Starting phenix.real_space_refine on Fri Mar 6 01:05:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nb4_0402/03_2026/6nb4_0402.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nb4_0402/03_2026/6nb4_0402.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6nb4_0402/03_2026/6nb4_0402.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nb4_0402/03_2026/6nb4_0402.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6nb4_0402/03_2026/6nb4_0402.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nb4_0402/03_2026/6nb4_0402.map" } resolution = 3.6 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= 0.002 sd= 0.057 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 133 5.16 5 C 16832 2.51 5 N 4285 2.21 5 O 5431 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 184 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26681 Number of models: 1 Model: "" Number of chains: 46 Chain: "A" Number of atoms: 9032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1169, 9032 Classifications: {'peptide': 1169} Link IDs: {'PTRANS': 59, 'TRANS': 1109} Chain breaks: 4 Chain: "B" Number of atoms: 7402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 958, 7402 Classifications: {'peptide': 958} Link IDs: {'PTRANS': 45, 'TRANS': 912} Chain breaks: 5 Chain: "C" Number of atoms: 7404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 959, 7404 Classifications: {'peptide': 959} Link IDs: {'PTRANS': 45, 'TRANS': 913} Chain breaks: 5 Chain: "H" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 738 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 3, 'TRANS': 119} Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 269 Unresolved non-hydrogen dihedrals: 162 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 5, 'ASN:plan1': 3, 'ASP:plan': 6, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 91 Chain: "L" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 607 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 5, 'TRANS': 100} Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 4, 'ARG:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 54 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} 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: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "X" 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: "Y" 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: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 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: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} 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: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} 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 Time building chain proxies: 6.12, per 1000 atoms: 0.23 Number of scatterers: 26681 At special positions: 0 Unit cell: (152.07, 146.59, 187.69, 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 133 16.00 O 5431 8.00 N 4285 7.00 C 16832 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS A 195 " distance=2.05 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 214 " distance=2.04 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 349 " distance=2.02 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS A 407 " distance=2.10 Simple disulfide: pdb=" SG CYS A 425 " - pdb=" SG CYS A 478 " distance=2.07 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 585 " distance=2.07 Simple disulfide: pdb=" SG CYS A 503 " - pdb=" SG CYS A 526 " distance=2.08 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 654 " distance=2.04 Simple disulfide: pdb=" SG CYS A 620 " - pdb=" SG CYS A 650 " distance=2.04 Simple disulfide: pdb=" SG CYS A 679 " - pdb=" SG CYS A 713 " distance=2.20 Simple disulfide: pdb=" SG CYS A 727 " - pdb=" SG CYS A 736 " distance=2.03 Simple disulfide: pdb=" SG CYS A 806 " - pdb=" SG CYS A 828 " distance=2.06 Simple disulfide: pdb=" SG CYS A 811 " - pdb=" SG CYS A 817 " distance=2.11 Simple disulfide: pdb=" SG CYS A 912 " - pdb=" SG CYS A 925 " distance=2.03 Simple disulfide: pdb=" SG CYS A1106 " - pdb=" SG CYS A1117 " distance=2.04 Simple disulfide: pdb=" SG CYS A1156 " - pdb=" SG CYS A1164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 30 " - pdb=" SG CYS B 195 " distance=2.03 Simple disulfide: pdb=" SG CYS B 176 " - pdb=" SG CYS B 214 " distance=2.04 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 339 " - pdb=" SG CYS B 349 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 654 " distance=2.04 Simple disulfide: pdb=" SG CYS B 620 " - pdb=" SG CYS B 650 " distance=2.03 Simple disulfide: pdb=" SG CYS B 679 " - pdb=" SG CYS B 713 " distance=2.15 Simple disulfide: pdb=" SG CYS B 727 " - pdb=" SG CYS B 736 " distance=2.03 Simple disulfide: pdb=" SG CYS B 806 " - pdb=" SG CYS B 828 " distance=2.03 Simple disulfide: pdb=" SG CYS B 811 " - pdb=" SG CYS B 817 " distance=2.12 Simple disulfide: pdb=" SG CYS B 912 " - pdb=" SG CYS B 925 " distance=2.09 Simple disulfide: pdb=" SG CYS B1106 " - pdb=" SG CYS B1117 " distance=2.04 Simple disulfide: pdb=" SG CYS B1156 " - pdb=" SG CYS B1164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 195 " distance=2.03 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 185 " - pdb=" SG CYS C 237 " distance=2.03 Simple disulfide: pdb=" SG CYS C 339 " - pdb=" SG CYS C 349 " distance=2.03 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 654 " distance=2.03 Simple disulfide: pdb=" SG CYS C 620 " - pdb=" SG CYS C 650 " distance=2.03 Simple disulfide: pdb=" SG CYS C 679 " - pdb=" SG CYS C 713 " distance=2.05 Simple disulfide: pdb=" SG CYS C 727 " - pdb=" SG CYS C 736 " distance=2.03 Simple disulfide: pdb=" SG CYS C 806 " - pdb=" SG CYS C 828 " distance=2.04 Simple disulfide: pdb=" SG CYS C 811 " - pdb=" SG CYS C 817 " distance=2.04 Simple disulfide: pdb=" SG CYS C 912 " - pdb=" SG CYS C 925 " distance=2.07 Simple disulfide: pdb=" SG CYS C1106 " - pdb=" SG CYS C1117 " distance=2.04 Simple disulfide: pdb=" SG CYS C1156 " - pdb=" SG CYS C1164 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 98 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.02 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 ALPHA1-2 " MAN U 4 " - " MAN U 5 " ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA I 3 " - " MAN I 4 " " BMA R 3 " - " MAN R 4 " " BMA U 3 " - " MAN U 4 " " BMA W 3 " - " MAN W 4 " " BMA X 3 " - " MAN X 4 " " BMA f 3 " - " MAN f 4 " " BMA i 3 " - " MAN i 4 " " BMA q 3 " - " MAN q 4 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " " BMA I 3 " - " MAN I 5 " " BMA R 3 " - " MAN R 5 " " BMA U 3 " - " MAN U 6 " " BMA W 3 " - " MAN W 5 " " BMA i 3 " - " MAN i 5 " " BMA q 3 " - " MAN q 5 " BETA1-4 " 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 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 P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 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 W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 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 k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " NAG-ASN " NAG A1401 " - " ASN A 66 " " NAG A1418 " - " ASN A 236 " " NAG A1423 " - " ASN A 487 " " NAG A1424 " - " ASN A 592 " " NAG B1433 " - " ASN B 774 " " NAG C1412 " - " ASN C 166 " " NAG C1416 " - " ASN C 236 " " NAG C1419 " - " ASN C 592 " " NAG C1424 " - " ASN C 774 " " NAG D 1 " - " ASN A 104 " " NAG E 1 " - " ASN A 125 " " NAG F 1 " - " ASN A 155 " " NAG G 1 " - " ASN A 166 " " NAG I 1 " - " ASN A 222 " " NAG J 1 " - " ASN A 244 " " NAG K 1 " - " ASN A 410 " " NAG M 1 " - " ASN A 619 " " NAG N 1 " - " ASN A 719 " " NAG O 1 " - " ASN A 774 " " NAG P 1 " - " ASN A 785 " " NAG Q 1 " - " ASN A 870 " " NAG R 1 " - " ASN A1213 " " NAG S 1 " - " ASN B 66 " " NAG T 1 " - " ASN B 104 " " NAG U 1 " - " ASN B 125 " " NAG V 1 " - " ASN B 155 " " NAG W 1 " - " ASN B 166 " " NAG X 1 " - " ASN B 222 " " NAG Y 1 " - " ASN B 236 " " NAG Z 1 " - " ASN B 244 " " NAG a 1 " - " ASN B 592 " " NAG b 1 " - " ASN B 619 " " NAG c 1 " - " ASN B 719 " " NAG d 1 " - " ASN B 785 " " NAG e 1 " - " ASN B 870 " " NAG f 1 " - " ASN B1213 " " NAG g 1 " - " ASN C 66 " " NAG h 1 " - " ASN C 104 " " NAG i 1 " - " ASN C 125 " " NAG j 1 " - " ASN C 155 " " NAG k 1 " - " ASN C 222 " " NAG l 1 " - " ASN C 244 " " NAG m 1 " - " ASN C 619 " " NAG n 1 " - " ASN C 719 " " NAG o 1 " - " ASN C 785 " " NAG p 1 " - " ASN C 870 " " NAG q 1 " - " ASN C1213 " Time building additional restraints: 2.58 Conformation dependent library (CDL) restraints added in 965.2 milliseconds 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6122 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 59 sheets defined 23.9% alpha, 27.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 36 through 41 Processing helix chain 'A' and resid 49 through 53 Processing helix chain 'A' and resid 209 through 213 Processing helix chain 'A' and resid 222 through 230 Processing helix chain 'A' and resid 269 through 271 No H-bonds generated for 'chain 'A' and resid 269 through 271' Processing helix chain 'A' and resid 342 through 351 Processing helix chain 'A' and resid 385 through 390 Processing helix chain 'A' and resid 395 through 399 removed outlier: 3.937A pdb=" N PHE A 399 " --> pdb=" O VAL A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 416 Processing helix chain 'A' and resid 431 through 435 Processing helix chain 'A' and resid 449 through 456 removed outlier: 4.839A pdb=" N SER A 454 " --> pdb=" O SER A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 550 Processing helix chain 'A' and resid 805 through 811 Processing helix chain 'A' and resid 814 through 822 Processing helix chain 'A' and resid 826 through 854 Processing helix chain 'A' and resid 888 through 898 Processing helix chain 'A' and resid 909 through 913 Processing helix chain 'A' and resid 926 through 931 removed outlier: 3.528A pdb=" N GLY A 931 " --> pdb=" O GLN A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 953 Processing helix chain 'A' and resid 971 through 982 Processing helix chain 'A' and resid 986 through 993 Processing helix chain 'A' and resid 993 through 1007 removed outlier: 3.676A pdb=" N ALA A 998 " --> pdb=" O GLN A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1008 through 1011 Processing helix chain 'A' and resid 1016 through 1040 removed outlier: 4.312A pdb=" N ALA A1032 " --> pdb=" O ASN A1028 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU A1033 " --> pdb=" O ASN A1029 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU A1036 " --> pdb=" O ALA A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1059 through 1107 removed outlier: 5.087A pdb=" N ALA A1065 " --> pdb=" O PRO A1061 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 40 Processing helix chain 'B' and resid 49 through 53 Processing helix chain 'B' and resid 209 through 214 Processing helix chain 'B' and resid 222 through 230 Processing helix chain 'B' and resid 342 through 351 Processing helix chain 'B' and resid 591 through 595 removed outlier: 4.195A pdb=" N LYS B 595 " --> pdb=" O ASN B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 805 through 811 Processing helix chain 'B' and resid 814 through 822 Processing helix chain 'B' and resid 826 through 854 Processing helix chain 'B' and resid 888 through 898 Processing helix chain 'B' and resid 908 through 913 Processing helix chain 'B' and resid 926 through 931 Processing helix chain 'B' and resid 940 through 954 Processing helix chain 'B' and resid 954 through 959 removed outlier: 3.985A pdb=" N GLY B 959 " --> pdb=" O ILE B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 971 through 982 Processing helix chain 'B' and resid 986 through 993 Processing helix chain 'B' and resid 993 through 1007 Processing helix chain 'B' and resid 1008 through 1011 Processing helix chain 'B' and resid 1016 through 1040 removed outlier: 3.940A pdb=" N ALA B1032 " --> pdb=" O ASN B1028 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU B1033 " --> pdb=" O ASN B1029 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER B1034 " --> pdb=" O ALA B1030 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU B1036 " --> pdb=" O ALA B1032 " (cutoff:3.500A) Processing helix chain 'B' and resid 1050 through 1056 Processing helix chain 'B' and resid 1059 through 1107 removed outlier: 3.536A pdb=" N ASP B1064 " --> pdb=" O PRO B1060 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ALA B1065 " --> pdb=" O PRO B1061 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN B1066 " --> pdb=" O GLU B1062 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 41 Processing helix chain 'C' and resid 49 through 53 Processing helix chain 'C' and resid 209 through 213 Processing helix chain 'C' and resid 222 through 230 Processing helix chain 'C' and resid 342 through 351 Processing helix chain 'C' and resid 805 through 812 Processing helix chain 'C' and resid 814 through 822 removed outlier: 3.989A pdb=" N LEU C 820 " --> pdb=" O LYS C 816 " (cutoff:3.500A) Processing helix chain 'C' and resid 823 through 825 No H-bonds generated for 'chain 'C' and resid 823 through 825' Processing helix chain 'C' and resid 826 through 854 Processing helix chain 'C' and resid 888 through 896 Processing helix chain 'C' and resid 907 through 915 removed outlier: 3.845A pdb=" N MET C 913 " --> pdb=" O TYR C 909 " (cutoff:3.500A) Processing helix chain 'C' and resid 926 through 931 removed outlier: 3.619A pdb=" N GLY C 931 " --> pdb=" O GLN C 927 " (cutoff:3.500A) Processing helix chain 'C' and resid 940 through 954 Processing helix chain 'C' and resid 971 through 982 Processing helix chain 'C' and resid 986 through 993 Processing helix chain 'C' and resid 993 through 1010 removed outlier: 4.059A pdb=" N THR C1010 " --> pdb=" O GLY C1006 " (cutoff:3.500A) Processing helix chain 'C' and resid 1016 through 1040 removed outlier: 4.067A pdb=" N ALA C1032 " --> pdb=" O ASN C1028 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEU C1033 " --> pdb=" O ASN C1029 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU C1036 " --> pdb=" O ALA C1032 " (cutoff:3.500A) Processing helix chain 'C' and resid 1050 through 1058 Processing helix chain 'C' and resid 1059 through 1107 removed outlier: 3.524A pdb=" N ASP C1064 " --> pdb=" O PRO C1060 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ALA C1065 " --> pdb=" O PRO C1061 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 53 through 57 Processing helix chain 'H' and resid 64 through 67 Processing helix chain 'H' and resid 89 through 93 Processing helix chain 'L' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 34 Processing sheet with id=AA2, first strand: chain 'A' and resid 67 through 75 removed outlier: 4.318A pdb=" N ARG A 335 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.006A pdb=" N SER A 267 " --> pdb=" O GLN A 280 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N GLN A 280 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 88 through 89 removed outlier: 7.653A pdb=" N SER A 88 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N THR A 206 " --> pdb=" O SER A 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 92 through 93 Processing sheet with id=AA6, first strand: chain 'A' and resid 110 through 111 removed outlier: 4.679A pdb=" N ALA A 146 " --> pdb=" O ILE A 296 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU A 180 " --> pdb=" O TYR A 241 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N TYR A 241 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ALA A 182 " --> pdb=" O PHE A 239 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N PHE A 239 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N TYR A 184 " --> pdb=" O CYS A 237 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N CYS A 237 " --> pdb=" O TYR A 184 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 127 through 129 removed outlier: 3.637A pdb=" N ALA A 309 " --> pdb=" O THR A 139 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 153 through 155 Processing sheet with id=AA9, first strand: chain 'A' and resid 214 through 215 removed outlier: 3.807A pdb=" N SER A 215 " --> pdb=" O ASN A 218 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 359 through 366 removed outlier: 4.554A pdb=" N VAL A 659 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N SER A 365 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL A 657 " --> pdb=" O SER A 365 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 371 through 376 removed outlier: 4.136A pdb=" N GLU A 605 " --> pdb=" O SER A 371 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N SER A 373 " --> pdb=" O GLU A 605 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N SER A 607 " --> pdb=" O SER A 373 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VAL A 375 " --> pdb=" O SER A 607 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N VAL A 639 " --> pdb=" O LEU A 651 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL A 631 " --> pdb=" O VAL A 639 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 400 through 404 removed outlier: 6.999A pdb=" N THR A 477 " --> pdb=" O CYS A 425 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N CYS A 425 " --> pdb=" O THR A 477 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N LEU A 479 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N PHE A 423 " --> pdb=" O LEU A 479 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU A 481 " --> pdb=" O ASN A 421 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 407 through 408 removed outlier: 5.999A pdb=" N CYS A 407 " --> pdb=" O CYS A 585 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 513 through 515 removed outlier: 5.504A pdb=" N SER A 498 " --> pdb=" O VAL A 561 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL A 561 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ILE A 500 " --> pdb=" O SER A 559 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N SER A 559 " --> pdb=" O ILE A 500 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 717 through 724 removed outlier: 6.529A pdb=" N VAL A 718 " --> pdb=" O LEU A 759 " (cutoff:3.500A) removed outlier: 9.011A pdb=" N SER A 761 " --> pdb=" O VAL A 718 " (cutoff:3.500A) removed outlier: 9.853A pdb=" N SER A 720 " --> pdb=" O SER A 761 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU A 735 " --> pdb=" O LEU A 731 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 768 through 769 removed outlier: 5.695A pdb=" N ILE A 768 " --> pdb=" O SER B 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1184 through 1188 removed outlier: 4.616A pdb=" N PHE A1172 " --> pdb=" O ALA A1152 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N VAL A1150 " --> pdb=" O LYS A1174 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 785 through 796 removed outlier: 3.601A pdb=" N ASN A 785 " --> pdb=" O SER A1144 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL A1124 " --> pdb=" O VAL A1139 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N TYR A1141 " --> pdb=" O HIS A1122 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N HIS A1122 " --> pdb=" O TYR A1141 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 802 through 804 Processing sheet with id=AC2, first strand: chain 'A' and resid 857 through 858 Processing sheet with id=AC3, first strand: chain 'A' and resid 967 through 968 removed outlier: 5.608A pdb=" N VAL C1150 " --> pdb=" O LYS C1174 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N PHE C1172 " --> pdb=" O ALA C1152 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1202 through 1205 removed outlier: 4.049A pdb=" N CYS A1164 " --> pdb=" O VAL A1205 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 33 through 35 Processing sheet with id=AC6, first strand: chain 'B' and resid 67 through 75 removed outlier: 4.181A pdb=" N ARG B 335 " --> pdb=" O ASP B 326 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.061A pdb=" N SER B 267 " --> pdb=" O GLN B 280 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N GLN B 280 " --> pdb=" O SER B 267 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 88 through 89 removed outlier: 7.469A pdb=" N SER B 88 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N THR B 206 " --> pdb=" O SER B 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 92 through 93 Processing sheet with id=AD1, first strand: chain 'B' and resid 110 through 111 removed outlier: 6.637A pdb=" N LEU B 180 " --> pdb=" O TYR B 241 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N TYR B 241 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ALA B 182 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N PHE B 239 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N TYR B 184 " --> pdb=" O CYS B 237 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N CYS B 237 " --> pdb=" O TYR B 184 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 127 through 129 removed outlier: 3.605A pdb=" N ALA B 309 " --> pdb=" O THR B 139 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 153 through 155 Processing sheet with id=AD4, first strand: chain 'B' and resid 359 through 366 removed outlier: 4.558A pdb=" N VAL B 659 " --> pdb=" O VAL B 363 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N SER B 365 " --> pdb=" O VAL B 657 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N VAL B 657 " --> pdb=" O SER B 365 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N CYS B 713 " --> pdb=" O PHE B 674 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 371 through 376 removed outlier: 4.243A pdb=" N GLU B 605 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N SER B 373 " --> pdb=" O GLU B 605 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N SER B 607 " --> pdb=" O SER B 373 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL B 375 " --> pdb=" O SER B 607 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL B 639 " --> pdb=" O LEU B 651 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL B 631 " --> pdb=" O VAL B 639 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 717 through 724 removed outlier: 6.393A pdb=" N VAL B 718 " --> pdb=" O LEU B 759 " (cutoff:3.500A) removed outlier: 8.860A pdb=" N SER B 761 " --> pdb=" O VAL B 718 " (cutoff:3.500A) removed outlier: 9.731A pdb=" N SER B 720 " --> pdb=" O SER B 761 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU B 735 " --> pdb=" O LEU B 731 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 768 through 769 removed outlier: 5.532A pdb=" N ILE B 768 " --> pdb=" O SER C 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'B' and resid 1121 through 1130 removed outlier: 5.795A pdb=" N HIS B1122 " --> pdb=" O TYR B1141 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N TYR B1141 " --> pdb=" O HIS B1122 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N VAL B1124 " --> pdb=" O VAL B1139 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N VAL B1150 " --> pdb=" O LYS B1174 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N PHE B1172 " --> pdb=" O ALA B1152 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1121 through 1130 removed outlier: 5.795A pdb=" N HIS B1122 " --> pdb=" O TYR B1141 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N TYR B1141 " --> pdb=" O HIS B1122 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N VAL B1124 " --> pdb=" O VAL B1139 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N HIS B1146 " --> pdb=" O PRO B 783 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N GLU B1148 " --> pdb=" O SER B 781 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N SER B 781 " --> pdb=" O GLU B1148 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL B1150 " --> pdb=" O LYS B 779 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LYS B 779 " --> pdb=" O VAL B1150 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 801 through 804 removed outlier: 4.547A pdb=" N LYS B 801 " --> pdb=" O LEU B 935 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 1202 through 1205 removed outlier: 3.914A pdb=" N CYS B1164 " --> pdb=" O VAL B1205 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ASN B1163 " --> pdb=" O ASP B1157 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 33 through 34 Processing sheet with id=AE4, first strand: chain 'C' and resid 67 through 75 removed outlier: 4.128A pdb=" N ARG C 335 " --> pdb=" O ASP C 326 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.116A pdb=" N SER C 267 " --> pdb=" O GLN C 280 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLN C 280 " --> pdb=" O SER C 267 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 88 through 89 removed outlier: 7.316A pdb=" N SER C 88 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N THR C 206 " --> pdb=" O SER C 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'C' and resid 92 through 93 Processing sheet with id=AE8, first strand: chain 'C' and resid 110 through 111 removed outlier: 6.647A pdb=" N LEU C 180 " --> pdb=" O TYR C 241 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TYR C 241 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ALA C 182 " --> pdb=" O PHE C 239 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N PHE C 239 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N TYR C 184 " --> pdb=" O CYS C 237 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N CYS C 237 " --> pdb=" O TYR C 184 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 127 through 129 Processing sheet with id=AF1, first strand: chain 'C' and resid 153 through 155 Processing sheet with id=AF2, first strand: chain 'C' and resid 214 through 215 removed outlier: 3.745A pdb=" N SER C 215 " --> pdb=" O ASN C 218 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 359 through 366 removed outlier: 4.696A pdb=" N VAL C 659 " --> pdb=" O VAL C 363 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N SER C 365 " --> pdb=" O VAL C 657 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N VAL C 657 " --> pdb=" O SER C 365 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 371 through 376 removed outlier: 4.189A pdb=" N GLU C 605 " --> pdb=" O SER C 371 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N SER C 373 " --> pdb=" O GLU C 605 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N SER C 607 " --> pdb=" O SER C 373 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL C 375 " --> pdb=" O SER C 607 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N VAL C 639 " --> pdb=" O LEU C 651 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL C 631 " --> pdb=" O VAL C 639 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 718 through 724 removed outlier: 6.541A pdb=" N VAL C 718 " --> pdb=" O LEU C 759 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N SER C 761 " --> pdb=" O VAL C 718 " (cutoff:3.500A) removed outlier: 9.995A pdb=" N SER C 720 " --> pdb=" O SER C 761 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'C' and resid 786 through 796 removed outlier: 4.412A pdb=" N VAL C1124 " --> pdb=" O VAL C1139 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N TYR C1141 " --> pdb=" O HIS C1122 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N HIS C1122 " --> pdb=" O TYR C1141 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 802 through 803 Processing sheet with id=AF8, first strand: chain 'C' and resid 1202 through 1205 removed outlier: 4.049A pdb=" N CYS C1164 " --> pdb=" O VAL C1205 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AG1, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.666A pdb=" N TRP H 33 " --> pdb=" O LEU H 101 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 10 through 11 Processing sheet with id=AG3, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AG4, first strand: chain 'L' and resid 46 through 50 removed outlier: 6.516A pdb=" N TRP L 37 " --> pdb=" O MET L 49 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 46 through 50 removed outlier: 6.516A pdb=" N TRP L 37 " --> pdb=" O MET L 49 " (cutoff:3.500A) 1053 hydrogen bonds defined for protein. 2802 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: 6.65 Time building geometry restraints manager: 3.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5115 1.32 - 1.45: 7667 1.45 - 1.58: 14305 1.58 - 1.71: 11 1.71 - 1.84: 175 Bond restraints: 27273 Sorted by residual: bond pdb=" C1 NAG O 2 " pdb=" O5 NAG O 2 " ideal model delta sigma weight residual 1.406 1.547 -0.141 2.00e-02 2.50e+03 4.95e+01 bond pdb=" C1 NAG K 2 " pdb=" O5 NAG K 2 " ideal model delta sigma weight residual 1.406 1.547 -0.141 2.00e-02 2.50e+03 4.94e+01 bond pdb=" C1 NAG A1423 " pdb=" O5 NAG A1423 " ideal model delta sigma weight residual 1.406 1.546 -0.140 2.00e-02 2.50e+03 4.93e+01 bond pdb=" C1 NAG k 2 " pdb=" O5 NAG k 2 " ideal model delta sigma weight residual 1.406 1.546 -0.140 2.00e-02 2.50e+03 4.93e+01 bond pdb=" C1 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.406 1.546 -0.140 2.00e-02 2.50e+03 4.90e+01 ... (remaining 27268 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.69: 36870 5.69 - 11.39: 239 11.39 - 17.08: 5 17.08 - 22.78: 5 22.78 - 28.47: 2 Bond angle restraints: 37121 Sorted by residual: angle pdb=" C VAL B 711 " pdb=" CA VAL B 711 " pdb=" CB VAL B 711 " ideal model delta sigma weight residual 111.29 135.81 -24.52 1.64e+00 3.72e-01 2.24e+02 angle pdb=" C TYR C 905 " pdb=" CA TYR C 905 " pdb=" CB TYR C 905 " ideal model delta sigma weight residual 110.42 138.89 -28.47 1.99e+00 2.53e-01 2.05e+02 angle pdb=" C LEU A 450 " pdb=" CA LEU A 450 " pdb=" CB LEU A 450 " ideal model delta sigma weight residual 110.79 129.97 -19.18 1.66e+00 3.63e-01 1.34e+02 angle pdb=" N MET C 906 " pdb=" CA MET C 906 " pdb=" C MET C 906 " ideal model delta sigma weight residual 110.28 127.08 -16.80 1.48e+00 4.57e-01 1.29e+02 angle pdb=" N TYR C 905 " pdb=" CA TYR C 905 " pdb=" C TYR C 905 " ideal model delta sigma weight residual 110.80 90.45 20.35 2.13e+00 2.20e-01 9.13e+01 ... (remaining 37116 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.85: 16884 21.85 - 43.70: 475 43.70 - 65.55: 102 65.55 - 87.40: 93 87.40 - 109.24: 47 Dihedral angle restraints: 17601 sinusoidal: 7994 harmonic: 9607 Sorted by residual: dihedral pdb=" C LEU A 450 " pdb=" N LEU A 450 " pdb=" CA LEU A 450 " pdb=" CB LEU A 450 " ideal model delta harmonic sigma weight residual -122.60 -159.37 36.77 0 2.50e+00 1.60e-01 2.16e+02 dihedral pdb=" C VAL B 711 " pdb=" N VAL B 711 " pdb=" CA VAL B 711 " pdb=" CB VAL B 711 " ideal model delta harmonic sigma weight residual -122.00 -158.60 36.60 0 2.50e+00 1.60e-01 2.14e+02 dihedral pdb=" N LEU A 450 " pdb=" C LEU A 450 " pdb=" CA LEU A 450 " pdb=" CB LEU A 450 " ideal model delta harmonic sigma weight residual 122.80 154.44 -31.64 0 2.50e+00 1.60e-01 1.60e+02 ... (remaining 17598 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.305: 4432 0.305 - 0.610: 22 0.610 - 0.915: 1 0.915 - 1.220: 0 1.220 - 1.525: 2 Chirality restraints: 4457 Sorted by residual: chirality pdb=" C1 BMA Y 3 " pdb=" O4 NAG Y 2 " pdb=" C2 BMA Y 3 " pdb=" O5 BMA Y 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 6.89e+01 chirality pdb=" CA LEU A 450 " pdb=" N LEU A 450 " pdb=" C LEU A 450 " pdb=" CB LEU A 450 " both_signs ideal model delta sigma weight residual False 2.51 0.99 1.53 2.00e-01 2.50e+01 5.82e+01 chirality pdb=" C1 NAG h 2 " pdb=" O4 NAG h 1 " pdb=" C2 NAG h 2 " pdb=" O5 NAG h 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.54 0.14 2.00e-02 2.50e+03 5.12e+01 ... (remaining 4454 not shown) Planarity restraints: 4724 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG q 2 " -0.044 2.00e-02 2.50e+03 3.62e-02 1.64e+01 pdb=" C7 NAG q 2 " 0.010 2.00e-02 2.50e+03 pdb=" C8 NAG q 2 " -0.033 2.00e-02 2.50e+03 pdb=" N2 NAG q 2 " 0.058 2.00e-02 2.50e+03 pdb=" O7 NAG q 2 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 166 " -0.033 2.00e-02 2.50e+03 3.48e-02 1.52e+01 pdb=" CG ASN B 166 " 0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN B 166 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN B 166 " 0.053 2.00e-02 2.50e+03 pdb=" C1 NAG W 1 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 2 " 0.035 2.00e-02 2.50e+03 2.84e-02 1.01e+01 pdb=" C7 NAG R 2 " -0.007 2.00e-02 2.50e+03 pdb=" C8 NAG R 2 " 0.026 2.00e-02 2.50e+03 pdb=" N2 NAG R 2 " -0.045 2.00e-02 2.50e+03 pdb=" O7 NAG R 2 " -0.008 2.00e-02 2.50e+03 ... (remaining 4721 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 110 2.57 - 3.15: 21986 3.15 - 3.73: 39357 3.73 - 4.32: 57613 4.32 - 4.90: 91153 Nonbonded interactions: 210219 Sorted by model distance: nonbonded pdb=" CB SER B 676 " pdb=" O TYR C 905 " model vdw 1.986 3.440 nonbonded pdb=" OG SER A 419 " pdb=" OG1 THR A 483 " model vdw 2.249 3.040 nonbonded pdb=" N ASN C 592 " pdb=" OD1 ASN C 592 " model vdw 2.284 3.120 nonbonded pdb=" OG1 THR A 709 " pdb=" O GLY A 712 " model vdw 2.295 3.040 nonbonded pdb=" OG SER A 328 " pdb=" OD1 ASP A 330 " model vdw 2.374 3.040 ... (remaining 210214 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 18 through 378 or resid 591 through 1433)) selection = (chain 'C' and (resid 18 through 378 or resid 591 through 1412)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'g' selection = chain 'h' selection = chain 'j' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' } ncs_group { reference = chain 'E' selection = chain 'I' selection = chain 'R' selection = chain 'W' selection = chain 'i' selection = chain 'q' } ncs_group { reference = chain 'X' selection = chain 'f' } ncs_group { reference = chain 'Y' 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 group one per residue 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: 3.610 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: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 25.990 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 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 : 0.016 0.173 27431 Z= 0.856 Angle : 1.363 28.470 37550 Z= 0.858 Chirality : 0.089 1.525 4457 Planarity : 0.006 0.057 4677 Dihedral : 13.877 109.244 11344 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.62 % Favored : 97.13 % Rotamer: Outliers : 0.45 % Allowed : 1.35 % Favored : 98.21 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.14), residues: 3277 helix: 0.40 (0.19), residues: 677 sheet: 0.49 (0.18), residues: 711 loop : -0.23 (0.14), residues: 1889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 401 TYR 0.042 0.006 TYR A 77 PHE 0.024 0.004 PHE C 313 TRP 0.035 0.006 TRP C1184 HIS 0.007 0.001 HIS C1138 Details of bonding type rmsd covalent geometry : bond 0.01603 (27273) covalent geometry : angle 1.33588 (37121) SS BOND : bond 0.04109 ( 45) SS BOND : angle 3.54204 ( 90) hydrogen bonds : bond 0.19240 ( 1031) hydrogen bonds : angle 7.71602 ( 2802) link_ALPHA1-2 : bond 0.04221 ( 1) link_ALPHA1-2 : angle 1.58040 ( 3) link_ALPHA1-3 : bond 0.03394 ( 9) link_ALPHA1-3 : angle 1.65944 ( 27) link_ALPHA1-6 : bond 0.03121 ( 7) link_ALPHA1-6 : angle 2.29878 ( 21) link_BETA1-4 : bond 0.03477 ( 49) link_BETA1-4 : angle 2.49143 ( 147) link_NAG-ASN : bond 0.03536 ( 47) link_NAG-ASN : angle 3.05587 ( 141) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 624 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.7564 (ttp) cc_final: 0.7298 (ttp) REVERT: A 225 LEU cc_start: 0.6792 (tp) cc_final: 0.6459 (tt) REVERT: A 231 TYR cc_start: 0.6438 (m-80) cc_final: 0.6209 (m-80) REVERT: A 290 ILE cc_start: 0.8228 (mt) cc_final: 0.7907 (mm) REVERT: A 469 TYR cc_start: 0.7951 (t80) cc_final: 0.7707 (t80) REVERT: A 473 PHE cc_start: 0.7428 (p90) cc_final: 0.7149 (p90) REVERT: A 491 ILE cc_start: 0.7187 (tt) cc_final: 0.6962 (pt) REVERT: B 199 ASN cc_start: 0.5801 (m-40) cc_final: 0.5424 (p0) REVERT: B 674 PHE cc_start: 0.7919 (m-80) cc_final: 0.7638 (m-80) REVERT: B 686 MET cc_start: 0.7533 (mmm) cc_final: 0.6921 (tpp) REVERT: B 724 VAL cc_start: 0.7658 (p) cc_final: 0.6989 (p) REVERT: B 798 THR cc_start: 0.8171 (p) cc_final: 0.7075 (p) REVERT: B 938 LEU cc_start: 0.8173 (tt) cc_final: 0.7612 (tt) REVERT: B 1043 THR cc_start: 0.8321 (m) cc_final: 0.7996 (p) REVERT: B 1054 ILE cc_start: 0.8377 (pt) cc_final: 0.8078 (mt) REVERT: C 677 VAL cc_start: 0.8909 (t) cc_final: 0.8682 (m) REVERT: C 807 LYS cc_start: 0.8577 (tttt) cc_final: 0.7999 (tppt) REVERT: C 913 MET cc_start: 0.6064 (mtm) cc_final: 0.5834 (mtp) REVERT: C 961 THR cc_start: 0.5897 (p) cc_final: 0.5571 (p) outliers start: 12 outliers final: 0 residues processed: 633 average time/residue: 0.1875 time to fit residues: 186.1322 Evaluate side-chains 247 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 0.0770 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.0470 chunk 298 optimal weight: 0.5980 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN A1009 GLN ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1097 GLN ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 808 GLN B 812 ASN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1027 ASN B1056 GLN B1129 ASN ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 GLN C 812 ASN C1042 ASN C1085 GLN C1129 ASN C1169 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.157106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.130272 restraints weight = 48394.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.130853 restraints weight = 38512.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.131820 restraints weight = 32415.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.132222 restraints weight = 27389.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.132374 restraints weight = 24139.736| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 27431 Z= 0.162 Angle : 0.704 10.121 37550 Z= 0.358 Chirality : 0.045 0.267 4457 Planarity : 0.005 0.060 4677 Dihedral : 10.265 82.733 5901 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.32 % Favored : 97.62 % Rotamer: Outliers : 2.43 % Allowed : 7.70 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.14), residues: 3277 helix: 1.73 (0.20), residues: 675 sheet: 0.54 (0.18), residues: 746 loop : -0.32 (0.14), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 181 TYR 0.020 0.001 TYR A 77 PHE 0.022 0.002 PHE B 254 TRP 0.014 0.001 TRP C 310 HIS 0.010 0.001 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00342 (27273) covalent geometry : angle 0.66771 (37121) SS BOND : bond 0.00880 ( 45) SS BOND : angle 2.05146 ( 90) hydrogen bonds : bond 0.06826 ( 1031) hydrogen bonds : angle 5.81086 ( 2802) link_ALPHA1-2 : bond 0.00227 ( 1) link_ALPHA1-2 : angle 1.41607 ( 3) link_ALPHA1-3 : bond 0.00653 ( 9) link_ALPHA1-3 : angle 3.10565 ( 27) link_ALPHA1-6 : bond 0.00645 ( 7) link_ALPHA1-6 : angle 2.00056 ( 21) link_BETA1-4 : bond 0.01202 ( 49) link_BETA1-4 : angle 2.24575 ( 147) link_NAG-ASN : bond 0.00412 ( 47) link_NAG-ASN : angle 2.06678 ( 141) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 310 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 473 PHE cc_start: 0.7740 (p90) cc_final: 0.7509 (p90) REVERT: A 812 ASN cc_start: 0.7580 (t0) cc_final: 0.6978 (t0) REVERT: B 636 GLN cc_start: 0.7640 (mm-40) cc_final: 0.7389 (mm110) REVERT: B 674 PHE cc_start: 0.8041 (m-80) cc_final: 0.7645 (m-80) REVERT: B 686 MET cc_start: 0.7557 (mmm) cc_final: 0.7018 (tpp) REVERT: B 1008 MET cc_start: 0.7162 (mtp) cc_final: 0.6793 (mtp) REVERT: B 1204 TYR cc_start: 0.8102 (m-80) cc_final: 0.7713 (m-10) REVERT: C 147 PHE cc_start: 0.7852 (m-80) cc_final: 0.7505 (m-10) REVERT: C 674 PHE cc_start: 0.8331 (m-80) cc_final: 0.7973 (m-80) REVERT: C 928 TYR cc_start: 0.8332 (m-80) cc_final: 0.8111 (m-80) outliers start: 65 outliers final: 36 residues processed: 364 average time/residue: 0.1644 time to fit residues: 98.8410 Evaluate side-chains 251 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 215 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 540 TYR Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 772 GLN Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 859 SER Chi-restraints excluded: chain B residue 1056 GLN Chi-restraints excluded: chain B residue 1210 THR Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 592 ASN Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain C residue 1041 SER Chi-restraints excluded: chain C residue 1042 ASN Chi-restraints excluded: chain C residue 1043 THR Chi-restraints excluded: chain C residue 1094 LEU Chi-restraints excluded: chain C residue 1121 THR Chi-restraints excluded: chain C residue 1202 THR Chi-restraints excluded: chain C residue 1205 VAL Chi-restraints excluded: chain C residue 1210 THR Chi-restraints excluded: chain H residue 62 TYR Chi-restraints excluded: chain L residue 33 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 66 optimal weight: 1.9990 chunk 213 optimal weight: 0.9990 chunk 240 optimal weight: 0.5980 chunk 130 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 100 optimal weight: 0.4980 chunk 229 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 HIS ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 516 GLN A 836 HIS ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1145 ASN B 258 GLN B 812 ASN B1056 GLN B1122 HIS B1169 ASN C 812 ASN C 927 GLN C1003 GLN C1042 ASN C1138 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.148737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.121300 restraints weight = 48806.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.122306 restraints weight = 42047.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.123343 restraints weight = 33902.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.123585 restraints weight = 27152.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.123708 restraints weight = 26371.642| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 27431 Z= 0.244 Angle : 0.757 14.507 37550 Z= 0.379 Chirality : 0.047 0.251 4457 Planarity : 0.005 0.064 4677 Dihedral : 8.813 73.065 5901 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.80 % Allowed : 9.64 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.14), residues: 3277 helix: 1.49 (0.20), residues: 672 sheet: 0.48 (0.18), residues: 752 loop : -0.69 (0.13), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 847 TYR 0.022 0.002 TYR C 85 PHE 0.033 0.002 PHE B1116 TRP 0.015 0.002 TRP A 535 HIS 0.012 0.002 HIS A1138 Details of bonding type rmsd covalent geometry : bond 0.00575 (27273) covalent geometry : angle 0.72626 (37121) SS BOND : bond 0.00477 ( 45) SS BOND : angle 1.93616 ( 90) hydrogen bonds : bond 0.06792 ( 1031) hydrogen bonds : angle 5.67748 ( 2802) link_ALPHA1-2 : bond 0.00240 ( 1) link_ALPHA1-2 : angle 0.69822 ( 3) link_ALPHA1-3 : bond 0.00913 ( 9) link_ALPHA1-3 : angle 2.44944 ( 27) link_ALPHA1-6 : bond 0.00597 ( 7) link_ALPHA1-6 : angle 1.66848 ( 21) link_BETA1-4 : bond 0.01078 ( 49) link_BETA1-4 : angle 2.15075 ( 147) link_NAG-ASN : bond 0.00701 ( 47) link_NAG-ASN : angle 2.23091 ( 141) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 230 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 ARG cc_start: 0.6095 (OUTLIER) cc_final: 0.5880 (ptp-170) REVERT: A 473 PHE cc_start: 0.7937 (p90) cc_final: 0.7694 (p90) REVERT: A 502 LYS cc_start: 0.7800 (OUTLIER) cc_final: 0.7552 (ptmm) REVERT: A 729 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8416 (pp) REVERT: A 812 ASN cc_start: 0.7599 (t0) cc_final: 0.6994 (t0) REVERT: A 820 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8373 (mp) REVERT: A 875 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7246 (mp0) REVERT: B 261 GLN cc_start: 0.7647 (tm-30) cc_final: 0.7418 (tm-30) REVERT: B 686 MET cc_start: 0.7716 (mmm) cc_final: 0.7466 (tpp) REVERT: B 1008 MET cc_start: 0.7483 (mtp) cc_final: 0.7281 (mtp) REVERT: B 1024 ASP cc_start: 0.7564 (t0) cc_final: 0.7249 (t70) REVERT: C 31 ILE cc_start: 0.8030 (mm) cc_final: 0.7762 (tp) REVERT: C 353 SER cc_start: 0.8702 (t) cc_final: 0.8454 (m) outliers start: 75 outliers final: 48 residues processed: 297 average time/residue: 0.1653 time to fit residues: 82.2058 Evaluate side-chains 234 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 182 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 307 ARG Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 502 LYS Chi-restraints excluded: chain A residue 540 TYR Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1190 SER Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 355 ASP Chi-restraints excluded: chain B residue 771 ASP Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain B residue 859 SER Chi-restraints excluded: chain B residue 888 SER Chi-restraints excluded: chain B residue 966 SER Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1056 GLN Chi-restraints excluded: chain B residue 1210 THR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 939 MET Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 986 THR Chi-restraints excluded: chain C residue 1041 SER Chi-restraints excluded: chain C residue 1094 LEU Chi-restraints excluded: chain C residue 1121 THR Chi-restraints excluded: chain C residue 1205 VAL Chi-restraints excluded: chain C residue 1210 THR Chi-restraints excluded: chain H residue 62 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 76 optimal weight: 0.9980 chunk 271 optimal weight: 0.0970 chunk 297 optimal weight: 0.6980 chunk 86 optimal weight: 0.5980 chunk 185 optimal weight: 0.9990 chunk 299 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 83 optimal weight: 0.2980 chunk 238 optimal weight: 3.9990 chunk 170 optimal weight: 0.7980 chunk 124 optimal weight: 0.4980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 ASN ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 927 GLN B 258 GLN B 636 GLN B 812 ASN B 836 HIS B1056 GLN C 304 GLN C 812 ASN C 915 GLN C1042 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.151296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.125292 restraints weight = 48367.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.124401 restraints weight = 44558.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.125319 restraints weight = 39478.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.125780 restraints weight = 32985.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.125930 restraints weight = 30687.404| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 27431 Z= 0.136 Angle : 0.636 16.789 37550 Z= 0.313 Chirality : 0.044 0.249 4457 Planarity : 0.004 0.060 4677 Dihedral : 7.778 65.740 5901 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.58 % Allowed : 11.06 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.14), residues: 3277 helix: 1.76 (0.20), residues: 678 sheet: 0.48 (0.18), residues: 736 loop : -0.64 (0.13), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 847 TYR 0.015 0.001 TYR A1141 PHE 0.022 0.001 PHE C 40 TRP 0.016 0.001 TRP H 117 HIS 0.008 0.001 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00300 (27273) covalent geometry : angle 0.60535 (37121) SS BOND : bond 0.00340 ( 45) SS BOND : angle 1.90757 ( 90) hydrogen bonds : bond 0.05542 ( 1031) hydrogen bonds : angle 5.29270 ( 2802) link_ALPHA1-2 : bond 0.00306 ( 1) link_ALPHA1-2 : angle 1.40138 ( 3) link_ALPHA1-3 : bond 0.01040 ( 9) link_ALPHA1-3 : angle 2.51148 ( 27) link_ALPHA1-6 : bond 0.00791 ( 7) link_ALPHA1-6 : angle 1.51507 ( 21) link_BETA1-4 : bond 0.01083 ( 49) link_BETA1-4 : angle 1.98016 ( 147) link_NAG-ASN : bond 0.00455 ( 47) link_NAG-ASN : angle 1.79385 ( 141) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 218 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 ARG cc_start: 0.5989 (OUTLIER) cc_final: 0.5505 (ttm170) REVERT: A 467 PHE cc_start: 0.6285 (m-10) cc_final: 0.5993 (m-10) REVERT: A 473 PHE cc_start: 0.7985 (p90) cc_final: 0.7779 (p90) REVERT: A 502 LYS cc_start: 0.7644 (OUTLIER) cc_final: 0.7443 (ptmm) REVERT: A 729 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8361 (pp) REVERT: A 812 ASN cc_start: 0.7438 (t0) cc_final: 0.6854 (t0) REVERT: A 820 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8385 (mp) REVERT: B 261 GLN cc_start: 0.7757 (tm-30) cc_final: 0.7524 (tm-30) REVERT: B 686 MET cc_start: 0.7683 (mmm) cc_final: 0.7387 (tpp) REVERT: B 726 ASP cc_start: 0.7862 (m-30) cc_final: 0.7137 (p0) REVERT: B 1056 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.8023 (pp30) REVERT: B 1204 TYR cc_start: 0.8170 (m-80) cc_final: 0.7892 (m-10) REVERT: C 31 ILE cc_start: 0.8029 (mm) cc_final: 0.7729 (tp) REVERT: C 147 PHE cc_start: 0.7736 (m-80) cc_final: 0.7516 (m-10) REVERT: C 240 MET cc_start: 0.7815 (tpp) cc_final: 0.7608 (tpp) REVERT: C 353 SER cc_start: 0.8629 (t) cc_final: 0.8428 (m) outliers start: 69 outliers final: 43 residues processed: 276 average time/residue: 0.1604 time to fit residues: 74.6346 Evaluate side-chains 235 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 187 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 307 ARG Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 502 LYS Chi-restraints excluded: chain A residue 540 TYR Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 772 GLN Chi-restraints excluded: chain A residue 819 GLN Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1190 SER Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 258 GLN Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain B residue 859 SER Chi-restraints excluded: chain B residue 966 SER Chi-restraints excluded: chain B residue 1020 GLN Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1056 GLN Chi-restraints excluded: chain B residue 1151 SER Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 592 ASN Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 986 THR Chi-restraints excluded: chain C residue 1041 SER Chi-restraints excluded: chain C residue 1042 ASN Chi-restraints excluded: chain C residue 1087 VAL Chi-restraints excluded: chain C residue 1094 LEU Chi-restraints excluded: chain C residue 1121 THR Chi-restraints excluded: chain C residue 1205 VAL Chi-restraints excluded: chain H residue 62 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 287 optimal weight: 1.9990 chunk 307 optimal weight: 10.0000 chunk 172 optimal weight: 3.9990 chunk 168 optimal weight: 0.7980 chunk 145 optimal weight: 2.9990 chunk 139 optimal weight: 0.0870 chunk 230 optimal weight: 4.9990 chunk 237 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 187 optimal weight: 0.9980 chunk 177 optimal weight: 0.3980 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 ASN ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 GLN A1122 HIS B 258 GLN B 348 HIS B 636 GLN B 812 ASN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1056 GLN B1066 GLN C 304 GLN C 618 GLN C 812 ASN C1042 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.149139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.122880 restraints weight = 48479.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.124242 restraints weight = 39983.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.124829 restraints weight = 34645.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.124987 restraints weight = 26810.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.125114 restraints weight = 25427.446| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.129 27431 Z= 0.180 Angle : 0.670 18.309 37550 Z= 0.331 Chirality : 0.045 0.255 4457 Planarity : 0.005 0.064 4677 Dihedral : 7.332 59.670 5901 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.73 % Allowed : 12.03 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.14), residues: 3277 helix: 1.69 (0.20), residues: 676 sheet: 0.43 (0.18), residues: 714 loop : -0.75 (0.13), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 269 TYR 0.016 0.001 TYR A1141 PHE 0.018 0.002 PHE A 778 TRP 0.018 0.001 TRP H 33 HIS 0.009 0.001 HIS A1138 Details of bonding type rmsd covalent geometry : bond 0.00421 (27273) covalent geometry : angle 0.63723 (37121) SS BOND : bond 0.00331 ( 45) SS BOND : angle 2.33506 ( 90) hydrogen bonds : bond 0.05779 ( 1031) hydrogen bonds : angle 5.28260 ( 2802) link_ALPHA1-2 : bond 0.00438 ( 1) link_ALPHA1-2 : angle 1.23856 ( 3) link_ALPHA1-3 : bond 0.01122 ( 9) link_ALPHA1-3 : angle 2.50757 ( 27) link_ALPHA1-6 : bond 0.00727 ( 7) link_ALPHA1-6 : angle 1.57035 ( 21) link_BETA1-4 : bond 0.01085 ( 49) link_BETA1-4 : angle 2.03287 ( 147) link_NAG-ASN : bond 0.00542 ( 47) link_NAG-ASN : angle 1.79255 ( 141) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 203 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 GLU cc_start: 0.7471 (pp20) cc_final: 0.7256 (tm-30) REVERT: A 467 PHE cc_start: 0.6254 (m-10) cc_final: 0.6005 (m-10) REVERT: A 473 PHE cc_start: 0.7927 (p90) cc_final: 0.7679 (p90) REVERT: A 474 SER cc_start: 0.8577 (OUTLIER) cc_final: 0.7934 (t) REVERT: A 502 LYS cc_start: 0.7363 (OUTLIER) cc_final: 0.7137 (ptmm) REVERT: A 729 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8418 (pp) REVERT: A 820 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8366 (mp) REVERT: A 875 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7364 (mp0) REVERT: B 185 CYS cc_start: 0.4141 (OUTLIER) cc_final: 0.3476 (m) REVERT: B 686 MET cc_start: 0.7659 (mmm) cc_final: 0.7428 (tpp) REVERT: B 725 GLU cc_start: 0.7447 (mt-10) cc_final: 0.7071 (mm-30) REVERT: B 726 ASP cc_start: 0.7802 (m-30) cc_final: 0.7011 (p0) REVERT: B 1056 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.8018 (pp30) REVERT: C 31 ILE cc_start: 0.8076 (mm) cc_final: 0.7840 (tp) REVERT: C 240 MET cc_start: 0.7847 (tpp) cc_final: 0.7601 (tpp) outliers start: 73 outliers final: 49 residues processed: 266 average time/residue: 0.1576 time to fit residues: 71.3392 Evaluate side-chains 236 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 181 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 438 TYR Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 502 LYS Chi-restraints excluded: chain A residue 540 TYR Chi-restraints excluded: chain A residue 541 TYR Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain A residue 1042 ASN Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1190 SER Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 355 ASP Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain B residue 859 SER Chi-restraints excluded: chain B residue 1020 GLN Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1056 GLN Chi-restraints excluded: chain B residue 1151 SER Chi-restraints excluded: chain B residue 1210 THR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 592 ASN Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 939 MET Chi-restraints excluded: chain C residue 986 THR Chi-restraints excluded: chain C residue 1087 VAL Chi-restraints excluded: chain C residue 1094 LEU Chi-restraints excluded: chain C residue 1205 VAL Chi-restraints excluded: chain C residue 1210 THR Chi-restraints excluded: chain H residue 62 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 209 optimal weight: 2.9990 chunk 196 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 309 optimal weight: 20.0000 chunk 39 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 97 optimal weight: 0.1980 chunk 100 optimal weight: 0.7980 chunk 304 optimal weight: 0.0980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1056 GLN C 91 HIS C 812 ASN C1042 ASN C1122 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.149948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.123930 restraints weight = 48614.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.122867 restraints weight = 42857.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.123744 restraints weight = 42132.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.124093 restraints weight = 35976.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.124491 restraints weight = 30531.313| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 27431 Z= 0.145 Angle : 0.651 19.936 37550 Z= 0.320 Chirality : 0.044 0.258 4457 Planarity : 0.004 0.062 4677 Dihedral : 6.855 55.650 5901 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.84 % Allowed : 12.26 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.14), residues: 3277 helix: 1.70 (0.20), residues: 685 sheet: 0.45 (0.18), residues: 737 loop : -0.75 (0.13), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 269 TYR 0.016 0.001 TYR A1141 PHE 0.015 0.001 PHE A 778 TRP 0.022 0.001 TRP H 117 HIS 0.007 0.001 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00333 (27273) covalent geometry : angle 0.61242 (37121) SS BOND : bond 0.00276 ( 45) SS BOND : angle 2.95439 ( 90) hydrogen bonds : bond 0.05308 ( 1031) hydrogen bonds : angle 5.15260 ( 2802) link_ALPHA1-2 : bond 0.00518 ( 1) link_ALPHA1-2 : angle 1.26002 ( 3) link_ALPHA1-3 : bond 0.01109 ( 9) link_ALPHA1-3 : angle 2.28762 ( 27) link_ALPHA1-6 : bond 0.00782 ( 7) link_ALPHA1-6 : angle 1.52838 ( 21) link_BETA1-4 : bond 0.01055 ( 49) link_BETA1-4 : angle 2.01286 ( 147) link_NAG-ASN : bond 0.00298 ( 47) link_NAG-ASN : angle 1.76093 ( 141) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 207 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 GLU cc_start: 0.7405 (pp20) cc_final: 0.7196 (tm-30) REVERT: A 467 PHE cc_start: 0.6381 (m-10) cc_final: 0.6057 (m-10) REVERT: A 474 SER cc_start: 0.8653 (OUTLIER) cc_final: 0.8012 (t) REVERT: A 674 PHE cc_start: 0.8832 (m-80) cc_final: 0.8514 (m-10) REVERT: A 729 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8440 (pp) REVERT: A 820 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8287 (mp) REVERT: A 875 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7372 (mp0) REVERT: B 185 CYS cc_start: 0.4117 (OUTLIER) cc_final: 0.3298 (m) REVERT: B 686 MET cc_start: 0.7614 (mmm) cc_final: 0.7382 (tpp) REVERT: B 725 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7067 (mm-30) REVERT: B 726 ASP cc_start: 0.7827 (m-30) cc_final: 0.7038 (p0) REVERT: B 871 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8116 (pp) REVERT: B 1056 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.7872 (pp30) REVERT: C 31 ILE cc_start: 0.7898 (mm) cc_final: 0.7654 (tp) REVERT: C 147 PHE cc_start: 0.7615 (m-80) cc_final: 0.7318 (m-10) REVERT: C 240 MET cc_start: 0.7865 (tpp) cc_final: 0.7645 (tpp) REVERT: C 964 LEU cc_start: 0.8035 (mm) cc_final: 0.7769 (mp) outliers start: 76 outliers final: 50 residues processed: 273 average time/residue: 0.1520 time to fit residues: 71.1313 Evaluate side-chains 241 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 185 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 438 TYR Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 540 TYR Chi-restraints excluded: chain A residue 541 TYR Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 772 GLN Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain A residue 1042 ASN Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1190 SER Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain B residue 859 SER Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 966 SER Chi-restraints excluded: chain B residue 1020 GLN Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1055 ILE Chi-restraints excluded: chain B residue 1056 GLN Chi-restraints excluded: chain B residue 1151 SER Chi-restraints excluded: chain B residue 1210 THR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 592 ASN Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 986 THR Chi-restraints excluded: chain C residue 1042 ASN Chi-restraints excluded: chain C residue 1087 VAL Chi-restraints excluded: chain C residue 1094 LEU Chi-restraints excluded: chain C residue 1205 VAL Chi-restraints excluded: chain C residue 1210 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 186 optimal weight: 0.0570 chunk 247 optimal weight: 0.3980 chunk 124 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 264 optimal weight: 0.6980 chunk 281 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 206 optimal weight: 0.6980 chunk 259 optimal weight: 1.9990 chunk 209 optimal weight: 0.9980 chunk 115 optimal weight: 0.0970 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN B 812 ASN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1056 GLN C 836 HIS C1042 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.150080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.123102 restraints weight = 47861.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.123622 restraints weight = 39752.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.124582 restraints weight = 34395.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.124941 restraints weight = 28174.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.125087 restraints weight = 24566.404| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.4439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 27431 Z= 0.125 Angle : 0.628 19.806 37550 Z= 0.306 Chirality : 0.043 0.256 4457 Planarity : 0.004 0.062 4677 Dihedral : 6.440 54.073 5901 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.35 % Allowed : 13.19 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.14), residues: 3277 helix: 1.86 (0.21), residues: 678 sheet: 0.50 (0.18), residues: 737 loop : -0.72 (0.14), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 847 TYR 0.016 0.001 TYR B 635 PHE 0.018 0.001 PHE C 40 TRP 0.024 0.001 TRP H 117 HIS 0.007 0.001 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00275 (27273) covalent geometry : angle 0.59549 (37121) SS BOND : bond 0.00310 ( 45) SS BOND : angle 2.30828 ( 90) hydrogen bonds : bond 0.04942 ( 1031) hydrogen bonds : angle 5.04171 ( 2802) link_ALPHA1-2 : bond 0.00632 ( 1) link_ALPHA1-2 : angle 1.31576 ( 3) link_ALPHA1-3 : bond 0.01105 ( 9) link_ALPHA1-3 : angle 2.16023 ( 27) link_ALPHA1-6 : bond 0.00825 ( 7) link_ALPHA1-6 : angle 1.50841 ( 21) link_BETA1-4 : bond 0.01055 ( 49) link_BETA1-4 : angle 1.99541 ( 147) link_NAG-ASN : bond 0.00284 ( 47) link_NAG-ASN : angle 1.65395 ( 141) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 203 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 GLU cc_start: 0.7621 (pp20) cc_final: 0.7297 (tm-30) REVERT: A 467 PHE cc_start: 0.6269 (m-10) cc_final: 0.6050 (m-10) REVERT: A 502 LYS cc_start: 0.7682 (pttm) cc_final: 0.7480 (ptmm) REVERT: A 674 PHE cc_start: 0.8838 (m-80) cc_final: 0.8507 (m-10) REVERT: A 729 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8454 (pp) REVERT: A 820 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8318 (mp) REVERT: A 875 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7447 (mp0) REVERT: B 185 CYS cc_start: 0.3957 (OUTLIER) cc_final: 0.3296 (m) REVERT: B 686 MET cc_start: 0.7636 (mmm) cc_final: 0.7406 (tpp) REVERT: B 725 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7085 (mm-30) REVERT: B 726 ASP cc_start: 0.7811 (m-30) cc_final: 0.7031 (p0) REVERT: B 871 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8112 (pp) REVERT: B 1056 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.8139 (pp30) REVERT: B 1204 TYR cc_start: 0.8189 (m-80) cc_final: 0.7930 (m-10) REVERT: C 31 ILE cc_start: 0.7940 (mm) cc_final: 0.7689 (tp) REVERT: C 240 MET cc_start: 0.7939 (tpp) cc_final: 0.7721 (tpp) REVERT: C 964 LEU cc_start: 0.8018 (mm) cc_final: 0.7749 (mp) outliers start: 63 outliers final: 45 residues processed: 255 average time/residue: 0.1554 time to fit residues: 67.5486 Evaluate side-chains 241 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 191 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 438 TYR Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 540 TYR Chi-restraints excluded: chain A residue 541 TYR Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 772 GLN Chi-restraints excluded: chain A residue 817 CYS Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain A residue 1042 ASN Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1190 SER Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain B residue 859 SER Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 966 SER Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1056 GLN Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 592 ASN Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 853 VAL Chi-restraints excluded: chain C residue 986 THR Chi-restraints excluded: chain C residue 1042 ASN Chi-restraints excluded: chain C residue 1087 VAL Chi-restraints excluded: chain C residue 1094 LEU Chi-restraints excluded: chain C residue 1205 VAL Chi-restraints excluded: chain C residue 1210 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 234 optimal weight: 2.9990 chunk 259 optimal weight: 1.9990 chunk 298 optimal weight: 0.7980 chunk 265 optimal weight: 0.5980 chunk 201 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 327 optimal weight: 7.9990 chunk 278 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 241 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1020 GLN B 81 HIS B 636 GLN B1056 GLN B1085 GLN C 277 ASN C 636 GLN C 812 ASN C1042 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.147547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.121052 restraints weight = 48367.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.121081 restraints weight = 40222.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.121941 restraints weight = 34485.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.122443 restraints weight = 28116.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.122511 restraints weight = 26078.921| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.4620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 27431 Z= 0.173 Angle : 0.654 20.655 37550 Z= 0.321 Chirality : 0.044 0.250 4457 Planarity : 0.004 0.058 4677 Dihedral : 6.415 53.174 5901 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.77 % Allowed : 13.23 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.14), residues: 3277 helix: 1.75 (0.21), residues: 679 sheet: 0.45 (0.18), residues: 741 loop : -0.79 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 119 TYR 0.017 0.001 TYR B 635 PHE 0.016 0.002 PHE A 778 TRP 0.022 0.001 TRP H 117 HIS 0.008 0.001 HIS A1138 Details of bonding type rmsd covalent geometry : bond 0.00409 (27273) covalent geometry : angle 0.62208 (37121) SS BOND : bond 0.00300 ( 45) SS BOND : angle 2.27922 ( 90) hydrogen bonds : bond 0.05412 ( 1031) hydrogen bonds : angle 5.12645 ( 2802) link_ALPHA1-2 : bond 0.00686 ( 1) link_ALPHA1-2 : angle 1.37512 ( 3) link_ALPHA1-3 : bond 0.01089 ( 9) link_ALPHA1-3 : angle 2.17003 ( 27) link_ALPHA1-6 : bond 0.00774 ( 7) link_ALPHA1-6 : angle 1.53639 ( 21) link_BETA1-4 : bond 0.01018 ( 49) link_BETA1-4 : angle 2.04339 ( 147) link_NAG-ASN : bond 0.00339 ( 47) link_NAG-ASN : angle 1.73262 ( 141) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 192 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 467 PHE cc_start: 0.6386 (m-10) cc_final: 0.6033 (m-10) REVERT: A 502 LYS cc_start: 0.7695 (pttm) cc_final: 0.7315 (ptmm) REVERT: A 674 PHE cc_start: 0.8896 (m-80) cc_final: 0.8515 (m-10) REVERT: A 729 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8509 (pp) REVERT: A 820 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8283 (mp) REVERT: A 875 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7412 (mp0) REVERT: B 686 MET cc_start: 0.7747 (mmm) cc_final: 0.7508 (tpp) REVERT: B 725 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7076 (mm-30) REVERT: B 726 ASP cc_start: 0.7892 (m-30) cc_final: 0.7057 (p0) REVERT: B 871 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8169 (pp) REVERT: B 1056 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.7450 (pp30) REVERT: C 31 ILE cc_start: 0.7934 (mm) cc_final: 0.7638 (tp) REVERT: C 272 ASP cc_start: 0.6960 (t70) cc_final: 0.6295 (t0) REVERT: C 964 LEU cc_start: 0.7939 (mm) cc_final: 0.7697 (mp) outliers start: 74 outliers final: 55 residues processed: 257 average time/residue: 0.1495 time to fit residues: 66.3455 Evaluate side-chains 239 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 180 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 438 TYR Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 540 TYR Chi-restraints excluded: chain A residue 541 TYR Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 817 CYS Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain A residue 1042 ASN Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1190 SER Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 355 ASP Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain B residue 859 SER Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 1020 GLN Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1056 GLN Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 592 ASN Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 853 VAL Chi-restraints excluded: chain C residue 986 THR Chi-restraints excluded: chain C residue 1042 ASN Chi-restraints excluded: chain C residue 1087 VAL Chi-restraints excluded: chain C residue 1094 LEU Chi-restraints excluded: chain C residue 1205 VAL Chi-restraints excluded: chain C residue 1210 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 43 optimal weight: 1.9990 chunk 200 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 152 optimal weight: 0.5980 chunk 278 optimal weight: 2.9990 chunk 172 optimal weight: 0.8980 chunk 229 optimal weight: 8.9990 chunk 80 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN B1056 GLN C1042 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.148084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.121668 restraints weight = 48156.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.121665 restraints weight = 40132.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.122668 restraints weight = 33706.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.123189 restraints weight = 27496.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.123267 restraints weight = 25116.067| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.4746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 27431 Z= 0.156 Angle : 0.651 21.042 37550 Z= 0.320 Chirality : 0.044 0.246 4457 Planarity : 0.004 0.061 4677 Dihedral : 6.335 52.605 5901 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.47 % Allowed : 13.64 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.14), residues: 3277 helix: 1.76 (0.21), residues: 684 sheet: 0.44 (0.18), residues: 740 loop : -0.80 (0.14), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 269 TYR 0.017 0.001 TYR B 635 PHE 0.015 0.001 PHE A 778 TRP 0.019 0.001 TRP H 117 HIS 0.007 0.001 HIS A1138 Details of bonding type rmsd covalent geometry : bond 0.00362 (27273) covalent geometry : angle 0.61964 (37121) SS BOND : bond 0.00331 ( 45) SS BOND : angle 2.30197 ( 90) hydrogen bonds : bond 0.05304 ( 1031) hydrogen bonds : angle 5.09540 ( 2802) link_ALPHA1-2 : bond 0.00690 ( 1) link_ALPHA1-2 : angle 1.35111 ( 3) link_ALPHA1-3 : bond 0.01064 ( 9) link_ALPHA1-3 : angle 2.04864 ( 27) link_ALPHA1-6 : bond 0.00784 ( 7) link_ALPHA1-6 : angle 1.50120 ( 21) link_BETA1-4 : bond 0.01027 ( 49) link_BETA1-4 : angle 2.03493 ( 147) link_NAG-ASN : bond 0.00320 ( 47) link_NAG-ASN : angle 1.71519 ( 141) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 192 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 LEU cc_start: 0.6257 (mt) cc_final: 0.5919 (mt) REVERT: A 502 LYS cc_start: 0.7694 (pttm) cc_final: 0.7398 (ptmm) REVERT: A 674 PHE cc_start: 0.8791 (m-80) cc_final: 0.8461 (m-10) REVERT: A 729 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8508 (pp) REVERT: A 820 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8308 (mp) REVERT: A 875 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7415 (mp0) REVERT: B 725 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7070 (mm-30) REVERT: B 726 ASP cc_start: 0.7901 (m-30) cc_final: 0.7066 (p0) REVERT: B 871 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8186 (pp) REVERT: B 1056 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.7538 (pp30) REVERT: C 31 ILE cc_start: 0.7930 (mm) cc_final: 0.7622 (tp) outliers start: 66 outliers final: 55 residues processed: 250 average time/residue: 0.1517 time to fit residues: 64.9798 Evaluate side-chains 241 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 182 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 438 TYR Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 540 TYR Chi-restraints excluded: chain A residue 541 TYR Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 772 GLN Chi-restraints excluded: chain A residue 817 CYS Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain A residue 1042 ASN Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1190 SER Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain B residue 859 SER Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 888 SER Chi-restraints excluded: chain B residue 1020 GLN Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1056 GLN Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 592 ASN Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 853 VAL Chi-restraints excluded: chain C residue 986 THR Chi-restraints excluded: chain C residue 1042 ASN Chi-restraints excluded: chain C residue 1087 VAL Chi-restraints excluded: chain C residue 1094 LEU Chi-restraints excluded: chain C residue 1205 VAL Chi-restraints excluded: chain C residue 1210 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 326 optimal weight: 10.0000 chunk 186 optimal weight: 0.8980 chunk 321 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 179 optimal weight: 0.9990 chunk 268 optimal weight: 0.5980 chunk 166 optimal weight: 0.4980 chunk 118 optimal weight: 0.9990 chunk 163 optimal weight: 1.9990 chunk 265 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN C1042 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.149368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.123992 restraints weight = 47988.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.123298 restraints weight = 43318.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.124342 restraints weight = 36943.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.124687 restraints weight = 31096.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.124930 restraints weight = 29699.361| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.4856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 27431 Z= 0.159 Angle : 0.658 21.027 37550 Z= 0.322 Chirality : 0.044 0.244 4457 Planarity : 0.004 0.060 4677 Dihedral : 6.286 51.991 5901 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.32 % Allowed : 13.94 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.14), residues: 3277 helix: 1.76 (0.21), residues: 684 sheet: 0.46 (0.18), residues: 728 loop : -0.82 (0.14), residues: 1865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 269 TYR 0.017 0.001 TYR B 635 PHE 0.017 0.002 PHE C 147 TRP 0.018 0.001 TRP H 117 HIS 0.007 0.001 HIS A1138 Details of bonding type rmsd covalent geometry : bond 0.00371 (27273) covalent geometry : angle 0.62747 (37121) SS BOND : bond 0.00267 ( 45) SS BOND : angle 2.26857 ( 90) hydrogen bonds : bond 0.05325 ( 1031) hydrogen bonds : angle 5.10281 ( 2802) link_ALPHA1-2 : bond 0.00702 ( 1) link_ALPHA1-2 : angle 1.36589 ( 3) link_ALPHA1-3 : bond 0.01037 ( 9) link_ALPHA1-3 : angle 1.98431 ( 27) link_ALPHA1-6 : bond 0.00791 ( 7) link_ALPHA1-6 : angle 1.49592 ( 21) link_BETA1-4 : bond 0.01007 ( 49) link_BETA1-4 : angle 2.03736 ( 147) link_NAG-ASN : bond 0.00323 ( 47) link_NAG-ASN : angle 1.71423 ( 141) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 190 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 LEU cc_start: 0.6264 (mt) cc_final: 0.5915 (mt) REVERT: A 467 PHE cc_start: 0.6576 (m-10) cc_final: 0.6233 (m-10) REVERT: A 502 LYS cc_start: 0.7655 (pttm) cc_final: 0.7237 (ptmm) REVERT: A 576 GLN cc_start: 0.8181 (mm-40) cc_final: 0.7738 (mm-40) REVERT: A 674 PHE cc_start: 0.8778 (m-80) cc_final: 0.8437 (m-10) REVERT: A 729 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8488 (pp) REVERT: A 820 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8325 (mp) REVERT: A 875 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7427 (mp0) REVERT: B 725 GLU cc_start: 0.7488 (mt-10) cc_final: 0.7020 (mm-30) REVERT: B 726 ASP cc_start: 0.7837 (m-30) cc_final: 0.7066 (p0) REVERT: B 871 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8168 (pp) REVERT: C 272 ASP cc_start: 0.6335 (t70) cc_final: 0.5553 (t0) REVERT: C 964 LEU cc_start: 0.7982 (mm) cc_final: 0.7765 (mp) outliers start: 62 outliers final: 57 residues processed: 244 average time/residue: 0.1498 time to fit residues: 62.6161 Evaluate side-chains 240 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 180 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 438 TYR Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 540 TYR Chi-restraints excluded: chain A residue 541 TYR Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 772 GLN Chi-restraints excluded: chain A residue 817 CYS Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain A residue 1042 ASN Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1190 SER Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain B residue 859 SER Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 888 SER Chi-restraints excluded: chain B residue 912 CYS Chi-restraints excluded: chain B residue 1020 GLN Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 592 ASN Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 853 VAL Chi-restraints excluded: chain C residue 986 THR Chi-restraints excluded: chain C residue 1042 ASN Chi-restraints excluded: chain C residue 1087 VAL Chi-restraints excluded: chain C residue 1094 LEU Chi-restraints excluded: chain C residue 1205 VAL Chi-restraints excluded: chain C residue 1210 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 7 optimal weight: 6.9990 chunk 178 optimal weight: 0.0030 chunk 290 optimal weight: 0.5980 chunk 150 optimal weight: 1.9990 chunk 269 optimal weight: 0.6980 chunk 113 optimal weight: 0.2980 chunk 87 optimal weight: 2.9990 chunk 167 optimal weight: 0.5980 chunk 234 optimal weight: 0.5980 chunk 245 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 overall best weight: 0.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1056 GLN C1042 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.151115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.126330 restraints weight = 48103.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.125391 restraints weight = 41955.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.126019 restraints weight = 39310.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.126443 restraints weight = 34834.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.126685 restraints weight = 30814.515| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.4957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 27431 Z= 0.124 Angle : 0.626 20.658 37550 Z= 0.305 Chirality : 0.043 0.249 4457 Planarity : 0.004 0.063 4677 Dihedral : 5.985 50.796 5901 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.02 % Allowed : 14.09 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.14), residues: 3277 helix: 1.90 (0.21), residues: 680 sheet: 0.49 (0.19), residues: 735 loop : -0.74 (0.14), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 847 TYR 0.018 0.001 TYR B 635 PHE 0.012 0.001 PHE A 778 TRP 0.020 0.001 TRP H 117 HIS 0.007 0.001 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00276 (27273) covalent geometry : angle 0.59714 (37121) SS BOND : bond 0.00241 ( 45) SS BOND : angle 2.09694 ( 90) hydrogen bonds : bond 0.04799 ( 1031) hydrogen bonds : angle 4.94291 ( 2802) link_ALPHA1-2 : bond 0.00697 ( 1) link_ALPHA1-2 : angle 1.32552 ( 3) link_ALPHA1-3 : bond 0.00989 ( 9) link_ALPHA1-3 : angle 1.79971 ( 27) link_ALPHA1-6 : bond 0.00830 ( 7) link_ALPHA1-6 : angle 1.44247 ( 21) link_BETA1-4 : bond 0.01008 ( 49) link_BETA1-4 : angle 1.99502 ( 147) link_NAG-ASN : bond 0.00332 ( 47) link_NAG-ASN : angle 1.60492 ( 141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3969.94 seconds wall clock time: 69 minutes 48.88 seconds (4188.88 seconds total)