Starting phenix.real_space_refine on Sat Jul 4 15:38:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ur6_26706/07_2026/7ur6_26706.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ur6_26706/07_2026/7ur6_26706.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7ur6_26706/07_2026/7ur6_26706.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ur6_26706/07_2026/7ur6_26706.cif" model { file = "/net/cci-nas-00/data/ceres_data/7ur6_26706/07_2026/7ur6_26706.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ur6_26706/07_2026/7ur6_26706.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ur6_26706/07_2026/7ur6_26706.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ur6_26706/07_2026/7ur6_26706.map" } resolution = 3.46 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= 0.004 sd= 0.025 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 129 5.16 5 C 13497 2.51 5 N 3429 2.21 5 O 4578 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 83 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21633 Number of models: 1 Model: "" Number of chains: 60 Chain: "G" Number of atoms: 3556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3556 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 23, 'TRANS': 428} Chain breaks: 4 Chain: "B" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1045 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "H" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1021 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain: "L" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 803 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "A" Number of atoms: 3556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3556 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 23, 'TRANS': 428} Chain breaks: 4 Chain: "C" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1045 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "D" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1021 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain: "E" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 803 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "F" Number of atoms: 3556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3556 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 23, 'TRANS': 428} Chain breaks: 4 Chain: "I" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1045 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "J" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1021 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain: "K" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 803 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" 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: "P" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "Q" 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: "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: 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: 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: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" 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: "d" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "e" 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: "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: 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: "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: 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: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "l" 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: "m" 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: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "r" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "s" 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: "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: 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: 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: 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: "z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "0" 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: "1" 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: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "B" 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 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 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 Chain: "F" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "I" 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: 4.73, per 1000 atoms: 0.22 Number of scatterers: 21633 At special positions: 0 Unit cell: (148.371, 153.786, 124.545, 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 129 16.00 O 4578 8.00 N 3429 7.00 C 13497 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.04 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.04 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS G 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS C 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 201 " - pdb=" SG CYS F 433 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.04 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 501 " - pdb=" SG CYS I 605 " distance=2.03 Simple disulfide: pdb=" SG CYS I 598 " - pdb=" SG CYS I 604 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " 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 P 5 " - " MAN P 6 " " MAN P 8 " - " MAN P 9 " " MAN Q 4 " - " MAN Q 5 " " MAN d 5 " - " MAN d 6 " " MAN d 8 " - " MAN d 9 " " MAN e 4 " - " MAN e 5 " " MAN r 5 " - " MAN r 6 " " MAN r 8 " - " MAN r 9 " " MAN s 4 " - " MAN s 5 " ALPHA1-3 " BMA 0 3 " - " MAN 0 4 " " BMA O 3 " - " MAN O 4 " " BMA P 3 " - " MAN P 8 " " MAN P 4 " - " MAN P 7 " " BMA Q 3 " - " MAN Q 4 " " BMA Y 3 " - " MAN Y 4 " " BMA c 3 " - " MAN c 4 " " BMA d 3 " - " MAN d 8 " " MAN d 4 " - " MAN d 7 " " BMA e 3 " - " MAN e 4 " " BMA m 3 " - " MAN m 4 " " BMA q 3 " - " MAN q 4 " " BMA r 3 " - " MAN r 8 " " MAN r 4 " - " MAN r 7 " " BMA s 3 " - " MAN s 4 " ALPHA1-6 " BMA 0 3 " - " MAN 0 5 " " BMA O 3 " - " MAN O 5 " " BMA P 3 " - " MAN P 4 " " MAN P 4 " - " MAN P 5 " " BMA Q 3 " - " MAN Q 6 " " BMA Y 3 " - " MAN Y 5 " " BMA c 3 " - " MAN c 5 " " BMA d 3 " - " MAN d 4 " " MAN d 4 " - " MAN d 5 " " BMA e 3 " - " MAN e 6 " " BMA m 3 " - " MAN m 5 " " BMA q 3 " - " MAN q 5 " " BMA r 3 " - " MAN r 4 " " MAN r 4 " - " MAN r 5 " " BMA s 3 " - " MAN s 6 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 1 1 " - " NAG 1 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " 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 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 Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " 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 h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " 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 y 1 " - " NAG y 2 " " NAG z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " NAG-ASN " NAG 0 1 " - " ASN F 339 " " NAG 1 1 " - " ASN I 637 " " NAG A 601 " - " ASN A 130 " " NAG A 602 " - " ASN A 230 " " NAG A 603 " - " ASN A 234 " " NAG A 604 " - " ASN A 276 " " NAG A 605 " - " ASN A 289 " " NAG A 606 " - " ASN A 301 " " NAG A 607 " - " ASN A 332 " " NAG A 608 " - " ASN A 386 " " NAG A 609 " - " ASN A 442 " " NAG A 610 " - " ASN A 448 " " NAG A 611 " - " ASN A 133 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 625 " " NAG B 703 " - " ASN B 616 " " NAG C 701 " - " ASN C 611 " " NAG C 702 " - " ASN C 625 " " NAG C 703 " - " ASN C 616 " " NAG F 601 " - " ASN F 130 " " NAG F 602 " - " ASN F 230 " " NAG F 603 " - " ASN F 234 " " NAG F 604 " - " ASN F 276 " " NAG F 605 " - " ASN F 289 " " NAG F 606 " - " ASN F 301 " " NAG F 607 " - " ASN F 332 " " NAG F 608 " - " ASN F 386 " " NAG F 609 " - " ASN F 442 " " NAG F 610 " - " ASN F 448 " " NAG F 611 " - " ASN F 133 " " NAG G 601 " - " ASN G 130 " " NAG G 602 " - " ASN G 230 " " NAG G 603 " - " ASN G 234 " " NAG G 604 " - " ASN G 276 " " NAG G 605 " - " ASN G 289 " " NAG G 606 " - " ASN G 301 " " NAG G 607 " - " ASN G 332 " " NAG G 608 " - " ASN G 386 " " NAG G 609 " - " ASN G 442 " " NAG G 610 " - " ASN G 448 " " NAG G 611 " - " ASN G 133 " " NAG I 701 " - " ASN I 611 " " NAG I 702 " - " ASN I 625 " " NAG I 703 " - " ASN I 616 " " NAG M 1 " - " ASN G 156 " " NAG N 1 " - " ASN G 197 " " NAG O 1 " - " ASN G 262 " " NAG P 1 " - " ASN G 241 " " NAG Q 1 " - " ASN G 88 " " NAG R 1 " - " ASN G 160 " " NAG S 1 " - " ASN G 407 " " NAG T 1 " - " ASN G 402 " " NAG U 1 " - " ASN G 398 " " NAG V 1 " - " ASN G 358 " " NAG W 1 " - " ASN G 362 " " NAG X 1 " - " ASN G 392 " " NAG Y 1 " - " ASN G 339 " " NAG Z 1 " - " ASN B 637 " " NAG a 1 " - " ASN A 156 " " NAG b 1 " - " ASN A 197 " " NAG c 1 " - " ASN A 262 " " NAG d 1 " - " ASN A 241 " " NAG e 1 " - " ASN A 88 " " NAG f 1 " - " ASN A 160 " " NAG g 1 " - " ASN A 407 " " NAG h 1 " - " ASN A 402 " " NAG i 1 " - " ASN A 398 " " NAG j 1 " - " ASN A 358 " " NAG k 1 " - " ASN A 362 " " NAG l 1 " - " ASN A 392 " " NAG m 1 " - " ASN A 339 " " NAG n 1 " - " ASN C 637 " " NAG o 1 " - " ASN F 156 " " NAG p 1 " - " ASN F 197 " " NAG q 1 " - " ASN F 262 " " NAG r 1 " - " ASN F 241 " " NAG s 1 " - " ASN F 88 " " NAG t 1 " - " ASN F 160 " " NAG u 1 " - " ASN F 407 " " NAG v 1 " - " ASN F 402 " " NAG w 1 " - " ASN F 398 " " NAG x 1 " - " ASN F 358 " " NAG y 1 " - " ASN F 362 " " NAG z 1 " - " ASN F 392 " Time building additional restraints: 2.41 Conformation dependent library (CDL) restraints added in 846.1 milliseconds 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4572 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 48 sheets defined 20.2% alpha, 30.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'G' and resid 70 through 74 Processing helix chain 'G' and resid 98 through 117 removed outlier: 3.929A pdb=" N ASP G 102 " --> pdb=" O ASN G 98 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU G 106 " --> pdb=" O ASP G 102 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE G 109 " --> pdb=" O HIS G 105 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS G 117 " --> pdb=" O ASP G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 Processing helix chain 'G' and resid 195 through 198 Processing helix chain 'G' and resid 335 through 353 removed outlier: 3.774A pdb=" N GLU G 351 " --> pdb=" O ARG G 347 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N HIS G 352 " --> pdb=" O LYS G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.535A pdb=" N THR G 373 " --> pdb=" O LEU G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 402 through 406 removed outlier: 3.569A pdb=" N ALA G 405 " --> pdb=" O ASN G 402 " (cutoff:3.500A) Processing helix chain 'G' and resid 476 through 481 removed outlier: 3.574A pdb=" N SER G 481 " --> pdb=" O ASP G 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 544 removed outlier: 4.233A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU B 544 " --> pdb=" O GLN B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 597 removed outlier: 3.625A pdb=" N VAL B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 624 removed outlier: 3.514A pdb=" N ASN B 624 " --> pdb=" O GLU B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 662 removed outlier: 3.661A pdb=" N GLU B 657 " --> pdb=" O GLN B 653 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.531A pdb=" N LYS H 64 " --> pdb=" O LEU H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.632A pdb=" N THR H 87 " --> pdb=" O PRO H 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 98 through 117 removed outlier: 3.876A pdb=" N ASP A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE A 109 " --> pdb=" O HIS A 105 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS A 117 " --> pdb=" O ASP A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 353 removed outlier: 3.501A pdb=" N THR A 341 " --> pdb=" O ASN A 337 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N HIS A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.562A pdb=" N THR A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 406 removed outlier: 3.560A pdb=" N ALA A 405 " --> pdb=" O ASN A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 484 removed outlier: 3.583A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 536 through 544 removed outlier: 4.274A pdb=" N GLN C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA C 541 " --> pdb=" O LEU C 537 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLN C 543 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU C 544 " --> pdb=" O GLN C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 597 removed outlier: 3.634A pdb=" N VAL C 589 " --> pdb=" O ARG C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 624 removed outlier: 3.514A pdb=" N ASN C 624 " --> pdb=" O GLU C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 635 Processing helix chain 'C' and resid 638 through 662 removed outlier: 3.673A pdb=" N GLU C 657 " --> pdb=" O GLN C 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 64 removed outlier: 3.579A pdb=" N LYS D 64 " --> pdb=" O LEU D 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 61 through 64' Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.628A pdb=" N THR D 87 " --> pdb=" O PRO D 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 74 Processing helix chain 'F' and resid 98 through 117 removed outlier: 3.952A pdb=" N ASP F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU F 106 " --> pdb=" O ASP F 102 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE F 109 " --> pdb=" O HIS F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 126 Processing helix chain 'F' and resid 195 through 198 Processing helix chain 'F' and resid 335 through 353 removed outlier: 3.765A pdb=" N GLU F 351 " --> pdb=" O ARG F 347 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N HIS F 352 " --> pdb=" O LYS F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 373 removed outlier: 3.533A pdb=" N THR F 373 " --> pdb=" O LEU F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 402 through 406 removed outlier: 3.569A pdb=" N ALA F 405 " --> pdb=" O ASN F 402 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 484 removed outlier: 3.629A pdb=" N SER F 481 " --> pdb=" O ASP F 477 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLU F 482 " --> pdb=" O ASN F 478 " (cutoff:3.500A) Processing helix chain 'I' and resid 529 through 534 Processing helix chain 'I' and resid 536 through 544 removed outlier: 4.272A pdb=" N GLN I 540 " --> pdb=" O THR I 536 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA I 541 " --> pdb=" O LEU I 537 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLN I 543 " --> pdb=" O VAL I 539 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU I 544 " --> pdb=" O GLN I 540 " (cutoff:3.500A) Processing helix chain 'I' and resid 569 through 597 removed outlier: 3.675A pdb=" N VAL I 589 " --> pdb=" O ARG I 585 " (cutoff:3.500A) Processing helix chain 'I' and resid 618 through 624 removed outlier: 3.528A pdb=" N ASN I 624 " --> pdb=" O GLU I 620 " (cutoff:3.500A) Processing helix chain 'I' and resid 627 through 635 Processing helix chain 'I' and resid 638 through 662 removed outlier: 3.670A pdb=" N GLU I 657 " --> pdb=" O GLN I 653 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 64 removed outlier: 3.613A pdb=" N LYS J 64 " --> pdb=" O LEU J 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 61 through 64' Processing helix chain 'J' and resid 83 through 87 removed outlier: 3.608A pdb=" N THR J 87 " --> pdb=" O PRO J 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 494 through 499 removed outlier: 3.532A pdb=" N ALA G 497 " --> pdb=" O THR G 37 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N VAL B 608 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N VAL G 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N THR B 606 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N TYR G 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N CYS B 604 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'G' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'G' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'G' and resid 130 through 133 Processing sheet with id=AA6, first strand: chain 'G' and resid 181 through 183 Processing sheet with id=AA7, first strand: chain 'G' and resid 202 through 203 removed outlier: 7.438A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 259 through 261 removed outlier: 6.434A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE G 443 " --> pdb=" O ARG G 298 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N GLY G 451 " --> pdb=" O GLU G 290 " (cutoff:3.500A) removed outlier: 10.900A pdb=" N GLU G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 12.033A pdb=" N LEU G 453 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 12.335A pdb=" N LEU G 288 " --> pdb=" O LEU G 453 " (cutoff:3.500A) removed outlier: 10.947A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 11.037A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 284 through 298 current: chain 'G' and resid 359 through 361 removed outlier: 3.753A pdb=" N GLY G 393 " --> pdb=" O PHE G 361 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 271 through 273 removed outlier: 11.037A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) removed outlier: 10.947A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 12.335A pdb=" N LEU G 288 " --> pdb=" O LEU G 453 " (cutoff:3.500A) removed outlier: 12.033A pdb=" N LEU G 453 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 10.900A pdb=" N GLU G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N GLY G 451 " --> pdb=" O GLU G 290 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE G 443 " --> pdb=" O ARG G 298 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 443 through 456 current: chain 'G' and resid 413 through 415 Processing sheet with id=AB1, first strand: chain 'G' and resid 302 through 312 removed outlier: 6.489A pdb=" N THR G 303 " --> pdb=" O GLY G 321 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 374 through 378 removed outlier: 3.617A pdb=" N PHE G 376 " --> pdb=" O PHE G 383 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 513 through 514 removed outlier: 7.071A pdb=" N ASP H 100H" --> pdb=" O TYR H 100 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N TYR H 100 " --> pdb=" O ASP H 100H" (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL H 100J" --> pdb=" O ARG H 98 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N ARG H 98 " --> pdb=" O VAL H 100J" (cutoff:3.500A) removed outlier: 5.197A pdb=" N VAL H 100L" --> pdb=" O ARG H 96 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ARG H 96 " --> pdb=" O VAL H 100L" (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 513 through 514 removed outlier: 7.071A pdb=" N ASP H 100H" --> pdb=" O TYR H 100 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N TYR H 100 " --> pdb=" O ASP H 100H" (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL H 100J" --> pdb=" O ARG H 98 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N ARG H 98 " --> pdb=" O VAL H 100J" (cutoff:3.500A) removed outlier: 5.197A pdb=" N VAL H 100L" --> pdb=" O ARG H 96 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ARG H 96 " --> pdb=" O VAL H 100L" (cutoff:3.500A) removed outlier: 5.025A pdb=" N GLY H 35 " --> pdb=" O ILE H 95 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE H 35A" --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N GLY H 50 " --> pdb=" O ILE H 35A" (cutoff:3.500A) removed outlier: 6.840A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.737A pdb=" N THR H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 19 through 24 removed outlier: 3.576A pdb=" N ILE L 21 " --> pdb=" O LEU L 73 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS L 23 " --> pdb=" O ALA L 71 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.565A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE L 97 " --> pdb=" O THR L 90 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 494 through 499 removed outlier: 3.512A pdb=" N ALA A 497 " --> pdb=" O THR A 37 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N VAL C 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N VAL A 38 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N THR C 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N TYR A 40 " --> pdb=" O CYS C 604 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N CYS C 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AC1, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AC2, first strand: chain 'A' and resid 154 through 162 Processing sheet with id=AC3, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AC4, first strand: chain 'A' and resid 202 through 203 removed outlier: 7.415A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.391A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL A 292 " --> pdb=" O ILE A 449 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.965A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 12.036A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 12.368A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 10.941A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.001A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 284 through 298 current: chain 'A' and resid 359 through 361 removed outlier: 3.637A pdb=" N GLY A 393 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 271 through 273 removed outlier: 11.001A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.941A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.368A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 12.036A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.965A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL A 292 " --> pdb=" O ILE A 449 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 443 through 456 current: chain 'A' and resid 413 through 415 Processing sheet with id=AC7, first strand: chain 'A' and resid 302 through 312 removed outlier: 6.539A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 374 through 378 removed outlier: 3.610A pdb=" N PHE A 376 " --> pdb=" O PHE A 383 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 513 through 514 removed outlier: 7.024A pdb=" N ASP D 100H" --> pdb=" O TYR D 100 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N TYR D 100 " --> pdb=" O ASP D 100H" (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL D 100J" --> pdb=" O ARG D 98 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N ARG D 98 " --> pdb=" O VAL D 100J" (cutoff:3.500A) removed outlier: 5.255A pdb=" N VAL D 100L" --> pdb=" O ARG D 96 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ARG D 96 " --> pdb=" O VAL D 100L" (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 513 through 514 removed outlier: 7.024A pdb=" N ASP D 100H" --> pdb=" O TYR D 100 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N TYR D 100 " --> pdb=" O ASP D 100H" (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL D 100J" --> pdb=" O ARG D 98 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N ARG D 98 " --> pdb=" O VAL D 100J" (cutoff:3.500A) removed outlier: 5.255A pdb=" N VAL D 100L" --> pdb=" O ARG D 96 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ARG D 96 " --> pdb=" O VAL D 100L" (cutoff:3.500A) removed outlier: 4.973A pdb=" N GLY D 35 " --> pdb=" O ILE D 95 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE D 35A" --> pdb=" O GLY D 50 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N GLY D 50 " --> pdb=" O ILE D 35A" (cutoff:3.500A) removed outlier: 6.898A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.755A pdb=" N THR D 3 " --> pdb=" O SER D 25 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER D 25 " --> pdb=" O THR D 3 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR D 21 " --> pdb=" O SER D 7 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 19 through 24 removed outlier: 3.584A pdb=" N ILE E 21 " --> pdb=" O LEU E 73 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS E 23 " --> pdb=" O ALA E 71 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA E 71 " --> pdb=" O CYS E 23 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 45 through 48 removed outlier: 6.547A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 494 through 499 removed outlier: 3.517A pdb=" N ALA F 497 " --> pdb=" O THR F 37 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N VAL I 608 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N VAL F 38 " --> pdb=" O THR I 606 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N THR I 606 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N TYR F 40 " --> pdb=" O CYS I 604 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N CYS I 604 " --> pdb=" O TYR F 40 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 45 through 47 Processing sheet with id=AD7, first strand: chain 'F' and resid 53 through 55 Processing sheet with id=AD8, first strand: chain 'F' and resid 66 through 67 removed outlier: 6.893A pdb=" N HIS F 66 " --> pdb=" O THR F 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'F' and resid 91 through 94 Processing sheet with id=AE1, first strand: chain 'F' and resid 130 through 133 Processing sheet with id=AE2, first strand: chain 'F' and resid 181 through 183 Processing sheet with id=AE3, first strand: chain 'F' and resid 259 through 261 removed outlier: 6.416A pdb=" N LEU F 260 " --> pdb=" O THR F 450 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE F 443 " --> pdb=" O ARG F 298 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL F 292 " --> pdb=" O ILE F 449 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N GLY F 451 " --> pdb=" O GLU F 290 " (cutoff:3.500A) removed outlier: 10.858A pdb=" N GLU F 290 " --> pdb=" O GLY F 451 " (cutoff:3.500A) removed outlier: 12.005A pdb=" N LEU F 453 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 12.270A pdb=" N LEU F 288 " --> pdb=" O LEU F 453 " (cutoff:3.500A) removed outlier: 10.975A pdb=" N THR F 455 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 11.109A pdb=" N VAL F 286 " --> pdb=" O THR F 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 284 through 298 current: chain 'F' and resid 359 through 361 removed outlier: 3.755A pdb=" N GLY F 393 " --> pdb=" O PHE F 361 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 271 through 273 removed outlier: 11.109A pdb=" N VAL F 286 " --> pdb=" O THR F 455 " (cutoff:3.500A) removed outlier: 10.975A pdb=" N THR F 455 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 12.270A pdb=" N LEU F 288 " --> pdb=" O LEU F 453 " (cutoff:3.500A) removed outlier: 12.005A pdb=" N LEU F 453 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 10.858A pdb=" N GLU F 290 " --> pdb=" O GLY F 451 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N GLY F 451 " --> pdb=" O GLU F 290 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL F 292 " --> pdb=" O ILE F 449 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE F 443 " --> pdb=" O ARG F 298 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 443 through 456 current: chain 'F' and resid 413 through 415 Processing sheet with id=AE5, first strand: chain 'F' and resid 302 through 312 removed outlier: 6.514A pdb=" N THR F 303 " --> pdb=" O GLY F 321 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N GLN F 315 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 374 through 378 removed outlier: 3.627A pdb=" N PHE F 376 " --> pdb=" O PHE F 383 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 423 through 424 removed outlier: 3.706A pdb=" N ILE F 424 " --> pdb=" O MET F 434 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 513 through 514 removed outlier: 7.098A pdb=" N ASP J 100H" --> pdb=" O TYR J 100 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N TYR J 100 " --> pdb=" O ASP J 100H" (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL J 100J" --> pdb=" O ARG J 98 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N ARG J 98 " --> pdb=" O VAL J 100J" (cutoff:3.500A) removed outlier: 5.216A pdb=" N VAL J 100L" --> pdb=" O ARG J 96 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ARG J 96 " --> pdb=" O VAL J 100L" (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA J 88 " --> pdb=" O VAL J 109 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 513 through 514 removed outlier: 7.098A pdb=" N ASP J 100H" --> pdb=" O TYR J 100 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N TYR J 100 " --> pdb=" O ASP J 100H" (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL J 100J" --> pdb=" O ARG J 98 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N ARG J 98 " --> pdb=" O VAL J 100J" (cutoff:3.500A) removed outlier: 5.216A pdb=" N VAL J 100L" --> pdb=" O ARG J 96 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ARG J 96 " --> pdb=" O VAL J 100L" (cutoff:3.500A) removed outlier: 4.935A pdb=" N GLY J 35 " --> pdb=" O ILE J 95 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE J 35A" --> pdb=" O GLY J 50 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N GLY J 50 " --> pdb=" O ILE J 35A" (cutoff:3.500A) removed outlier: 6.934A pdb=" N TRP J 36 " --> pdb=" O LEU J 48 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 3 through 7 removed outlier: 3.716A pdb=" N THR J 3 " --> pdb=" O SER J 25 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR J 21 " --> pdb=" O SER J 7 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 19 through 24 removed outlier: 3.619A pdb=" N ILE K 21 " --> pdb=" O LEU K 73 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N CYS K 23 " --> pdb=" O ALA K 71 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA K 71 " --> pdb=" O CYS K 23 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 45 through 48 removed outlier: 6.573A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) 665 hydrogen bonds defined for protein. 1743 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: 4.04 Time building geometry restraints manager: 3.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6506 1.35 - 1.47: 5853 1.47 - 1.59: 9508 1.59 - 1.71: 0 1.71 - 1.83: 174 Bond restraints: 22041 Sorted by residual: bond pdb=" C1 BMA Y 3 " pdb=" C2 BMA Y 3 " ideal model delta sigma weight residual 1.519 1.588 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C1 BMA m 3 " pdb=" C2 BMA m 3 " ideal model delta sigma weight residual 1.519 1.587 -0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" C1 BMA 0 3 " pdb=" C2 BMA 0 3 " ideal model delta sigma weight residual 1.519 1.586 -0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" C1 BMA X 3 " pdb=" C2 BMA X 3 " ideal model delta sigma weight residual 1.519 1.558 -0.039 2.00e-02 2.50e+03 3.78e+00 bond pdb=" C1 BMA l 3 " pdb=" C2 BMA l 3 " ideal model delta sigma weight residual 1.519 1.557 -0.038 2.00e-02 2.50e+03 3.70e+00 ... (remaining 22036 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 28275 1.58 - 3.16: 1282 3.16 - 4.74: 282 4.74 - 6.32: 89 6.32 - 7.91: 15 Bond angle restraints: 29943 Sorted by residual: angle pdb=" CA GLU G 164 " pdb=" C GLU G 164 " pdb=" O GLU G 164 " ideal model delta sigma weight residual 120.55 116.89 3.66 1.06e+00 8.90e-01 1.19e+01 angle pdb=" N GLU G 164 " pdb=" CA GLU G 164 " pdb=" C GLU G 164 " ideal model delta sigma weight residual 111.28 107.57 3.71 1.09e+00 8.42e-01 1.16e+01 angle pdb=" O GLU G 164 " pdb=" C GLU G 164 " pdb=" N ILE G 165 " ideal model delta sigma weight residual 122.12 125.46 -3.34 1.06e+00 8.90e-01 9.91e+00 angle pdb=" N VAL K 39 " pdb=" CA VAL K 39 " pdb=" C VAL K 39 " ideal model delta sigma weight residual 109.02 106.10 2.92 9.30e-01 1.16e+00 9.88e+00 angle pdb=" N GLU F 164 " pdb=" CA GLU F 164 " pdb=" C GLU F 164 " ideal model delta sigma weight residual 111.82 108.22 3.60 1.16e+00 7.43e-01 9.64e+00 ... (remaining 29938 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 10254 17.93 - 35.86: 1226 35.86 - 53.78: 256 53.78 - 71.71: 34 71.71 - 89.64: 29 Dihedral angle restraints: 11799 sinusoidal: 4695 harmonic: 7104 Sorted by residual: dihedral pdb=" CB CYS F 119 " pdb=" SG CYS F 119 " pdb=" SG CYS F 205 " pdb=" CB CYS F 205 " ideal model delta sinusoidal sigma weight residual -86.00 -143.45 57.45 1 1.00e+01 1.00e-02 4.44e+01 dihedral pdb=" CB CYS G 119 " pdb=" SG CYS G 119 " pdb=" SG CYS G 205 " pdb=" CB CYS G 205 " ideal model delta sinusoidal sigma weight residual -86.00 -143.44 57.44 1 1.00e+01 1.00e-02 4.43e+01 dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -143.18 57.18 1 1.00e+01 1.00e-02 4.40e+01 ... (remaining 11796 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 3654 0.105 - 0.210: 243 0.210 - 0.315: 21 0.315 - 0.420: 0 0.420 - 0.525: 6 Chirality restraints: 3924 Sorted by residual: chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN G 398 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 6.89e+00 chirality pdb=" C1 NAG w 1 " pdb=" ND2 ASN F 398 " pdb=" C2 NAG w 1 " pdb=" O5 NAG w 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.85e+00 chirality pdb=" C1 NAG i 1 " pdb=" ND2 ASN A 398 " pdb=" C2 NAG i 1 " pdb=" O5 NAG i 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.73e+00 ... (remaining 3921 not shown) Planarity restraints: 3615 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN D 39 " 0.034 5.00e-02 4.00e+02 5.16e-02 4.26e+00 pdb=" N PRO D 40 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO D 40 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 40 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO J 40 " 0.034 5.00e-02 4.00e+02 5.09e-02 4.15e+00 pdb=" N PRO J 41 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO J 41 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO J 41 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP G 78 " -0.032 5.00e-02 4.00e+02 4.90e-02 3.84e+00 pdb=" N PRO G 79 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO G 79 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO G 79 " -0.027 5.00e-02 4.00e+02 ... (remaining 3612 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 406 2.64 - 3.21: 19600 3.21 - 3.77: 30846 3.77 - 4.34: 43053 4.34 - 4.90: 71166 Nonbonded interactions: 165071 Sorted by model distance: nonbonded pdb=" OG SER K 12 " pdb=" O ILE K 105 " model vdw 2.075 3.040 nonbonded pdb=" OG SER E 12 " pdb=" O ILE E 105 " model vdw 2.083 3.040 nonbonded pdb=" OG SER L 12 " pdb=" O ILE L 105 " model vdw 2.084 3.040 nonbonded pdb=" OG1 THR A 404 " pdb=" O5 NAG h 1 " model vdw 2.103 3.040 nonbonded pdb=" OG1 THR G 404 " pdb=" O5 NAG T 1 " model vdw 2.106 3.040 ... (remaining 165066 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain '0' selection = chain 'O' selection = chain 'Y' selection = chain 'c' selection = chain 'm' selection = chain 'q' } ncs_group { reference = chain '1' selection = chain 'M' selection = chain 'N' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' } ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'P' selection = chain 'd' selection = chain 'r' } ncs_group { reference = chain 'Q' selection = chain 'e' selection = chain 's' } ncs_group { reference = chain 'X' selection = chain 'l' selection = chain 'z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 19.520 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.070 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 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 : 0.005 0.069 22263 Z= 0.262 Angle : 0.863 10.797 30567 Z= 0.355 Chirality : 0.056 0.525 3924 Planarity : 0.004 0.074 3531 Dihedral : 15.881 89.638 7101 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.23 % Allowed : 17.83 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.17), residues: 2412 helix: 0.97 (0.29), residues: 375 sheet: -0.05 (0.20), residues: 720 loop : -0.45 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 617 TYR 0.008 0.001 TYR K 36 PHE 0.004 0.001 PHE G 210 TRP 0.009 0.001 TRP J 47 HIS 0.004 0.000 HIS F 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.26 (22041) covalent geometry : angle 0.80873 / 0.34 (29943) SS BOND : bond 0.00242 / 0.16 ( 42) SS BOND : angle 0.94698 / 0.69 ( 84) hydrogen bonds : bond 0.27757 / 18.26 ( 634) hydrogen bonds : angle 8.62388 / 5.91 ( 1743) link_ALPHA1-2 : bond 0.00477 / 0.27 ( 9) link_ALPHA1-2 : angle 2.04639 / 1.28 ( 27) link_ALPHA1-3 : bond 0.00423 / 0.25 ( 15) link_ALPHA1-3 : angle 1.94522 / 1.37 ( 45) link_ALPHA1-6 : bond 0.00439 / 0.27 ( 15) link_ALPHA1-6 : angle 1.86092 / 1.31 ( 45) link_BETA1-4 : bond 0.00817 / 0.54 ( 57) link_BETA1-4 : angle 2.43127 / 1.79 ( 171) link_NAG-ASN : bond 0.00562 / 0.35 ( 84) link_NAG-ASN : angle 2.54883 / 1.63 ( 252) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 418 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 449 ILE cc_start: 0.9015 (mt) cc_final: 0.8772 (tt) REVERT: B 652 GLN cc_start: 0.8477 (tp-100) cc_final: 0.7848 (tp40) REVERT: H 46 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7716 (tm-30) REVERT: H 82 ASN cc_start: 0.8644 (t0) cc_final: 0.8184 (t0) REVERT: H 86 ASP cc_start: 0.8876 (t0) cc_final: 0.8640 (t0) REVERT: H 90 TYR cc_start: 0.8276 (m-80) cc_final: 0.8056 (m-10) REVERT: L 28 ILE cc_start: 0.9207 (mm) cc_final: 0.8795 (tt) REVERT: L 78 LEU cc_start: 0.8240 (tp) cc_final: 0.7950 (tt) REVERT: L 82 ASP cc_start: 0.8373 (m-30) cc_final: 0.7977 (m-30) REVERT: L 85 ASP cc_start: 0.7700 (m-30) cc_final: 0.7295 (m-30) REVERT: A 217 TYR cc_start: 0.7360 (m-80) cc_final: 0.7050 (m-80) REVERT: C 652 GLN cc_start: 0.8470 (tp-100) cc_final: 0.7870 (tp40) REVERT: D 46 GLU cc_start: 0.7655 (tm-30) cc_final: 0.7202 (tm-30) REVERT: D 82 ASN cc_start: 0.8823 (t0) cc_final: 0.8577 (t0) REVERT: D 82 MET cc_start: 0.7854 (mpp) cc_final: 0.7505 (mpp) REVERT: D 95 ILE cc_start: 0.9052 (pt) cc_final: 0.8785 (pt) REVERT: E 28 ILE cc_start: 0.9300 (mm) cc_final: 0.8947 (tt) REVERT: E 78 LEU cc_start: 0.8159 (mp) cc_final: 0.7863 (tt) REVERT: F 426 MET cc_start: 0.7639 (ttm) cc_final: 0.6807 (ttp) REVERT: F 434 MET cc_start: 0.7419 (mtm) cc_final: 0.7143 (mtm) REVERT: I 648 GLU cc_start: 0.8556 (tm-30) cc_final: 0.8330 (tm-30) REVERT: J 29 MET cc_start: 0.8905 (mmm) cc_final: 0.8698 (tpt) REVERT: J 46 GLU cc_start: 0.7706 (tm-30) cc_final: 0.6890 (tm-30) REVERT: J 82 ASN cc_start: 0.8797 (t0) cc_final: 0.8334 (t0) REVERT: K 28 ILE cc_start: 0.9380 (mm) cc_final: 0.8999 (tt) outliers start: 5 outliers final: 3 residues processed: 423 average time/residue: 0.1578 time to fit residues: 100.0763 Evaluate side-chains 310 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 307 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 339 ASN Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain F residue 339 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.0980 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 235 optimal weight: 10.0000 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 653 GLN L 31 ASN C 653 GLN E 31 ASN E 79 GLN F 280 ASN F 343 GLN I 653 GLN K 79 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.074247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.057615 restraints weight = 65417.961| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 3.78 r_work: 0.2780 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22263 Z= 0.156 Angle : 0.717 9.951 30567 Z= 0.331 Chirality : 0.048 0.371 3924 Planarity : 0.004 0.048 3531 Dihedral : 4.304 50.253 2634 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.18 % Allowed : 18.76 % Favored : 79.06 % 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 (0.17), residues: 2412 helix: 1.40 (0.28), residues: 399 sheet: 0.40 (0.21), residues: 660 loop : -0.79 (0.17), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 38 TYR 0.015 0.001 TYR J 90 PHE 0.012 0.001 PHE H 100G TRP 0.016 0.001 TRP F 427 HIS 0.003 0.001 HIS G 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (22041) covalent geometry : angle 0.65762 / 0.32 (29943) SS BOND : bond 0.00270 / 0.18 ( 42) SS BOND : angle 0.81587 / 0.55 ( 84) hydrogen bonds : bond 0.06276 / 4.18 ( 634) hydrogen bonds : angle 5.75633 / 4.00 ( 1743) link_ALPHA1-2 : bond 0.00778 / 0.45 ( 9) link_ALPHA1-2 : angle 1.93107 / 1.19 ( 27) link_ALPHA1-3 : bond 0.00593 / 0.36 ( 15) link_ALPHA1-3 : angle 1.50016 / 1.02 ( 45) link_ALPHA1-6 : bond 0.00530 / 0.34 ( 15) link_ALPHA1-6 : angle 1.53004 / 1.09 ( 45) link_BETA1-4 : bond 0.01011 / 0.69 ( 57) link_BETA1-4 : angle 1.98448 / 1.45 ( 171) link_NAG-ASN : bond 0.00628 / 0.40 ( 84) link_NAG-ASN : angle 2.62391 / 1.71 ( 252) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 316 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 217 TYR cc_start: 0.8154 (m-80) cc_final: 0.7730 (m-80) REVERT: G 449 ILE cc_start: 0.9209 (mt) cc_final: 0.8925 (tt) REVERT: B 588 GLU cc_start: 0.9151 (tt0) cc_final: 0.8917 (mt-10) REVERT: B 646 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9110 (mt) REVERT: B 652 GLN cc_start: 0.8367 (tp-100) cc_final: 0.7828 (tp40) REVERT: H 46 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7819 (tm-30) REVERT: H 75 LYS cc_start: 0.9085 (tptp) cc_final: 0.8876 (tptp) REVERT: H 82 ASN cc_start: 0.9231 (t0) cc_final: 0.8806 (t0) REVERT: H 86 ASP cc_start: 0.9041 (t0) cc_final: 0.8724 (t0) REVERT: L 28 ILE cc_start: 0.9243 (mm) cc_final: 0.8732 (tt) REVERT: L 54 ARG cc_start: 0.8873 (ptt180) cc_final: 0.8575 (ptt180) REVERT: L 82 ASP cc_start: 0.8384 (m-30) cc_final: 0.7914 (m-30) REVERT: A 84 MET cc_start: 0.9013 (tpp) cc_final: 0.8750 (tpp) REVERT: A 217 TYR cc_start: 0.8035 (m-80) cc_final: 0.7689 (m-80) REVERT: A 426 MET cc_start: 0.7304 (ttp) cc_final: 0.6928 (ttp) REVERT: C 588 GLU cc_start: 0.9205 (tt0) cc_final: 0.8868 (pt0) REVERT: C 648 GLU cc_start: 0.8984 (tm-30) cc_final: 0.8625 (tm-30) REVERT: C 652 GLN cc_start: 0.8311 (tp-100) cc_final: 0.7613 (tp40) REVERT: D 46 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7439 (tm-30) REVERT: D 82 ASN cc_start: 0.9309 (t0) cc_final: 0.9107 (t0) REVERT: D 82 MET cc_start: 0.7943 (mpp) cc_final: 0.7675 (mpp) REVERT: E 28 ILE cc_start: 0.9211 (mm) cc_final: 0.8762 (tt) REVERT: F 217 TYR cc_start: 0.8248 (m-80) cc_final: 0.7589 (m-80) REVERT: I 588 GLU cc_start: 0.9137 (tt0) cc_final: 0.8887 (mt-10) REVERT: I 601 LYS cc_start: 0.8907 (ttmm) cc_final: 0.8687 (mtmm) REVERT: I 630 GLU cc_start: 0.9027 (mt-10) cc_final: 0.8677 (mt-10) REVERT: I 648 GLU cc_start: 0.9148 (tm-30) cc_final: 0.8890 (tm-30) REVERT: J 46 GLU cc_start: 0.7842 (tm-30) cc_final: 0.7062 (tm-30) REVERT: J 72 ASP cc_start: 0.8644 (t0) cc_final: 0.8393 (t0) REVERT: J 82 ASN cc_start: 0.9309 (t0) cc_final: 0.8917 (t0) REVERT: K 28 ILE cc_start: 0.9384 (mm) cc_final: 0.9083 (tt) REVERT: K 78 LEU cc_start: 0.8134 (tt) cc_final: 0.7838 (tt) REVERT: K 79 GLN cc_start: 0.8960 (mm110) cc_final: 0.8651 (mp10) outliers start: 47 outliers final: 22 residues processed: 352 average time/residue: 0.1466 time to fit residues: 79.3705 Evaluate side-chains 309 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 286 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 151 PHE Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 339 ASN Chi-restraints excluded: chain G residue 398 ASN Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 398 ASN Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain E residue 27 ASN Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 151 PHE Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 280 ASN Chi-restraints excluded: chain F residue 339 ASN Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain K residue 3 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 21 optimal weight: 3.9990 chunk 210 optimal weight: 8.9990 chunk 7 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 144 optimal weight: 6.9990 chunk 90 optimal weight: 7.9990 chunk 142 optimal weight: 0.7980 chunk 197 optimal weight: 8.9990 chunk 86 optimal weight: 2.9990 chunk 13 optimal weight: 0.0170 chunk 111 optimal weight: 2.9990 overall best weight: 1.5624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 6 GLN K 53 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.073271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.056600 restraints weight = 64993.517| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 3.70 r_work: 0.2762 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22263 Z= 0.162 Angle : 0.680 10.400 30567 Z= 0.312 Chirality : 0.047 0.353 3924 Planarity : 0.004 0.047 3531 Dihedral : 4.177 49.168 2632 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.14 % Allowed : 19.73 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.17), residues: 2412 helix: 1.42 (0.29), residues: 402 sheet: 0.33 (0.21), residues: 636 loop : -0.81 (0.16), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 27 TYR 0.016 0.002 TYR F 217 PHE 0.009 0.001 PHE G 53 TRP 0.009 0.001 TRP F 427 HIS 0.007 0.001 HIS G 396 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (22041) covalent geometry : angle 0.62009 / 0.30 (29943) SS BOND : bond 0.00281 / 0.19 ( 42) SS BOND : angle 0.80939 / 0.54 ( 84) hydrogen bonds : bond 0.05158 / 3.44 ( 634) hydrogen bonds : angle 5.17056 / 3.60 ( 1743) link_ALPHA1-2 : bond 0.00694 / 0.41 ( 9) link_ALPHA1-2 : angle 1.78414 / 1.11 ( 27) link_ALPHA1-3 : bond 0.00496 / 0.28 ( 15) link_ALPHA1-3 : angle 1.44203 / 0.99 ( 45) link_ALPHA1-6 : bond 0.00431 / 0.26 ( 15) link_ALPHA1-6 : angle 1.49673 / 1.06 ( 45) link_BETA1-4 : bond 0.00930 / 0.63 ( 57) link_BETA1-4 : angle 1.85075 / 1.37 ( 171) link_NAG-ASN : bond 0.00518 / 0.31 ( 84) link_NAG-ASN : angle 2.59031 / 1.71 ( 252) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 285 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 154 MET cc_start: 0.6580 (mtm) cc_final: 0.6176 (mtm) REVERT: G 217 TYR cc_start: 0.8103 (m-80) cc_final: 0.7810 (m-80) REVERT: H 46 GLU cc_start: 0.8291 (tm-30) cc_final: 0.8014 (tm-30) REVERT: H 57 LYS cc_start: 0.9428 (mptt) cc_final: 0.9083 (mmtp) REVERT: H 82 ASN cc_start: 0.9055 (t0) cc_final: 0.8632 (t0) REVERT: L 28 ILE cc_start: 0.9326 (mm) cc_final: 0.8898 (tt) REVERT: L 54 ARG cc_start: 0.9017 (ptt180) cc_final: 0.8704 (ptt180) REVERT: L 82 ASP cc_start: 0.8553 (m-30) cc_final: 0.8121 (m-30) REVERT: L 103 ARG cc_start: 0.8767 (mmm-85) cc_final: 0.8506 (mmm-85) REVERT: A 84 MET cc_start: 0.9188 (tpp) cc_final: 0.8936 (tpp) REVERT: A 217 TYR cc_start: 0.8125 (m-80) cc_final: 0.7782 (m-80) REVERT: A 426 MET cc_start: 0.7196 (ttp) cc_final: 0.6948 (ttp) REVERT: C 648 GLU cc_start: 0.8763 (tm-30) cc_final: 0.8343 (tm-30) REVERT: C 652 GLN cc_start: 0.8618 (tp-100) cc_final: 0.7954 (tp40) REVERT: D 46 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7715 (tm-30) REVERT: D 82 MET cc_start: 0.8131 (mpp) cc_final: 0.7929 (mpp) REVERT: E 28 ILE cc_start: 0.9313 (mm) cc_final: 0.8957 (tt) REVERT: F 84 MET cc_start: 0.9123 (tpp) cc_final: 0.8717 (tpp) REVERT: I 601 LYS cc_start: 0.9034 (ttmm) cc_final: 0.8786 (mtmm) REVERT: I 630 GLU cc_start: 0.8783 (mt-10) cc_final: 0.8527 (mt-10) REVERT: I 648 GLU cc_start: 0.9052 (tm-30) cc_final: 0.8801 (tm-30) REVERT: J 46 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7357 (tm-30) REVERT: J 82 ASN cc_start: 0.9111 (t0) cc_final: 0.8734 (t0) REVERT: K 28 ILE cc_start: 0.9446 (mm) cc_final: 0.9073 (tt) REVERT: K 78 LEU cc_start: 0.8332 (tt) cc_final: 0.7994 (tt) REVERT: K 79 GLN cc_start: 0.8923 (mm110) cc_final: 0.8615 (mp10) REVERT: K 90 THR cc_start: 0.8960 (OUTLIER) cc_final: 0.8745 (m) REVERT: K 103 ARG cc_start: 0.8811 (mmm-85) cc_final: 0.8321 (mmm160) outliers start: 46 outliers final: 27 residues processed: 321 average time/residue: 0.1465 time to fit residues: 72.3675 Evaluate side-chains 294 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 266 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 151 PHE Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 327 ARG Chi-restraints excluded: chain G residue 339 ASN Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 398 ASN Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 398 ASN Chi-restraints excluded: chain C residue 601 LYS Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 151 PHE Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain I residue 523 LEU Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain K residue 95 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 108 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 237 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 221 optimal weight: 0.9980 chunk 227 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 343 GLN A 336 GLN J 100CASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.073643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.057082 restraints weight = 64925.237| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 3.70 r_work: 0.2769 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22263 Z= 0.125 Angle : 0.660 10.062 30567 Z= 0.300 Chirality : 0.046 0.357 3924 Planarity : 0.003 0.044 3531 Dihedral : 4.038 49.799 2630 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.27 % Allowed : 20.94 % Favored : 76.79 % 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: -0.11 (0.17), residues: 2412 helix: 1.54 (0.28), residues: 402 sheet: 0.41 (0.21), residues: 639 loop : -0.80 (0.17), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 27 TYR 0.012 0.001 TYR B 586 PHE 0.007 0.001 PHE G 53 TRP 0.009 0.001 TRP I 631 HIS 0.003 0.001 HIS F 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (22041) covalent geometry : angle 0.60293 / 0.29 (29943) SS BOND : bond 0.00254 / 0.17 ( 42) SS BOND : angle 0.63732 / 0.44 ( 84) hydrogen bonds : bond 0.04364 / 2.93 ( 634) hydrogen bonds : angle 4.85181 / 3.38 ( 1743) link_ALPHA1-2 : bond 0.00640 / 0.37 ( 9) link_ALPHA1-2 : angle 1.74333 / 1.10 ( 27) link_ALPHA1-3 : bond 0.00500 / 0.29 ( 15) link_ALPHA1-3 : angle 1.36868 / 0.94 ( 45) link_ALPHA1-6 : bond 0.00448 / 0.27 ( 15) link_ALPHA1-6 : angle 1.45373 / 1.02 ( 45) link_BETA1-4 : bond 0.00904 / 0.62 ( 57) link_BETA1-4 : angle 1.77691 / 1.32 ( 171) link_NAG-ASN : bond 0.00504 / 0.30 ( 84) link_NAG-ASN : angle 2.52854 / 1.66 ( 252) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 289 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 154 MET cc_start: 0.6583 (mtm) cc_final: 0.6119 (mtm) REVERT: G 217 TYR cc_start: 0.8127 (m-80) cc_final: 0.7736 (m-80) REVERT: H 46 GLU cc_start: 0.8324 (tm-30) cc_final: 0.8081 (tm-30) REVERT: H 57 LYS cc_start: 0.9410 (mptt) cc_final: 0.9052 (mmtp) REVERT: H 82 ASN cc_start: 0.9053 (t0) cc_final: 0.8631 (t0) REVERT: L 28 ILE cc_start: 0.9329 (mm) cc_final: 0.8892 (tt) REVERT: A 84 MET cc_start: 0.9185 (tpp) cc_final: 0.8964 (tpp) REVERT: A 217 TYR cc_start: 0.8070 (m-80) cc_final: 0.7660 (m-80) REVERT: A 426 MET cc_start: 0.7503 (ttp) cc_final: 0.7293 (ttp) REVERT: C 652 GLN cc_start: 0.8640 (tp-100) cc_final: 0.7858 (tp40) REVERT: D 35 TYR cc_start: 0.8771 (m-10) cc_final: 0.8557 (m-10) REVERT: D 46 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7678 (tm-30) REVERT: E 28 ILE cc_start: 0.9257 (mm) cc_final: 0.8897 (tt) REVERT: E 78 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7849 (tt) REVERT: F 84 MET cc_start: 0.9172 (tpp) cc_final: 0.8677 (tpp) REVERT: I 601 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8754 (mtmm) REVERT: I 630 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8560 (mt-10) REVERT: J 46 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7382 (tm-30) REVERT: J 82 ASN cc_start: 0.9115 (t0) cc_final: 0.8736 (t0) REVERT: K 28 ILE cc_start: 0.9450 (mm) cc_final: 0.9089 (tt) REVERT: K 78 LEU cc_start: 0.8439 (tt) cc_final: 0.8141 (tt) REVERT: K 103 ARG cc_start: 0.8864 (mmm-85) cc_final: 0.8412 (mmm160) outliers start: 49 outliers final: 23 residues processed: 326 average time/residue: 0.1484 time to fit residues: 74.5289 Evaluate side-chains 293 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 268 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 327 ARG Chi-restraints excluded: chain G residue 339 ASN Chi-restraints excluded: chain G residue 398 ASN Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 398 ASN Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain E residue 27 ASN Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain I residue 538 THR Chi-restraints excluded: chain I residue 601 LYS Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 95 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 178 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 208 optimal weight: 6.9990 chunk 129 optimal weight: 9.9990 chunk 77 optimal weight: 8.9990 chunk 164 optimal weight: 7.9990 chunk 82 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 242 optimal weight: 0.9980 chunk 216 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 356 ASN F 356 ASN I 619 GLN I 653 GLN J 39 GLN K 79 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.070146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.053584 restraints weight = 65448.682| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 3.67 r_work: 0.2679 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 22263 Z= 0.241 Angle : 0.755 9.820 30567 Z= 0.345 Chirality : 0.049 0.364 3924 Planarity : 0.004 0.047 3531 Dihedral : 4.307 49.417 2630 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.74 % Allowed : 21.36 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.17), residues: 2412 helix: 1.37 (0.28), residues: 402 sheet: 0.38 (0.20), residues: 666 loop : -0.91 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 27 TYR 0.024 0.002 TYR G 401 PHE 0.014 0.002 PHE G 53 TRP 0.024 0.001 TRP F 427 HIS 0.009 0.001 HIS A 396 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.24 (22041) covalent geometry : angle 0.69637 / 0.33 (29943) SS BOND : bond 0.00376 / 0.25 ( 42) SS BOND : angle 0.96994 / 0.65 ( 84) hydrogen bonds : bond 0.04774 / 3.21 ( 634) hydrogen bonds : angle 4.92449 / 3.42 ( 1743) link_ALPHA1-2 : bond 0.00539 / 0.30 ( 9) link_ALPHA1-2 : angle 1.88207 / 1.18 ( 27) link_ALPHA1-3 : bond 0.00415 / 0.23 ( 15) link_ALPHA1-3 : angle 1.55623 / 1.07 ( 45) link_ALPHA1-6 : bond 0.00274 / 0.16 ( 15) link_ALPHA1-6 : angle 1.59793 / 1.11 ( 45) link_BETA1-4 : bond 0.00823 / 0.56 ( 57) link_BETA1-4 : angle 1.84907 / 1.37 ( 171) link_NAG-ASN : bond 0.00555 / 0.34 ( 84) link_NAG-ASN : angle 2.75671 / 1.82 ( 252) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 265 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 154 MET cc_start: 0.6680 (mtm) cc_final: 0.6101 (mtt) REVERT: H 46 GLU cc_start: 0.8400 (tm-30) cc_final: 0.7935 (tm-30) REVERT: H 57 LYS cc_start: 0.9431 (mptt) cc_final: 0.9120 (mmtp) REVERT: H 82 ASN cc_start: 0.9204 (t0) cc_final: 0.8900 (t0) REVERT: L 28 ILE cc_start: 0.9320 (mm) cc_final: 0.8874 (tt) REVERT: L 78 LEU cc_start: 0.8361 (tt) cc_final: 0.8135 (tt) REVERT: L 79 GLN cc_start: 0.8857 (mm110) cc_final: 0.8604 (mm110) REVERT: A 84 MET cc_start: 0.9240 (tpp) cc_final: 0.8988 (tpp) REVERT: A 217 TYR cc_start: 0.8349 (m-80) cc_final: 0.8047 (m-80) REVERT: A 426 MET cc_start: 0.7641 (ttp) cc_final: 0.7414 (ttp) REVERT: C 630 GLU cc_start: 0.8987 (mt-10) cc_final: 0.8785 (mt-10) REVERT: C 648 GLU cc_start: 0.8938 (tm-30) cc_final: 0.8693 (tp30) REVERT: D 46 GLU cc_start: 0.8267 (tm-30) cc_final: 0.7655 (tm-30) REVERT: E 28 ILE cc_start: 0.9188 (mm) cc_final: 0.8822 (tt) REVERT: E 103 ARG cc_start: 0.9039 (mmm-85) cc_final: 0.8304 (mmm160) REVERT: F 84 MET cc_start: 0.9182 (tpp) cc_final: 0.8537 (tpp) REVERT: I 601 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8868 (mtmm) REVERT: J 82 ASN cc_start: 0.9207 (t0) cc_final: 0.8926 (t0) REVERT: K 28 ILE cc_start: 0.9473 (mm) cc_final: 0.9062 (tt) REVERT: K 103 ARG cc_start: 0.8922 (mmm-85) cc_final: 0.8456 (mmm160) outliers start: 59 outliers final: 40 residues processed: 310 average time/residue: 0.1389 time to fit residues: 67.0366 Evaluate side-chains 294 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 253 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 151 PHE Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 327 ARG Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 398 ASN Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 398 ASN Chi-restraints excluded: chain C residue 601 LYS Chi-restraints excluded: chain C residue 657 GLU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain E residue 27 ASN Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 151 PHE Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain I residue 601 LYS Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 95 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 34 optimal weight: 0.9980 chunk 214 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 180 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 206 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 177 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 575 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.070073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.053452 restraints weight = 65630.596| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 3.69 r_work: 0.2681 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 22263 Z= 0.198 Angle : 0.711 9.742 30567 Z= 0.324 Chirality : 0.047 0.353 3924 Planarity : 0.004 0.046 3531 Dihedral : 4.177 18.358 2628 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.55 % Allowed : 21.82 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.17), residues: 2412 helix: 1.56 (0.29), residues: 384 sheet: 0.44 (0.20), residues: 660 loop : -0.93 (0.17), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 27 TYR 0.026 0.002 TYR F 401 PHE 0.011 0.001 PHE G 53 TRP 0.012 0.001 TRP G 338 HIS 0.004 0.001 HIS A 396 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.20 (22041) covalent geometry : angle 0.65243 / 0.31 (29943) SS BOND : bond 0.00336 / 0.22 ( 42) SS BOND : angle 0.86885 / 0.58 ( 84) hydrogen bonds : bond 0.04472 / 2.99 ( 634) hydrogen bonds : angle 4.78380 / 3.32 ( 1743) link_ALPHA1-2 : bond 0.00513 / 0.30 ( 9) link_ALPHA1-2 : angle 1.86087 / 1.17 ( 27) link_ALPHA1-3 : bond 0.00432 / 0.24 ( 15) link_ALPHA1-3 : angle 1.42806 / 0.99 ( 45) link_ALPHA1-6 : bond 0.00317 / 0.18 ( 15) link_ALPHA1-6 : angle 1.54908 / 1.08 ( 45) link_BETA1-4 : bond 0.00818 / 0.55 ( 57) link_BETA1-4 : angle 1.80803 / 1.35 ( 171) link_NAG-ASN : bond 0.00520 / 0.31 ( 84) link_NAG-ASN : angle 2.66365 / 1.76 ( 252) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 266 time to evaluate : 0.623 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: G 154 MET cc_start: 0.6644 (mtm) cc_final: 0.6062 (mtt) REVERT: H 46 GLU cc_start: 0.8446 (tm-30) cc_final: 0.8126 (tm-30) REVERT: H 57 LYS cc_start: 0.9430 (mptt) cc_final: 0.9124 (mmtp) REVERT: H 72 ASP cc_start: 0.8738 (t0) cc_final: 0.8487 (t0) REVERT: H 82 ASN cc_start: 0.9237 (t0) cc_final: 0.8910 (t0) REVERT: L 28 ILE cc_start: 0.9299 (mm) cc_final: 0.8860 (tt) REVERT: L 78 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8168 (tp) REVERT: A 84 MET cc_start: 0.9223 (tpp) cc_final: 0.9008 (tpp) REVERT: C 601 LYS cc_start: 0.9029 (OUTLIER) cc_final: 0.8660 (mtmm) REVERT: C 648 GLU cc_start: 0.8933 (tm-30) cc_final: 0.8683 (tp30) REVERT: C 652 GLN cc_start: 0.8749 (tp-100) cc_final: 0.8520 (tp40) REVERT: D 46 GLU cc_start: 0.8332 (tm-30) cc_final: 0.7760 (tm-30) REVERT: D 71 LYS cc_start: 0.9195 (ptmm) cc_final: 0.8806 (ptmm) REVERT: E 28 ILE cc_start: 0.9168 (mm) cc_final: 0.8823 (tt) REVERT: E 103 ARG cc_start: 0.9056 (mmm-85) cc_final: 0.8403 (mmm160) REVERT: F 84 MET cc_start: 0.9191 (tpp) cc_final: 0.8512 (tpp) REVERT: J 46 GLU cc_start: 0.8294 (tm-30) cc_final: 0.7635 (tm-30) REVERT: J 82 ASN cc_start: 0.9217 (t0) cc_final: 0.8907 (t0) REVERT: K 28 ILE cc_start: 0.9461 (mm) cc_final: 0.9050 (tt) REVERT: K 103 ARG cc_start: 0.8957 (mmm-85) cc_final: 0.8489 (mmm160) outliers start: 55 outliers final: 36 residues processed: 309 average time/residue: 0.1390 time to fit residues: 67.4396 Evaluate side-chains 295 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 257 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 151 PHE Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 327 ARG Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 398 ASN Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 398 ASN Chi-restraints excluded: chain C residue 601 LYS Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain E residue 27 ASN Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 151 PHE Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 95 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 109 optimal weight: 0.9980 chunk 160 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 236 optimal weight: 7.9990 chunk 168 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 162 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 199 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 356 ASN B 653 GLN C 575 GLN C 619 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.069271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.052559 restraints weight = 66183.685| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 3.66 r_work: 0.2665 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 22263 Z= 0.233 Angle : 0.765 10.136 30567 Z= 0.348 Chirality : 0.048 0.365 3924 Planarity : 0.004 0.051 3531 Dihedral : 4.286 18.556 2628 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.69 % Allowed : 21.77 % Favored : 75.53 % 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: -0.30 (0.17), residues: 2412 helix: 1.45 (0.28), residues: 384 sheet: 0.48 (0.21), residues: 609 loop : -1.01 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 16 TYR 0.022 0.002 TYR F 401 PHE 0.012 0.001 PHE G 53 TRP 0.008 0.001 TRP F 338 HIS 0.005 0.001 HIS A 396 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.23 (22041) covalent geometry : angle 0.70831 / 0.34 (29943) SS BOND : bond 0.00361 / 0.24 ( 42) SS BOND : angle 1.05618 / 0.72 ( 84) hydrogen bonds : bond 0.04569 / 3.08 ( 634) hydrogen bonds : angle 4.82567 / 3.34 ( 1743) link_ALPHA1-2 : bond 0.00513 / 0.29 ( 9) link_ALPHA1-2 : angle 1.86555 / 1.17 ( 27) link_ALPHA1-3 : bond 0.00417 / 0.23 ( 15) link_ALPHA1-3 : angle 1.47308 / 1.02 ( 45) link_ALPHA1-6 : bond 0.00264 / 0.15 ( 15) link_ALPHA1-6 : angle 1.55585 / 1.08 ( 45) link_BETA1-4 : bond 0.00921 / 0.63 ( 57) link_BETA1-4 : angle 1.84680 / 1.38 ( 171) link_NAG-ASN : bond 0.00955 / 0.63 ( 84) link_NAG-ASN : angle 2.72713 / 1.81 ( 252) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 254 time to evaluate : 0.819 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: G 154 MET cc_start: 0.6923 (mtm) cc_final: 0.6329 (mtt) REVERT: H 29 MET cc_start: 0.9242 (mmm) cc_final: 0.8898 (tpt) REVERT: H 46 GLU cc_start: 0.8434 (tm-30) cc_final: 0.8041 (tm-30) REVERT: H 57 LYS cc_start: 0.9420 (mptt) cc_final: 0.9157 (mmtp) REVERT: H 82 ASN cc_start: 0.9186 (t0) cc_final: 0.8875 (t0) REVERT: L 28 ILE cc_start: 0.9354 (mm) cc_final: 0.8927 (tt) REVERT: L 78 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8185 (tp) REVERT: C 601 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8735 (mtmm) REVERT: C 648 GLU cc_start: 0.8877 (tm-30) cc_final: 0.8638 (tp30) REVERT: D 46 GLU cc_start: 0.8431 (tm-30) cc_final: 0.7921 (tm-30) REVERT: D 71 LYS cc_start: 0.9208 (ptmm) cc_final: 0.8848 (ptmm) REVERT: D 72 ASP cc_start: 0.8720 (t0) cc_final: 0.7967 (t0) REVERT: D 75 LYS cc_start: 0.8965 (tptp) cc_final: 0.8724 (tptp) REVERT: D 77 GLN cc_start: 0.8843 (pt0) cc_final: 0.8423 (pm20) REVERT: D 82 MET cc_start: 0.8007 (mpp) cc_final: 0.7615 (mpp) REVERT: E 28 ILE cc_start: 0.9259 (mm) cc_final: 0.8899 (tt) REVERT: E 103 ARG cc_start: 0.8997 (mmm-85) cc_final: 0.8392 (mmm160) REVERT: F 84 MET cc_start: 0.9209 (tpp) cc_final: 0.8527 (tpp) REVERT: J 46 GLU cc_start: 0.8268 (tm-30) cc_final: 0.7792 (tm-30) REVERT: J 82 ASN cc_start: 0.9146 (t0) cc_final: 0.8841 (t0) REVERT: K 28 ILE cc_start: 0.9470 (mm) cc_final: 0.9092 (tt) outliers start: 58 outliers final: 46 residues processed: 299 average time/residue: 0.1482 time to fit residues: 68.7705 Evaluate side-chains 293 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 245 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 151 PHE Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 327 ARG Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 398 ASN Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 398 ASN Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain C residue 515 ILE Chi-restraints excluded: chain C residue 601 LYS Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain E residue 27 ASN Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 151 PHE Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain I residue 615 SER Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 95 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 153 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 chunk 242 optimal weight: 0.7980 chunk 204 optimal weight: 1.9990 chunk 196 optimal weight: 0.7980 chunk 116 optimal weight: 0.3980 chunk 142 optimal weight: 5.9990 chunk 220 optimal weight: 10.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 280 ASN C 575 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.069788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.053132 restraints weight = 65478.411| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 3.72 r_work: 0.2679 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 22263 Z= 0.169 Angle : 1.058 59.200 30567 Z= 0.522 Chirality : 0.049 0.572 3924 Planarity : 0.004 0.050 3531 Dihedral : 4.294 18.038 2628 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.69 % Allowed : 22.24 % Favored : 75.07 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.17), residues: 2412 helix: 1.46 (0.29), residues: 384 sheet: 0.48 (0.21), residues: 609 loop : -0.99 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 16 TYR 0.017 0.001 TYR F 401 PHE 0.008 0.001 PHE F 53 TRP 0.034 0.001 TRP B 571 HIS 0.003 0.001 HIS F 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (22041) covalent geometry : angle 0.94759 / 0.50 (29943) SS BOND : bond 0.00340 / 0.23 ( 42) SS BOND : angle 1.08266 / 0.70 ( 84) hydrogen bonds : bond 0.04556 / 3.08 ( 634) hydrogen bonds : angle 4.79904 / 3.32 ( 1743) link_ALPHA1-2 : bond 0.00516 / 0.30 ( 9) link_ALPHA1-2 : angle 1.85261 / 1.16 ( 27) link_ALPHA1-3 : bond 0.00427 / 0.24 ( 15) link_ALPHA1-3 : angle 1.47102 / 1.01 ( 45) link_ALPHA1-6 : bond 0.00281 / 0.16 ( 15) link_ALPHA1-6 : angle 1.52476 / 1.06 ( 45) link_BETA1-4 : bond 0.01320 / 0.99 ( 57) link_BETA1-4 : angle 2.14841 / 1.57 ( 171) link_NAG-ASN : bond 0.00793 / 0.41 ( 84) link_NAG-ASN : angle 4.94366 / 2.92 ( 252) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 251 time to evaluate : 0.871 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: G 154 MET cc_start: 0.6821 (mtm) cc_final: 0.6192 (mtt) REVERT: G 178 LYS cc_start: 0.9152 (mmmt) cc_final: 0.8883 (tptp) REVERT: H 46 GLU cc_start: 0.8453 (tm-30) cc_final: 0.8026 (tm-30) REVERT: H 57 LYS cc_start: 0.9428 (mptt) cc_final: 0.9133 (mmtp) REVERT: H 82 ASN cc_start: 0.9237 (t0) cc_final: 0.8918 (t0) REVERT: L 28 ILE cc_start: 0.9327 (mm) cc_final: 0.8885 (tt) REVERT: L 78 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8237 (tp) REVERT: A 302 MET cc_start: 0.6317 (mmt) cc_final: 0.5826 (mtt) REVERT: C 601 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8738 (mtmm) REVERT: C 648 GLU cc_start: 0.8913 (tm-30) cc_final: 0.8666 (tp30) REVERT: D 46 GLU cc_start: 0.8434 (tm-30) cc_final: 0.7880 (tm-30) REVERT: D 71 LYS cc_start: 0.9224 (ptmm) cc_final: 0.8848 (ptmm) REVERT: D 82 MET cc_start: 0.7982 (mpp) cc_final: 0.7685 (mpp) REVERT: E 28 ILE cc_start: 0.9227 (mm) cc_final: 0.8854 (tt) REVERT: E 103 ARG cc_start: 0.9032 (mmm-85) cc_final: 0.8391 (mmm160) REVERT: F 84 MET cc_start: 0.9197 (tpp) cc_final: 0.8500 (tpp) REVERT: J 46 GLU cc_start: 0.8280 (tm-30) cc_final: 0.7755 (tm-30) REVERT: J 82 ASN cc_start: 0.9204 (t0) cc_final: 0.8882 (t0) REVERT: K 28 ILE cc_start: 0.9454 (mm) cc_final: 0.9056 (tt) REVERT: K 79 GLN cc_start: 0.8547 (mp-120) cc_final: 0.7847 (mp10) outliers start: 58 outliers final: 47 residues processed: 298 average time/residue: 0.1429 time to fit residues: 66.3921 Evaluate side-chains 296 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 247 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 151 PHE Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 327 ARG Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 398 ASN Chi-restraints excluded: chain G residue 407 ASN Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 398 ASN Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain C residue 515 ILE Chi-restraints excluded: chain C residue 601 LYS Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain E residue 27 ASN Chi-restraints excluded: chain E residue 51 ASN Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 151 PHE Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain I residue 615 SER Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 95 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 60 optimal weight: 4.9990 chunk 193 optimal weight: 7.9990 chunk 62 optimal weight: 0.2980 chunk 40 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 653 GLN C 575 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.069883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.053183 restraints weight = 65677.860| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 3.67 r_work: 0.2673 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.165 22263 Z= 0.179 Angle : 1.070 59.200 30567 Z= 0.525 Chirality : 0.049 0.572 3924 Planarity : 0.004 0.050 3531 Dihedral : 4.294 18.038 2628 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.27 % Allowed : 22.56 % Favored : 75.16 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.17), residues: 2412 helix: 1.46 (0.29), residues: 384 sheet: 0.48 (0.21), residues: 609 loop : -0.99 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 16 TYR 0.017 0.001 TYR F 401 PHE 0.008 0.001 PHE F 53 TRP 0.034 0.001 TRP B 571 HIS 0.003 0.001 HIS F 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (22041) covalent geometry : angle 0.94759 / 0.50 (29943) SS BOND : bond 0.00698 / 0.53 ( 42) SS BOND : angle 1.36202 / 0.95 ( 84) hydrogen bonds : bond 0.04556 / 3.08 ( 634) hydrogen bonds : angle 4.79904 / 3.32 ( 1743) link_ALPHA1-2 : bond 0.00516 / 0.30 ( 9) link_ALPHA1-2 : angle 1.85261 / 1.16 ( 27) link_ALPHA1-3 : bond 0.00427 / 0.24 ( 15) link_ALPHA1-3 : angle 1.47102 / 1.01 ( 45) link_ALPHA1-6 : bond 0.00281 / 0.16 ( 15) link_ALPHA1-6 : angle 1.52476 / 1.06 ( 45) link_BETA1-4 : bond 0.01320 / 0.99 ( 57) link_BETA1-4 : angle 2.14841 / 1.57 ( 171) link_NAG-ASN : bond 0.01963 / 1.48 ( 84) link_NAG-ASN : angle 5.21479 / 3.08 ( 252) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 247 time to evaluate : 0.557 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: G 154 MET cc_start: 0.6845 (mtm) cc_final: 0.6219 (mtt) REVERT: G 178 LYS cc_start: 0.9141 (mmmt) cc_final: 0.8886 (tptp) REVERT: H 46 GLU cc_start: 0.8454 (tm-30) cc_final: 0.8035 (tm-30) REVERT: H 57 LYS cc_start: 0.9424 (mptt) cc_final: 0.9136 (mmtp) REVERT: H 82 ASN cc_start: 0.9236 (t0) cc_final: 0.8910 (t0) REVERT: L 28 ILE cc_start: 0.9333 (mm) cc_final: 0.8892 (tt) REVERT: L 78 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8238 (tp) REVERT: A 302 MET cc_start: 0.6375 (mmt) cc_final: 0.5839 (mtt) REVERT: C 601 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8727 (mtmm) REVERT: C 648 GLU cc_start: 0.8901 (tm-30) cc_final: 0.8656 (tp30) REVERT: D 46 GLU cc_start: 0.8423 (tm-30) cc_final: 0.7887 (tm-30) REVERT: D 71 LYS cc_start: 0.9217 (ptmm) cc_final: 0.8842 (ptmm) REVERT: D 82 MET cc_start: 0.7982 (mpp) cc_final: 0.7693 (mpp) REVERT: E 28 ILE cc_start: 0.9232 (mm) cc_final: 0.8863 (tt) REVERT: E 103 ARG cc_start: 0.9015 (mmm-85) cc_final: 0.8386 (mmm160) REVERT: F 84 MET cc_start: 0.9202 (tpp) cc_final: 0.8507 (tpp) REVERT: J 46 GLU cc_start: 0.8270 (tm-30) cc_final: 0.7760 (tm-30) REVERT: J 82 ASN cc_start: 0.9192 (t0) cc_final: 0.8869 (t0) REVERT: K 28 ILE cc_start: 0.9455 (mm) cc_final: 0.9061 (tt) REVERT: K 79 GLN cc_start: 0.8603 (mp-120) cc_final: 0.7848 (mp10) outliers start: 49 outliers final: 47 residues processed: 285 average time/residue: 0.1428 time to fit residues: 63.3641 Evaluate side-chains 295 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 246 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 151 PHE Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 327 ARG Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 398 ASN Chi-restraints excluded: chain G residue 407 ASN Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 398 ASN Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain C residue 515 ILE Chi-restraints excluded: chain C residue 601 LYS Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain E residue 27 ASN Chi-restraints excluded: chain E residue 51 ASN Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 151 PHE Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain I residue 615 SER Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 95 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 106 optimal weight: 5.9990 chunk 202 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 218 optimal weight: 0.6980 chunk 141 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 212 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 194 optimal weight: 0.1980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 653 GLN C 575 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.069845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.053218 restraints weight = 65716.654| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 3.66 r_work: 0.2676 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.165 22263 Z= 0.179 Angle : 1.070 59.200 30567 Z= 0.525 Chirality : 0.049 0.572 3924 Planarity : 0.004 0.050 3531 Dihedral : 4.294 18.038 2628 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.27 % Allowed : 22.56 % Favored : 75.16 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.17), residues: 2412 helix: 1.46 (0.29), residues: 384 sheet: 0.48 (0.21), residues: 609 loop : -0.99 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 16 TYR 0.017 0.001 TYR F 401 PHE 0.008 0.001 PHE F 53 TRP 0.034 0.001 TRP B 571 HIS 0.003 0.001 HIS F 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (22041) covalent geometry : angle 0.94759 / 0.50 (29943) SS BOND : bond 0.00698 / 0.53 ( 42) SS BOND : angle 1.36202 / 0.95 ( 84) hydrogen bonds : bond 0.04556 / 3.08 ( 634) hydrogen bonds : angle 4.79904 / 3.32 ( 1743) link_ALPHA1-2 : bond 0.00516 / 0.30 ( 9) link_ALPHA1-2 : angle 1.85261 / 1.16 ( 27) link_ALPHA1-3 : bond 0.00427 / 0.24 ( 15) link_ALPHA1-3 : angle 1.47102 / 1.01 ( 45) link_ALPHA1-6 : bond 0.00281 / 0.16 ( 15) link_ALPHA1-6 : angle 1.52476 / 1.06 ( 45) link_BETA1-4 : bond 0.01320 / 0.99 ( 57) link_BETA1-4 : angle 2.14841 / 1.57 ( 171) link_NAG-ASN : bond 0.01963 / 1.48 ( 84) link_NAG-ASN : angle 5.21479 / 3.08 ( 252) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 246 time to evaluate : 0.781 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: G 154 MET cc_start: 0.6843 (mtm) cc_final: 0.6216 (mtt) REVERT: G 178 LYS cc_start: 0.9142 (mmmt) cc_final: 0.8886 (tptp) REVERT: H 46 GLU cc_start: 0.8451 (tm-30) cc_final: 0.8037 (tm-30) REVERT: H 57 LYS cc_start: 0.9425 (mptt) cc_final: 0.9137 (mmtp) REVERT: H 82 ASN cc_start: 0.9226 (t0) cc_final: 0.8898 (t0) REVERT: L 28 ILE cc_start: 0.9334 (mm) cc_final: 0.8896 (tt) REVERT: L 78 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8242 (tp) REVERT: A 302 MET cc_start: 0.6373 (mmt) cc_final: 0.5837 (mtt) REVERT: C 601 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8727 (mtmm) REVERT: C 648 GLU cc_start: 0.8895 (tm-30) cc_final: 0.8653 (tp30) REVERT: D 46 GLU cc_start: 0.8423 (tm-30) cc_final: 0.7891 (tm-30) REVERT: D 71 LYS cc_start: 0.9216 (ptmm) cc_final: 0.8844 (ptmm) REVERT: D 82 MET cc_start: 0.7984 (mpp) cc_final: 0.7697 (mpp) REVERT: E 28 ILE cc_start: 0.9233 (mm) cc_final: 0.8866 (tt) REVERT: E 103 ARG cc_start: 0.9010 (mmm-85) cc_final: 0.8386 (mmm160) REVERT: F 84 MET cc_start: 0.9201 (tpp) cc_final: 0.8505 (tpp) REVERT: J 46 GLU cc_start: 0.8274 (tm-30) cc_final: 0.7767 (tm-30) REVERT: J 82 ASN cc_start: 0.9174 (t0) cc_final: 0.8852 (t0) REVERT: K 28 ILE cc_start: 0.9456 (mm) cc_final: 0.9064 (tt) REVERT: K 79 GLN cc_start: 0.8602 (mp-120) cc_final: 0.7847 (mp10) outliers start: 49 outliers final: 47 residues processed: 284 average time/residue: 0.1489 time to fit residues: 65.7604 Evaluate side-chains 295 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 246 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 151 PHE Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 327 ARG Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 398 ASN Chi-restraints excluded: chain G residue 407 ASN Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 398 ASN Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain C residue 515 ILE Chi-restraints excluded: chain C residue 601 LYS Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain E residue 27 ASN Chi-restraints excluded: chain E residue 51 ASN Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 151 PHE Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain I residue 615 SER Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 95 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 180 optimal weight: 3.9990 chunk 183 optimal weight: 7.9990 chunk 116 optimal weight: 10.0000 chunk 127 optimal weight: 0.7980 chunk 214 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 225 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 chunk 148 optimal weight: 10.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 653 GLN C 575 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.069845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.053218 restraints weight = 65745.236| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 3.66 r_work: 0.2675 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.165 22263 Z= 0.179 Angle : 1.070 59.200 30567 Z= 0.525 Chirality : 0.049 0.572 3924 Planarity : 0.004 0.050 3531 Dihedral : 4.294 18.038 2628 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.27 % Allowed : 22.56 % Favored : 75.16 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.17), residues: 2412 helix: 1.46 (0.29), residues: 384 sheet: 0.48 (0.21), residues: 609 loop : -0.99 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 16 TYR 0.017 0.001 TYR F 401 PHE 0.008 0.001 PHE F 53 TRP 0.034 0.001 TRP B 571 HIS 0.003 0.001 HIS F 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (22041) covalent geometry : angle 0.94759 / 0.50 (29943) SS BOND : bond 0.00698 / 0.53 ( 42) SS BOND : angle 1.36202 / 0.95 ( 84) hydrogen bonds : bond 0.04556 / 3.08 ( 634) hydrogen bonds : angle 4.79904 / 3.32 ( 1743) link_ALPHA1-2 : bond 0.00516 / 0.30 ( 9) link_ALPHA1-2 : angle 1.85261 / 1.16 ( 27) link_ALPHA1-3 : bond 0.00427 / 0.24 ( 15) link_ALPHA1-3 : angle 1.47102 / 1.01 ( 45) link_ALPHA1-6 : bond 0.00281 / 0.16 ( 15) link_ALPHA1-6 : angle 1.52476 / 1.06 ( 45) link_BETA1-4 : bond 0.01320 / 0.99 ( 57) link_BETA1-4 : angle 2.14841 / 1.57 ( 171) link_NAG-ASN : bond 0.01963 / 1.48 ( 84) link_NAG-ASN : angle 5.21479 / 3.08 ( 252) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3891.30 seconds wall clock time: 68 minutes 14.64 seconds (4094.64 seconds total)