14.69 Time building geometry restraints manager: 9.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9665 1.34 - 1.47: 8058 1.47 - 1.60: 13402 1.60 - 1.72: 0 1.72 - 1.85: 162 Bond restraints: 31287 Sorted by residual: bond pdb=" C1 NAG A1306 " pdb=" O5 NAG A1306 " ideal model delta sigma weight residual 1.406 1.482 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C1 NAG B1306 " pdb=" O5 NAG B1306 " ideal model delta sigma weight residual 1.406 1.482 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C1 NAG S1306 " pdb=" O5 NAG S1306 " ideal model delta sigma weight residual 1.406 1.480 -0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" C1 NAG c 2 " pdb=" O5 NAG c 2 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.41e+00 bond pdb=" C1 NAG T 2 " pdb=" O5 NAG T 2 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.88e+00 ... (remaining 31282 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 42175 2.71 - 5.41: 385 5.41 - 8.12: 38 8.12 - 10.83: 4 10.83 - 13.54: 1 Bond angle restraints: 42603 Sorted by residual: angle pdb=" CA CYS B 166 " pdb=" CB CYS B 166 " pdb=" SG CYS B 166 " ideal model delta sigma weight residual 114.40 127.94 -13.54 2.30e+00 1.89e-01 3.46e+01 angle pdb=" N ASN A 657 " pdb=" CA ASN A 657 " pdb=" C ASN A 657 " ideal model delta sigma weight residual 113.97 108.26 5.71 1.28e+00 6.10e-01 1.99e+01 angle pdb=" C ASN B 282 " pdb=" CA ASN B 282 " pdb=" CB ASN B 282 " ideal model delta sigma weight residual 112.63 122.01 -9.38 2.16e+00 2.14e-01 1.89e+01 angle pdb=" CA CYS S 166 " pdb=" CB CYS S 166 " pdb=" SG CYS S 166 " ideal model delta sigma weight residual 114.40 124.21 -9.81 2.30e+00 1.89e-01 1.82e+01 angle pdb=" N CYS B 131 " pdb=" CA CYS B 131 " pdb=" C CYS B 131 " ideal model delta sigma weight residual 109.18 115.20 -6.02 1.42e+00 4.96e-01 1.80e+01 ... (remaining 42598 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.34: 17920 24.34 - 48.68: 1457 48.68 - 73.02: 286 73.02 - 97.36: 71 97.36 - 121.70: 45 Dihedral angle restraints: 19779 sinusoidal: 8727 harmonic: 11052 Sorted by residual: dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual 93.00 7.20 85.80 1 1.00e+01 1.00e-02 8.90e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual 93.00 8.61 84.39 1 1.00e+01 1.00e-02 8.66e+01 dihedral pdb=" CB CYS S 538 " pdb=" SG CYS S 538 " pdb=" SG CYS S 590 " pdb=" CB CYS S 590 " ideal model delta sinusoidal sigma weight residual 93.00 9.94 83.06 1 1.00e+01 1.00e-02 8.44e+01 ... (remaining 19776 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 5034 0.124 - 0.248: 68 0.248 - 0.372: 16 0.372 - 0.496: 1 0.496 - 0.619: 2 Chirality restraints: 5121 Sorted by residual: chirality pdb=" C1 NAG B1305 " pdb=" ND2 ASN B 657 " pdb=" C2 NAG B1305 " pdb=" O5 NAG B1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.78 -0.62 2.00e-01 2.50e+01 9.59e+00 chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN A 801 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.94e+00 chirality pdb=" C1 NAG f 2 " pdb=" O4 NAG f 1 " pdb=" C2 NAG f 2 " pdb=" O5 NAG f 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.44 0.04 2.00e-02 2.50e+03 4.85e+00 ... (remaining 5118 not shown) Planarity restraints: 5427 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 657 " 0.054 2.00e-02 2.50e+03 5.08e-02 3.23e+01 pdb=" CG ASN B 657 " -0.056 2.00e-02 2.50e+03 pdb=" OD1 ASN B 657 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN B 657 " -0.061 2.00e-02 2.50e+03 pdb=" C1 NAG B1305 " 0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 657 " 0.045 2.00e-02 2.50e+03 4.42e-02 2.44e+01 pdb=" CG ASN A 657 " -0.058 2.00e-02 2.50e+03 pdb=" OD1 ASN A 657 " 0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN A 657 " -0.047 2.00e-02 2.50e+03 pdb=" C1 NAG A1305 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 717 " 0.044 2.00e-02 2.50e+03 4.04e-02 2.04e+01 pdb=" CG ASN A 717 " -0.059 2.00e-02 2.50e+03 pdb=" OD1 ASN A 717 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN A 717 " -0.033 2.00e-02 2.50e+03 pdb=" C1 NAG O 1 " 0.039 2.00e-02 2.50e+03 ... (remaining 5424 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 818 2.70 - 3.25: 26595 3.25 - 3.80: 41293 3.80 - 4.35: 54461 4.35 - 4.90: 97834 Nonbonded interactions: 221001 Sorted by model distance: nonbonded pdb=" O VAL A 308 " pdb=" OG1 THR A 602 " model vdw 2.144 3.040 nonbonded pdb=" O ILE E 56 " pdb=" OH TYR E 100E" model vdw 2.207 3.040 nonbonded pdb=" O ILE H 56 " pdb=" OH TYR H 100E" model vdw 2.207 3.040 nonbonded pdb=" O ILE C 56 " pdb=" OH TYR C 100E" model vdw 2.210 3.040 nonbonded pdb=" O VAL B 308 " pdb=" OG1 THR B 602 " model vdw 2.223 3.040 ... (remaining 220996 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'S' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'L' } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'l' selection = chain 'm' } ncs_group { reference = chain 'I' selection = chain 'U' selection = chain 'e' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Z' selection = chain 'a' selection = chain 'j' selection = chain 'k' } 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: 0.010 Normalize map: mean=0, sd=1: 7.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.260 Check model and map are aligned: 0.240 Set scattering table: 0.280 Process input model: 73.840 Find NCS groups from input model: 1.590 Set up NCS constraints: 0.380 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 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 : 0.004 0.076 31422 Z= 0.186 Angle : 0.728 20.381 42963 Z= 0.354 Chirality : 0.052 0.619 5121 Planarity : 0.004 0.081 5379 Dihedral : 18.607 121.703 12552 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 0.28 % Allowed : 25.66 % Favored : 74.07 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.13), residues: 3753 helix: -0.44 (0.22), residues: 606 sheet: -0.06 (0.17), residues: 1008 loop : -1.90 (0.12), residues: 2139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP S 436 HIS 0.007 0.001 HIS A 655 PHE 0.032 0.001 PHE A 802 TYR 0.013 0.001 TYR B 707 ARG 0.002 0.000 ARG A 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00848 ( 48) link_NAG-ASN : angle 4.88313 ( 144) link_BETA1-4 : bond 0.00836 ( 39) link_BETA1-4 : angle 2.19816 ( 117) link_ALPHA1-3 : bond 0.00327 ( 3) link_ALPHA1-3 : angle 1.92264 ( 9) hydrogen bonds : bond 0.18827 ( 991) hydrogen bonds : angle 7.15181 ( 2766) SS BOND : bond 0.00465 ( 45) SS BOND : angle 1.66066 ( 90) covalent geometry : bond 0.00368 (31287) covalent geometry : angle 0.65865 (42603) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 219 time to evaluate : 3.038 Fit side-chains REVERT: A 403 ARG cc_start: 0.6242 (OUTLIER) cc_final: 0.5964 (mtp85) outliers start: 9 outliers final: 3 residues processed: 226 average time/residue: 0.4169 time to fit residues: 153.7761 Evaluate side-chains 205 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 201 time to evaluate : 3.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain L residue 33 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 316 optimal weight: 0.6980 chunk 284 optimal weight: 4.9990 chunk 157 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 chunk 191 optimal weight: 6.9990 chunk 151 optimal weight: 4.9990 chunk 293 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 178 optimal weight: 0.6980 chunk 218 optimal weight: 6.9990 chunk 340 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 146 HIS A 207 HIS A 422 ASN A 448 ASN A 540 ASN A 542 ASN A 544 ASN A 613 GLN A 787 GLN A 907 ASN A 914 ASN A1010 GLN A1101 HIS B 125 ASN B 146 HIS B 207 HIS B 422 ASN B 448 ASN B 540 ASN B 542 ASN B 613 GLN B 703 ASN B 907 ASN B 914 ASN B 949 GLN B1010 GLN B1101 HIS F 42 GLN H 6 GLN S 14 GLN S 115 GLN S 146 HIS S 207 HIS S 422 ASN S 448 ASN S 540 ASN S 542 ASN S 544 ASN S 613 GLN S 784 GLN S 907 ASN S 914 ASN S1010 GLN S1101 HIS Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.158160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.124064 restraints weight = 37153.845| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 3.30 r_work: 0.3061 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.0675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31422 Z= 0.148 Angle : 0.661 14.602 42963 Z= 0.327 Chirality : 0.048 0.278 5121 Planarity : 0.005 0.054 5379 Dihedral : 11.386 111.373 5966 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 2.62 % Allowed : 23.81 % Favored : 73.57 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.13), residues: 3753 helix: 0.19 (0.22), residues: 633 sheet: -0.02 (0.17), residues: 1026 loop : -1.98 (0.12), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 886 HIS 0.004 0.001 HIS S1064 PHE 0.017 0.001 PHE B1121 TYR 0.019 0.001 TYR B1067 ARG 0.002 0.000 ARG A 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00575 ( 48) link_NAG-ASN : angle 3.17511 ( 144) link_BETA1-4 : bond 0.00631 ( 39) link_BETA1-4 : angle 1.96362 ( 117) link_ALPHA1-3 : bond 0.00527 ( 3) link_ALPHA1-3 : angle 1.62134 ( 9) hydrogen bonds : bond 0.05797 ( 991) hydrogen bonds : angle 5.40055 ( 2766) SS BOND : bond 0.00545 ( 45) SS BOND : angle 1.57486 ( 90) covalent geometry : bond 0.00342 (31287) covalent geometry : angle 0.62477 (42603) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 226 time to evaluate : 3.153 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 389 ASP cc_start: 0.8042 (t0) cc_final: 0.7759 (t0) REVERT: B 226 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7980 (mp) REVERT: B 703 ASN cc_start: 0.8124 (OUTLIER) cc_final: 0.7891 (t0) REVERT: B 784 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7561 (mt0) REVERT: E 69 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.8205 (mt) REVERT: F 45 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7390 (ttp-170) REVERT: S 226 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8133 (mt) REVERT: S 245 HIS cc_start: 0.6269 (OUTLIER) cc_final: 0.5401 (t70) REVERT: S 914 ASN cc_start: 0.9186 (OUTLIER) cc_final: 0.8957 (p0) outliers start: 85 outliers final: 28 residues processed: 299 average time/residue: 0.3753 time to fit residues: 188.9941 Evaluate side-chains 250 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 214 time to evaluate : 3.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 226 LEU Chi-restraints excluded: chain S residue 245 HIS Chi-restraints excluded: chain S residue 791 THR Chi-restraints excluded: chain S residue 907 ASN Chi-restraints excluded: chain S residue 914 ASN Chi-restraints excluded: chain S residue 1010 GLN Chi-restraints excluded: chain S residue 1133 VAL Chi-restraints excluded: chain S residue 1136 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 90 optimal weight: 2.9990 chunk 263 optimal weight: 7.9990 chunk 151 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 80 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 189 optimal weight: 0.0870 chunk 372 optimal weight: 1.9990 chunk 201 optimal weight: 0.9990 chunk 205 optimal weight: 3.9990 chunk 289 optimal weight: 0.7980 overall best weight: 1.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 784 GLN A 787 GLN A1010 GLN B 207 HIS B 703 ASN B 949 GLN B1010 GLN F 42 GLN S 207 HIS S1010 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.158688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.124509 restraints weight = 37282.080| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 4.97 r_work: 0.3082 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.0825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 31422 Z= 0.130 Angle : 0.639 13.889 42963 Z= 0.315 Chirality : 0.047 0.299 5121 Planarity : 0.004 0.045 5379 Dihedral : 9.871 110.294 5958 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 3.24 % Allowed : 23.99 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.13), residues: 3753 helix: 0.54 (0.22), residues: 630 sheet: 0.09 (0.17), residues: 1008 loop : -1.91 (0.12), residues: 2115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP S 886 HIS 0.003 0.001 HIS S1064 PHE 0.015 0.001 PHE B1121 TYR 0.018 0.001 TYR B1067 ARG 0.003 0.000 ARG S 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00520 ( 48) link_NAG-ASN : angle 2.89781 ( 144) link_BETA1-4 : bond 0.00578 ( 39) link_BETA1-4 : angle 1.92767 ( 117) link_ALPHA1-3 : bond 0.00781 ( 3) link_ALPHA1-3 : angle 1.48852 ( 9) hydrogen bonds : bond 0.05102 ( 991) hydrogen bonds : angle 5.16259 ( 2766) SS BOND : bond 0.00618 ( 45) SS BOND : angle 2.01969 ( 90) covalent geometry : bond 0.00295 (31287) covalent geometry : angle 0.60323 (42603) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 228 time to evaluate : 3.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 ASP cc_start: 0.8034 (t0) cc_final: 0.7742 (t0) REVERT: B 226 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7934 (mp) REVERT: B 703 ASN cc_start: 0.8023 (OUTLIER) cc_final: 0.7756 (t0) REVERT: F 45 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7310 (ttp-170) REVERT: H 13 LYS cc_start: 0.7712 (mttt) cc_final: 0.6842 (mptt) REVERT: S 226 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8051 (mt) REVERT: S 245 HIS cc_start: 0.6229 (OUTLIER) cc_final: 0.5365 (t70) REVERT: S 960 ASN cc_start: 0.8517 (m-40) cc_final: 0.8276 (m-40) outliers start: 105 outliers final: 50 residues processed: 316 average time/residue: 0.3671 time to fit residues: 195.3458 Evaluate side-chains 264 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 209 time to evaluate : 3.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 690 GLN Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain D residue 70 ASP Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain S residue 23 GLN Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 226 LEU Chi-restraints excluded: chain S residue 241 LEU Chi-restraints excluded: chain S residue 244 LEU Chi-restraints excluded: chain S residue 245 HIS Chi-restraints excluded: chain S residue 291 CYS Chi-restraints excluded: chain S residue 576 VAL Chi-restraints excluded: chain S residue 645 THR Chi-restraints excluded: chain S residue 690 GLN Chi-restraints excluded: chain S residue 747 THR Chi-restraints excluded: chain S residue 791 THR Chi-restraints excluded: chain S residue 1136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 91 optimal weight: 3.9990 chunk 276 optimal weight: 0.0970 chunk 172 optimal weight: 4.9990 chunk 275 optimal weight: 0.2980 chunk 121 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 203 optimal weight: 4.9990 chunk 224 optimal weight: 8.9990 chunk 238 optimal weight: 5.9990 chunk 360 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A1010 GLN B 207 HIS B 784 GLN B 907 ASN B 949 GLN B1010 GLN S 207 HIS S 907 ASN S 914 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.158527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.122882 restraints weight = 37288.816| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 4.75 r_work: 0.3068 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.0962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31422 Z= 0.132 Angle : 0.628 13.283 42963 Z= 0.310 Chirality : 0.047 0.356 5121 Planarity : 0.004 0.044 5379 Dihedral : 8.761 109.579 5958 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 3.36 % Allowed : 24.39 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.14), residues: 3753 helix: 0.87 (0.22), residues: 618 sheet: 0.11 (0.17), residues: 1008 loop : -1.86 (0.12), residues: 2127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP S 436 HIS 0.004 0.001 HIS S1064 PHE 0.015 0.001 PHE B1121 TYR 0.018 0.001 TYR S 369 ARG 0.003 0.000 ARG S 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00476 ( 48) link_NAG-ASN : angle 2.79379 ( 144) link_BETA1-4 : bond 0.00563 ( 39) link_BETA1-4 : angle 1.76353 ( 117) link_ALPHA1-3 : bond 0.00846 ( 3) link_ALPHA1-3 : angle 1.58595 ( 9) hydrogen bonds : bond 0.05007 ( 991) hydrogen bonds : angle 5.02837 ( 2766) SS BOND : bond 0.00606 ( 45) SS BOND : angle 1.99166 ( 90) covalent geometry : bond 0.00304 (31287) covalent geometry : angle 0.59451 (42603) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 222 time to evaluate : 3.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 ASP cc_start: 0.8090 (t0) cc_final: 0.7806 (t0) REVERT: B 226 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7924 (mp) REVERT: F 45 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7347 (ttp-170) REVERT: H 13 LYS cc_start: 0.7808 (mttt) cc_final: 0.6951 (mptt) REVERT: S 53 ASP cc_start: 0.8463 (OUTLIER) cc_final: 0.8049 (t70) REVERT: S 226 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8049 (mt) REVERT: S 245 HIS cc_start: 0.6148 (OUTLIER) cc_final: 0.5382 (t70) REVERT: S 960 ASN cc_start: 0.8499 (m-40) cc_final: 0.8259 (m-40) outliers start: 109 outliers final: 67 residues processed: 320 average time/residue: 0.3532 time to fit residues: 191.0363 Evaluate side-chains 282 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 210 time to evaluate : 3.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 690 GLN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain S residue 23 GLN Chi-restraints excluded: chain S residue 53 ASP Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 162 SER Chi-restraints excluded: chain S residue 226 LEU Chi-restraints excluded: chain S residue 241 LEU Chi-restraints excluded: chain S residue 244 LEU Chi-restraints excluded: chain S residue 245 HIS Chi-restraints excluded: chain S residue 291 CYS Chi-restraints excluded: chain S residue 442 ASP Chi-restraints excluded: chain S residue 534 VAL Chi-restraints excluded: chain S residue 576 VAL Chi-restraints excluded: chain S residue 645 THR Chi-restraints excluded: chain S residue 690 GLN Chi-restraints excluded: chain S residue 723 THR Chi-restraints excluded: chain S residue 747 THR Chi-restraints excluded: chain S residue 791 THR Chi-restraints excluded: chain S residue 907 ASN Chi-restraints excluded: chain S residue 1133 VAL Chi-restraints excluded: chain S residue 1136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 125 optimal weight: 8.9990 chunk 3 optimal weight: 0.3980 chunk 178 optimal weight: 0.3980 chunk 290 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 253 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 186 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 274 optimal weight: 0.6980 chunk 44 optimal weight: 20.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A1010 GLN B 207 HIS B 703 ASN B 907 ASN B 949 GLN B1010 GLN S 207 HIS S 907 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.160623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.124855 restraints weight = 37193.357| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 4.28 r_work: 0.3104 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 31422 Z= 0.109 Angle : 0.590 10.966 42963 Z= 0.293 Chirality : 0.046 0.462 5121 Planarity : 0.004 0.043 5379 Dihedral : 8.167 108.583 5958 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 3.08 % Allowed : 24.88 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.14), residues: 3753 helix: 1.08 (0.22), residues: 618 sheet: 0.20 (0.17), residues: 1005 loop : -1.76 (0.12), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 886 HIS 0.002 0.000 HIS S1064 PHE 0.011 0.001 PHE B1121 TYR 0.018 0.001 TYR S 369 ARG 0.003 0.000 ARG B 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00533 ( 48) link_NAG-ASN : angle 2.61124 ( 144) link_BETA1-4 : bond 0.00536 ( 39) link_BETA1-4 : angle 1.61192 ( 117) link_ALPHA1-3 : bond 0.00875 ( 3) link_ALPHA1-3 : angle 1.42924 ( 9) hydrogen bonds : bond 0.04228 ( 991) hydrogen bonds : angle 4.89397 ( 2766) SS BOND : bond 0.00461 ( 45) SS BOND : angle 1.81933 ( 90) covalent geometry : bond 0.00231 (31287) covalent geometry : angle 0.55972 (42603) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 216 time to evaluate : 3.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 ASP cc_start: 0.8065 (t0) cc_final: 0.7780 (t0) REVERT: B 226 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7890 (mp) REVERT: S 226 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7983 (mt) REVERT: S 245 HIS cc_start: 0.6113 (OUTLIER) cc_final: 0.5345 (t70) REVERT: S 914 ASN cc_start: 0.9178 (OUTLIER) cc_final: 0.8964 (p0) REVERT: S 960 ASN cc_start: 0.8472 (m-40) cc_final: 0.8230 (m-40) REVERT: S 1072 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8261 (mp0) outliers start: 100 outliers final: 72 residues processed: 302 average time/residue: 0.3644 time to fit residues: 188.0177 Evaluate side-chains 284 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 207 time to evaluate : 3.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 690 GLN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 70 ASP Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 70 ASP Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain S residue 23 GLN Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 162 SER Chi-restraints excluded: chain S residue 226 LEU Chi-restraints excluded: chain S residue 241 LEU Chi-restraints excluded: chain S residue 244 LEU Chi-restraints excluded: chain S residue 245 HIS Chi-restraints excluded: chain S residue 284 THR Chi-restraints excluded: chain S residue 291 CYS Chi-restraints excluded: chain S residue 380 TYR Chi-restraints excluded: chain S residue 576 VAL Chi-restraints excluded: chain S residue 645 THR Chi-restraints excluded: chain S residue 723 THR Chi-restraints excluded: chain S residue 747 THR Chi-restraints excluded: chain S residue 791 THR Chi-restraints excluded: chain S residue 907 ASN Chi-restraints excluded: chain S residue 914 ASN Chi-restraints excluded: chain S residue 1072 GLU Chi-restraints excluded: chain S residue 1136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 206 optimal weight: 6.9990 chunk 118 optimal weight: 0.5980 chunk 345 optimal weight: 0.7980 chunk 307 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 chunk 203 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 187 optimal weight: 5.9990 chunk 338 optimal weight: 4.9990 chunk 141 optimal weight: 5.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 703 ASN A1010 GLN B 207 HIS S 207 HIS S 907 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.156978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.120690 restraints weight = 37209.424| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 4.32 r_work: 0.3057 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 31422 Z= 0.175 Angle : 0.662 11.783 42963 Z= 0.331 Chirality : 0.048 0.424 5121 Planarity : 0.005 0.045 5379 Dihedral : 8.243 109.398 5958 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 4.10 % Allowed : 24.21 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.14), residues: 3753 helix: 0.85 (0.22), residues: 621 sheet: 0.00 (0.17), residues: 1044 loop : -1.84 (0.12), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP S 436 HIS 0.005 0.001 HIS A1064 PHE 0.020 0.002 PHE B1121 TYR 0.021 0.002 TYR B1067 ARG 0.003 0.000 ARG S 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00504 ( 48) link_NAG-ASN : angle 2.76247 ( 144) link_BETA1-4 : bond 0.00530 ( 39) link_BETA1-4 : angle 1.51792 ( 117) link_ALPHA1-3 : bond 0.00765 ( 3) link_ALPHA1-3 : angle 1.51946 ( 9) hydrogen bonds : bond 0.05855 ( 991) hydrogen bonds : angle 4.97828 ( 2766) SS BOND : bond 0.00623 ( 45) SS BOND : angle 2.14285 ( 90) covalent geometry : bond 0.00430 (31287) covalent geometry : angle 0.63170 (42603) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 227 time to evaluate : 3.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8437 (mt) REVERT: A 389 ASP cc_start: 0.8117 (t0) cc_final: 0.7829 (t0) REVERT: A 726 ILE cc_start: 0.9207 (OUTLIER) cc_final: 0.8823 (mt) REVERT: B 226 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8056 (mp) REVERT: B 529 LYS cc_start: 0.8204 (mtpt) cc_final: 0.7363 (mmmt) REVERT: B 726 ILE cc_start: 0.9127 (OUTLIER) cc_final: 0.8864 (mt) REVERT: E 85 GLU cc_start: 0.7578 (mp0) cc_final: 0.7241 (mp0) REVERT: F 45 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7378 (ttp-170) REVERT: H 85 GLU cc_start: 0.7594 (mp0) cc_final: 0.7220 (mp0) REVERT: S 53 ASP cc_start: 0.8494 (OUTLIER) cc_final: 0.8037 (t70) REVERT: S 226 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8168 (mt) REVERT: S 245 HIS cc_start: 0.6241 (OUTLIER) cc_final: 0.5528 (t70) REVERT: S 537 LYS cc_start: 0.7651 (OUTLIER) cc_final: 0.7239 (mmtp) REVERT: S 726 ILE cc_start: 0.9141 (OUTLIER) cc_final: 0.8873 (mt) REVERT: S 820 ASP cc_start: 0.8561 (OUTLIER) cc_final: 0.8355 (m-30) REVERT: S 914 ASN cc_start: 0.9278 (OUTLIER) cc_final: 0.8998 (p0) REVERT: S 960 ASN cc_start: 0.8532 (m-40) cc_final: 0.8274 (m-40) REVERT: S 987 PRO cc_start: 0.7753 (Cg_exo) cc_final: 0.7470 (Cg_endo) REVERT: S 1072 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8341 (mp0) outliers start: 133 outliers final: 84 residues processed: 345 average time/residue: 0.3698 time to fit residues: 217.5591 Evaluate side-chains 313 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 216 time to evaluate : 3.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 690 GLN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain S residue 23 GLN Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 53 ASP Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 162 SER Chi-restraints excluded: chain S residue 226 LEU Chi-restraints excluded: chain S residue 241 LEU Chi-restraints excluded: chain S residue 244 LEU Chi-restraints excluded: chain S residue 245 HIS Chi-restraints excluded: chain S residue 291 CYS Chi-restraints excluded: chain S residue 380 TYR Chi-restraints excluded: chain S residue 386 LYS Chi-restraints excluded: chain S residue 534 VAL Chi-restraints excluded: chain S residue 537 LYS Chi-restraints excluded: chain S residue 576 VAL Chi-restraints excluded: chain S residue 723 THR Chi-restraints excluded: chain S residue 726 ILE Chi-restraints excluded: chain S residue 747 THR Chi-restraints excluded: chain S residue 791 THR Chi-restraints excluded: chain S residue 813 SER Chi-restraints excluded: chain S residue 820 ASP Chi-restraints excluded: chain S residue 878 LEU Chi-restraints excluded: chain S residue 907 ASN Chi-restraints excluded: chain S residue 914 ASN Chi-restraints excluded: chain S residue 1055 SER Chi-restraints excluded: chain S residue 1072 GLU Chi-restraints excluded: chain S residue 1133 VAL Chi-restraints excluded: chain S residue 1136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 276 optimal weight: 0.8980 chunk 156 optimal weight: 7.9990 chunk 13 optimal weight: 0.0570 chunk 354 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 204 optimal weight: 0.9990 chunk 91 optimal weight: 0.5980 chunk 338 optimal weight: 5.9990 chunk 312 optimal weight: 10.0000 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 450 ASN B 207 HIS B 907 ASN B 949 GLN B1010 GLN F 42 GLN S 125 ASN S 207 HIS S 907 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.160584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.126215 restraints weight = 37104.161| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 4.79 r_work: 0.3103 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 31422 Z= 0.105 Angle : 0.578 10.385 42963 Z= 0.288 Chirality : 0.045 0.375 5121 Planarity : 0.004 0.044 5379 Dihedral : 7.847 108.264 5958 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.02 % Allowed : 25.50 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.14), residues: 3753 helix: 1.15 (0.22), residues: 618 sheet: 0.15 (0.17), residues: 1029 loop : -1.71 (0.12), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 886 HIS 0.002 0.000 HIS S1064 PHE 0.010 0.001 PHE B1121 TYR 0.020 0.001 TYR S 369 ARG 0.003 0.000 ARG S 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00467 ( 48) link_NAG-ASN : angle 2.47782 ( 144) link_BETA1-4 : bond 0.00536 ( 39) link_BETA1-4 : angle 1.43160 ( 117) link_ALPHA1-3 : bond 0.00852 ( 3) link_ALPHA1-3 : angle 1.33354 ( 9) hydrogen bonds : bond 0.04153 ( 991) hydrogen bonds : angle 4.83688 ( 2766) SS BOND : bond 0.00473 ( 45) SS BOND : angle 1.60023 ( 90) covalent geometry : bond 0.00221 (31287) covalent geometry : angle 0.55173 (42603) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 213 time to evaluate : 3.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8479 (mt) REVERT: A 389 ASP cc_start: 0.8070 (t0) cc_final: 0.7806 (t0) REVERT: B 529 LYS cc_start: 0.8154 (mtpt) cc_final: 0.7343 (mmmt) REVERT: B 820 ASP cc_start: 0.8522 (OUTLIER) cc_final: 0.8313 (m-30) REVERT: B 987 PRO cc_start: 0.7720 (Cg_exo) cc_final: 0.7459 (Cg_endo) REVERT: E 85 GLU cc_start: 0.7533 (mp0) cc_final: 0.7192 (mp0) REVERT: F 45 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.7362 (ttp-170) REVERT: H 85 GLU cc_start: 0.7573 (mp0) cc_final: 0.7200 (mp0) REVERT: S 53 ASP cc_start: 0.8379 (OUTLIER) cc_final: 0.7984 (t70) REVERT: S 226 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7991 (mt) REVERT: S 229 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8511 (mt) REVERT: S 245 HIS cc_start: 0.6210 (OUTLIER) cc_final: 0.5530 (t70) REVERT: S 914 ASN cc_start: 0.9213 (OUTLIER) cc_final: 0.8971 (p0) REVERT: S 960 ASN cc_start: 0.8503 (m-40) cc_final: 0.8261 (m-40) REVERT: S 987 PRO cc_start: 0.7655 (Cg_exo) cc_final: 0.7368 (Cg_endo) outliers start: 98 outliers final: 71 residues processed: 299 average time/residue: 0.3749 time to fit residues: 189.0930 Evaluate side-chains 288 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 209 time to evaluate : 3.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 70 ASP Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain F residue 70 ASP Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain S residue 23 GLN Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 53 ASP Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain S residue 162 SER Chi-restraints excluded: chain S residue 226 LEU Chi-restraints excluded: chain S residue 229 LEU Chi-restraints excluded: chain S residue 241 LEU Chi-restraints excluded: chain S residue 244 LEU Chi-restraints excluded: chain S residue 245 HIS Chi-restraints excluded: chain S residue 284 THR Chi-restraints excluded: chain S residue 291 CYS Chi-restraints excluded: chain S residue 380 TYR Chi-restraints excluded: chain S residue 534 VAL Chi-restraints excluded: chain S residue 576 VAL Chi-restraints excluded: chain S residue 645 THR Chi-restraints excluded: chain S residue 723 THR Chi-restraints excluded: chain S residue 791 THR Chi-restraints excluded: chain S residue 878 LEU Chi-restraints excluded: chain S residue 907 ASN Chi-restraints excluded: chain S residue 914 ASN Chi-restraints excluded: chain S residue 1136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 43 optimal weight: 30.0000 chunk 19 optimal weight: 2.9990 chunk 176 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 344 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 356 optimal weight: 3.9990 chunk 194 optimal weight: 0.9980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS B 207 HIS B 690 GLN S 207 HIS S 907 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.159118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.125150 restraints weight = 37621.243| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 3.54 r_work: 0.3065 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 31422 Z= 0.133 Angle : 0.604 10.531 42963 Z= 0.302 Chirality : 0.046 0.396 5121 Planarity : 0.004 0.043 5379 Dihedral : 7.861 108.969 5958 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 3.24 % Allowed : 25.16 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.14), residues: 3753 helix: 1.11 (0.22), residues: 621 sheet: 0.13 (0.17), residues: 1032 loop : -1.75 (0.12), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP S 886 HIS 0.004 0.001 HIS A1064 PHE 0.016 0.001 PHE B1121 TYR 0.019 0.001 TYR S 369 ARG 0.003 0.000 ARG S 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00426 ( 48) link_NAG-ASN : angle 2.55575 ( 144) link_BETA1-4 : bond 0.00530 ( 39) link_BETA1-4 : angle 1.37253 ( 117) link_ALPHA1-3 : bond 0.00773 ( 3) link_ALPHA1-3 : angle 1.42853 ( 9) hydrogen bonds : bond 0.04842 ( 991) hydrogen bonds : angle 4.81528 ( 2766) SS BOND : bond 0.00536 ( 45) SS BOND : angle 1.77378 ( 90) covalent geometry : bond 0.00313 (31287) covalent geometry : angle 0.57754 (42603) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 224 time to evaluate : 3.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8502 (mt) REVERT: A 389 ASP cc_start: 0.8104 (t0) cc_final: 0.7848 (t0) REVERT: B 389 ASP cc_start: 0.7892 (t0) cc_final: 0.7659 (t0) REVERT: B 529 LYS cc_start: 0.8188 (mtpt) cc_final: 0.7402 (mmmt) REVERT: B 987 PRO cc_start: 0.7756 (Cg_exo) cc_final: 0.7502 (Cg_endo) REVERT: C 85 GLU cc_start: 0.7717 (mp0) cc_final: 0.7421 (mp0) REVERT: E 85 GLU cc_start: 0.7600 (mp0) cc_final: 0.7297 (mp0) REVERT: F 45 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7450 (ttp-170) REVERT: H 85 GLU cc_start: 0.7615 (mp0) cc_final: 0.7291 (mp0) REVERT: S 53 ASP cc_start: 0.8478 (OUTLIER) cc_final: 0.8057 (t70) REVERT: S 226 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8078 (mt) REVERT: S 229 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8514 (mt) REVERT: S 245 HIS cc_start: 0.6285 (OUTLIER) cc_final: 0.5656 (t70) REVERT: S 914 ASN cc_start: 0.9206 (OUTLIER) cc_final: 0.8969 (p0) REVERT: S 960 ASN cc_start: 0.8603 (m-40) cc_final: 0.8368 (m-40) REVERT: S 987 PRO cc_start: 0.7681 (Cg_exo) cc_final: 0.7391 (Cg_endo) outliers start: 105 outliers final: 83 residues processed: 318 average time/residue: 0.3683 time to fit residues: 196.6417 Evaluate side-chains 305 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 215 time to evaluate : 3.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 70 ASP Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain S residue 23 GLN Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 53 ASP Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 162 SER Chi-restraints excluded: chain S residue 226 LEU Chi-restraints excluded: chain S residue 229 LEU Chi-restraints excluded: chain S residue 241 LEU Chi-restraints excluded: chain S residue 244 LEU Chi-restraints excluded: chain S residue 245 HIS Chi-restraints excluded: chain S residue 284 THR Chi-restraints excluded: chain S residue 291 CYS Chi-restraints excluded: chain S residue 380 TYR Chi-restraints excluded: chain S residue 386 LYS Chi-restraints excluded: chain S residue 534 VAL Chi-restraints excluded: chain S residue 576 VAL Chi-restraints excluded: chain S residue 645 THR Chi-restraints excluded: chain S residue 723 THR Chi-restraints excluded: chain S residue 747 THR Chi-restraints excluded: chain S residue 791 THR Chi-restraints excluded: chain S residue 878 LEU Chi-restraints excluded: chain S residue 907 ASN Chi-restraints excluded: chain S residue 914 ASN Chi-restraints excluded: chain S residue 1055 SER Chi-restraints excluded: chain S residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 324 optimal weight: 5.9990 chunk 323 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 50 optimal weight: 0.0980 chunk 309 optimal weight: 0.9990 chunk 354 optimal weight: 0.8980 chunk 160 optimal weight: 0.9980 chunk 298 optimal weight: 0.0570 chunk 125 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 201 optimal weight: 4.9990 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS B 207 HIS B 907 ASN B 949 GLN B1010 GLN S 207 HIS ** S 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.161203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.127709 restraints weight = 37132.621| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 3.20 r_work: 0.3092 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 31422 Z= 0.104 Angle : 0.569 9.830 42963 Z= 0.283 Chirality : 0.045 0.367 5121 Planarity : 0.004 0.042 5379 Dihedral : 7.649 107.577 5958 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.02 % Allowed : 25.19 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.14), residues: 3753 helix: 1.21 (0.22), residues: 636 sheet: 0.18 (0.17), residues: 1029 loop : -1.67 (0.12), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP S 886 HIS 0.002 0.000 HIS S1064 PHE 0.010 0.001 PHE B 65 TYR 0.019 0.001 TYR S 369 ARG 0.005 0.000 ARG S 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00443 ( 48) link_NAG-ASN : angle 2.53785 ( 144) link_BETA1-4 : bond 0.00515 ( 39) link_BETA1-4 : angle 1.32494 ( 117) link_ALPHA1-3 : bond 0.00741 ( 3) link_ALPHA1-3 : angle 1.33366 ( 9) hydrogen bonds : bond 0.03983 ( 991) hydrogen bonds : angle 4.72878 ( 2766) SS BOND : bond 0.00445 ( 45) SS BOND : angle 1.46786 ( 90) covalent geometry : bond 0.00222 (31287) covalent geometry : angle 0.54329 (42603) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 224 time to evaluate : 3.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8502 (mt) REVERT: A 389 ASP cc_start: 0.8003 (t0) cc_final: 0.7767 (t0) REVERT: A 987 PRO cc_start: 0.7745 (Cg_exo) cc_final: 0.7472 (Cg_endo) REVERT: B 529 LYS cc_start: 0.8118 (mtpt) cc_final: 0.7394 (mmmt) REVERT: B 987 PRO cc_start: 0.7750 (Cg_exo) cc_final: 0.7503 (Cg_endo) REVERT: C 85 GLU cc_start: 0.7664 (mp0) cc_final: 0.7373 (mp0) REVERT: E 85 GLU cc_start: 0.7539 (mp0) cc_final: 0.7236 (mp0) REVERT: F 45 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7443 (ttp-170) REVERT: H 85 GLU cc_start: 0.7553 (mp0) cc_final: 0.7230 (mp0) REVERT: S 53 ASP cc_start: 0.8385 (OUTLIER) cc_final: 0.7973 (t70) REVERT: S 226 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7975 (mt) REVERT: S 229 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8512 (mt) REVERT: S 245 HIS cc_start: 0.6296 (OUTLIER) cc_final: 0.5681 (t70) REVERT: S 914 ASN cc_start: 0.9153 (OUTLIER) cc_final: 0.8926 (p0) REVERT: S 960 ASN cc_start: 0.8574 (m-40) cc_final: 0.8346 (m-40) REVERT: S 987 PRO cc_start: 0.7631 (Cg_exo) cc_final: 0.7355 (Cg_endo) outliers start: 98 outliers final: 80 residues processed: 310 average time/residue: 0.3622 time to fit residues: 189.9954 Evaluate side-chains 302 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 215 time to evaluate : 3.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 70 ASP Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 53 ASP Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 162 SER Chi-restraints excluded: chain S residue 226 LEU Chi-restraints excluded: chain S residue 229 LEU Chi-restraints excluded: chain S residue 244 LEU Chi-restraints excluded: chain S residue 245 HIS Chi-restraints excluded: chain S residue 284 THR Chi-restraints excluded: chain S residue 291 CYS Chi-restraints excluded: chain S residue 380 TYR Chi-restraints excluded: chain S residue 386 LYS Chi-restraints excluded: chain S residue 518 LEU Chi-restraints excluded: chain S residue 534 VAL Chi-restraints excluded: chain S residue 576 VAL Chi-restraints excluded: chain S residue 645 THR Chi-restraints excluded: chain S residue 723 THR Chi-restraints excluded: chain S residue 791 THR Chi-restraints excluded: chain S residue 878 LEU Chi-restraints excluded: chain S residue 914 ASN Chi-restraints excluded: chain S residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 239 optimal weight: 0.6980 chunk 162 optimal weight: 0.0980 chunk 281 optimal weight: 2.9990 chunk 303 optimal weight: 7.9990 chunk 184 optimal weight: 0.0570 chunk 146 optimal weight: 3.9990 chunk 240 optimal weight: 6.9990 chunk 143 optimal weight: 10.0000 chunk 98 optimal weight: 0.0970 chunk 324 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 overall best weight: 0.7898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS B 207 HIS B1010 GLN S 207 HIS S1002 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.160937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.126097 restraints weight = 37217.595| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 4.53 r_work: 0.3109 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 31422 Z= 0.109 Angle : 0.574 9.715 42963 Z= 0.286 Chirality : 0.045 0.370 5121 Planarity : 0.004 0.042 5379 Dihedral : 7.591 107.148 5958 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 2.87 % Allowed : 25.32 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.14), residues: 3753 helix: 1.24 (0.22), residues: 636 sheet: 0.18 (0.17), residues: 1035 loop : -1.65 (0.12), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP S 886 HIS 0.003 0.000 HIS S1064 PHE 0.012 0.001 PHE B1121 TYR 0.019 0.001 TYR S 369 ARG 0.002 0.000 ARG S 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00404 ( 48) link_NAG-ASN : angle 2.46874 ( 144) link_BETA1-4 : bond 0.00517 ( 39) link_BETA1-4 : angle 1.29254 ( 117) link_ALPHA1-3 : bond 0.00719 ( 3) link_ALPHA1-3 : angle 1.37469 ( 9) hydrogen bonds : bond 0.04073 ( 991) hydrogen bonds : angle 4.68813 ( 2766) SS BOND : bond 0.00453 ( 45) SS BOND : angle 1.48468 ( 90) covalent geometry : bond 0.00241 (31287) covalent geometry : angle 0.54934 (42603) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 214 time to evaluate : 3.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 ASP cc_start: 0.8046 (t0) cc_final: 0.7789 (t0) REVERT: A 987 PRO cc_start: 0.7657 (Cg_exo) cc_final: 0.7377 (Cg_endo) REVERT: B 80 ASP cc_start: 0.7392 (p0) cc_final: 0.7127 (p0) REVERT: B 529 LYS cc_start: 0.8106 (mtpt) cc_final: 0.7287 (mmmt) REVERT: B 987 PRO cc_start: 0.7664 (Cg_exo) cc_final: 0.7400 (Cg_endo) REVERT: C 85 GLU cc_start: 0.7626 (mp0) cc_final: 0.7306 (mp0) REVERT: E 85 GLU cc_start: 0.7469 (mp0) cc_final: 0.7139 (mp0) REVERT: F 45 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7362 (ttp-170) REVERT: H 85 GLU cc_start: 0.7503 (mp0) cc_final: 0.7163 (mp0) REVERT: S 53 ASP cc_start: 0.8405 (OUTLIER) cc_final: 0.7972 (t70) REVERT: S 226 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.8037 (mt) REVERT: S 229 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8489 (mt) REVERT: S 245 HIS cc_start: 0.6160 (OUTLIER) cc_final: 0.5608 (t70) REVERT: S 914 ASN cc_start: 0.9197 (OUTLIER) cc_final: 0.8965 (p0) REVERT: S 960 ASN cc_start: 0.8476 (m-40) cc_final: 0.8229 (m-40) REVERT: S 987 PRO cc_start: 0.7560 (Cg_exo) cc_final: 0.7275 (Cg_endo) outliers start: 93 outliers final: 80 residues processed: 295 average time/residue: 0.3768 time to fit residues: 187.8194 Evaluate side-chains 298 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 212 time to evaluate : 3.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 70 ASP Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 53 ASP Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 162 SER Chi-restraints excluded: chain S residue 226 LEU Chi-restraints excluded: chain S residue 229 LEU Chi-restraints excluded: chain S residue 244 LEU Chi-restraints excluded: chain S residue 245 HIS Chi-restraints excluded: chain S residue 284 THR Chi-restraints excluded: chain S residue 291 CYS Chi-restraints excluded: chain S residue 380 TYR Chi-restraints excluded: chain S residue 386 LYS Chi-restraints excluded: chain S residue 518 LEU Chi-restraints excluded: chain S residue 534 VAL Chi-restraints excluded: chain S residue 576 VAL Chi-restraints excluded: chain S residue 645 THR Chi-restraints excluded: chain S residue 723 THR Chi-restraints excluded: chain S residue 791 THR Chi-restraints excluded: chain S residue 813 SER Chi-restraints excluded: chain S residue 878 LEU Chi-restraints excluded: chain S residue 914 ASN Chi-restraints excluded: chain S residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 18 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 263 optimal weight: 8.9990 chunk 6 optimal weight: 4.9990 chunk 269 optimal weight: 9.9990 chunk 143 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 147 optimal weight: 8.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A1010 GLN B 207 HIS S 207 HIS S1002 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.155194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.118739 restraints weight = 37262.549| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 4.89 r_work: 0.3019 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 31422 Z= 0.232 Angle : 0.719 11.159 42963 Z= 0.363 Chirality : 0.050 0.466 5121 Planarity : 0.005 0.046 5379 Dihedral : 8.248 109.873 5958 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 3.11 % Allowed : 25.16 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.14), residues: 3753 helix: 0.76 (0.22), residues: 624 sheet: -0.04 (0.17), residues: 1059 loop : -1.90 (0.12), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP S 436 HIS 0.007 0.001 HIS A1064 PHE 0.023 0.002 PHE A1121 TYR 0.025 0.002 TYR B1067 ARG 0.004 0.000 ARG B1000 Details of bonding type rmsd link_NAG-ASN : bond 0.00508 ( 48) link_NAG-ASN : angle 2.82651 ( 144) link_BETA1-4 : bond 0.00562 ( 39) link_BETA1-4 : angle 1.39631 ( 117) link_ALPHA1-3 : bond 0.00609 ( 3) link_ALPHA1-3 : angle 1.60274 ( 9) hydrogen bonds : bond 0.06878 ( 991) hydrogen bonds : angle 5.02954 ( 2766) SS BOND : bond 0.00774 ( 45) SS BOND : angle 2.34709 ( 90) covalent geometry : bond 0.00581 (31287) covalent geometry : angle 0.69076 (42603) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15034.53 seconds wall clock time: 261 minutes 24.82 seconds (15684.82 seconds total)