Starting phenix.real_space_refine on Mon Aug 25 20:34:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bj3_44628/08_2025/9bj3_44628_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bj3_44628/08_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_44628/08_2025/9bj3_44628.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bj3_44628/08_2025/9bj3_44628.map" model { file = "/net/cci-nas-00/data/ceres_data/9bj3_44628/08_2025/9bj3_44628_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bj3_44628/08_2025/9bj3_44628_neut.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.031 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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, 'GLU:plan': 2, 'ARG:plan': 2, 'PHE:plan': 2, 'HIS:plan': 1} 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, 'GLU:plan': 2, 'ARG:plan': 2, 'PHE:plan': 2, 'HIS:plan': 1} 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, 'GLU:plan': 2, 'ARG:plan': 2, 'PHE:plan': 2, 'HIS:plan': 1} 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: 6.47, per 1000 atoms: 0.21 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: 2.74 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.49 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: 6.98 Time building geometry restraints manager: 3.63 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: 0.02 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: 0.000 Normalize map: mean=0, sd=1: 6.020 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: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 27.120 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.360 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG A 237 TYR 0.013 0.001 TYR B 707 PHE 0.032 0.001 PHE A 802 TRP 0.008 0.001 TRP S 436 HIS 0.007 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00368 (31287) covalent geometry : angle 0.65865 (42603) SS BOND : bond 0.00465 ( 45) SS BOND : angle 1.66066 ( 90) hydrogen bonds : bond 0.18827 ( 991) hydrogen bonds : angle 7.15181 ( 2766) link_ALPHA1-3 : bond 0.00327 ( 3) link_ALPHA1-3 : angle 1.92264 ( 9) link_BETA1-4 : bond 0.00836 ( 39) link_BETA1-4 : angle 2.19816 ( 117) link_NAG-ASN : bond 0.00848 ( 48) link_NAG-ASN : angle 4.88313 ( 144) *********************** 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 : 0.975 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: 0.1674 time to fit residues: 61.8066 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 : 0.919 ------------------------------------------------------------------------------- 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 197 optimal weight: 2.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 784 GLN A 787 GLN A 907 ASN A 914 ASN A1010 GLN A1101 HIS 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 784 GLN 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 = 0.3805 r_free = 0.3805 target = 0.155030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.119956 restraints weight = 37367.791| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 4.76 r_work: 0.3040 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.0920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 31422 Z= 0.223 Angle : 0.751 14.561 42963 Z= 0.374 Chirality : 0.051 0.285 5121 Planarity : 0.005 0.054 5379 Dihedral : 11.368 112.125 5966 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 3.70 % Allowed : 24.30 % Favored : 72.00 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.69 (0.13), residues: 3753 helix: 0.06 (0.21), residues: 621 sheet: -0.20 (0.17), residues: 1032 loop : -2.06 (0.12), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 905 TYR 0.021 0.002 TYR B1067 PHE 0.023 0.002 PHE A1121 TRP 0.012 0.001 TRP A 436 HIS 0.007 0.001 HIS S1064 Details of bonding type rmsd covalent geometry : bond 0.00557 (31287) covalent geometry : angle 0.71471 (42603) SS BOND : bond 0.00685 ( 45) SS BOND : angle 1.99023 ( 90) hydrogen bonds : bond 0.07149 ( 991) hydrogen bonds : angle 5.50396 ( 2766) link_ALPHA1-3 : bond 0.00548 ( 3) link_ALPHA1-3 : angle 1.71170 ( 9) link_BETA1-4 : bond 0.00634 ( 39) link_BETA1-4 : angle 2.04778 ( 117) link_NAG-ASN : bond 0.00668 ( 48) link_NAG-ASN : angle 3.31983 ( 144) *********************** 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 352 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 232 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 389 ASP cc_start: 0.8125 (t0) cc_final: 0.7834 (t0) REVERT: A 396 TYR cc_start: 0.8220 (m-80) cc_final: 0.7789 (m-80) REVERT: B 226 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8156 (mp) REVERT: B 245 HIS cc_start: 0.6159 (OUTLIER) cc_final: 0.5657 (t70) REVERT: B 703 ASN cc_start: 0.8119 (OUTLIER) cc_final: 0.7856 (t0) REVERT: E 69 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.8176 (mt) REVERT: F 45 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.7314 (ttp-170) REVERT: S 226 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8263 (mt) REVERT: S 245 HIS cc_start: 0.6246 (OUTLIER) cc_final: 0.5366 (t70) REVERT: S 537 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7466 (mmtp) REVERT: S 914 ASN cc_start: 0.9315 (OUTLIER) cc_final: 0.9036 (p0) REVERT: S 960 ASN cc_start: 0.8518 (m-40) cc_final: 0.8300 (m-40) outliers start: 120 outliers final: 53 residues processed: 335 average time/residue: 0.1560 time to fit residues: 87.4540 Evaluate side-chains 283 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 221 time to evaluate : 0.817 ------------------------------------------------------------------------------- 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 291 CYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 590 CYS 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 916 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 90 VAL 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 226 LEU Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 703 ASN 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 1010 GLN Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain D residue 45 ARG 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 77 THR Chi-restraints excluded: chain E residue 81 GLU 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 77 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 85 VAL 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 245 HIS Chi-restraints excluded: chain S residue 537 LYS 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 1010 GLN Chi-restraints excluded: chain S residue 1133 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 94 optimal weight: 1.9990 chunk 205 optimal weight: 0.9990 chunk 290 optimal weight: 0.0010 chunk 257 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 319 optimal weight: 8.9990 chunk 111 optimal weight: 3.9990 chunk 339 optimal weight: 2.9990 chunk 297 optimal weight: 0.0980 chunk 153 optimal weight: 0.7980 chunk 268 optimal weight: 10.0000 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 207 HIS A1010 GLN B 125 ASN B 207 HIS B 703 ASN B 949 GLN B1010 GLN F 42 GLN S 17 ASN S 207 HIS S1010 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.159648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.124459 restraints weight = 37296.921| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 4.65 r_work: 0.3105 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.0875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 31422 Z= 0.113 Angle : 0.615 13.564 42963 Z= 0.303 Chirality : 0.047 0.269 5121 Planarity : 0.004 0.046 5379 Dihedral : 9.632 110.127 5958 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.71 % Allowed : 24.95 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.33 (0.13), residues: 3753 helix: 0.50 (0.22), residues: 633 sheet: 0.06 (0.17), residues: 1011 loop : -1.88 (0.12), residues: 2109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 403 TYR 0.018 0.001 TYR S 369 PHE 0.010 0.001 PHE A 238 TRP 0.009 0.001 TRP A 886 HIS 0.002 0.001 HIS S1064 Details of bonding type rmsd covalent geometry : bond 0.00235 (31287) covalent geometry : angle 0.58207 (42603) SS BOND : bond 0.00580 ( 45) SS BOND : angle 1.51054 ( 90) hydrogen bonds : bond 0.04573 ( 991) hydrogen bonds : angle 5.17311 ( 2766) link_ALPHA1-3 : bond 0.00815 ( 3) link_ALPHA1-3 : angle 1.40363 ( 9) link_BETA1-4 : bond 0.00579 ( 39) link_BETA1-4 : angle 1.95461 ( 117) link_NAG-ASN : bond 0.00518 ( 48) link_NAG-ASN : angle 2.85082 ( 144) *********************** 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 315 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 227 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 ASP cc_start: 0.8034 (t0) cc_final: 0.7751 (t0) REVERT: A 823 PHE cc_start: 0.8072 (OUTLIER) cc_final: 0.7377 (t80) REVERT: A 1072 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8133 (mp0) REVERT: B 226 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7854 (mp) REVERT: B 703 ASN cc_start: 0.7966 (OUTLIER) cc_final: 0.7697 (t0) REVERT: S 226 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7929 (mt) REVERT: S 245 HIS cc_start: 0.6264 (OUTLIER) cc_final: 0.5415 (t70) outliers start: 88 outliers final: 40 residues processed: 295 average time/residue: 0.1538 time to fit residues: 76.8356 Evaluate side-chains 252 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 206 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 221 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 823 PHE Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain B residue 117 LEU 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 549 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 690 GLN Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 813 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 45 ARG Chi-restraints excluded: chain D residue 70 ASP Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 87 THR 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 33 LEU Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain S residue 23 GLN Chi-restraints excluded: chain S residue 226 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 645 THR Chi-restraints excluded: chain S residue 690 GLN 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 344 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 162 optimal weight: 0.7980 chunk 167 optimal weight: 3.9990 chunk 273 optimal weight: 0.0370 chunk 327 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 overall best weight: 0.6858 ------------------------------------------------------------------------------- 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 907 ASN B1010 GLN S 207 HIS S 907 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.160525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.125545 restraints weight = 37012.365| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 3.62 r_work: 0.3085 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 31422 Z= 0.109 Angle : 0.599 12.578 42963 Z= 0.295 Chirality : 0.046 0.328 5121 Planarity : 0.004 0.042 5379 Dihedral : 8.486 108.757 5958 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.93 % Allowed : 25.07 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.14), residues: 3753 helix: 0.98 (0.22), residues: 618 sheet: 0.14 (0.17), residues: 1011 loop : -1.78 (0.12), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 403 TYR 0.018 0.001 TYR S 369 PHE 0.013 0.001 PHE A 135 TRP 0.009 0.001 TRP S 436 HIS 0.002 0.000 HIS S1064 Details of bonding type rmsd covalent geometry : bond 0.00235 (31287) covalent geometry : angle 0.56687 (42603) SS BOND : bond 0.00488 ( 45) SS BOND : angle 1.96167 ( 90) hydrogen bonds : bond 0.04236 ( 991) hydrogen bonds : angle 4.92856 ( 2766) link_ALPHA1-3 : bond 0.00871 ( 3) link_ALPHA1-3 : angle 1.52701 ( 9) link_BETA1-4 : bond 0.00559 ( 39) link_BETA1-4 : angle 1.74116 ( 117) link_NAG-ASN : bond 0.00469 ( 48) link_NAG-ASN : angle 2.65454 ( 144) *********************** 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 318 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 223 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 ASP cc_start: 0.8032 (t0) cc_final: 0.7746 (t0) REVERT: A 1072 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.8129 (mp0) REVERT: B 226 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7869 (mp) REVERT: B 960 ASN cc_start: 0.8614 (m-40) cc_final: 0.8344 (m110) REVERT: F 45 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.7369 (ttp-170) REVERT: S 53 ASP cc_start: 0.8399 (OUTLIER) cc_final: 0.7966 (t70) REVERT: S 226 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7997 (mt) REVERT: S 245 HIS cc_start: 0.6177 (OUTLIER) cc_final: 0.5415 (t70) REVERT: S 1072 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8260 (mp0) outliers start: 95 outliers final: 53 residues processed: 307 average time/residue: 0.1497 time to fit residues: 77.4484 Evaluate side-chains 270 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 210 time to evaluate : 0.841 ------------------------------------------------------------------------------- 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 241 LEU 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 576 VAL 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 791 THR Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 117 LEU 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 645 THR Chi-restraints excluded: chain B residue 690 GLN 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 45 ARG 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 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 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 244 LEU Chi-restraints excluded: chain S residue 245 HIS Chi-restraints excluded: chain S residue 291 CYS Chi-restraints excluded: chain S residue 534 VAL Chi-restraints excluded: chain S residue 645 THR Chi-restraints excluded: chain S residue 791 THR Chi-restraints excluded: chain S residue 907 ASN Chi-restraints excluded: chain S residue 1072 GLU 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 367 optimal weight: 3.9990 chunk 121 optimal weight: 0.1980 chunk 32 optimal weight: 2.9990 chunk 196 optimal weight: 0.8980 chunk 56 optimal weight: 10.0000 chunk 54 optimal weight: 0.7980 chunk 292 optimal weight: 5.9990 chunk 298 optimal weight: 0.1980 chunk 159 optimal weight: 0.7980 chunk 187 optimal weight: 4.9990 chunk 185 optimal weight: 5.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 A 787 GLN A1010 GLN B 207 HIS B 703 ASN B 907 ASN B1010 GLN S 125 ASN S 207 HIS S 907 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.161552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.126994 restraints weight = 37279.815| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 4.81 r_work: 0.3118 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 31422 Z= 0.103 Angle : 0.581 12.065 42963 Z= 0.287 Chirality : 0.046 0.457 5121 Planarity : 0.004 0.041 5379 Dihedral : 8.015 107.754 5958 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 3.11 % Allowed : 25.29 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.14), residues: 3753 helix: 1.20 (0.22), residues: 618 sheet: 0.19 (0.17), residues: 1011 loop : -1.70 (0.12), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 905 TYR 0.018 0.001 TYR S 369 PHE 0.011 0.001 PHE A 800 TRP 0.008 0.001 TRP A 886 HIS 0.002 0.000 HIS S1064 Details of bonding type rmsd covalent geometry : bond 0.00218 (31287) covalent geometry : angle 0.55140 (42603) SS BOND : bond 0.00446 ( 45) SS BOND : angle 1.78249 ( 90) hydrogen bonds : bond 0.03955 ( 991) hydrogen bonds : angle 4.82586 ( 2766) link_ALPHA1-3 : bond 0.00859 ( 3) link_ALPHA1-3 : angle 1.41107 ( 9) link_BETA1-4 : bond 0.00546 ( 39) link_BETA1-4 : angle 1.58193 ( 117) link_NAG-ASN : bond 0.00465 ( 48) link_NAG-ASN : angle 2.55567 ( 144) *********************** 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: 101 poor density : 215 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8472 (mt) REVERT: A 389 ASP cc_start: 0.8035 (t0) cc_final: 0.7748 (t0) REVERT: A 1072 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8186 (mp0) REVERT: F 45 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.7363 (ttp-170) REVERT: S 53 ASP cc_start: 0.8370 (OUTLIER) cc_final: 0.7942 (t70) REVERT: S 226 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7987 (mt) REVERT: S 245 HIS cc_start: 0.6109 (OUTLIER) cc_final: 0.5402 (t70) REVERT: S 987 PRO cc_start: 0.7745 (Cg_exo) cc_final: 0.7473 (Cg_endo) REVERT: S 1072 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8264 (mp0) outliers start: 101 outliers final: 69 residues processed: 305 average time/residue: 0.1608 time to fit residues: 83.2860 Evaluate side-chains 284 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 208 time to evaluate : 0.810 ------------------------------------------------------------------------------- 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 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 576 VAL 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 907 ASN Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 100 ILE 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 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 791 THR Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU 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 45 ARG 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 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 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 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 534 VAL Chi-restraints excluded: chain S residue 645 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 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 4 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 50 optimal weight: 0.0030 chunk 126 optimal weight: 3.9990 chunk 156 optimal weight: 7.9990 chunk 62 optimal weight: 0.1980 chunk 353 optimal weight: 4.9990 chunk 328 optimal weight: 0.5980 chunk 206 optimal weight: 6.9990 chunk 314 optimal weight: 20.0000 overall best weight: 0.9594 ------------------------------------------------------------------------------- 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 B1010 GLN 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 = 0.3867 r_free = 0.3867 target = 0.160637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.125999 restraints weight = 37328.135| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 3.52 r_work: 0.3075 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 31422 Z= 0.115 Angle : 0.589 11.280 42963 Z= 0.292 Chirality : 0.046 0.390 5121 Planarity : 0.004 0.041 5379 Dihedral : 7.856 107.388 5958 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 3.21 % Allowed : 24.95 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.14), residues: 3753 helix: 1.28 (0.23), residues: 618 sheet: 0.23 (0.17), residues: 1017 loop : -1.68 (0.12), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 905 TYR 0.018 0.001 TYR B1067 PHE 0.014 0.001 PHE B1121 TRP 0.007 0.001 TRP A 886 HIS 0.003 0.001 HIS S1064 Details of bonding type rmsd covalent geometry : bond 0.00257 (31287) covalent geometry : angle 0.56117 (42603) SS BOND : bond 0.00485 ( 45) SS BOND : angle 1.89739 ( 90) hydrogen bonds : bond 0.04293 ( 991) hydrogen bonds : angle 4.78959 ( 2766) link_ALPHA1-3 : bond 0.00849 ( 3) link_ALPHA1-3 : angle 1.42500 ( 9) link_BETA1-4 : bond 0.00520 ( 39) link_BETA1-4 : angle 1.47155 ( 117) link_NAG-ASN : bond 0.00439 ( 48) link_NAG-ASN : angle 2.51009 ( 144) *********************** 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 322 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 218 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 ASP cc_start: 0.8061 (t0) cc_final: 0.7785 (t0) REVERT: A 900 MET cc_start: 0.8586 (mtt) cc_final: 0.8350 (mtt) REVERT: B 529 LYS cc_start: 0.8157 (mtpt) cc_final: 0.7372 (mmmt) REVERT: F 45 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7450 (ttp-170) REVERT: S 53 ASP cc_start: 0.8399 (OUTLIER) cc_final: 0.7978 (t70) REVERT: S 226 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.8019 (mt) REVERT: S 245 HIS cc_start: 0.6186 (OUTLIER) cc_final: 0.5499 (t70) REVERT: S 987 PRO cc_start: 0.7670 (Cg_exo) cc_final: 0.7389 (Cg_endo) REVERT: S 1072 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8286 (mp0) outliers start: 104 outliers final: 75 residues processed: 307 average time/residue: 0.1644 time to fit residues: 85.3379 Evaluate side-chains 289 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 209 time to evaluate : 1.295 ------------------------------------------------------------------------------- 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 176 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 433 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 576 VAL 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 907 ASN 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 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 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 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 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 45 ARG 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 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 284 THR Chi-restraints excluded: chain S residue 291 CYS Chi-restraints excluded: chain S residue 380 TYR Chi-restraints excluded: chain S residue 433 VAL Chi-restraints excluded: chain S residue 534 VAL Chi-restraints excluded: chain S residue 645 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 1072 GLU 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 313 optimal weight: 20.0000 chunk 331 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 98 optimal weight: 0.0050 chunk 176 optimal weight: 0.7980 chunk 183 optimal weight: 2.9990 chunk 283 optimal weight: 0.9980 chunk 346 optimal weight: 9.9990 chunk 30 optimal weight: 0.5980 chunk 78 optimal weight: 0.9980 chunk 333 optimal weight: 0.8980 overall best weight: 0.6594 ------------------------------------------------------------------------------- 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 B 907 ASN S 207 HIS S 907 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.161801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.127263 restraints weight = 37324.623| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 3.55 r_work: 0.3094 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1247 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= 0.103 Angle : 0.563 10.342 42963 Z= 0.279 Chirality : 0.045 0.347 5121 Planarity : 0.004 0.041 5379 Dihedral : 7.631 106.657 5958 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 3.05 % Allowed : 25.04 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.14), residues: 3753 helix: 1.40 (0.23), residues: 618 sheet: 0.26 (0.18), residues: 1017 loop : -1.63 (0.12), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 905 TYR 0.018 0.001 TYR S 369 PHE 0.011 0.001 PHE B1121 TRP 0.007 0.001 TRP A 886 HIS 0.002 0.000 HIS S1064 Details of bonding type rmsd covalent geometry : bond 0.00221 (31287) covalent geometry : angle 0.53784 (42603) SS BOND : bond 0.00433 ( 45) SS BOND : angle 1.52263 ( 90) hydrogen bonds : bond 0.03892 ( 991) hydrogen bonds : angle 4.72835 ( 2766) link_ALPHA1-3 : bond 0.00788 ( 3) link_ALPHA1-3 : angle 1.34211 ( 9) link_BETA1-4 : bond 0.00530 ( 39) link_BETA1-4 : angle 1.36907 ( 117) link_NAG-ASN : bond 0.00416 ( 48) link_NAG-ASN : angle 2.42823 ( 144) *********************** 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 309 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 210 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8494 (mt) REVERT: A 389 ASP cc_start: 0.8012 (t0) cc_final: 0.7755 (t0) REVERT: A 900 MET cc_start: 0.8568 (mtt) cc_final: 0.8300 (mtt) REVERT: B 529 LYS cc_start: 0.8138 (mtpt) cc_final: 0.7337 (mmmt) REVERT: B 987 PRO cc_start: 0.7720 (Cg_exo) cc_final: 0.7459 (Cg_endo) REVERT: F 45 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7443 (ttp-170) REVERT: S 53 ASP cc_start: 0.8365 (OUTLIER) cc_final: 0.7948 (t70) REVERT: S 226 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7978 (mt) REVERT: S 229 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8508 (mt) REVERT: S 245 HIS cc_start: 0.6142 (OUTLIER) cc_final: 0.5523 (t70) REVERT: S 987 PRO cc_start: 0.7617 (Cg_exo) cc_final: 0.7331 (Cg_endo) outliers start: 99 outliers final: 73 residues processed: 295 average time/residue: 0.1731 time to fit residues: 85.8712 Evaluate side-chains 281 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 202 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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 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 433 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 576 VAL 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 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 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 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 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 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 45 ARG 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 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 70 ASP 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 114 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 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 433 VAL Chi-restraints excluded: chain S residue 645 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 1055 SER 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 165 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 172 optimal weight: 4.9990 chunk 360 optimal weight: 0.9980 chunk 324 optimal weight: 0.5980 chunk 181 optimal weight: 0.8980 chunk 171 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 chunk 152 optimal weight: 4.9990 chunk 173 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 690 GLN S 207 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.161427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.129139 restraints weight = 37338.396| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 3.33 r_work: 0.3089 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 31422 Z= 0.108 Angle : 0.569 10.277 42963 Z= 0.283 Chirality : 0.045 0.339 5121 Planarity : 0.004 0.040 5379 Dihedral : 7.565 107.201 5958 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.02 % Allowed : 24.95 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.14), residues: 3753 helix: 1.42 (0.23), residues: 618 sheet: 0.22 (0.17), residues: 1035 loop : -1.61 (0.12), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 357 TYR 0.017 0.001 TYR S 369 PHE 0.013 0.001 PHE B1121 TRP 0.007 0.001 TRP A 886 HIS 0.003 0.000 HIS S1064 Details of bonding type rmsd covalent geometry : bond 0.00237 (31287) covalent geometry : angle 0.54494 (42603) SS BOND : bond 0.00438 ( 45) SS BOND : angle 1.61560 ( 90) hydrogen bonds : bond 0.04031 ( 991) hydrogen bonds : angle 4.68269 ( 2766) link_ALPHA1-3 : bond 0.00767 ( 3) link_ALPHA1-3 : angle 1.37321 ( 9) link_BETA1-4 : bond 0.00515 ( 39) link_BETA1-4 : angle 1.31262 ( 117) link_NAG-ASN : bond 0.00407 ( 48) link_NAG-ASN : angle 2.38542 ( 144) *********************** 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 309 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 211 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8506 (mt) REVERT: A 389 ASP cc_start: 0.8040 (t0) cc_final: 0.7779 (t0) REVERT: B 80 ASP cc_start: 0.7370 (p0) cc_final: 0.7142 (p0) REVERT: B 529 LYS cc_start: 0.8115 (mtpt) cc_final: 0.7322 (mmmt) REVERT: B 987 PRO cc_start: 0.7675 (Cg_exo) cc_final: 0.7414 (Cg_endo) REVERT: F 45 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7466 (ttp-170) REVERT: S 53 ASP cc_start: 0.8396 (OUTLIER) cc_final: 0.7978 (t70) REVERT: S 226 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.8034 (mt) REVERT: S 229 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8515 (mt) REVERT: S 245 HIS cc_start: 0.6177 (OUTLIER) cc_final: 0.5560 (t70) REVERT: S 987 PRO cc_start: 0.7578 (Cg_exo) cc_final: 0.7298 (Cg_endo) outliers start: 98 outliers final: 78 residues processed: 294 average time/residue: 0.1590 time to fit residues: 79.1877 Evaluate side-chains 287 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 203 time to evaluate : 1.152 ------------------------------------------------------------------------------- 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 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 433 VAL Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 576 VAL 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 791 THR 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 386 LYS Chi-restraints excluded: chain B residue 515 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 735 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 902 MET 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 87 THR Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 45 ARG 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 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 114 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 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 645 THR Chi-restraints excluded: chain S residue 791 THR Chi-restraints excluded: chain S residue 878 LEU 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 192 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 chunk 163 optimal weight: 5.9990 chunk 276 optimal weight: 0.9990 chunk 360 optimal weight: 4.9990 chunk 295 optimal weight: 1.9990 chunk 230 optimal weight: 6.9990 chunk 62 optimal weight: 0.6980 chunk 326 optimal weight: 0.7980 chunk 267 optimal weight: 6.9990 chunk 137 optimal weight: 9.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN A 207 HIS A1010 GLN B 207 HIS S 207 HIS S 914 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.158044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.122347 restraints weight = 37265.743| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 5.11 r_work: 0.3046 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 31422 Z= 0.151 Angle : 0.629 13.256 42963 Z= 0.315 Chirality : 0.047 0.511 5121 Planarity : 0.004 0.043 5379 Dihedral : 7.848 107.925 5958 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 3.30 % Allowed : 24.70 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.14), residues: 3753 helix: 1.15 (0.22), residues: 624 sheet: 0.12 (0.17), residues: 1041 loop : -1.75 (0.12), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1000 TYR 0.020 0.001 TYR B1067 PHE 0.019 0.002 PHE B1121 TRP 0.007 0.001 TRP B 886 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00360 (31287) covalent geometry : angle 0.60160 (42603) SS BOND : bond 0.00565 ( 45) SS BOND : angle 1.95613 ( 90) hydrogen bonds : bond 0.05398 ( 991) hydrogen bonds : angle 4.84447 ( 2766) link_ALPHA1-3 : bond 0.00644 ( 3) link_ALPHA1-3 : angle 1.43049 ( 9) link_BETA1-4 : bond 0.00528 ( 39) link_BETA1-4 : angle 1.30538 ( 117) link_NAG-ASN : bond 0.00477 ( 48) link_NAG-ASN : angle 2.65283 ( 144) *********************** 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 330 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 223 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8495 (mt) REVERT: A 389 ASP cc_start: 0.8115 (t0) cc_final: 0.7852 (t0) REVERT: A 987 PRO cc_start: 0.7718 (Cg_exo) cc_final: 0.7426 (Cg_endo) REVERT: B 80 ASP cc_start: 0.7429 (p0) cc_final: 0.7145 (p0) REVERT: B 389 ASP cc_start: 0.7996 (t0) cc_final: 0.7781 (t0) REVERT: B 529 LYS cc_start: 0.8121 (mtpt) cc_final: 0.7315 (mmmt) REVERT: B 987 PRO cc_start: 0.7696 (Cg_exo) cc_final: 0.7428 (Cg_endo) REVERT: F 45 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7419 (ttp-170) REVERT: S 53 ASP cc_start: 0.8466 (OUTLIER) cc_final: 0.8030 (t70) REVERT: S 226 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8133 (mt) REVERT: S 229 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8516 (mt) REVERT: S 245 HIS cc_start: 0.6255 (OUTLIER) cc_final: 0.5614 (t70) REVERT: S 389 ASP cc_start: 0.8081 (t0) cc_final: 0.7810 (t0) outliers start: 107 outliers final: 82 residues processed: 313 average time/residue: 0.1598 time to fit residues: 83.8962 Evaluate side-chains 305 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 217 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN 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 576 VAL 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 735 SER 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 878 LEU Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 916 LEU 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 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 386 LYS 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 735 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 902 MET 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 87 THR Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 45 ARG 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 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 221 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 645 THR 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 878 LEU Chi-restraints excluded: chain S residue 1055 SER 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 160 optimal weight: 0.8980 chunk 353 optimal weight: 3.9990 chunk 347 optimal weight: 6.9990 chunk 121 optimal weight: 6.9990 chunk 236 optimal weight: 1.9990 chunk 189 optimal weight: 0.7980 chunk 323 optimal weight: 3.9990 chunk 145 optimal weight: 0.9980 chunk 86 optimal weight: 0.0770 chunk 163 optimal weight: 0.2980 chunk 14 optimal weight: 0.7980 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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 907 ASN S 207 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.161334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.126138 restraints weight = 37130.616| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 4.64 r_work: 0.3110 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 31422 Z= 0.103 Angle : 0.569 12.474 42963 Z= 0.283 Chirality : 0.045 0.446 5121 Planarity : 0.004 0.042 5379 Dihedral : 7.623 107.347 5958 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.53 % Allowed : 25.41 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.14), residues: 3753 helix: 1.26 (0.22), residues: 636 sheet: 0.23 (0.18), residues: 1029 loop : -1.66 (0.12), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 403 TYR 0.020 0.001 TYR S 369 PHE 0.010 0.001 PHE A 800 TRP 0.010 0.001 TRP A 886 HIS 0.002 0.000 HIS S1064 Details of bonding type rmsd covalent geometry : bond 0.00220 (31287) covalent geometry : angle 0.54317 (42603) SS BOND : bond 0.00429 ( 45) SS BOND : angle 1.50349 ( 90) hydrogen bonds : bond 0.03920 ( 991) hydrogen bonds : angle 4.73152 ( 2766) link_ALPHA1-3 : bond 0.00725 ( 3) link_ALPHA1-3 : angle 1.34917 ( 9) link_BETA1-4 : bond 0.00509 ( 39) link_BETA1-4 : angle 1.29565 ( 117) link_NAG-ASN : bond 0.00458 ( 48) link_NAG-ASN : angle 2.54578 ( 144) ********************** 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 291 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 209 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8511 (mt) REVERT: A 389 ASP cc_start: 0.8061 (t0) cc_final: 0.7810 (t0) REVERT: A 987 PRO cc_start: 0.7616 (Cg_exo) cc_final: 0.7333 (Cg_endo) REVERT: B 389 ASP cc_start: 0.7967 (t0) cc_final: 0.7749 (t0) REVERT: B 987 PRO cc_start: 0.7644 (Cg_exo) cc_final: 0.7368 (Cg_endo) REVERT: F 45 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.7422 (ttp-170) REVERT: S 53 ASP cc_start: 0.8403 (OUTLIER) cc_final: 0.7976 (t70) REVERT: S 226 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7997 (mt) REVERT: S 229 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8501 (mt) REVERT: S 245 HIS cc_start: 0.6198 (OUTLIER) cc_final: 0.5657 (t70) REVERT: S 987 PRO cc_start: 0.7572 (Cg_exo) cc_final: 0.7283 (Cg_endo) outliers start: 82 outliers final: 71 residues processed: 278 average time/residue: 0.1588 time to fit residues: 73.9035 Evaluate side-chains 282 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 205 time to evaluate : 1.123 ------------------------------------------------------------------------------- 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 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 576 VAL 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 735 SER 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 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 386 LYS 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 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 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 45 ARG 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 85 VAL Chi-restraints excluded: chain S residue 23 GLN 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 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 645 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 1055 SER Chi-restraints excluded: chain S residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.4402 > 50: distance: 4 - 9: 14.312 distance: 9 - 10: 6.631 distance: 10 - 11: 11.095 distance: 10 - 13: 5.002 distance: 11 - 12: 27.838 distance: 11 - 17: 18.038 distance: 13 - 14: 24.810 distance: 14 - 15: 16.271 distance: 14 - 16: 6.035 distance: 17 - 18: 13.554 distance: 18 - 19: 25.415 distance: 18 - 21: 4.128 distance: 19 - 20: 42.454 distance: 19 - 25: 11.763 distance: 21 - 22: 13.804 distance: 22 - 23: 6.098 distance: 22 - 24: 34.191 distance: 25 - 26: 4.602 distance: 26 - 27: 30.668 distance: 26 - 29: 32.976 distance: 27 - 28: 17.939 distance: 27 - 31: 10.489 distance: 29 - 30: 47.420 distance: 30 - 112: 28.583 distance: 31 - 32: 7.002 distance: 31 - 37: 16.503 distance: 32 - 33: 9.824 distance: 32 - 35: 44.727 distance: 33 - 34: 13.557 distance: 33 - 38: 18.264 distance: 35 - 36: 11.241 distance: 36 - 37: 33.819 distance: 38 - 39: 12.256 distance: 39 - 40: 20.789 distance: 39 - 42: 7.967 distance: 40 - 41: 9.319 distance: 40 - 49: 21.995 distance: 42 - 43: 12.048 distance: 43 - 44: 9.625 distance: 43 - 45: 14.714 distance: 44 - 46: 8.402 distance: 45 - 47: 9.763 distance: 46 - 48: 15.559 distance: 47 - 48: 18.032 distance: 49 - 50: 15.702 distance: 51 - 52: 8.806 distance: 51 - 53: 15.402 distance: 52 - 80: 14.756 distance: 53 - 54: 14.988 distance: 54 - 55: 5.087 distance: 54 - 57: 12.970 distance: 55 - 56: 13.764 distance: 55 - 62: 3.770 distance: 57 - 58: 3.406 distance: 58 - 59: 17.481 distance: 59 - 60: 15.614 distance: 59 - 61: 8.528 distance: 62 - 63: 27.344 distance: 63 - 64: 9.757 distance: 63 - 66: 11.987 distance: 64 - 65: 13.267 distance: 64 - 69: 20.277 distance: 66 - 67: 29.130 distance: 66 - 68: 25.107 distance: 69 - 70: 5.307 distance: 70 - 71: 8.983 distance: 70 - 73: 10.130 distance: 71 - 72: 13.905 distance: 71 - 80: 7.527 distance: 73 - 74: 3.482 distance: 74 - 75: 4.712 distance: 74 - 76: 6.302 distance: 75 - 77: 3.842 distance: 76 - 78: 3.359 distance: 77 - 79: 7.046 distance: 78 - 79: 3.910 distance: 80 - 81: 15.608 distance: 81 - 82: 17.710 distance: 81 - 84: 9.564 distance: 82 - 83: 17.686 distance: 82 - 88: 4.431 distance: 84 - 85: 12.213 distance: 85 - 86: 11.269 distance: 85 - 87: 15.863 distance: 87 - 153: 3.295