Starting phenix.real_space_refine on Mon Sep 14 14:29:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6nb3_0401/09_2026/6nb3_0401.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nb3_0401/09_2026/6nb3_0401.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6nb3_0401/09_2026/6nb3_0401.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6nb3_0401/09_2026/6nb3_0401.cif" model { file = "/net/cci-nas-00/data/ceres_data/6nb3_0401/09_2026/6nb3_0401.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nb3_0401/09_2026/6nb3_0401.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6nb3_0401/09_2026/6nb3_0401.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nb3_0401/09_2026/6nb3_0401.map" } resolution = 3.5 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= 0.061 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 155 5.16 5 C 19492 2.51 5 N 4892 2.21 5 O 6421 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 199 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30960 Number of models: 1 Model: "" Number of chains: 54 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: "L" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 773 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 958 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "D" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 951 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "E" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 773 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} 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: 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: "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 chiralities: 2 Chain: "G" 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 chiralities: 3 Chain: "I" 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 chiralities: 6 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "K" 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 chiralities: 6 Chain: "M" 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 chiralities: 6 Chain: "N" 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 chiralities: 5 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "P" 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 chiralities: 6 Chain: "Q" 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 chiralities: 4 Chain: "R" 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 chiralities: 3 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 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 chiralities: 2 Chain: "U" 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 chiralities: 2 Chain: "V" 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 chiralities: 3 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 chiralities: 5 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 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 chiralities: 3 Chain: "Z" 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 chiralities: 6 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "b" 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 chiralities: 6 Chain: "c" 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 chiralities: 6 Chain: "d" 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 chiralities: 5 Chain: "e" 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 chiralities: 3 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 chiralities: 2 Chain: "g" 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 chiralities: 3 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "k" 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 chiralities: 5 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 chiralities: 2 Chain: "m" 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 chiralities: 3 Chain: "n" 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 chiralities: 6 Chain: "o" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "p" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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 chiralities: 5 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 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 chiralities: 2 Chain: "t" 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 chiralities: 3 Chain: "u" 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 chiralities: 2 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 chiralities: 2 Chain: "w" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "x" 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 chiralities: 3 Chain: "y" 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 chiralities: 5 Chain: "A" 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 chiralities: 1 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 chiralities: 1 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 6.35, per 1000 atoms: 0.21 Number of scatterers: 30960 At special positions: 0 Unit cell: (153.44, 147.96, 194.54, 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 155 16.00 O 6421 8.00 N 4892 7.00 C 19492 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS A 195 " distance=2.06 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=2.07 Simple disulfide: pdb=" SG CYS A 425 " - pdb=" SG CYS A 478 " distance=2.05 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 585 " distance=2.06 Simple disulfide: pdb=" SG CYS A 503 " - pdb=" SG CYS A 526 " distance=2.04 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 654 " distance=2.03 Simple disulfide: pdb=" SG CYS A 620 " - pdb=" SG CYS A 650 " distance=2.03 Simple disulfide: pdb=" SG CYS A 679 " - pdb=" SG CYS A 713 " distance=2.23 Simple disulfide: pdb=" SG CYS A 727 " - pdb=" SG CYS A 736 " distance=2.04 Simple disulfide: pdb=" SG CYS A 806 " - pdb=" SG CYS A 828 " distance=2.04 Simple disulfide: pdb=" SG CYS A 811 " - pdb=" SG CYS A 817 " distance=2.08 Simple disulfide: pdb=" SG CYS A 912 " - pdb=" SG CYS A 925 " distance=2.04 Simple disulfide: pdb=" SG CYS A1106 " - pdb=" SG CYS A1117 " distance=2.04 Simple disulfide: pdb=" SG CYS A1156 " - pdb=" SG CYS A1164 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 98 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 98 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 90 " distance=2.02 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=2.03 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=2.16 Simple disulfide: pdb=" SG CYS B 727 " - pdb=" SG CYS B 736 " distance=2.04 Simple disulfide: pdb=" SG CYS B 806 " - pdb=" SG CYS B 828 " distance=2.02 Simple disulfide: pdb=" SG CYS B 811 " - pdb=" SG CYS B 817 " distance=2.11 Simple disulfide: pdb=" SG CYS B 912 " - pdb=" SG CYS B 925 " distance=2.13 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 383 " - pdb=" SG CYS C 407 " distance=2.04 Simple disulfide: pdb=" SG CYS C 425 " - pdb=" SG CYS C 478 " distance=2.04 Simple disulfide: pdb=" SG CYS C 437 " - pdb=" SG CYS C 585 " distance=2.08 Simple disulfide: pdb=" SG CYS C 503 " - pdb=" SG CYS C 526 " distance=2.02 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 654 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 727 " - pdb=" SG CYS C 736 " distance=2.02 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=2.06 Simple disulfide: pdb=" SG CYS C 912 " - pdb=" SG CYS C 925 " distance=2.08 Simple disulfide: pdb=" SG CYS C1106 " - pdb=" SG CYS C1117 " distance=2.03 Simple disulfide: pdb=" SG CYS C1156 " - pdb=" SG CYS C1164 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN I 4 " - " MAN I 5 " " MAN K 4 " - " MAN K 5 " " MAN M 4 " - " MAN M 5 " " MAN P 4 " - " MAN P 5 " " MAN Z 4 " - " MAN Z 5 " " MAN b 4 " - " MAN b 5 " " MAN c 4 " - " MAN c 5 " " MAN n 4 " - " MAN n 5 " " MAN q 4 " - " MAN q 5 " ALPHA1-3 " BMA I 3 " - " MAN I 4 " " BMA K 3 " - " MAN K 4 " " BMA M 3 " - " MAN M 4 " " BMA N 3 " - " MAN N 4 " " BMA P 3 " - " MAN P 4 " " BMA Q 3 " - " MAN Q 4 " " BMA W 3 " - " MAN W 4 " " BMA Z 3 " - " MAN Z 4 " " BMA b 3 " - " MAN b 4 " " BMA c 3 " - " MAN c 4 " " BMA d 3 " - " MAN d 4 " " BMA k 3 " - " MAN k 4 " " BMA n 3 " - " MAN n 4 " " BMA q 3 " - " MAN q 4 " " BMA y 3 " - " MAN y 4 " ALPHA1-6 " BMA I 3 " - " MAN I 6 " " BMA K 3 " - " MAN K 6 " " BMA M 3 " - " MAN M 6 " " BMA N 3 " - " MAN N 5 " " BMA P 3 " - " MAN P 6 " " BMA W 3 " - " MAN W 5 " " BMA Z 3 " - " MAN Z 6 " " BMA b 3 " - " MAN b 6 " " BMA c 3 " - " MAN c 6 " " BMA d 3 " - " MAN d 5 " " BMA k 3 " - " MAN k 5 " " BMA n 3 " - " MAN n 6 " " BMA y 3 " - " MAN y 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " 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 V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " 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 g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " NAG-ASN " NAG A1445 " - " ASN A 592 " " NAG B1442 " - " ASN B 774 " " NAG C1423 " - " ASN C 236 " " NAG C1428 " - " ASN C 487 " " NAG C1429 " - " ASN C 592 " " NAG F 1 " - " ASN A 66 " " NAG G 1 " - " ASN A 104 " " NAG I 1 " - " ASN A 125 " " NAG J 1 " - " ASN A 155 " " NAG K 1 " - " ASN A 166 " " NAG M 1 " - " ASN A 222 " " NAG N 1 " - " ASN A 236 " " NAG O 1 " - " ASN A 244 " " NAG P 1 " - " ASN A 410 " " NAG Q 1 " - " ASN A 487 " " NAG R 1 " - " ASN A 619 " " NAG S 1 " - " ASN A 719 " " NAG T 1 " - " ASN A 774 " " NAG U 1 " - " ASN A 785 " " NAG V 1 " - " ASN A 870 " " NAG W 1 " - " ASN A1213 " " NAG X 1 " - " ASN B 66 " " NAG Y 1 " - " ASN B 104 " " NAG Z 1 " - " ASN B 125 " " NAG a 1 " - " ASN B 155 " " NAG b 1 " - " ASN B 166 " " NAG c 1 " - " ASN B 222 " " NAG d 1 " - " ASN B 236 " " NAG e 1 " - " ASN B 244 " " NAG f 1 " - " ASN B 592 " " NAG g 1 " - " ASN B 619 " " NAG h 1 " - " ASN B 719 " " NAG i 1 " - " ASN B 785 " " NAG j 1 " - " ASN B 870 " " NAG k 1 " - " ASN B1213 " " NAG l 1 " - " ASN C 66 " " NAG m 1 " - " ASN C 104 " " NAG n 1 " - " ASN C 125 " " NAG o 1 " - " ASN C 155 " " NAG p 1 " - " ASN C 166 " " NAG q 1 " - " ASN C 222 " " NAG r 1 " - " ASN C 244 " " NAG s 1 " - " ASN C 410 " " NAG t 1 " - " ASN C 619 " " NAG u 1 " - " ASN C 719 " " NAG v 1 " - " ASN C 774 " " NAG w 1 " - " ASN C 785 " " NAG x 1 " - " ASN C 870 " " NAG y 1 " - " ASN C1213 " Time building additional restraints: 3.09 Conformation dependent library (CDL) restraints added in 1.2 seconds 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6928 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 69 sheets defined 22.2% alpha, 28.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 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 395 through 399 removed outlier: 3.925A pdb=" N PHE A 399 " --> pdb=" O VAL A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 416 removed outlier: 3.760A pdb=" N LEU A 414 " --> pdb=" O ASN A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 435 Processing helix chain 'A' and resid 449 through 456 removed outlier: 4.583A 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 812 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: 3.525A 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: 3.697A 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: 4.295A pdb=" N ALA A1032 " --> pdb=" O ASN A1028 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU A1033 " --> pdb=" O ASN A1029 " (cutoff:3.500A) removed outlier: 3.982A 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: 4.842A pdb=" N ALA A1065 " --> pdb=" O PRO A1061 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 85 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 53 through 57 Processing helix chain 'H' and resid 89 through 93 Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 53 through 57 Processing helix chain 'D' and resid 64 through 67 Processing helix chain 'D' and resid 89 through 93 Processing helix chain 'E' and resid 81 through 85 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 213 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: 4.137A 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: 4.614A 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: 4.056A pdb=" N ALA B1032 " --> pdb=" O ASN B1028 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LEU B1033 " --> pdb=" O ASN B1029 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER B1034 " --> pdb=" O ALA B1030 " (cutoff:3.500A) removed outlier: 4.264A 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: 3.515A pdb=" N ASP B1064 " --> pdb=" O PRO B1060 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ALA B1065 " --> pdb=" O PRO B1061 " (cutoff:3.500A) removed outlier: 3.533A 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 395 through 399 removed outlier: 3.564A pdb=" N PHE C 399 " --> pdb=" O VAL C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 417 removed outlier: 3.554A pdb=" N LEU C 414 " --> pdb=" O ASN C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 435 Processing helix chain 'C' and resid 449 through 457 removed outlier: 5.268A pdb=" N SER C 454 " --> pdb=" O SER C 451 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER C 457 " --> pdb=" O SER C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 805 through 812 Processing helix chain 'C' and resid 814 through 822 removed outlier: 3.700A pdb=" N GLN C 819 " --> pdb=" O GLN C 815 " (cutoff:3.500A) removed outlier: 4.271A 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: 3.761A pdb=" N MET C 913 " --> pdb=" O TYR C 909 " (cutoff:3.500A) Processing helix chain 'C' and resid 926 through 931 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: 4.003A pdb=" N THR C1010 " --> pdb=" O GLY C1006 " (cutoff:3.500A) Processing helix chain 'C' and resid 1016 through 1040 removed outlier: 3.508A pdb=" N VAL C1022 " --> pdb=" O ALA C1018 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA C1032 " --> pdb=" O ASN C1028 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LEU C1033 " --> pdb=" O ASN C1029 " (cutoff:3.500A) removed outlier: 4.060A 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: 5.205A pdb=" N ALA C1065 " --> pdb=" O PRO C1061 " (cutoff:3.500A) 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: 4.402A 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: 6.042A pdb=" N SER A 267 " --> pdb=" O GLN A 280 " (cutoff:3.500A) removed outlier: 5.631A 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: 7.274A pdb=" N SER A 88 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 6.445A 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: 4.687A pdb=" N ALA A 146 " --> pdb=" O ILE A 296 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU A 180 " --> pdb=" O TYR A 241 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TYR A 241 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ALA A 182 " --> pdb=" O PHE A 239 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N PHE A 239 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N TYR A 184 " --> pdb=" O CYS A 237 " (cutoff:3.500A) removed outlier: 4.520A 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: 3.759A 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: 3.736A 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: 4.483A pdb=" N VAL A 659 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N SER A 365 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 6.144A 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: 4.167A pdb=" N GLU A 605 " --> pdb=" O SER A 371 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N SER A 373 " --> pdb=" O GLU A 605 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N SER A 607 " --> pdb=" O SER A 373 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N VAL A 375 " --> pdb=" O SER A 607 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N VAL A 639 " --> pdb=" O LEU A 651 " (cutoff:3.500A) removed outlier: 6.829A 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: 6.898A pdb=" N THR A 477 " --> pdb=" O CYS A 425 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N CYS A 425 " --> pdb=" O THR A 477 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU A 479 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N PHE A 423 " --> pdb=" O LEU A 479 " (cutoff:3.500A) removed outlier: 6.813A 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: 6.086A 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: 5.535A pdb=" N SER A 498 " --> pdb=" O VAL A 561 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL A 561 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ILE A 500 " --> pdb=" O SER A 559 " (cutoff:3.500A) removed outlier: 6.170A 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: 6.496A pdb=" N VAL A 718 " --> pdb=" O LEU A 759 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N SER A 761 " --> pdb=" O VAL A 718 " (cutoff:3.500A) removed outlier: 9.884A pdb=" N SER A 720 " --> pdb=" O SER A 761 " (cutoff:3.500A) removed outlier: 6.771A 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: 5.651A 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: 4.541A pdb=" N PHE A1172 " --> pdb=" O ALA A1152 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N VAL A1150 " --> pdb=" O LYS A1174 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 786 through 796 removed outlier: 4.493A pdb=" N VAL A1124 " --> pdb=" O VAL A1139 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N TYR A1141 " --> pdb=" O HIS A1122 " (cutoff:3.500A) removed outlier: 5.744A 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: 5.692A pdb=" N VAL C1150 " --> pdb=" O LYS C1174 " (cutoff:3.500A) removed outlier: 4.785A 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: 4.149A pdb=" N CYS A1164 " --> pdb=" O VAL A1205 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.474A pdb=" N TRP L 37 " --> pdb=" O MET L 49 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 9 through 11 Processing sheet with id=AC7, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AC8, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC9, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.954A pdb=" N TRP H 33 " --> pdb=" O LEU H 101 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N MET H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ARG H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 10 through 11 Processing sheet with id=AD2, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AD3, first strand: chain 'D' and resid 10 through 11 removed outlier: 3.710A pdb=" N TRP D 33 " --> pdb=" O LEU D 101 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N MET D 34 " --> pdb=" O ARG D 50 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ARG D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 10 through 11 Processing sheet with id=AD5, first strand: chain 'E' and resid 9 through 11 removed outlier: 6.477A pdb=" N TRP E 37 " --> pdb=" O MET E 49 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 9 through 11 Processing sheet with id=AD7, first strand: chain 'E' and resid 18 through 23 Processing sheet with id=AD8, first strand: chain 'B' and resid 33 through 35 Processing sheet with id=AD9, first strand: chain 'B' and resid 67 through 75 removed outlier: 4.161A pdb=" N ARG B 335 " --> pdb=" O ASP B 326 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.031A pdb=" N SER B 267 " --> pdb=" O GLN B 280 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N GLN B 280 " --> pdb=" O SER B 267 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 88 through 89 removed outlier: 7.562A 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=AE2 Processing sheet with id=AE3, first strand: chain 'B' and resid 92 through 93 Processing sheet with id=AE4, first strand: chain 'B' and resid 110 through 111 removed outlier: 6.584A pdb=" N LEU B 180 " --> pdb=" O TYR B 241 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TYR B 241 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ALA B 182 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N PHE B 239 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N TYR B 184 " --> pdb=" O CYS B 237 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N CYS B 237 " --> pdb=" O TYR B 184 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 127 through 130 removed outlier: 5.514A pdb=" N THR B 136 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA B 309 " --> pdb=" O THR B 139 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 153 through 155 Processing sheet with id=AE7, first strand: chain 'B' and resid 214 through 215 removed outlier: 3.742A pdb=" N SER B 215 " --> pdb=" O ASN B 218 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 359 through 366 removed outlier: 4.652A pdb=" N VAL B 659 " --> pdb=" O VAL B 363 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N SER B 365 " --> pdb=" O VAL B 657 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N VAL B 657 " --> pdb=" O SER B 365 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N CYS B 713 " --> pdb=" O PHE B 674 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 371 through 376 removed outlier: 4.245A pdb=" N GLU B 605 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N SER B 373 " --> pdb=" O GLU B 605 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N SER B 607 " --> pdb=" O SER B 373 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL B 375 " --> pdb=" O SER B 607 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL B 639 " --> pdb=" O LEU B 651 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL B 631 " --> pdb=" O VAL B 639 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 717 through 724 removed outlier: 6.330A pdb=" N VAL B 718 " --> pdb=" O LEU B 759 " (cutoff:3.500A) removed outlier: 8.807A pdb=" N SER B 761 " --> pdb=" O VAL B 718 " (cutoff:3.500A) removed outlier: 9.632A pdb=" N SER B 720 " --> pdb=" O SER B 761 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N LEU B 735 " --> pdb=" O LEU B 731 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 768 through 769 removed outlier: 5.718A pdb=" N ILE B 768 " --> pdb=" O SER C 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'B' and resid 1184 through 1188 removed outlier: 4.698A pdb=" N PHE B1172 " --> pdb=" O ALA B1152 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N VAL B1150 " --> pdb=" O LYS B1174 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 785 through 796 removed outlier: 3.617A pdb=" N ASN B 785 " --> pdb=" O SER B1144 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N VAL B1124 " --> pdb=" O VAL B1139 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N TYR B1141 " --> pdb=" O HIS B1122 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N HIS B1122 " --> pdb=" O TYR B1141 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 801 through 804 removed outlier: 4.609A pdb=" N LYS B 801 " --> pdb=" O LEU B 935 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 1202 through 1205 removed outlier: 3.931A pdb=" N CYS B1164 " --> pdb=" O VAL B1205 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ASN B1163 " --> pdb=" O ASP B1157 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 33 through 34 Processing sheet with id=AF8, first strand: chain 'C' and resid 67 through 75 removed outlier: 4.075A pdb=" N ARG C 335 " --> pdb=" O ASP C 326 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.157A pdb=" N SER C 267 " --> pdb=" O GLN C 280 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N GLN C 280 " --> pdb=" O SER C 267 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 88 through 89 removed outlier: 7.159A pdb=" N SER C 88 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N THR C 206 " --> pdb=" O SER C 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'C' and resid 92 through 93 Processing sheet with id=AG3, first strand: chain 'C' and resid 109 through 111 removed outlier: 6.700A pdb=" N LEU C 180 " --> pdb=" O TYR C 241 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N TYR C 241 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ALA C 182 " --> pdb=" O PHE C 239 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N PHE C 239 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N TYR C 184 " --> pdb=" O CYS C 237 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N CYS C 237 " --> pdb=" O TYR C 184 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 127 through 129 removed outlier: 3.611A pdb=" N ALA C 309 " --> pdb=" O THR C 139 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 153 through 155 Processing sheet with id=AG6, first strand: chain 'C' and resid 214 through 215 removed outlier: 3.938A pdb=" N SER C 215 " --> pdb=" O ASN C 218 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'C' and resid 359 through 366 removed outlier: 4.671A pdb=" N VAL C 659 " --> pdb=" O VAL C 363 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N SER C 365 " --> pdb=" O VAL C 657 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N VAL C 657 " --> pdb=" O SER C 365 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 371 through 376 removed outlier: 4.233A pdb=" N GLU C 605 " --> pdb=" O SER C 371 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N SER C 373 " --> pdb=" O GLU C 605 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N SER C 607 " --> pdb=" O SER C 373 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N VAL C 375 " --> pdb=" O SER C 607 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N VAL C 639 " --> pdb=" O LEU C 651 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL C 631 " --> pdb=" O VAL C 639 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'C' and resid 400 through 404 removed outlier: 3.538A pdb=" N SER C 440 " --> pdb=" O GLN C 576 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N THR C 477 " --> pdb=" O CYS C 425 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N CYS C 425 " --> pdb=" O THR C 477 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU C 479 " --> pdb=" O PHE C 423 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N PHE C 423 " --> pdb=" O LEU C 479 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU C 481 " --> pdb=" O ASN C 421 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'C' and resid 407 through 409 Processing sheet with id=AH2, first strand: chain 'C' and resid 513 through 515 removed outlier: 5.592A pdb=" N SER C 498 " --> pdb=" O VAL C 561 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL C 561 " --> pdb=" O SER C 498 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ILE C 500 " --> pdb=" O SER C 559 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N SER C 559 " --> pdb=" O ILE C 500 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'C' and resid 718 through 724 removed outlier: 6.340A pdb=" N VAL C 718 " --> pdb=" O LEU C 759 " (cutoff:3.500A) removed outlier: 8.723A pdb=" N SER C 761 " --> pdb=" O VAL C 718 " (cutoff:3.500A) removed outlier: 9.885A pdb=" N SER C 720 " --> pdb=" O SER C 761 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH3 Processing sheet with id=AH4, first strand: chain 'C' and resid 786 through 796 removed outlier: 4.379A pdb=" N VAL C1124 " --> pdb=" O VAL C1139 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N TYR C1141 " --> pdb=" O HIS C1122 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N HIS C1122 " --> pdb=" O TYR C1141 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'C' and resid 802 through 803 Processing sheet with id=AH6, first strand: chain 'C' and resid 1202 through 1205 removed outlier: 4.058A pdb=" N CYS C1164 " --> pdb=" O VAL C1205 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N ASN C1163 " --> pdb=" O ASP C1157 " (cutoff:3.500A) 1178 hydrogen bonds defined for protein. 3063 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: 8.01 Time building geometry restraints manager: 3.97 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: 5851 1.32 - 1.45: 9056 1.45 - 1.58: 16515 1.58 - 1.71: 6 1.71 - 1.84: 206 Bond restraints: 31634 Sorted by residual: bond pdb=" CA PRO A1220 " pdb=" C PRO A1220 " ideal model delta sigma weight residual 1.517 1.581 -0.064 9.30e-03 1.16e+04 4.71e+01 bond pdb=" CA PRO C1220 " pdb=" C PRO C1220 " ideal model delta sigma weight residual 1.517 1.578 -0.061 9.30e-03 1.16e+04 4.31e+01 bond pdb=" CA PRO B1220 " pdb=" C PRO B1220 " ideal model delta sigma weight residual 1.517 1.573 -0.056 9.30e-03 1.16e+04 3.65e+01 bond pdb=" CA PRO B1219 " pdb=" C PRO B1219 " ideal model delta sigma weight residual 1.517 1.570 -0.053 9.30e-03 1.16e+04 3.23e+01 bond pdb=" N PRO C1221 " pdb=" CD PRO C1221 " ideal model delta sigma weight residual 1.473 1.402 0.071 1.40e-02 5.10e+03 2.59e+01 ... (remaining 31629 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.56: 42601 5.56 - 11.12: 409 11.12 - 16.68: 3 16.68 - 22.24: 5 22.24 - 27.79: 2 Bond angle restraints: 43020 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 111.29 134.84 -23.55 1.64e+00 3.72e-01 2.06e+02 angle pdb=" C TYR C 905 " pdb=" CA TYR C 905 " pdb=" CB TYR C 905 " ideal model delta sigma weight residual 110.42 138.21 -27.79 1.99e+00 2.53e-01 1.95e+02 angle pdb=" N MET C 906 " pdb=" CA MET C 906 " pdb=" C MET C 906 " ideal model delta sigma weight residual 110.28 125.89 -15.61 1.48e+00 4.57e-01 1.11e+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 88.98 21.82 2.13e+00 2.20e-01 1.05e+02 angle pdb=" CD1 LEU C 506 " pdb=" CG LEU C 506 " pdb=" CD2 LEU C 506 " ideal model delta sigma weight residual 110.80 131.55 -20.75 2.20e+00 2.07e-01 8.90e+01 ... (remaining 43015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 16870 17.50 - 35.00: 483 35.00 - 52.51: 159 52.51 - 70.01: 59 70.01 - 87.51: 36 Dihedral angle restraints: 17607 sinusoidal: 6727 harmonic: 10880 Sorted by residual: 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 -158.42 36.42 0 2.50e+00 1.60e-01 2.12e+02 dihedral pdb=" N VAL B 711 " pdb=" C VAL B 711 " pdb=" CA VAL B 711 " pdb=" CB VAL B 711 " ideal model delta harmonic sigma weight residual 123.40 150.91 -27.51 0 2.50e+00 1.60e-01 1.21e+02 dihedral pdb=" CB CYS C 806 " pdb=" SG CYS C 806 " pdb=" SG CYS C 828 " pdb=" CB CYS C 828 " ideal model delta sinusoidal sigma weight residual 93.00 178.95 -85.95 1 1.00e+01 1.00e-02 8.92e+01 ... (remaining 17604 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.267: 5215 0.267 - 0.534: 58 0.534 - 0.802: 4 0.802 - 1.069: 0 1.069 - 1.336: 1 Chirality restraints: 5278 Sorted by residual: chirality pdb=" C1 BMA Q 3 " pdb=" O4 NAG Q 2 " pdb=" C2 BMA Q 3 " pdb=" O5 BMA Q 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.31e+01 chirality pdb=" C1 BMA a 3 " pdb=" O4 NAG a 2 " pdb=" C2 BMA a 3 " pdb=" O5 BMA a 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.22e+01 chirality pdb=" C1 BMA o 3 " pdb=" O4 NAG o 2 " pdb=" C2 BMA o 3 " pdb=" O5 BMA o 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.55 0.15 2.00e-02 2.50e+03 5.77e+01 ... (remaining 5275 not shown) Planarity restraints: 5366 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 166 " -0.042 2.00e-02 2.50e+03 4.22e-02 2.23e+01 pdb=" CG ASN B 166 " 0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN B 166 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN B 166 " 0.064 2.00e-02 2.50e+03 pdb=" C1 NAG b 1 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 166 " 0.036 2.00e-02 2.50e+03 3.68e-02 1.70e+01 pdb=" CG ASN A 166 " -0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN A 166 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A 166 " -0.056 2.00e-02 2.50e+03 pdb=" C1 NAG K 1 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 77 " 0.049 2.00e-02 2.50e+03 2.47e-02 1.22e+01 pdb=" CG TYR A 77 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR A 77 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR A 77 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR A 77 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 77 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 77 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 77 " 0.027 2.00e-02 2.50e+03 ... (remaining 5363 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 871 2.69 - 3.24: 29800 3.24 - 3.80: 48629 3.80 - 4.35: 63141 4.35 - 4.90: 102110 Nonbonded interactions: 244551 Sorted by model distance: nonbonded pdb=" OG SER C 419 " pdb=" OG1 THR C 483 " model vdw 2.139 3.040 nonbonded pdb=" OG SER A 419 " pdb=" OG1 THR A 483 " model vdw 2.238 3.040 nonbonded pdb=" N ASN C 592 " pdb=" OD1 ASN C 592 " model vdw 2.253 3.120 nonbonded pdb=" CB SER B 676 " pdb=" O TYR C 905 " model vdw 2.256 3.440 nonbonded pdb=" OG1 THR A 709 " pdb=" O GLY A 712 " model vdw 2.298 3.040 ... (remaining 244546 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and resid 18 through 1423) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 2 through 124) } ncs_group { reference = chain 'E' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'X' selection = chain 'f' selection = chain 'h' selection = chain 'i' selection = chain 'l' selection = chain 'r' selection = chain 's' selection = chain 'u' selection = chain 'v' selection = chain 'w' } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'O' selection = chain 'R' selection = chain 'V' selection = chain 'Y' selection = chain 'a' selection = chain 'e' selection = chain 'g' selection = chain 'j' selection = chain 'm' selection = chain 'o' selection = chain 'p' selection = chain 't' selection = chain 'x' } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'P' selection = chain 'Z' selection = chain 'b' selection = chain 'c' selection = chain 'n' } ncs_group { reference = chain 'N' selection = chain 'W' selection = chain 'd' selection = chain 'k' selection = chain 'q' selection = chain 'y' } 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: 3.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 29.550 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.200 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 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 : 0.015 0.201 31845 Z= 0.789 Angle : 1.419 27.795 43602 Z= 0.860 Chirality : 0.090 1.336 5278 Planarity : 0.006 0.059 5317 Dihedral : 10.924 87.511 10526 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.69 % Favored : 97.12 % Rotamer: Outliers : 0.41 % Allowed : 1.44 % Favored : 98.15 % Cbeta Deviations : 0.09 % 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: 0.07 (0.13), residues: 3717 helix: 0.47 (0.19), residues: 682 sheet: 0.59 (0.16), residues: 897 loop : -0.27 (0.13), residues: 2138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 401 TYR 0.049 0.006 TYR A 77 PHE 0.030 0.004 PHE C 313 TRP 0.036 0.006 TRP C1184 HIS 0.006 0.001 HIS A1138 Details of bonding type rmsd/Z covalent geometry : bond 0.01462 / 0.78 (31634) covalent geometry : angle 1.39741 / 0.86 (43020) SS BOND : bond 0.04067 / 3.00 ( 51) SS BOND : angle 3.78031 / 2.62 ( 102) hydrogen bonds : bond 0.18874 / 12.67 ( 1154) hydrogen bonds : angle 7.83260 / 5.41 ( 3063) link_ALPHA1-2 : bond 0.04072 / 2.48 ( 9) link_ALPHA1-2 : angle 1.84735 / 1.18 ( 27) link_ALPHA1-3 : bond 0.03453 / 2.20 ( 15) link_ALPHA1-3 : angle 1.52567 / 1.04 ( 45) link_ALPHA1-6 : bond 0.03038 / 1.96 ( 13) link_ALPHA1-6 : angle 2.24264 / 1.51 ( 39) link_BETA1-4 : bond 0.03616 / 2.40 ( 74) link_BETA1-4 : angle 2.43756 / 1.70 ( 222) link_NAG-ASN : bond 0.02549 / 1.74 ( 49) link_NAG-ASN : angle 1.95172 / 1.32 ( 147) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 852 residues out of total 3194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 839 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.7676 (ttp) cc_final: 0.7234 (ttm) REVERT: A 444 ASP cc_start: 0.7617 (m-30) cc_final: 0.7275 (m-30) REVERT: A 817 CYS cc_start: 0.6670 (t) cc_final: 0.6433 (t) REVERT: H 83 LEU cc_start: 0.5935 (tp) cc_final: 0.5664 (tt) REVERT: H 88 LEU cc_start: 0.7166 (mt) cc_final: 0.6911 (mt) REVERT: H 92 ASP cc_start: 0.6545 (m-30) cc_final: 0.5164 (t70) REVERT: H 100 THR cc_start: 0.6187 (p) cc_final: 0.5962 (p) REVERT: H 108 TRP cc_start: 0.6890 (t-100) cc_final: 0.6404 (t60) REVERT: D 60 THR cc_start: 0.7052 (p) cc_final: 0.6761 (t) REVERT: D 62 TYR cc_start: 0.8066 (m-80) cc_final: 0.7688 (m-10) REVERT: D 72 LEU cc_start: 0.7149 (mp) cc_final: 0.6661 (tt) REVERT: D 95 VAL cc_start: 0.7588 (t) cc_final: 0.7382 (m) REVERT: E 64 PHE cc_start: 0.5375 (m-80) cc_final: 0.4594 (m-10) REVERT: E 97 SER cc_start: 0.8310 (m) cc_final: 0.7875 (p) REVERT: E 108 VAL cc_start: 0.6319 (t) cc_final: 0.6037 (t) REVERT: B 68 THR cc_start: 0.8641 (m) cc_final: 0.8336 (p) REVERT: B 220 ASN cc_start: 0.5262 (t0) cc_final: 0.4688 (t0) REVERT: B 677 VAL cc_start: 0.8872 (t) cc_final: 0.8591 (m) REVERT: B 816 LYS cc_start: 0.8229 (tptt) cc_final: 0.7764 (mmtt) REVERT: B 1054 ILE cc_start: 0.9101 (pt) cc_final: 0.8828 (mt) REVERT: C 84 MET cc_start: 0.7002 (ptm) cc_final: 0.6648 (ptm) REVERT: C 144 TYR cc_start: 0.7922 (m-80) cc_final: 0.7699 (m-10) REVERT: C 245 ILE cc_start: 0.8034 (mt) cc_final: 0.7807 (mt) REVERT: C 292 TYR cc_start: 0.8153 (m-80) cc_final: 0.7917 (m-10) REVERT: C 859 SER cc_start: 0.8795 (m) cc_final: 0.8514 (p) REVERT: C 1040 LEU cc_start: 0.8397 (tp) cc_final: 0.7856 (tp) outliers start: 13 outliers final: 1 residues processed: 848 average time/residue: 0.1864 time to fit residues: 254.7758 Evaluate side-chains 397 residues out of total 3194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 396 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 592 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 346 GLN A 466 GLN A 522 GLN A 833 GLN A 857 GLN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 ASN H 119 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 GLN B 277 ASN B 298 HIS B 346 GLN B 914 GLN B 993 ASN ** B1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1132 ASN C 36 GLN C 60 GLN ** C 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 468 ASN ** C 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 708 GLN C1056 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.145671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.114228 restraints weight = 60727.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.118436 restraints weight = 32605.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.120180 restraints weight = 20072.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.120384 restraints weight = 18397.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.120422 restraints weight = 15932.864| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 31845 Z= 0.186 Angle : 0.757 11.061 43602 Z= 0.377 Chirality : 0.046 0.421 5278 Planarity : 0.005 0.059 5317 Dihedral : 4.827 49.941 4073 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.61 % Favored : 97.36 % Rotamer: Outliers : 2.35 % Allowed : 8.86 % Favored : 88.79 % 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: 0.34 (0.13), residues: 3717 helix: 1.48 (0.20), residues: 698 sheet: 0.50 (0.16), residues: 933 loop : -0.29 (0.13), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 181 TYR 0.028 0.002 TYR C 87 PHE 0.025 0.002 PHE A 977 TRP 0.019 0.002 TRP C 253 HIS 0.007 0.002 HIS C 681 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 (31634) covalent geometry : angle 0.71872 / 0.37 (43020) SS BOND : bond 0.00646 / 0.47 ( 51) SS BOND : angle 1.79768 / 1.24 ( 102) hydrogen bonds : bond 0.06650 / 4.44 ( 1154) hydrogen bonds : angle 6.08499 / 4.21 ( 3063) link_ALPHA1-2 : bond 0.00312 / 0.17 ( 9) link_ALPHA1-2 : angle 1.63644 / 1.06 ( 27) link_ALPHA1-3 : bond 0.00512 / 0.35 ( 15) link_ALPHA1-3 : angle 1.74658 / 1.24 ( 45) link_ALPHA1-6 : bond 0.00540 / 0.35 ( 13) link_ALPHA1-6 : angle 1.97691 / 1.28 ( 39) link_BETA1-4 : bond 0.01208 / 0.86 ( 74) link_BETA1-4 : angle 2.52182 / 1.76 ( 222) link_NAG-ASN : bond 0.00425 / 0.29 ( 49) link_NAG-ASN : angle 2.14720 / 1.43 ( 147) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 3194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 460 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.7882 (ttp) cc_final: 0.7658 (ttm) REVERT: A 686 MET cc_start: 0.8039 (ttt) cc_final: 0.7641 (ttt) REVERT: A 943 MET cc_start: 0.6986 (mmt) cc_final: 0.6763 (mmt) REVERT: A 944 GLU cc_start: 0.6501 (tt0) cc_final: 0.6165 (tt0) REVERT: A 1137 MET cc_start: 0.8035 (mpp) cc_final: 0.7633 (mtm) REVERT: A 1190 SER cc_start: 0.8686 (m) cc_final: 0.8208 (t) REVERT: L 87 ASP cc_start: 0.7591 (OUTLIER) cc_final: 0.7301 (m-30) REVERT: H 100 THR cc_start: 0.6837 (p) cc_final: 0.6332 (t) REVERT: H 108 TRP cc_start: 0.6943 (t-100) cc_final: 0.6599 (t60) REVERT: D 28 THR cc_start: 0.8444 (t) cc_final: 0.7786 (t) REVERT: D 62 TYR cc_start: 0.8037 (m-80) cc_final: 0.7550 (m-10) REVERT: B 57 ILE cc_start: 0.8454 (mt) cc_final: 0.8163 (pt) REVERT: B 644 ASP cc_start: 0.7337 (m-30) cc_final: 0.6873 (m-30) REVERT: B 808 GLN cc_start: 0.7831 (mm-40) cc_final: 0.7331 (tp40) REVERT: B 943 MET cc_start: 0.7898 (mtm) cc_final: 0.7696 (ttm) REVERT: B 977 PHE cc_start: 0.7657 (m-80) cc_final: 0.7418 (m-80) REVERT: B 1054 ILE cc_start: 0.8966 (pt) cc_final: 0.8757 (mt) REVERT: B 1084 GLN cc_start: 0.8127 (tp40) cc_final: 0.7666 (tp40) REVERT: B 1186 TYR cc_start: 0.8662 (t80) cc_final: 0.8326 (t80) REVERT: C 84 MET cc_start: 0.6334 (ptm) cc_final: 0.6026 (ptm) REVERT: C 254 PHE cc_start: 0.8075 (t80) cc_final: 0.7838 (t80) REVERT: C 292 TYR cc_start: 0.8530 (m-80) cc_final: 0.8235 (m-10) REVERT: C 563 MET cc_start: 0.8106 (tpt) cc_final: 0.7863 (tpt) REVERT: C 664 ASP cc_start: 0.7466 (t0) cc_final: 0.7122 (t70) REVERT: C 689 TYR cc_start: 0.7183 (m-10) cc_final: 0.6857 (m-10) REVERT: C 859 SER cc_start: 0.8906 (m) cc_final: 0.8603 (p) REVERT: C 970 ILE cc_start: 0.8624 (mm) cc_final: 0.8392 (mm) REVERT: C 1161 PRO cc_start: 0.7865 (Cg_endo) cc_final: 0.7620 (Cg_exo) outliers start: 75 outliers final: 43 residues processed: 504 average time/residue: 0.1812 time to fit residues: 152.0328 Evaluate side-chains 377 residues out of total 3194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 333 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 HIS Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain A residue 844 ASP Chi-restraints excluded: chain A residue 978 TYR Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 87 ASP Chi-restraints excluded: chain L residue 106 THR Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 119 GLN Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 346 GLN Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 948 THR Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 993 ASN Chi-restraints excluded: chain B residue 1197 ILE Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 726 ASP Chi-restraints excluded: chain C residue 1041 SER Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1218 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 308 optimal weight: 0.8980 chunk 125 optimal weight: 0.0970 chunk 89 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 281 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 193 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 247 optimal weight: 0.3980 chunk 120 optimal weight: 1.9990 chunk 351 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 421 ASN A 842 GLN L 39 GLN D 39 GLN ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1122 HIS ** B1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 GLN C 436 ASN ** C 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 927 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.141115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.109855 restraints weight = 60685.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.113136 restraints weight = 32449.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.116154 restraints weight = 21737.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.116343 restraints weight = 18861.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.116193 restraints weight = 15878.840| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 31845 Z= 0.205 Angle : 0.721 12.367 43602 Z= 0.355 Chirality : 0.045 0.351 5278 Planarity : 0.005 0.056 5317 Dihedral : 4.890 47.858 4073 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.15 % Favored : 96.83 % Rotamer: Outliers : 2.66 % Allowed : 11.24 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.13), residues: 3717 helix: 1.40 (0.21), residues: 686 sheet: 0.39 (0.16), residues: 944 loop : -0.48 (0.13), residues: 2087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 19 TYR 0.030 0.002 TYR L 88 PHE 0.023 0.002 PHE C 850 TRP 0.011 0.002 TRP D 108 HIS 0.010 0.002 HIS C1138 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.20 (31634) covalent geometry : angle 0.68794 / 0.35 (43020) SS BOND : bond 0.00373 / 0.26 ( 51) SS BOND : angle 1.64391 / 1.18 ( 102) hydrogen bonds : bond 0.06233 / 4.16 ( 1154) hydrogen bonds : angle 5.73201 / 4.00 ( 3063) link_ALPHA1-2 : bond 0.00400 / 0.21 ( 9) link_ALPHA1-2 : angle 1.47013 / 0.94 ( 27) link_ALPHA1-3 : bond 0.00593 / 0.41 ( 15) link_ALPHA1-3 : angle 1.54931 / 1.08 ( 45) link_ALPHA1-6 : bond 0.00678 / 0.44 ( 13) link_ALPHA1-6 : angle 1.46442 / 1.01 ( 39) link_BETA1-4 : bond 0.01195 / 0.85 ( 74) link_BETA1-4 : angle 2.28567 / 1.59 ( 222) link_NAG-ASN : bond 0.00452 / 0.32 ( 49) link_NAG-ASN : angle 2.07488 / 1.40 ( 147) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 352 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8068 (ttp) cc_final: 0.7832 (ttm) REVERT: A 168 THR cc_start: 0.9160 (m) cc_final: 0.8920 (p) REVERT: A 218 ASN cc_start: 0.7072 (m-40) cc_final: 0.6820 (m-40) REVERT: A 415 LEU cc_start: 0.8148 (mt) cc_final: 0.7942 (mt) REVERT: A 444 ASP cc_start: 0.8077 (m-30) cc_final: 0.7662 (m-30) REVERT: A 686 MET cc_start: 0.8077 (ttt) cc_final: 0.7666 (ttt) REVERT: A 871 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7294 (pp) REVERT: A 943 MET cc_start: 0.7254 (mmt) cc_final: 0.6810 (mmt) REVERT: A 1020 GLN cc_start: 0.7808 (tm-30) cc_final: 0.7496 (tm-30) REVERT: L 87 ASP cc_start: 0.7373 (OUTLIER) cc_final: 0.6822 (m-30) REVERT: L 92 LEU cc_start: 0.8673 (tp) cc_final: 0.8470 (tt) REVERT: H 51 ILE cc_start: 0.7251 (tp) cc_final: 0.6984 (tt) REVERT: H 100 THR cc_start: 0.7186 (p) cc_final: 0.6590 (t) REVERT: D 62 TYR cc_start: 0.8348 (m-80) cc_final: 0.7819 (m-10) REVERT: D 115 ASP cc_start: 0.8436 (p0) cc_final: 0.7965 (p0) REVERT: E 84 ASP cc_start: 0.6860 (t0) cc_final: 0.6400 (t0) REVERT: B 179 LEU cc_start: 0.8760 (pp) cc_final: 0.8541 (pp) REVERT: B 808 GLN cc_start: 0.7912 (mm-40) cc_final: 0.7484 (tp40) REVERT: B 822 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7910 (mtm-85) REVERT: B 907 GLN cc_start: 0.7519 (tm-30) cc_final: 0.7039 (tm-30) REVERT: B 911 ASP cc_start: 0.7228 (t0) cc_final: 0.5886 (t0) REVERT: B 939 MET cc_start: 0.8212 (tpp) cc_final: 0.8009 (mmt) REVERT: B 943 MET cc_start: 0.7842 (mtm) cc_final: 0.7363 (ttm) REVERT: B 1084 GLN cc_start: 0.8191 (tp40) cc_final: 0.7680 (tp40) REVERT: C 84 MET cc_start: 0.6431 (ptm) cc_final: 0.6125 (ptm) REVERT: C 254 PHE cc_start: 0.8192 (t80) cc_final: 0.7902 (t80) REVERT: C 292 TYR cc_start: 0.8603 (m-80) cc_final: 0.8400 (m-80) REVERT: C 296 ILE cc_start: 0.8436 (mt) cc_final: 0.8174 (mt) REVERT: C 970 ILE cc_start: 0.8787 (mm) cc_final: 0.8570 (mm) outliers start: 85 outliers final: 56 residues processed: 414 average time/residue: 0.1784 time to fit residues: 123.4118 Evaluate side-chains 345 residues out of total 3194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 286 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 HIS Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 844 ASP Chi-restraints excluded: chain A residue 848 ASN Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 1047 ILE Chi-restraints excluded: chain A residue 1121 THR Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain L residue 87 ASP Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 822 ARG Chi-restraints excluded: chain B residue 846 VAL Chi-restraints excluded: chain B residue 1040 LEU Chi-restraints excluded: chain B residue 1197 ILE Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 513 GLU Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 726 ASP Chi-restraints excluded: chain C residue 1041 SER Chi-restraints excluded: chain C residue 1062 GLU Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1086 LEU Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain C residue 1218 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 360 optimal weight: 0.7980 chunk 217 optimal weight: 0.5980 chunk 108 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 chunk 166 optimal weight: 0.9980 chunk 248 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 305 optimal weight: 0.6980 chunk 274 optimal weight: 9.9990 chunk 347 optimal weight: 0.5980 chunk 150 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 421 ASN A 708 GLN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN B 346 GLN B 796 GLN B 857 GLN B1042 ASN ** B1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 GLN ** C 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1129 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.141070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.109765 restraints weight = 60252.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.113022 restraints weight = 31899.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.115703 restraints weight = 21316.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.115864 restraints weight = 18573.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.115838 restraints weight = 16290.877| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31845 Z= 0.156 Angle : 0.672 12.750 43602 Z= 0.327 Chirality : 0.044 0.304 5278 Planarity : 0.004 0.064 5317 Dihedral : 4.735 47.618 4073 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.01 % Allowed : 11.83 % Favored : 85.16 % 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: 0.03 (0.13), residues: 3717 helix: 1.53 (0.21), residues: 673 sheet: 0.24 (0.15), residues: 993 loop : -0.58 (0.13), residues: 2051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 56 TYR 0.038 0.001 TYR C 87 PHE 0.022 0.002 PHE A 850 TRP 0.012 0.001 TRP H 108 HIS 0.007 0.001 HIS C1138 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (31634) covalent geometry : angle 0.64053 / 0.32 (43020) SS BOND : bond 0.00289 / 0.21 ( 51) SS BOND : angle 1.34258 / 0.98 ( 102) hydrogen bonds : bond 0.05516 / 3.67 ( 1154) hydrogen bonds : angle 5.42874 / 3.78 ( 3063) link_ALPHA1-2 : bond 0.00377 / 0.20 ( 9) link_ALPHA1-2 : angle 1.47883 / 0.94 ( 27) link_ALPHA1-3 : bond 0.00552 / 0.38 ( 15) link_ALPHA1-3 : angle 1.57957 / 1.10 ( 45) link_ALPHA1-6 : bond 0.00649 / 0.43 ( 13) link_ALPHA1-6 : angle 1.50435 / 1.04 ( 39) link_BETA1-4 : bond 0.01160 / 0.82 ( 74) link_BETA1-4 : angle 2.16552 / 1.52 ( 222) link_NAG-ASN : bond 0.00375 / 0.26 ( 49) link_NAG-ASN : angle 1.97946 / 1.33 ( 147) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 3194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 343 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.7938 (ttp) cc_final: 0.7683 (ttm) REVERT: A 168 THR cc_start: 0.9129 (m) cc_final: 0.8814 (p) REVERT: A 218 ASN cc_start: 0.7142 (m-40) cc_final: 0.6879 (m-40) REVERT: A 686 MET cc_start: 0.8097 (ttt) cc_final: 0.7608 (ttt) REVERT: A 871 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7545 (pp) REVERT: A 1020 GLN cc_start: 0.7806 (tm-30) cc_final: 0.7396 (tm-30) REVERT: A 1068 ASP cc_start: 0.7763 (t0) cc_final: 0.7514 (m-30) REVERT: L 87 ASP cc_start: 0.7640 (m-30) cc_final: 0.7433 (m-30) REVERT: L 92 LEU cc_start: 0.8674 (tp) cc_final: 0.8460 (tt) REVERT: H 29 PHE cc_start: 0.5573 (t80) cc_final: 0.5147 (t80) REVERT: H 34 MET cc_start: 0.6316 (mmm) cc_final: 0.5534 (mmm) REVERT: H 92 ASP cc_start: 0.7852 (m-30) cc_final: 0.5405 (t70) REVERT: H 100 THR cc_start: 0.7328 (p) cc_final: 0.6729 (t) REVERT: D 52 LYS cc_start: 0.8266 (mttp) cc_final: 0.7863 (mtmt) REVERT: D 62 TYR cc_start: 0.8321 (m-80) cc_final: 0.7891 (m-10) REVERT: D 115 ASP cc_start: 0.8423 (p0) cc_final: 0.7925 (p0) REVERT: B 179 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8342 (pp) REVERT: B 213 ASP cc_start: 0.6653 (m-30) cc_final: 0.6199 (m-30) REVERT: B 808 GLN cc_start: 0.7977 (mm-40) cc_final: 0.7571 (tp40) REVERT: B 822 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7913 (mtm-85) REVERT: B 943 MET cc_start: 0.7642 (mtm) cc_final: 0.7245 (ttm) REVERT: B 1084 GLN cc_start: 0.8217 (tp40) cc_final: 0.7725 (tp40) REVERT: C 84 MET cc_start: 0.6419 (ptm) cc_final: 0.6131 (ptm) REVERT: C 254 PHE cc_start: 0.8221 (t80) cc_final: 0.7950 (t80) REVERT: C 858 SER cc_start: 0.8592 (p) cc_final: 0.8379 (t) REVERT: C 994 GLN cc_start: 0.7131 (pm20) cc_final: 0.6806 (pm20) REVERT: C 1008 MET cc_start: 0.8438 (tmm) cc_final: 0.8177 (tmm) outliers start: 96 outliers final: 63 residues processed: 414 average time/residue: 0.1695 time to fit residues: 119.0025 Evaluate side-chains 365 residues out of total 3194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 299 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 HIS Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 844 ASP Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 1047 ILE Chi-restraints excluded: chain A residue 1121 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 346 GLN Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 822 ARG Chi-restraints excluded: chain B residue 846 VAL Chi-restraints excluded: chain B residue 1197 ILE Chi-restraints excluded: chain B residue 1222 LEU Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 513 GLU Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 1041 SER Chi-restraints excluded: chain C residue 1062 GLU Chi-restraints excluded: chain C residue 1070 LEU Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1086 LEU Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain C residue 1214 ILE Chi-restraints excluded: chain C residue 1218 LEU Chi-restraints excluded: chain C residue 1222 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 41 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 125 optimal weight: 3.9990 chunk 211 optimal weight: 0.7980 chunk 212 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 116 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 215 optimal weight: 0.6980 chunk 143 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 521 ASN A1129 ASN D 119 GLN B 346 GLN ** B1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 GLN C 769 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.140395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.109168 restraints weight = 60346.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.113161 restraints weight = 32184.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.114603 restraints weight = 20292.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.114892 restraints weight = 19045.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.114870 restraints weight = 16570.234| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 31845 Z= 0.158 Angle : 0.671 12.316 43602 Z= 0.325 Chirality : 0.043 0.293 5278 Planarity : 0.004 0.063 5317 Dihedral : 4.689 47.202 4073 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.44 % Favored : 96.53 % Rotamer: Outliers : 3.10 % Allowed : 12.68 % Favored : 84.22 % 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: -0.04 (0.13), residues: 3717 helix: 1.54 (0.21), residues: 673 sheet: 0.21 (0.16), residues: 975 loop : -0.66 (0.13), residues: 2069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1057 TYR 0.030 0.001 TYR L 88 PHE 0.017 0.002 PHE B 674 TRP 0.044 0.002 TRP H 36 HIS 0.007 0.001 HIS C1138 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (31634) covalent geometry : angle 0.63914 / 0.32 (43020) SS BOND : bond 0.00315 / 0.23 ( 51) SS BOND : angle 1.41410 / 0.99 ( 102) hydrogen bonds : bond 0.05362 / 3.56 ( 1154) hydrogen bonds : angle 5.36134 / 3.72 ( 3063) link_ALPHA1-2 : bond 0.00388 / 0.21 ( 9) link_ALPHA1-2 : angle 1.47497 / 0.94 ( 27) link_ALPHA1-3 : bond 0.00550 / 0.38 ( 15) link_ALPHA1-3 : angle 1.59409 / 1.11 ( 45) link_ALPHA1-6 : bond 0.00668 / 0.44 ( 13) link_ALPHA1-6 : angle 1.50530 / 1.05 ( 39) link_BETA1-4 : bond 0.01142 / 0.81 ( 74) link_BETA1-4 : angle 2.15484 / 1.50 ( 222) link_NAG-ASN : bond 0.00405 / 0.28 ( 49) link_NAG-ASN : angle 1.97513 / 1.33 ( 147) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 324 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.7910 (ttp) cc_final: 0.7645 (ttm) REVERT: A 161 MET cc_start: 0.7541 (mmt) cc_final: 0.6977 (tpp) REVERT: A 168 THR cc_start: 0.9178 (m) cc_final: 0.8884 (p) REVERT: A 218 ASN cc_start: 0.7403 (m-40) cc_final: 0.7124 (m-40) REVERT: A 871 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7579 (pp) REVERT: A 943 MET cc_start: 0.7268 (mmt) cc_final: 0.7033 (mmt) REVERT: A 1020 GLN cc_start: 0.7805 (tm-30) cc_final: 0.7458 (tm-30) REVERT: A 1038 SER cc_start: 0.8896 (t) cc_final: 0.8620 (p) REVERT: L 87 ASP cc_start: 0.7580 (m-30) cc_final: 0.7367 (m-30) REVERT: H 13 LYS cc_start: 0.8251 (tppt) cc_final: 0.8021 (tppt) REVERT: H 29 PHE cc_start: 0.5446 (t80) cc_final: 0.4347 (t80) REVERT: H 36 TRP cc_start: 0.5841 (m100) cc_final: 0.5610 (m100) REVERT: H 92 ASP cc_start: 0.7832 (m-30) cc_final: 0.5537 (t70) REVERT: H 100 THR cc_start: 0.7463 (p) cc_final: 0.6878 (t) REVERT: D 62 TYR cc_start: 0.8385 (m-80) cc_final: 0.8060 (m-80) REVERT: D 82 TYR cc_start: 0.8450 (m-10) cc_final: 0.8176 (m-10) REVERT: D 115 ASP cc_start: 0.8454 (p0) cc_final: 0.7963 (p0) REVERT: D 119 GLN cc_start: 0.7003 (OUTLIER) cc_final: 0.6767 (pm20) REVERT: E 81 GLN cc_start: 0.7816 (pp30) cc_final: 0.7451 (pp30) REVERT: E 88 TYR cc_start: 0.6550 (m-80) cc_final: 0.5509 (m-10) REVERT: B 78 GLN cc_start: 0.9036 (OUTLIER) cc_final: 0.7610 (tp-100) REVERT: B 213 ASP cc_start: 0.6739 (m-30) cc_final: 0.6364 (m-30) REVERT: B 240 MET cc_start: 0.7265 (ttt) cc_final: 0.6267 (ttt) REVERT: B 822 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7914 (mtm-85) REVERT: B 943 MET cc_start: 0.7680 (mtm) cc_final: 0.7186 (ttm) REVERT: B 1019 PHE cc_start: 0.8154 (t80) cc_final: 0.7883 (t80) REVERT: B 1084 GLN cc_start: 0.8228 (tp40) cc_final: 0.7741 (tp40) REVERT: C 84 MET cc_start: 0.6401 (ptm) cc_final: 0.6113 (ptm) REVERT: C 254 PHE cc_start: 0.8263 (t80) cc_final: 0.7996 (t80) REVERT: C 827 PHE cc_start: 0.7719 (t80) cc_final: 0.7454 (t80) REVERT: C 994 GLN cc_start: 0.7179 (pm20) cc_final: 0.6894 (pm20) REVERT: C 1008 MET cc_start: 0.8405 (tmm) cc_final: 0.8180 (tmm) outliers start: 99 outliers final: 67 residues processed: 397 average time/residue: 0.1692 time to fit residues: 113.0627 Evaluate side-chains 363 residues out of total 3194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 292 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 HIS Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 844 ASP Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 1121 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 106 THR Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 119 GLN Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 804 VAL Chi-restraints excluded: chain B residue 822 ARG Chi-restraints excluded: chain B residue 846 VAL Chi-restraints excluded: chain B residue 1197 ILE Chi-restraints excluded: chain B residue 1218 LEU Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 513 GLU Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 939 MET Chi-restraints excluded: chain C residue 1041 SER Chi-restraints excluded: chain C residue 1062 GLU Chi-restraints excluded: chain C residue 1070 LEU Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1086 LEU Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain C residue 1218 LEU Chi-restraints excluded: chain C residue 1222 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 21 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 307 optimal weight: 1.9990 chunk 272 optimal weight: 0.9980 chunk 209 optimal weight: 0.9980 chunk 313 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 268 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 231 optimal weight: 0.3980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 348 HIS ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 GLN B 836 HIS B1129 ASN C 36 GLN C 348 HIS C 421 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.138455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.107785 restraints weight = 59439.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.111904 restraints weight = 31450.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.113910 restraints weight = 18963.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.114233 restraints weight = 16995.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.114069 restraints weight = 14305.641| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 31845 Z= 0.187 Angle : 0.701 12.480 43602 Z= 0.339 Chirality : 0.044 0.327 5278 Planarity : 0.004 0.064 5317 Dihedral : 4.798 46.826 4073 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.79 % Favored : 96.18 % Rotamer: Outliers : 3.35 % Allowed : 13.12 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.13), residues: 3717 helix: 1.44 (0.21), residues: 671 sheet: 0.09 (0.16), residues: 945 loop : -0.74 (0.13), residues: 2101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 63 TYR 0.031 0.002 TYR L 88 PHE 0.019 0.002 PHE C 116 TRP 0.021 0.001 TRP H 36 HIS 0.008 0.001 HIS C1138 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.19 (31634) covalent geometry : angle 0.66901 / 0.33 (43020) SS BOND : bond 0.00441 / 0.27 ( 51) SS BOND : angle 1.55002 / 1.09 ( 102) hydrogen bonds : bond 0.05586 / 3.70 ( 1154) hydrogen bonds : angle 5.43013 / 3.77 ( 3063) link_ALPHA1-2 : bond 0.00416 / 0.22 ( 9) link_ALPHA1-2 : angle 1.49871 / 0.95 ( 27) link_ALPHA1-3 : bond 0.00546 / 0.38 ( 15) link_ALPHA1-3 : angle 1.68233 / 1.18 ( 45) link_ALPHA1-6 : bond 0.00662 / 0.44 ( 13) link_ALPHA1-6 : angle 1.56207 / 1.09 ( 39) link_BETA1-4 : bond 0.01142 / 0.81 ( 74) link_BETA1-4 : angle 2.18213 / 1.52 ( 222) link_NAG-ASN : bond 0.00400 / 0.28 ( 49) link_NAG-ASN : angle 1.99023 / 1.35 ( 147) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 3194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 309 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.7983 (ttp) cc_final: 0.7718 (ttm) REVERT: A 168 THR cc_start: 0.9178 (m) cc_final: 0.8891 (p) REVERT: A 218 ASN cc_start: 0.7409 (m-40) cc_final: 0.7113 (m-40) REVERT: A 871 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7533 (pp) REVERT: A 1020 GLN cc_start: 0.7735 (tm-30) cc_final: 0.7379 (tm-30) REVERT: H 27 LEU cc_start: 0.2132 (OUTLIER) cc_final: 0.1746 (pp) REVERT: H 92 ASP cc_start: 0.7843 (m-30) cc_final: 0.5584 (t70) REVERT: H 100 THR cc_start: 0.7264 (p) cc_final: 0.6674 (t) REVERT: D 28 THR cc_start: 0.9523 (t) cc_final: 0.9207 (p) REVERT: D 52 LYS cc_start: 0.8363 (mttp) cc_final: 0.8019 (mtmt) REVERT: D 62 TYR cc_start: 0.8252 (m-80) cc_final: 0.7912 (m-80) REVERT: D 82 TYR cc_start: 0.8431 (m-10) cc_final: 0.8179 (m-10) REVERT: D 115 ASP cc_start: 0.8455 (p0) cc_final: 0.7991 (p0) REVERT: E 81 GLN cc_start: 0.7813 (pp30) cc_final: 0.7506 (pp30) REVERT: E 84 ASP cc_start: 0.7824 (t0) cc_final: 0.6943 (t0) REVERT: E 88 TYR cc_start: 0.6628 (m-80) cc_final: 0.5524 (m-10) REVERT: B 78 GLN cc_start: 0.8982 (OUTLIER) cc_final: 0.7962 (tp-100) REVERT: B 179 LEU cc_start: 0.8955 (pp) cc_final: 0.8601 (pp) REVERT: B 240 MET cc_start: 0.7466 (ttt) cc_final: 0.6433 (ttt) REVERT: B 1084 GLN cc_start: 0.8241 (tp40) cc_final: 0.7730 (tp40) REVERT: B 1105 GLU cc_start: 0.7133 (tt0) cc_final: 0.6843 (tt0) REVERT: C 84 MET cc_start: 0.6461 (ptm) cc_final: 0.6173 (ptm) REVERT: C 156 PHE cc_start: 0.5228 (OUTLIER) cc_final: 0.4781 (m-10) REVERT: C 254 PHE cc_start: 0.8313 (t80) cc_final: 0.7982 (t80) REVERT: C 827 PHE cc_start: 0.8144 (t80) cc_final: 0.7917 (t80) REVERT: C 994 GLN cc_start: 0.7075 (pm20) cc_final: 0.6872 (pm20) REVERT: C 1008 MET cc_start: 0.8453 (tmm) cc_final: 0.8248 (tmm) outliers start: 107 outliers final: 75 residues processed: 387 average time/residue: 0.1632 time to fit residues: 106.9893 Evaluate side-chains 369 residues out of total 3194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 290 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 HIS Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 844 ASP Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 1121 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 71 ASN Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 804 VAL Chi-restraints excluded: chain B residue 846 VAL Chi-restraints excluded: chain B residue 1040 LEU Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1197 ILE Chi-restraints excluded: chain B residue 1218 LEU Chi-restraints excluded: chain B residue 1222 LEU Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 513 GLU Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 939 MET Chi-restraints excluded: chain C residue 1041 SER Chi-restraints excluded: chain C residue 1062 GLU Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1086 LEU Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain C residue 1214 ILE Chi-restraints excluded: chain C residue 1218 LEU Chi-restraints excluded: chain C residue 1222 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 10 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 350 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 242 optimal weight: 0.7980 chunk 339 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 96 optimal weight: 0.0370 chunk 168 optimal weight: 0.7980 chunk 237 optimal weight: 0.1980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 842 GLN ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 GLN B1042 ASN C 36 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.139789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.109296 restraints weight = 59086.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.113731 restraints weight = 30413.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.115157 restraints weight = 17904.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.115407 restraints weight = 16435.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.115393 restraints weight = 14520.081| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.4609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 31845 Z= 0.136 Angle : 0.666 14.826 43602 Z= 0.322 Chirality : 0.043 0.292 5278 Planarity : 0.004 0.062 5317 Dihedral : 4.601 46.833 4073 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.20 % Favored : 96.77 % Rotamer: Outliers : 2.97 % Allowed : 13.81 % Favored : 83.22 % 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: -0.09 (0.14), residues: 3717 helix: 1.65 (0.21), residues: 669 sheet: 0.08 (0.16), residues: 987 loop : -0.68 (0.13), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 63 TYR 0.030 0.001 TYR L 88 PHE 0.022 0.001 PHE C 40 TRP 0.030 0.001 TRP H 36 HIS 0.005 0.001 HIS C 681 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (31634) covalent geometry : angle 0.62981 / 0.31 (43020) SS BOND : bond 0.00402 / 0.24 ( 51) SS BOND : angle 2.09991 / 1.34 ( 102) hydrogen bonds : bond 0.05025 / 3.32 ( 1154) hydrogen bonds : angle 5.25545 / 3.65 ( 3063) link_ALPHA1-2 : bond 0.00427 / 0.23 ( 9) link_ALPHA1-2 : angle 1.45172 / 0.93 ( 27) link_ALPHA1-3 : bond 0.00567 / 0.39 ( 15) link_ALPHA1-3 : angle 1.56916 / 1.10 ( 45) link_ALPHA1-6 : bond 0.00691 / 0.46 ( 13) link_ALPHA1-6 : angle 1.51991 / 1.06 ( 39) link_BETA1-4 : bond 0.01132 / 0.80 ( 74) link_BETA1-4 : angle 2.16119 / 1.50 ( 222) link_NAG-ASN : bond 0.00386 / 0.27 ( 49) link_NAG-ASN : angle 1.90056 / 1.29 ( 147) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 324 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.7946 (ttp) cc_final: 0.7684 (ttm) REVERT: A 161 MET cc_start: 0.8278 (tpp) cc_final: 0.8020 (mmm) REVERT: A 686 MET cc_start: 0.8447 (tpp) cc_final: 0.8008 (tpp) REVERT: A 871 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7608 (pp) REVERT: A 955 ILE cc_start: 0.8786 (mm) cc_final: 0.8574 (tp) REVERT: A 1020 GLN cc_start: 0.7771 (tm-30) cc_final: 0.7464 (tm-30) REVERT: A 1038 SER cc_start: 0.8850 (t) cc_final: 0.8559 (p) REVERT: L 54 ILE cc_start: 0.7616 (tp) cc_final: 0.7176 (mm) REVERT: L 88 TYR cc_start: 0.7535 (m-80) cc_final: 0.7043 (m-80) REVERT: H 92 ASP cc_start: 0.7758 (m-30) cc_final: 0.5585 (t70) REVERT: H 100 THR cc_start: 0.7288 (p) cc_final: 0.6692 (t) REVERT: D 52 LYS cc_start: 0.8322 (mttp) cc_final: 0.7912 (mtmt) REVERT: D 62 TYR cc_start: 0.8235 (m-80) cc_final: 0.7902 (m-80) REVERT: D 85 MET cc_start: 0.3635 (mtt) cc_final: 0.3363 (mtt) REVERT: E 84 ASP cc_start: 0.7881 (t0) cc_final: 0.7551 (t0) REVERT: E 107 LYS cc_start: 0.6941 (tptt) cc_final: 0.6628 (mmmt) REVERT: B 78 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.7950 (tp-100) REVERT: B 213 ASP cc_start: 0.6668 (m-30) cc_final: 0.6271 (m-30) REVERT: B 240 MET cc_start: 0.7101 (ttt) cc_final: 0.6002 (ttt) REVERT: B 819 GLN cc_start: 0.8630 (tp40) cc_final: 0.8363 (mt0) REVERT: B 1019 PHE cc_start: 0.8132 (t80) cc_final: 0.7930 (t80) REVERT: B 1084 GLN cc_start: 0.8194 (tp40) cc_final: 0.7689 (tp40) REVERT: C 84 MET cc_start: 0.6428 (ptm) cc_final: 0.6171 (ptm) REVERT: C 156 PHE cc_start: 0.5215 (OUTLIER) cc_final: 0.4754 (m-10) REVERT: C 254 PHE cc_start: 0.8282 (t80) cc_final: 0.7979 (t80) REVERT: C 1200 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8521 (mm) outliers start: 95 outliers final: 68 residues processed: 394 average time/residue: 0.1751 time to fit residues: 116.4028 Evaluate side-chains 371 residues out of total 3194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 299 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 844 ASP Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 1047 ILE Chi-restraints excluded: chain A residue 1121 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 804 VAL Chi-restraints excluded: chain B residue 1197 ILE Chi-restraints excluded: chain B residue 1218 LEU Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 513 GLU Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 681 HIS Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 811 CYS Chi-restraints excluded: chain C residue 939 MET Chi-restraints excluded: chain C residue 1041 SER Chi-restraints excluded: chain C residue 1062 GLU Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1086 LEU Chi-restraints excluded: chain C residue 1200 LEU Chi-restraints excluded: chain C residue 1218 LEU Chi-restraints excluded: chain C residue 1222 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 54 optimal weight: 0.9990 chunk 233 optimal weight: 2.9990 chunk 333 optimal weight: 0.7980 chunk 214 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 175 optimal weight: 0.6980 chunk 182 optimal weight: 0.5980 chunk 67 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 224 optimal weight: 0.0370 overall best weight: 0.6260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1122 HIS ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1042 ASN C 36 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.139929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.108848 restraints weight = 60657.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.113096 restraints weight = 32289.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.114372 restraints weight = 19741.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.114639 restraints weight = 18908.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.114566 restraints weight = 16237.947| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.4722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 31845 Z= 0.142 Angle : 0.671 12.733 43602 Z= 0.323 Chirality : 0.043 0.293 5278 Planarity : 0.004 0.064 5317 Dihedral : 4.568 46.585 4073 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.55 % Favored : 96.42 % Rotamer: Outliers : 2.79 % Allowed : 14.46 % Favored : 82.75 % 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: -0.10 (0.14), residues: 3717 helix: 1.66 (0.21), residues: 669 sheet: 0.11 (0.16), residues: 976 loop : -0.71 (0.13), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 53 TYR 0.020 0.001 TYR B1186 PHE 0.023 0.001 PHE C 40 TRP 0.022 0.001 TRP H 36 HIS 0.005 0.001 HIS B 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (31634) covalent geometry : angle 0.63679 / 0.32 (43020) SS BOND : bond 0.00342 / 0.22 ( 51) SS BOND : angle 1.91940 / 1.25 ( 102) hydrogen bonds : bond 0.04969 / 3.28 ( 1154) hydrogen bonds : angle 5.23590 / 3.64 ( 3063) link_ALPHA1-2 : bond 0.00413 / 0.22 ( 9) link_ALPHA1-2 : angle 1.45938 / 0.94 ( 27) link_ALPHA1-3 : bond 0.00547 / 0.38 ( 15) link_ALPHA1-3 : angle 1.60713 / 1.13 ( 45) link_ALPHA1-6 : bond 0.00697 / 0.46 ( 13) link_ALPHA1-6 : angle 1.53231 / 1.07 ( 39) link_BETA1-4 : bond 0.01136 / 0.81 ( 74) link_BETA1-4 : angle 2.14762 / 1.49 ( 222) link_NAG-ASN : bond 0.00388 / 0.27 ( 49) link_NAG-ASN : angle 1.88989 / 1.29 ( 147) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 311 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.7927 (ttp) cc_final: 0.7645 (ttm) REVERT: A 161 MET cc_start: 0.8377 (tpp) cc_final: 0.8130 (mmm) REVERT: A 871 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7632 (pp) REVERT: A 955 ILE cc_start: 0.8871 (mm) cc_final: 0.8640 (tp) REVERT: A 1020 GLN cc_start: 0.7768 (tm-30) cc_final: 0.7451 (tm-30) REVERT: A 1038 SER cc_start: 0.8925 (t) cc_final: 0.8648 (p) REVERT: L 47 LYS cc_start: 0.7467 (pttm) cc_final: 0.6281 (tppt) REVERT: L 49 MET cc_start: 0.7847 (mpp) cc_final: 0.7316 (mpp) REVERT: L 54 ILE cc_start: 0.7814 (tp) cc_final: 0.7397 (mm) REVERT: L 88 TYR cc_start: 0.7459 (m-80) cc_final: 0.7106 (m-80) REVERT: H 27 LEU cc_start: 0.2014 (OUTLIER) cc_final: 0.1622 (pp) REVERT: H 92 ASP cc_start: 0.7806 (m-30) cc_final: 0.5622 (t70) REVERT: H 100 THR cc_start: 0.7304 (p) cc_final: 0.6705 (t) REVERT: D 52 LYS cc_start: 0.8183 (mttp) cc_final: 0.7804 (mtmt) REVERT: D 62 TYR cc_start: 0.8245 (m-80) cc_final: 0.7904 (m-80) REVERT: D 82 TYR cc_start: 0.8630 (m-10) cc_final: 0.8364 (m-10) REVERT: E 81 GLN cc_start: 0.7777 (pp30) cc_final: 0.7517 (pp30) REVERT: E 107 LYS cc_start: 0.7028 (tptt) cc_final: 0.6659 (mmmt) REVERT: B 78 GLN cc_start: 0.9010 (OUTLIER) cc_final: 0.7820 (tp-100) REVERT: B 240 MET cc_start: 0.7085 (ttt) cc_final: 0.5986 (ttt) REVERT: B 830 LYS cc_start: 0.8845 (mmtt) cc_final: 0.8351 (mmtm) REVERT: B 1084 GLN cc_start: 0.8213 (tp40) cc_final: 0.7711 (tp40) REVERT: B 1137 MET cc_start: 0.8622 (mtm) cc_final: 0.8246 (ptp) REVERT: C 84 MET cc_start: 0.6424 (ptm) cc_final: 0.6172 (ptm) REVERT: C 156 PHE cc_start: 0.5240 (OUTLIER) cc_final: 0.4775 (m-10) REVERT: C 254 PHE cc_start: 0.8284 (t80) cc_final: 0.7988 (t80) REVERT: C 452 MET cc_start: 0.8282 (mtm) cc_final: 0.8014 (mtp) REVERT: C 757 MET cc_start: 0.8312 (mtp) cc_final: 0.7785 (mtp) REVERT: C 1200 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8475 (mm) outliers start: 89 outliers final: 76 residues processed: 375 average time/residue: 0.1570 time to fit residues: 101.3311 Evaluate side-chains 371 residues out of total 3194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 290 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 844 ASP Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 1047 ILE Chi-restraints excluded: chain A residue 1121 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 71 ASN Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 804 VAL Chi-restraints excluded: chain B residue 806 CYS Chi-restraints excluded: chain B residue 846 VAL Chi-restraints excluded: chain B residue 1040 LEU Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1197 ILE Chi-restraints excluded: chain B residue 1218 LEU Chi-restraints excluded: chain B residue 1222 LEU Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 513 GLU Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 681 HIS Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 811 CYS Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 939 MET Chi-restraints excluded: chain C residue 1041 SER Chi-restraints excluded: chain C residue 1062 GLU Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1086 LEU Chi-restraints excluded: chain C residue 1200 LEU Chi-restraints excluded: chain C residue 1218 LEU Chi-restraints excluded: chain C residue 1222 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 203 optimal weight: 0.8980 chunk 233 optimal weight: 2.9990 chunk 50 optimal weight: 0.0050 chunk 193 optimal weight: 0.9990 chunk 191 optimal weight: 1.9990 chunk 273 optimal weight: 0.4980 chunk 222 optimal weight: 1.9990 chunk 258 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 ASN ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 819 GLN ** B1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.141432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.112726 restraints weight = 60120.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.114939 restraints weight = 36488.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.115048 restraints weight = 26278.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.115615 restraints weight = 24450.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.115617 restraints weight = 21769.962| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.4913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 31845 Z= 0.169 Angle : 0.694 11.917 43602 Z= 0.335 Chirality : 0.044 0.307 5278 Planarity : 0.004 0.062 5317 Dihedral : 4.696 46.276 4073 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.09 % Favored : 95.88 % Rotamer: Outliers : 3.04 % Allowed : 14.68 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.13), residues: 3717 helix: 1.58 (0.21), residues: 669 sheet: 0.08 (0.16), residues: 950 loop : -0.79 (0.13), residues: 2098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 53 TYR 0.020 0.001 TYR B1186 PHE 0.031 0.002 PHE H 29 TRP 0.027 0.001 TRP H 36 HIS 0.006 0.001 HIS B 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (31634) covalent geometry : angle 0.65994 / 0.33 (43020) SS BOND : bond 0.00367 / 0.25 ( 51) SS BOND : angle 1.91157 / 1.30 ( 102) hydrogen bonds : bond 0.05251 / 3.47 ( 1154) hydrogen bonds : angle 5.33578 / 3.71 ( 3063) link_ALPHA1-2 : bond 0.00433 / 0.23 ( 9) link_ALPHA1-2 : angle 1.48122 / 0.95 ( 27) link_ALPHA1-3 : bond 0.00570 / 0.40 ( 15) link_ALPHA1-3 : angle 1.69805 / 1.19 ( 45) link_ALPHA1-6 : bond 0.00699 / 0.46 ( 13) link_ALPHA1-6 : angle 1.56661 / 1.09 ( 39) link_BETA1-4 : bond 0.01137 / 0.80 ( 74) link_BETA1-4 : angle 2.17847 / 1.51 ( 222) link_NAG-ASN : bond 0.00392 / 0.27 ( 49) link_NAG-ASN : angle 1.93521 / 1.32 ( 147) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 3194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 305 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.7733 (ttp) cc_final: 0.7400 (ttm) REVERT: A 871 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7763 (pp) REVERT: A 955 ILE cc_start: 0.8847 (mm) cc_final: 0.8523 (tt) REVERT: A 1020 GLN cc_start: 0.7776 (tm-30) cc_final: 0.7501 (tm-30) REVERT: L 47 LYS cc_start: 0.7675 (pttm) cc_final: 0.6609 (tppt) REVERT: L 49 MET cc_start: 0.7803 (mpp) cc_final: 0.7243 (mpp) REVERT: L 54 ILE cc_start: 0.7670 (tp) cc_final: 0.7277 (mm) REVERT: H 27 LEU cc_start: 0.1613 (OUTLIER) cc_final: 0.1175 (pp) REVERT: H 41 PRO cc_start: 0.8486 (Cg_exo) cc_final: 0.8230 (Cg_endo) REVERT: H 92 ASP cc_start: 0.7721 (m-30) cc_final: 0.5636 (t70) REVERT: H 100 THR cc_start: 0.7280 (p) cc_final: 0.6733 (t) REVERT: D 52 LYS cc_start: 0.8234 (mttp) cc_final: 0.7811 (mtmt) REVERT: D 62 TYR cc_start: 0.8078 (m-80) cc_final: 0.7835 (m-80) REVERT: D 82 TYR cc_start: 0.8423 (m-10) cc_final: 0.8116 (m-10) REVERT: D 85 MET cc_start: 0.3687 (mtt) cc_final: 0.3357 (mtt) REVERT: D 98 CYS cc_start: 0.6946 (OUTLIER) cc_final: 0.6646 (t) REVERT: E 81 GLN cc_start: 0.7744 (pp30) cc_final: 0.7520 (pp30) REVERT: E 107 LYS cc_start: 0.6873 (tptt) cc_final: 0.6656 (mmmt) REVERT: B 78 GLN cc_start: 0.9032 (OUTLIER) cc_final: 0.8053 (tp-100) REVERT: B 240 MET cc_start: 0.7090 (ttt) cc_final: 0.5986 (ttt) REVERT: B 303 ILE cc_start: 0.7102 (pp) cc_final: 0.6877 (tt) REVERT: B 830 LYS cc_start: 0.8924 (mmtt) cc_final: 0.8646 (mmtm) REVERT: B 1084 GLN cc_start: 0.8185 (tp40) cc_final: 0.7687 (tp40) REVERT: B 1137 MET cc_start: 0.8563 (mtm) cc_final: 0.8349 (ptp) REVERT: C 84 MET cc_start: 0.6580 (ptm) cc_final: 0.6333 (ptm) REVERT: C 156 PHE cc_start: 0.5218 (OUTLIER) cc_final: 0.4754 (m-10) REVERT: C 254 PHE cc_start: 0.8103 (t80) cc_final: 0.7847 (t80) REVERT: C 452 MET cc_start: 0.8387 (mtm) cc_final: 0.8133 (mtp) REVERT: C 757 MET cc_start: 0.8315 (mtp) cc_final: 0.7790 (mtp) REVERT: C 1200 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8349 (mm) outliers start: 97 outliers final: 80 residues processed: 377 average time/residue: 0.1661 time to fit residues: 106.8029 Evaluate side-chains 375 residues out of total 3194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 289 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 844 ASP Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 1047 ILE Chi-restraints excluded: chain A residue 1121 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 71 ASN Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 804 VAL Chi-restraints excluded: chain B residue 806 CYS Chi-restraints excluded: chain B residue 846 VAL Chi-restraints excluded: chain B residue 1040 LEU Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1197 ILE Chi-restraints excluded: chain B residue 1218 LEU Chi-restraints excluded: chain B residue 1222 LEU Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 513 GLU Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain C residue 569 MET Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 726 ASP Chi-restraints excluded: chain C residue 811 CYS Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 939 MET Chi-restraints excluded: chain C residue 1041 SER Chi-restraints excluded: chain C residue 1062 GLU Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1086 LEU Chi-restraints excluded: chain C residue 1144 SER Chi-restraints excluded: chain C residue 1200 LEU Chi-restraints excluded: chain C residue 1218 LEU Chi-restraints excluded: chain C residue 1222 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 148 optimal weight: 4.9990 chunk 368 optimal weight: 2.9990 chunk 299 optimal weight: 1.9990 chunk 241 optimal weight: 1.9990 chunk 308 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 294 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 chunk 313 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 ASN A 516 GLN A 815 GLN ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS ** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 800 GLN B 988 GLN ** B1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 857 GLN C 927 GLN C1146 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.141020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.112720 restraints weight = 59316.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.115306 restraints weight = 36207.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.115763 restraints weight = 26593.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.115812 restraints weight = 24000.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.115879 restraints weight = 21871.428| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.5277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 31845 Z= 0.286 Angle : 0.838 13.242 43602 Z= 0.408 Chirality : 0.048 0.349 5278 Planarity : 0.005 0.068 5317 Dihedral : 5.401 45.583 4073 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.27 % Favored : 94.70 % Rotamer: Outliers : 2.91 % Allowed : 14.97 % Favored : 82.12 % 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: -0.62 (0.13), residues: 3717 helix: 1.19 (0.21), residues: 641 sheet: -0.04 (0.17), residues: 912 loop : -1.10 (0.13), residues: 2164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 53 TYR 0.031 0.002 TYR A 641 PHE 0.030 0.003 PHE C 116 TRP 0.025 0.002 TRP H 36 HIS 0.009 0.002 HIS A1138 Details of bonding type rmsd/Z covalent geometry : bond 0.00676 / 0.29 (31634) covalent geometry : angle 0.80200 / 0.40 (43020) SS BOND : bond 0.00547 / 0.39 ( 51) SS BOND : angle 2.39139 / 1.71 ( 102) hydrogen bonds : bond 0.06679 / 4.42 ( 1154) hydrogen bonds : angle 5.90387 / 4.11 ( 3063) link_ALPHA1-2 : bond 0.00522 / 0.27 ( 9) link_ALPHA1-2 : angle 1.56164 / 0.99 ( 27) link_ALPHA1-3 : bond 0.00601 / 0.43 ( 15) link_ALPHA1-3 : angle 2.01506 / 1.42 ( 45) link_ALPHA1-6 : bond 0.00680 / 0.45 ( 13) link_ALPHA1-6 : angle 1.73719 / 1.21 ( 39) link_BETA1-4 : bond 0.01160 / 0.82 ( 74) link_BETA1-4 : angle 2.38033 / 1.64 ( 222) link_NAG-ASN : bond 0.00516 / 0.35 ( 49) link_NAG-ASN : angle 2.23327 / 1.52 ( 147) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 3194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 289 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.7794 (ttp) cc_final: 0.7395 (ttm) REVERT: A 161 MET cc_start: 0.8136 (mmm) cc_final: 0.7930 (mmm) REVERT: A 444 ASP cc_start: 0.8187 (m-30) cc_final: 0.7949 (m-30) REVERT: A 871 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7808 (pp) REVERT: A 1020 GLN cc_start: 0.7815 (tm-30) cc_final: 0.7536 (tm-30) REVERT: L 47 LYS cc_start: 0.7787 (pttm) cc_final: 0.6860 (tppt) REVERT: L 54 ILE cc_start: 0.8042 (tp) cc_final: 0.7636 (mm) REVERT: H 27 LEU cc_start: 0.1539 (OUTLIER) cc_final: 0.1133 (pp) REVERT: H 92 ASP cc_start: 0.7507 (m-30) cc_final: 0.5571 (t70) REVERT: H 100 THR cc_start: 0.7037 (p) cc_final: 0.6502 (t) REVERT: D 52 LYS cc_start: 0.8258 (mttp) cc_final: 0.7870 (mtmt) REVERT: D 62 TYR cc_start: 0.7963 (m-80) cc_final: 0.7721 (m-80) REVERT: D 82 TYR cc_start: 0.8389 (m-10) cc_final: 0.8187 (m-10) REVERT: E 4 LEU cc_start: 0.8156 (mt) cc_final: 0.7949 (mt) REVERT: B 78 GLN cc_start: 0.9057 (OUTLIER) cc_final: 0.8115 (tp-100) REVERT: B 88 SER cc_start: 0.8898 (m) cc_final: 0.8677 (t) REVERT: B 240 MET cc_start: 0.7390 (ttt) cc_final: 0.6403 (ttt) REVERT: B 303 ILE cc_start: 0.7189 (pp) cc_final: 0.6986 (mm) REVERT: B 830 LYS cc_start: 0.9002 (mmtt) cc_final: 0.8716 (mmtm) REVERT: B 1031 GLN cc_start: 0.8551 (tt0) cc_final: 0.8313 (tm-30) REVERT: B 1084 GLN cc_start: 0.8197 (tp40) cc_final: 0.7734 (tp40) REVERT: C 84 MET cc_start: 0.6682 (ptm) cc_final: 0.6422 (ptm) REVERT: C 156 PHE cc_start: 0.5439 (OUTLIER) cc_final: 0.4852 (m-10) REVERT: C 172 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7786 (tp) REVERT: C 224 SER cc_start: 0.9000 (m) cc_final: 0.8612 (p) REVERT: C 254 PHE cc_start: 0.8150 (t80) cc_final: 0.7868 (t80) REVERT: C 452 MET cc_start: 0.8452 (mtm) cc_final: 0.8222 (mtp) REVERT: C 757 MET cc_start: 0.8238 (mtp) cc_final: 0.7701 (mtp) REVERT: C 1200 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8294 (mm) outliers start: 93 outliers final: 79 residues processed: 359 average time/residue: 0.1665 time to fit residues: 101.2325 Evaluate side-chains 362 residues out of total 3194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 277 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 844 ASP Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 1047 ILE Chi-restraints excluded: chain A residue 1121 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain L residue 71 ASN Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 804 VAL Chi-restraints excluded: chain B residue 806 CYS Chi-restraints excluded: chain B residue 846 VAL Chi-restraints excluded: chain B residue 1040 LEU Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1197 ILE Chi-restraints excluded: chain B residue 1218 LEU Chi-restraints excluded: chain B residue 1222 LEU Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 513 GLU Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain C residue 569 MET Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 726 ASP Chi-restraints excluded: chain C residue 811 CYS Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 939 MET Chi-restraints excluded: chain C residue 1041 SER Chi-restraints excluded: chain C residue 1054 ILE Chi-restraints excluded: chain C residue 1062 GLU Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1144 SER Chi-restraints excluded: chain C residue 1200 LEU Chi-restraints excluded: chain C residue 1218 LEU Chi-restraints excluded: chain C residue 1222 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 32 optimal weight: 0.7980 chunk 168 optimal weight: 0.8980 chunk 299 optimal weight: 0.8980 chunk 283 optimal weight: 3.9990 chunk 328 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 199 optimal weight: 0.3980 chunk 125 optimal weight: 2.9990 chunk 249 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 353 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 ASN ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.140722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.111783 restraints weight = 60218.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.114665 restraints weight = 35879.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.115097 restraints weight = 24657.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.115138 restraints weight = 23959.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.115269 restraints weight = 21007.353| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.5305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 31845 Z= 0.159 Angle : 0.716 11.865 43602 Z= 0.346 Chirality : 0.045 0.356 5278 Planarity : 0.004 0.061 5317 Dihedral : 4.965 45.537 4073 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.71 % Favored : 96.26 % Rotamer: Outliers : 2.63 % Allowed : 15.53 % Favored : 81.84 % 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: -0.47 (0.13), residues: 3717 helix: 1.37 (0.21), residues: 669 sheet: -0.08 (0.16), residues: 950 loop : -0.98 (0.13), residues: 2098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 53 TYR 0.020 0.001 TYR A 641 PHE 0.030 0.002 PHE H 29 TRP 0.025 0.002 TRP H 36 HIS 0.007 0.001 HIS B 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (31634) covalent geometry : angle 0.68147 / 0.34 (43020) SS BOND : bond 0.00381 / 0.26 ( 51) SS BOND : angle 2.00996 / 1.39 ( 102) hydrogen bonds : bond 0.05490 / 3.63 ( 1154) hydrogen bonds : angle 5.53414 / 3.85 ( 3063) link_ALPHA1-2 : bond 0.00474 / 0.26 ( 9) link_ALPHA1-2 : angle 1.47671 / 0.95 ( 27) link_ALPHA1-3 : bond 0.00614 / 0.43 ( 15) link_ALPHA1-3 : angle 1.73684 / 1.22 ( 45) link_ALPHA1-6 : bond 0.00711 / 0.48 ( 13) link_ALPHA1-6 : angle 1.59747 / 1.12 ( 39) link_BETA1-4 : bond 0.01126 / 0.80 ( 74) link_BETA1-4 : angle 2.20947 / 1.54 ( 222) link_NAG-ASN : bond 0.00404 / 0.28 ( 49) link_NAG-ASN : angle 2.01768 / 1.38 ( 147) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4889.27 seconds wall clock time: 85 minutes 47.75 seconds (5147.75 seconds total)