Starting phenix.real_space_refine on Sun Jul 5 08:48:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6nb4_0402/07_2026/6nb4_0402.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nb4_0402/07_2026/6nb4_0402.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6nb4_0402/07_2026/6nb4_0402.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nb4_0402/07_2026/6nb4_0402.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6nb4_0402/07_2026/6nb4_0402.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6nb4_0402/07_2026/6nb4_0402.cif" model { file = "/net/cci-nas-00/data/ceres_data/6nb4_0402/07_2026/6nb4_0402.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nb4_0402/07_2026/6nb4_0402.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.057 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 133 5.16 5 C 16832 2.51 5 N 4285 2.21 5 O 5431 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 184 residue(s): 0.02s 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: 26681 Number of models: 1 Model: "" Number of chains: 46 Chain: "A" Number of atoms: 9032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1169, 9032 Classifications: {'peptide': 1169} Link IDs: {'PTRANS': 59, 'TRANS': 1109} Chain breaks: 4 Chain: "B" Number of atoms: 7402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 958, 7402 Classifications: {'peptide': 958} Link IDs: {'PTRANS': 45, 'TRANS': 912} Chain breaks: 5 Chain: "C" Number of atoms: 7404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 959, 7404 Classifications: {'peptide': 959} Link IDs: {'PTRANS': 45, 'TRANS': 913} Chain breaks: 5 Chain: "H" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 738 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 3, 'TRANS': 119} Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 269 Unresolved non-hydrogen dihedrals: 162 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 5, 'ASN:plan1': 3, 'ASP:plan': 6, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 91 Chain: "L" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 607 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 5, 'TRANS': 100} Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 4, 'ARG:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: "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: 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: 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: "R" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: 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: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "X" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 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: 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: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: 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: "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: 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: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 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: 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: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 5.40, per 1000 atoms: 0.20 Number of scatterers: 26681 At special positions: 0 Unit cell: (152.07, 146.59, 187.69, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 133 16.00 O 5431 8.00 N 4285 7.00 C 16832 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS A 195 " distance=2.05 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 214 " distance=2.04 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 349 " distance=2.02 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS A 407 " distance=2.10 Simple disulfide: pdb=" SG CYS A 425 " - pdb=" SG CYS A 478 " distance=2.07 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 585 " distance=2.07 Simple disulfide: pdb=" SG CYS A 503 " - pdb=" SG CYS A 526 " distance=2.08 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 654 " distance=2.04 Simple disulfide: pdb=" SG CYS A 620 " - pdb=" SG CYS A 650 " distance=2.04 Simple disulfide: pdb=" SG CYS A 679 " - pdb=" SG CYS A 713 " distance=2.20 Simple disulfide: pdb=" SG CYS A 727 " - pdb=" SG CYS A 736 " distance=2.03 Simple disulfide: pdb=" SG CYS A 806 " - pdb=" SG CYS A 828 " distance=2.06 Simple disulfide: pdb=" SG CYS A 811 " - pdb=" SG CYS A 817 " distance=2.11 Simple disulfide: pdb=" SG CYS A 912 " - pdb=" SG CYS A 925 " distance=2.03 Simple disulfide: pdb=" SG CYS A1106 " - pdb=" SG CYS A1117 " distance=2.04 Simple disulfide: pdb=" SG CYS A1156 " - pdb=" SG CYS A1164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 30 " - pdb=" SG CYS B 195 " distance=2.03 Simple disulfide: pdb=" SG CYS B 176 " - pdb=" SG CYS B 214 " distance=2.04 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 339 " - pdb=" SG CYS B 349 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 654 " distance=2.04 Simple disulfide: pdb=" SG CYS B 620 " - pdb=" SG CYS B 650 " distance=2.03 Simple disulfide: pdb=" SG CYS B 679 " - pdb=" SG CYS B 713 " distance=2.15 Simple disulfide: pdb=" SG CYS B 727 " - pdb=" SG CYS B 736 " distance=2.03 Simple disulfide: pdb=" SG CYS B 806 " - pdb=" SG CYS B 828 " distance=2.03 Simple disulfide: pdb=" SG CYS B 811 " - pdb=" SG CYS B 817 " distance=2.12 Simple disulfide: pdb=" SG CYS B 912 " - pdb=" SG CYS B 925 " distance=2.09 Simple disulfide: pdb=" SG CYS B1106 " - pdb=" SG CYS B1117 " distance=2.04 Simple disulfide: pdb=" SG CYS B1156 " - pdb=" SG CYS B1164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 195 " distance=2.03 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 185 " - pdb=" SG CYS C 237 " distance=2.03 Simple disulfide: pdb=" SG CYS C 339 " - pdb=" SG CYS C 349 " distance=2.03 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 654 " distance=2.03 Simple disulfide: pdb=" SG CYS C 620 " - pdb=" SG CYS C 650 " distance=2.03 Simple disulfide: pdb=" SG CYS C 679 " - pdb=" SG CYS C 713 " distance=2.05 Simple disulfide: pdb=" SG CYS C 727 " - pdb=" SG CYS C 736 " distance=2.03 Simple disulfide: pdb=" SG CYS C 806 " - pdb=" SG CYS C 828 " distance=2.04 Simple disulfide: pdb=" SG CYS C 811 " - pdb=" SG CYS C 817 " distance=2.04 Simple disulfide: pdb=" SG CYS C 912 " - pdb=" SG CYS C 925 " distance=2.07 Simple disulfide: pdb=" SG CYS C1106 " - pdb=" SG CYS C1117 " distance=2.04 Simple disulfide: pdb=" SG CYS C1156 " - pdb=" SG CYS C1164 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 98 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN U 4 " - " MAN U 5 " ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA I 3 " - " MAN I 4 " " BMA R 3 " - " MAN R 4 " " BMA U 3 " - " MAN U 4 " " BMA W 3 " - " MAN W 4 " " BMA X 3 " - " MAN X 4 " " BMA f 3 " - " MAN f 4 " " BMA i 3 " - " MAN i 4 " " BMA q 3 " - " MAN q 4 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " " BMA I 3 " - " MAN I 5 " " BMA R 3 " - " MAN R 5 " " BMA U 3 " - " MAN U 6 " " BMA W 3 " - " MAN W 5 " " BMA i 3 " - " MAN i 5 " " BMA q 3 " - " MAN q 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " NAG-ASN " NAG A1401 " - " ASN A 66 " " NAG A1418 " - " ASN A 236 " " NAG A1423 " - " ASN A 487 " " NAG A1424 " - " ASN A 592 " " NAG B1433 " - " ASN B 774 " " NAG C1412 " - " ASN C 166 " " NAG C1416 " - " ASN C 236 " " NAG C1419 " - " ASN C 592 " " NAG C1424 " - " ASN C 774 " " NAG D 1 " - " ASN A 104 " " NAG E 1 " - " ASN A 125 " " NAG F 1 " - " ASN A 155 " " NAG G 1 " - " ASN A 166 " " NAG I 1 " - " ASN A 222 " " NAG J 1 " - " ASN A 244 " " NAG K 1 " - " ASN A 410 " " NAG M 1 " - " ASN A 619 " " NAG N 1 " - " ASN A 719 " " NAG O 1 " - " ASN A 774 " " NAG P 1 " - " ASN A 785 " " NAG Q 1 " - " ASN A 870 " " NAG R 1 " - " ASN A1213 " " NAG S 1 " - " ASN B 66 " " NAG T 1 " - " ASN B 104 " " NAG U 1 " - " ASN B 125 " " NAG V 1 " - " ASN B 155 " " NAG W 1 " - " ASN B 166 " " NAG X 1 " - " ASN B 222 " " NAG Y 1 " - " ASN B 236 " " NAG Z 1 " - " ASN B 244 " " NAG a 1 " - " ASN B 592 " " NAG b 1 " - " ASN B 619 " " NAG c 1 " - " ASN B 719 " " NAG d 1 " - " ASN B 785 " " NAG e 1 " - " ASN B 870 " " NAG f 1 " - " ASN B1213 " " NAG g 1 " - " ASN C 66 " " NAG h 1 " - " ASN C 104 " " NAG i 1 " - " ASN C 125 " " NAG j 1 " - " ASN C 155 " " NAG k 1 " - " ASN C 222 " " NAG l 1 " - " ASN C 244 " " NAG m 1 " - " ASN C 619 " " NAG n 1 " - " ASN C 719 " " NAG o 1 " - " ASN C 785 " " NAG p 1 " - " ASN C 870 " " NAG q 1 " - " ASN C1213 " Time building additional restraints: 2.94 Conformation dependent library (CDL) restraints added in 1.3 seconds 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6122 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 59 sheets defined 23.9% alpha, 27.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 36 through 41 Processing helix chain 'A' and resid 49 through 53 Processing helix chain 'A' and resid 209 through 213 Processing helix chain 'A' and resid 222 through 230 Processing helix chain 'A' and resid 269 through 271 No H-bonds generated for 'chain 'A' and resid 269 through 271' Processing helix chain 'A' and resid 342 through 351 Processing helix chain 'A' and resid 385 through 390 Processing helix chain 'A' and resid 395 through 399 removed outlier: 3.937A pdb=" N PHE A 399 " --> pdb=" O VAL A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 416 Processing helix chain 'A' and resid 431 through 435 Processing helix chain 'A' and resid 449 through 456 removed outlier: 4.839A pdb=" N SER A 454 " --> pdb=" O SER A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 550 Processing helix chain 'A' and resid 805 through 811 Processing helix chain 'A' and resid 814 through 822 Processing helix chain 'A' and resid 826 through 854 Processing helix chain 'A' and resid 888 through 898 Processing helix chain 'A' and resid 909 through 913 Processing helix chain 'A' and resid 926 through 931 removed outlier: 3.528A pdb=" N GLY A 931 " --> pdb=" O GLN A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 953 Processing helix chain 'A' and resid 971 through 982 Processing helix chain 'A' and resid 986 through 993 Processing helix chain 'A' and resid 993 through 1007 removed outlier: 3.676A pdb=" N ALA A 998 " --> pdb=" O GLN A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1008 through 1011 Processing helix chain 'A' and resid 1016 through 1040 removed outlier: 4.312A pdb=" N ALA A1032 " --> pdb=" O ASN A1028 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU A1033 " --> pdb=" O ASN A1029 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU A1036 " --> pdb=" O ALA A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1059 through 1107 removed outlier: 5.087A pdb=" N ALA A1065 " --> pdb=" O PRO A1061 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 40 Processing helix chain 'B' and resid 49 through 53 Processing helix chain 'B' and resid 209 through 214 Processing helix chain 'B' and resid 222 through 230 Processing helix chain 'B' and resid 342 through 351 Processing helix chain 'B' and resid 591 through 595 removed outlier: 4.195A pdb=" N LYS B 595 " --> pdb=" O ASN B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 805 through 811 Processing helix chain 'B' and resid 814 through 822 Processing helix chain 'B' and resid 826 through 854 Processing helix chain 'B' and resid 888 through 898 Processing helix chain 'B' and resid 908 through 913 Processing helix chain 'B' and resid 926 through 931 Processing helix chain 'B' and resid 940 through 954 Processing helix chain 'B' and resid 954 through 959 removed outlier: 3.985A pdb=" N GLY B 959 " --> pdb=" O ILE B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 971 through 982 Processing helix chain 'B' and resid 986 through 993 Processing helix chain 'B' and resid 993 through 1007 Processing helix chain 'B' and resid 1008 through 1011 Processing helix chain 'B' and resid 1016 through 1040 removed outlier: 3.940A pdb=" N ALA B1032 " --> pdb=" O ASN B1028 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU B1033 " --> pdb=" O ASN B1029 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER B1034 " --> pdb=" O ALA B1030 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU B1036 " --> pdb=" O ALA B1032 " (cutoff:3.500A) Processing helix chain 'B' and resid 1050 through 1056 Processing helix chain 'B' and resid 1059 through 1107 removed outlier: 3.536A pdb=" N ASP B1064 " --> pdb=" O PRO B1060 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ALA B1065 " --> pdb=" O PRO B1061 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN B1066 " --> pdb=" O GLU B1062 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 41 Processing helix chain 'C' and resid 49 through 53 Processing helix chain 'C' and resid 209 through 213 Processing helix chain 'C' and resid 222 through 230 Processing helix chain 'C' and resid 342 through 351 Processing helix chain 'C' and resid 805 through 812 Processing helix chain 'C' and resid 814 through 822 removed outlier: 3.989A pdb=" N LEU C 820 " --> pdb=" O LYS C 816 " (cutoff:3.500A) Processing helix chain 'C' and resid 823 through 825 No H-bonds generated for 'chain 'C' and resid 823 through 825' Processing helix chain 'C' and resid 826 through 854 Processing helix chain 'C' and resid 888 through 896 Processing helix chain 'C' and resid 907 through 915 removed outlier: 3.845A pdb=" N MET C 913 " --> pdb=" O TYR C 909 " (cutoff:3.500A) Processing helix chain 'C' and resid 926 through 931 removed outlier: 3.619A pdb=" N GLY C 931 " --> pdb=" O GLN C 927 " (cutoff:3.500A) Processing helix chain 'C' and resid 940 through 954 Processing helix chain 'C' and resid 971 through 982 Processing helix chain 'C' and resid 986 through 993 Processing helix chain 'C' and resid 993 through 1010 removed outlier: 4.059A pdb=" N THR C1010 " --> pdb=" O GLY C1006 " (cutoff:3.500A) Processing helix chain 'C' and resid 1016 through 1040 removed outlier: 4.067A pdb=" N ALA C1032 " --> pdb=" O ASN C1028 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEU C1033 " --> pdb=" O ASN C1029 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU C1036 " --> pdb=" O ALA C1032 " (cutoff:3.500A) Processing helix chain 'C' and resid 1050 through 1058 Processing helix chain 'C' and resid 1059 through 1107 removed outlier: 3.524A pdb=" N ASP C1064 " --> pdb=" O PRO C1060 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ALA C1065 " --> pdb=" O PRO C1061 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 53 through 57 Processing helix chain 'H' and resid 64 through 67 Processing helix chain 'H' and resid 89 through 93 Processing helix chain 'L' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 34 Processing sheet with id=AA2, first strand: chain 'A' and resid 67 through 75 removed outlier: 4.318A pdb=" N ARG A 335 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.006A pdb=" N SER A 267 " --> pdb=" O GLN A 280 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N GLN A 280 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 88 through 89 removed outlier: 7.653A pdb=" N SER A 88 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N THR A 206 " --> pdb=" O SER A 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 92 through 93 Processing sheet with id=AA6, first strand: chain 'A' and resid 110 through 111 removed outlier: 4.679A pdb=" N ALA A 146 " --> pdb=" O ILE A 296 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU A 180 " --> pdb=" O TYR A 241 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N TYR A 241 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ALA A 182 " --> pdb=" O PHE A 239 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N PHE A 239 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N TYR A 184 " --> pdb=" O CYS A 237 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N CYS A 237 " --> pdb=" O TYR A 184 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 127 through 129 removed outlier: 3.637A pdb=" N ALA A 309 " --> pdb=" O THR A 139 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 153 through 155 Processing sheet with id=AA9, first strand: chain 'A' and resid 214 through 215 removed outlier: 3.807A pdb=" N SER A 215 " --> pdb=" O ASN A 218 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 359 through 366 removed outlier: 4.554A pdb=" N VAL A 659 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N SER A 365 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL A 657 " --> pdb=" O SER A 365 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 371 through 376 removed outlier: 4.136A pdb=" N GLU A 605 " --> pdb=" O SER A 371 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N SER A 373 " --> pdb=" O GLU A 605 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N SER A 607 " --> pdb=" O SER A 373 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VAL A 375 " --> pdb=" O SER A 607 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N VAL A 639 " --> pdb=" O LEU A 651 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL A 631 " --> pdb=" O VAL A 639 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 400 through 404 removed outlier: 6.999A pdb=" N THR A 477 " --> pdb=" O CYS A 425 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N CYS A 425 " --> pdb=" O THR A 477 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N LEU A 479 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N PHE A 423 " --> pdb=" O LEU A 479 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU A 481 " --> pdb=" O ASN A 421 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 407 through 408 removed outlier: 5.999A pdb=" N CYS A 407 " --> pdb=" O CYS A 585 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 513 through 515 removed outlier: 5.504A pdb=" N SER A 498 " --> pdb=" O VAL A 561 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL A 561 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ILE A 500 " --> pdb=" O SER A 559 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N SER A 559 " --> pdb=" O ILE A 500 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 717 through 724 removed outlier: 6.529A pdb=" N VAL A 718 " --> pdb=" O LEU A 759 " (cutoff:3.500A) removed outlier: 9.011A pdb=" N SER A 761 " --> pdb=" O VAL A 718 " (cutoff:3.500A) removed outlier: 9.853A pdb=" N SER A 720 " --> pdb=" O SER A 761 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU A 735 " --> pdb=" O LEU A 731 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 768 through 769 removed outlier: 5.695A pdb=" N ILE A 768 " --> pdb=" O SER B 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1184 through 1188 removed outlier: 4.616A pdb=" N PHE A1172 " --> pdb=" O ALA A1152 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N VAL A1150 " --> pdb=" O LYS A1174 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 785 through 796 removed outlier: 3.601A pdb=" N ASN A 785 " --> pdb=" O SER A1144 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL A1124 " --> pdb=" O VAL A1139 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N TYR A1141 " --> pdb=" O HIS A1122 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N HIS A1122 " --> pdb=" O TYR A1141 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 802 through 804 Processing sheet with id=AC2, first strand: chain 'A' and resid 857 through 858 Processing sheet with id=AC3, first strand: chain 'A' and resid 967 through 968 removed outlier: 5.608A pdb=" N VAL C1150 " --> pdb=" O LYS C1174 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N PHE C1172 " --> pdb=" O ALA C1152 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1202 through 1205 removed outlier: 4.049A pdb=" N CYS A1164 " --> pdb=" O VAL A1205 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 33 through 35 Processing sheet with id=AC6, first strand: chain 'B' and resid 67 through 75 removed outlier: 4.181A pdb=" N ARG B 335 " --> pdb=" O ASP B 326 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.061A pdb=" N SER B 267 " --> pdb=" O GLN B 280 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N GLN B 280 " --> pdb=" O SER B 267 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 88 through 89 removed outlier: 7.469A pdb=" N SER B 88 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N THR B 206 " --> pdb=" O SER B 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 92 through 93 Processing sheet with id=AD1, first strand: chain 'B' and resid 110 through 111 removed outlier: 6.637A pdb=" N LEU B 180 " --> pdb=" O TYR B 241 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N TYR B 241 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ALA B 182 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N PHE B 239 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N TYR B 184 " --> pdb=" O CYS B 237 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N CYS B 237 " --> pdb=" O TYR B 184 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 127 through 129 removed outlier: 3.605A pdb=" N ALA B 309 " --> pdb=" O THR B 139 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 153 through 155 Processing sheet with id=AD4, first strand: chain 'B' and resid 359 through 366 removed outlier: 4.558A pdb=" N VAL B 659 " --> pdb=" O VAL B 363 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N SER B 365 " --> pdb=" O VAL B 657 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N VAL B 657 " --> pdb=" O SER B 365 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N CYS B 713 " --> pdb=" O PHE B 674 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 371 through 376 removed outlier: 4.243A pdb=" N GLU B 605 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N SER B 373 " --> pdb=" O GLU B 605 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N SER B 607 " --> pdb=" O SER B 373 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL B 375 " --> pdb=" O SER B 607 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL B 639 " --> pdb=" O LEU B 651 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL B 631 " --> pdb=" O VAL B 639 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 717 through 724 removed outlier: 6.393A pdb=" N VAL B 718 " --> pdb=" O LEU B 759 " (cutoff:3.500A) removed outlier: 8.860A pdb=" N SER B 761 " --> pdb=" O VAL B 718 " (cutoff:3.500A) removed outlier: 9.731A pdb=" N SER B 720 " --> pdb=" O SER B 761 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU B 735 " --> pdb=" O LEU B 731 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 768 through 769 removed outlier: 5.532A pdb=" N ILE B 768 " --> pdb=" O SER C 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'B' and resid 1121 through 1130 removed outlier: 5.795A pdb=" N HIS B1122 " --> pdb=" O TYR B1141 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N TYR B1141 " --> pdb=" O HIS B1122 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N VAL B1124 " --> pdb=" O VAL B1139 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N VAL B1150 " --> pdb=" O LYS B1174 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N PHE B1172 " --> pdb=" O ALA B1152 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1121 through 1130 removed outlier: 5.795A pdb=" N HIS B1122 " --> pdb=" O TYR B1141 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N TYR B1141 " --> pdb=" O HIS B1122 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N VAL B1124 " --> pdb=" O VAL B1139 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N HIS B1146 " --> pdb=" O PRO B 783 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N GLU B1148 " --> pdb=" O SER B 781 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N SER B 781 " --> pdb=" O GLU B1148 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL B1150 " --> pdb=" O LYS B 779 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LYS B 779 " --> pdb=" O VAL B1150 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 801 through 804 removed outlier: 4.547A pdb=" N LYS B 801 " --> pdb=" O LEU B 935 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 1202 through 1205 removed outlier: 3.914A pdb=" N CYS B1164 " --> pdb=" O VAL B1205 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ASN B1163 " --> pdb=" O ASP B1157 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 33 through 34 Processing sheet with id=AE4, first strand: chain 'C' and resid 67 through 75 removed outlier: 4.128A pdb=" N ARG C 335 " --> pdb=" O ASP C 326 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.116A pdb=" N SER C 267 " --> pdb=" O GLN C 280 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLN C 280 " --> pdb=" O SER C 267 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 88 through 89 removed outlier: 7.316A pdb=" N SER C 88 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N THR C 206 " --> pdb=" O SER C 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'C' and resid 92 through 93 Processing sheet with id=AE8, first strand: chain 'C' and resid 110 through 111 removed outlier: 6.647A pdb=" N LEU C 180 " --> pdb=" O TYR C 241 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TYR C 241 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ALA C 182 " --> pdb=" O PHE C 239 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N PHE C 239 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N TYR C 184 " --> pdb=" O CYS C 237 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N CYS C 237 " --> pdb=" O TYR C 184 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 127 through 129 Processing sheet with id=AF1, first strand: chain 'C' and resid 153 through 155 Processing sheet with id=AF2, first strand: chain 'C' and resid 214 through 215 removed outlier: 3.745A pdb=" N SER C 215 " --> pdb=" O ASN C 218 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 359 through 366 removed outlier: 4.696A pdb=" N VAL C 659 " --> pdb=" O VAL C 363 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N SER C 365 " --> pdb=" O VAL C 657 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N VAL C 657 " --> pdb=" O SER C 365 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 371 through 376 removed outlier: 4.189A pdb=" N GLU C 605 " --> pdb=" O SER C 371 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N SER C 373 " --> pdb=" O GLU C 605 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N SER C 607 " --> pdb=" O SER C 373 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL C 375 " --> pdb=" O SER C 607 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N VAL C 639 " --> pdb=" O LEU C 651 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL C 631 " --> pdb=" O VAL C 639 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 718 through 724 removed outlier: 6.541A pdb=" N VAL C 718 " --> pdb=" O LEU C 759 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N SER C 761 " --> pdb=" O VAL C 718 " (cutoff:3.500A) removed outlier: 9.995A pdb=" N SER C 720 " --> pdb=" O SER C 761 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'C' and resid 786 through 796 removed outlier: 4.412A pdb=" N VAL C1124 " --> pdb=" O VAL C1139 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N TYR C1141 " --> pdb=" O HIS C1122 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N HIS C1122 " --> pdb=" O TYR C1141 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 802 through 803 Processing sheet with id=AF8, first strand: chain 'C' and resid 1202 through 1205 removed outlier: 4.049A pdb=" N CYS C1164 " --> pdb=" O VAL C1205 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AG1, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.666A pdb=" N TRP H 33 " --> pdb=" O LEU H 101 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 10 through 11 Processing sheet with id=AG3, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AG4, first strand: chain 'L' and resid 46 through 50 removed outlier: 6.516A pdb=" N TRP L 37 " --> pdb=" O MET L 49 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 46 through 50 removed outlier: 6.516A pdb=" N TRP L 37 " --> pdb=" O MET L 49 " (cutoff:3.500A) 1053 hydrogen bonds defined for protein. 2802 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.17 Time building geometry restraints manager: 3.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5115 1.32 - 1.45: 7667 1.45 - 1.58: 14305 1.58 - 1.71: 11 1.71 - 1.84: 175 Bond restraints: 27273 Sorted by residual: bond pdb=" C1 NAG O 2 " pdb=" O5 NAG O 2 " ideal model delta sigma weight residual 1.406 1.547 -0.141 2.00e-02 2.50e+03 4.95e+01 bond pdb=" C1 NAG K 2 " pdb=" O5 NAG K 2 " ideal model delta sigma weight residual 1.406 1.547 -0.141 2.00e-02 2.50e+03 4.94e+01 bond pdb=" C1 NAG A1423 " pdb=" O5 NAG A1423 " ideal model delta sigma weight residual 1.406 1.546 -0.140 2.00e-02 2.50e+03 4.93e+01 bond pdb=" C1 NAG k 2 " pdb=" O5 NAG k 2 " ideal model delta sigma weight residual 1.406 1.546 -0.140 2.00e-02 2.50e+03 4.93e+01 bond pdb=" C1 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.406 1.546 -0.140 2.00e-02 2.50e+03 4.90e+01 ... (remaining 27268 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.69: 36870 5.69 - 11.39: 239 11.39 - 17.08: 5 17.08 - 22.78: 5 22.78 - 28.47: 2 Bond angle restraints: 37121 Sorted by residual: angle pdb=" C VAL B 711 " pdb=" CA VAL B 711 " pdb=" CB VAL B 711 " ideal model delta sigma weight residual 111.29 135.81 -24.52 1.64e+00 3.72e-01 2.24e+02 angle pdb=" C TYR C 905 " pdb=" CA TYR C 905 " pdb=" CB TYR C 905 " ideal model delta sigma weight residual 110.42 138.89 -28.47 1.99e+00 2.53e-01 2.05e+02 angle pdb=" C LEU A 450 " pdb=" CA LEU A 450 " pdb=" CB LEU A 450 " ideal model delta sigma weight residual 110.79 129.97 -19.18 1.66e+00 3.63e-01 1.34e+02 angle pdb=" N MET C 906 " pdb=" CA MET C 906 " pdb=" C MET C 906 " ideal model delta sigma weight residual 110.28 127.08 -16.80 1.48e+00 4.57e-01 1.29e+02 angle pdb=" N TYR C 905 " pdb=" CA TYR C 905 " pdb=" C TYR C 905 " ideal model delta sigma weight residual 110.80 90.45 20.35 2.13e+00 2.20e-01 9.13e+01 ... (remaining 37116 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 14682 17.87 - 35.74: 398 35.74 - 53.61: 127 53.61 - 71.48: 51 71.48 - 89.35: 26 Dihedral angle restraints: 15284 sinusoidal: 5677 harmonic: 9607 Sorted by residual: dihedral pdb=" C LEU A 450 " pdb=" N LEU A 450 " pdb=" CA LEU A 450 " pdb=" CB LEU A 450 " ideal model delta harmonic sigma weight residual -122.60 -159.37 36.77 0 2.50e+00 1.60e-01 2.16e+02 dihedral pdb=" C VAL B 711 " pdb=" N VAL B 711 " pdb=" CA VAL B 711 " pdb=" CB VAL B 711 " ideal model delta harmonic sigma weight residual -122.00 -158.60 36.60 0 2.50e+00 1.60e-01 2.14e+02 dihedral pdb=" N LEU A 450 " pdb=" C LEU A 450 " pdb=" CA LEU A 450 " pdb=" CB LEU A 450 " ideal model delta harmonic sigma weight residual 122.80 154.44 -31.64 0 2.50e+00 1.60e-01 1.60e+02 ... (remaining 15281 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.305: 4432 0.305 - 0.610: 22 0.610 - 0.915: 1 0.915 - 1.220: 0 1.220 - 1.525: 2 Chirality restraints: 4457 Sorted by residual: chirality pdb=" C1 BMA Y 3 " pdb=" O4 NAG Y 2 " pdb=" C2 BMA Y 3 " pdb=" O5 BMA Y 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 6.89e+01 chirality pdb=" CA LEU A 450 " pdb=" N LEU A 450 " pdb=" C LEU A 450 " pdb=" CB LEU A 450 " both_signs ideal model delta sigma weight residual False 2.51 0.99 1.53 2.00e-01 2.50e+01 5.82e+01 chirality pdb=" C1 NAG h 2 " pdb=" O4 NAG h 1 " pdb=" C2 NAG h 2 " pdb=" O5 NAG h 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.54 0.14 2.00e-02 2.50e+03 5.12e+01 ... (remaining 4454 not shown) Planarity restraints: 4724 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG q 2 " -0.044 2.00e-02 2.50e+03 3.62e-02 1.64e+01 pdb=" C7 NAG q 2 " 0.010 2.00e-02 2.50e+03 pdb=" C8 NAG q 2 " -0.033 2.00e-02 2.50e+03 pdb=" N2 NAG q 2 " 0.058 2.00e-02 2.50e+03 pdb=" O7 NAG q 2 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 166 " -0.033 2.00e-02 2.50e+03 3.48e-02 1.52e+01 pdb=" CG ASN B 166 " 0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN B 166 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN B 166 " 0.053 2.00e-02 2.50e+03 pdb=" C1 NAG W 1 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 2 " 0.035 2.00e-02 2.50e+03 2.84e-02 1.01e+01 pdb=" C7 NAG R 2 " -0.007 2.00e-02 2.50e+03 pdb=" C8 NAG R 2 " 0.026 2.00e-02 2.50e+03 pdb=" N2 NAG R 2 " -0.045 2.00e-02 2.50e+03 pdb=" O7 NAG R 2 " -0.008 2.00e-02 2.50e+03 ... (remaining 4721 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 110 2.57 - 3.15: 21986 3.15 - 3.73: 39357 3.73 - 4.32: 57613 4.32 - 4.90: 91153 Nonbonded interactions: 210219 Sorted by model distance: nonbonded pdb=" CB SER B 676 " pdb=" O TYR C 905 " model vdw 1.986 3.440 nonbonded pdb=" OG SER A 419 " pdb=" OG1 THR A 483 " model vdw 2.249 3.040 nonbonded pdb=" N ASN C 592 " pdb=" OD1 ASN C 592 " model vdw 2.284 3.120 nonbonded pdb=" OG1 THR A 709 " pdb=" O GLY A 712 " model vdw 2.295 3.040 nonbonded pdb=" OG SER A 328 " pdb=" OD1 ASP A 330 " model vdw 2.374 3.040 ... (remaining 210214 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 18 through 378 or resid 591 through 1433)) selection = (chain 'C' and (resid 18 through 378 or resid 591 through 1412)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'g' selection = chain 'h' selection = chain 'j' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' } ncs_group { reference = chain 'E' selection = chain 'I' selection = chain 'R' selection = chain 'W' selection = chain 'i' selection = chain 'q' } ncs_group { reference = chain 'X' selection = chain 'f' } ncs_group { reference = chain 'Y' selection = chain 'k' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 28.300 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.100 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:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.173 27431 Z= 0.856 Angle : 1.363 28.470 37550 Z= 0.858 Chirality : 0.089 1.525 4457 Planarity : 0.006 0.057 4677 Dihedral : 10.807 89.347 9027 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.62 % Favored : 97.13 % Rotamer: Outliers : 0.45 % Allowed : 1.35 % Favored : 98.21 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.14), residues: 3277 helix: 0.40 (0.19), residues: 677 sheet: 0.49 (0.18), residues: 711 loop : -0.23 (0.14), residues: 1889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 401 TYR 0.042 0.006 TYR A 77 PHE 0.024 0.004 PHE C 313 TRP 0.035 0.006 TRP C1184 HIS 0.007 0.001 HIS C1138 Details of bonding type rmsd/Z covalent geometry : bond 0.01603 / 0.85 (27273) covalent geometry : angle 1.33588 / 0.85 (37121) SS BOND : bond 0.04109 / 3.07 ( 45) SS BOND : angle 3.54204 / 2.48 ( 90) hydrogen bonds : bond 0.19240 / 12.94 ( 1031) hydrogen bonds : angle 7.71602 / 5.34 ( 2802) link_ALPHA1-2 : bond 0.04221 / 2.22 ( 1) link_ALPHA1-2 : angle 1.58040 / 0.78 ( 3) link_ALPHA1-3 : bond 0.03394 / 2.02 ( 9) link_ALPHA1-3 : angle 1.65944 / 1.03 ( 27) link_ALPHA1-6 : bond 0.03121 / 1.58 ( 7) link_ALPHA1-6 : angle 2.29878 / 1.49 ( 21) link_BETA1-4 : bond 0.03477 / 2.30 ( 49) link_BETA1-4 : angle 2.49143 / 1.69 ( 147) link_NAG-ASN : bond 0.03536 / 2.32 ( 47) link_NAG-ASN : angle 3.05587 / 2.10 ( 141) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 624 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.7564 (ttp) cc_final: 0.7298 (ttp) REVERT: A 225 LEU cc_start: 0.6792 (tp) cc_final: 0.6459 (tt) REVERT: A 231 TYR cc_start: 0.6438 (m-80) cc_final: 0.6209 (m-80) REVERT: A 290 ILE cc_start: 0.8228 (mt) cc_final: 0.7907 (mm) REVERT: A 469 TYR cc_start: 0.7951 (t80) cc_final: 0.7707 (t80) REVERT: A 473 PHE cc_start: 0.7428 (p90) cc_final: 0.7149 (p90) REVERT: A 491 ILE cc_start: 0.7187 (tt) cc_final: 0.6962 (pt) REVERT: B 199 ASN cc_start: 0.5801 (m-40) cc_final: 0.5424 (p0) REVERT: B 674 PHE cc_start: 0.7919 (m-80) cc_final: 0.7638 (m-80) REVERT: B 686 MET cc_start: 0.7533 (mmm) cc_final: 0.6921 (tpp) REVERT: B 724 VAL cc_start: 0.7658 (p) cc_final: 0.6989 (p) REVERT: B 798 THR cc_start: 0.8171 (p) cc_final: 0.7075 (p) REVERT: B 938 LEU cc_start: 0.8173 (tt) cc_final: 0.7612 (tt) REVERT: B 1043 THR cc_start: 0.8321 (m) cc_final: 0.7996 (p) REVERT: B 1054 ILE cc_start: 0.8377 (pt) cc_final: 0.8078 (mt) REVERT: C 677 VAL cc_start: 0.8909 (t) cc_final: 0.8682 (m) REVERT: C 807 LYS cc_start: 0.8577 (tttt) cc_final: 0.7999 (tppt) REVERT: C 913 MET cc_start: 0.6064 (mtm) cc_final: 0.5834 (mtp) REVERT: C 961 THR cc_start: 0.5897 (p) cc_final: 0.5571 (p) outliers start: 12 outliers final: 0 residues processed: 633 average time/residue: 0.1757 time to fit residues: 174.9853 Evaluate side-chains 247 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 0.0770 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.0470 chunk 298 optimal weight: 0.5980 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 GLN A1009 GLN ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1097 GLN ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 812 ASN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1027 ASN B1056 GLN B1129 ASN ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 GLN C 812 ASN C1042 ASN C1085 GLN C1169 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.156693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.128602 restraints weight = 48044.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.129994 restraints weight = 32066.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.130561 restraints weight = 24614.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.131309 restraints weight = 22503.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.131538 restraints weight = 19332.665| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 27431 Z= 0.156 Angle : 0.699 9.418 37550 Z= 0.355 Chirality : 0.045 0.303 4457 Planarity : 0.005 0.060 4677 Dihedral : 4.689 25.922 3584 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.29 % Favored : 97.65 % Rotamer: Outliers : 2.50 % Allowed : 7.70 % Favored : 89.80 % 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: 0.41 (0.14), residues: 3277 helix: 1.71 (0.20), residues: 676 sheet: 0.54 (0.17), residues: 748 loop : -0.35 (0.13), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 181 TYR 0.019 0.001 TYR H 112 PHE 0.024 0.002 PHE B 254 TRP 0.014 0.001 TRP C 310 HIS 0.010 0.001 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (27273) covalent geometry : angle 0.66857 / 0.35 (37121) SS BOND : bond 0.00600 / 0.29 ( 45) SS BOND : angle 1.89110 / 1.38 ( 90) hydrogen bonds : bond 0.06581 / 4.52 ( 1031) hydrogen bonds : angle 5.74963 / 3.97 ( 2802) link_ALPHA1-2 : bond 0.00367 / 0.19 ( 1) link_ALPHA1-2 : angle 1.36631 / 0.74 ( 3) link_ALPHA1-3 : bond 0.00446 / 0.26 ( 9) link_ALPHA1-3 : angle 2.18481 / 1.39 ( 27) link_ALPHA1-6 : bond 0.00364 / 0.20 ( 7) link_ALPHA1-6 : angle 2.05724 / 1.41 ( 21) link_BETA1-4 : bond 0.01125 / 0.71 ( 49) link_BETA1-4 : angle 2.10012 / 1.47 ( 147) link_NAG-ASN : bond 0.00344 / 0.23 ( 47) link_NAG-ASN : angle 2.00142 / 1.41 ( 141) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 320 time to evaluate : 0.979 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: A 473 PHE cc_start: 0.7798 (p90) cc_final: 0.7575 (p90) REVERT: A 812 ASN cc_start: 0.7666 (t0) cc_final: 0.7001 (t0) REVERT: B 636 GLN cc_start: 0.7692 (mm-40) cc_final: 0.7421 (mm110) REVERT: B 686 MET cc_start: 0.7605 (mmm) cc_final: 0.7332 (tpp) REVERT: B 1008 MET cc_start: 0.7188 (mtp) cc_final: 0.6815 (mtp) REVERT: B 1204 TYR cc_start: 0.8124 (m-80) cc_final: 0.7724 (m-10) REVERT: C 147 PHE cc_start: 0.7958 (m-80) cc_final: 0.7560 (m-80) REVERT: C 674 PHE cc_start: 0.8365 (m-80) cc_final: 0.7983 (m-80) REVERT: C 928 TYR cc_start: 0.8301 (m-80) cc_final: 0.8077 (m-80) REVERT: C 1008 MET cc_start: 0.8319 (tmm) cc_final: 0.8108 (tmm) outliers start: 67 outliers final: 38 residues processed: 373 average time/residue: 0.1590 time to fit residues: 97.7881 Evaluate side-chains 249 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 211 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 502 LYS Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 772 GLN Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 859 SER Chi-restraints excluded: chain B residue 1056 GLN Chi-restraints excluded: chain B residue 1210 THR Chi-restraints excluded: chain C residue 592 ASN Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain C residue 986 THR Chi-restraints excluded: chain C residue 1041 SER Chi-restraints excluded: chain C residue 1042 ASN Chi-restraints excluded: chain C residue 1043 THR Chi-restraints excluded: chain C residue 1094 LEU Chi-restraints excluded: chain C residue 1121 THR Chi-restraints excluded: chain C residue 1202 THR Chi-restraints excluded: chain C residue 1205 VAL Chi-restraints excluded: chain C residue 1210 THR Chi-restraints excluded: chain H residue 62 TYR Chi-restraints excluded: chain L residue 33 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 66 optimal weight: 1.9990 chunk 213 optimal weight: 0.6980 chunk 240 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 229 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 54 optimal weight: 8.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 348 HIS ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 516 GLN A 836 HIS ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1145 ASN B 258 GLN B 348 HIS B 812 ASN ** B1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1122 HIS B1169 ASN C 91 HIS C 812 ASN C 927 GLN C1003 GLN C1042 ASN C1129 ASN C1138 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.148469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.121744 restraints weight = 48846.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.122978 restraints weight = 44008.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.123662 restraints weight = 36013.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.124101 restraints weight = 29086.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.124182 restraints weight = 28252.873| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.106 27431 Z= 0.253 Angle : 0.762 14.349 37550 Z= 0.384 Chirality : 0.047 0.273 4457 Planarity : 0.005 0.066 4677 Dihedral : 4.971 34.121 3584 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.23 % Favored : 96.73 % Rotamer: Outliers : 2.91 % Allowed : 9.90 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.14), residues: 3277 helix: 1.38 (0.20), residues: 677 sheet: 0.44 (0.18), residues: 741 loop : -0.68 (0.13), residues: 1859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B1113 TYR 0.023 0.002 TYR C 85 PHE 0.027 0.002 PHE A 850 TRP 0.015 0.002 TRP C 253 HIS 0.013 0.002 HIS A1138 Details of bonding type rmsd/Z covalent geometry : bond 0.00600 / 0.25 (27273) covalent geometry : angle 0.73466 / 0.38 (37121) SS BOND : bond 0.00418 / 0.27 ( 45) SS BOND : angle 2.11722 / 1.35 ( 90) hydrogen bonds : bond 0.06954 / 4.75 ( 1031) hydrogen bonds : angle 5.71162 / 3.96 ( 2802) link_ALPHA1-2 : bond 0.00550 / 0.29 ( 1) link_ALPHA1-2 : angle 1.25457 / 0.68 ( 3) link_ALPHA1-3 : bond 0.00705 / 0.46 ( 9) link_ALPHA1-3 : angle 1.52208 / 0.94 ( 27) link_ALPHA1-6 : bond 0.00467 / 0.26 ( 7) link_ALPHA1-6 : angle 1.49506 / 1.06 ( 21) link_BETA1-4 : bond 0.01079 / 0.70 ( 49) link_BETA1-4 : angle 2.08233 / 1.46 ( 147) link_NAG-ASN : bond 0.00562 / 0.36 ( 47) link_NAG-ASN : angle 2.10883 / 1.55 ( 141) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 232 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 473 PHE cc_start: 0.7748 (p90) cc_final: 0.7520 (p90) REVERT: A 729 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8428 (pp) REVERT: A 812 ASN cc_start: 0.7578 (t0) cc_final: 0.6992 (t0) REVERT: A 820 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8278 (mp) REVERT: B 261 GLN cc_start: 0.7656 (tm-30) cc_final: 0.7433 (tm-30) REVERT: B 686 MET cc_start: 0.7750 (mmm) cc_final: 0.7374 (tpp) REVERT: C 31 ILE cc_start: 0.8015 (mm) cc_final: 0.7754 (tp) REVERT: C 353 SER cc_start: 0.8613 (t) cc_final: 0.8374 (m) outliers start: 78 outliers final: 50 residues processed: 303 average time/residue: 0.1454 time to fit residues: 74.7050 Evaluate side-chains 234 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 182 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 540 TYR Chi-restraints excluded: chain A residue 541 TYR Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 819 GLN Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1190 SER Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 355 ASP Chi-restraints excluded: chain B residue 771 ASP Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain B residue 859 SER Chi-restraints excluded: chain B residue 888 SER Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1210 THR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 592 ASN Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 986 THR Chi-restraints excluded: chain C residue 1041 SER Chi-restraints excluded: chain C residue 1071 ILE Chi-restraints excluded: chain C residue 1094 LEU Chi-restraints excluded: chain C residue 1121 THR Chi-restraints excluded: chain C residue 1205 VAL Chi-restraints excluded: chain C residue 1210 THR Chi-restraints excluded: chain H residue 62 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 76 optimal weight: 0.5980 chunk 271 optimal weight: 0.2980 chunk 297 optimal weight: 0.7980 chunk 86 optimal weight: 0.4980 chunk 185 optimal weight: 0.5980 chunk 299 optimal weight: 0.7980 chunk 111 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 238 optimal weight: 2.9990 chunk 170 optimal weight: 0.8980 chunk 124 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 421 ASN ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 927 GLN B 258 GLN B 636 GLN B 812 ASN B 836 HIS B1056 GLN C 304 GLN C 812 ASN C 915 GLN C1042 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.150888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.124869 restraints weight = 48315.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.123918 restraints weight = 43733.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.124860 restraints weight = 41659.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.125158 restraints weight = 36174.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.126317 restraints weight = 30897.556| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 27431 Z= 0.142 Angle : 0.645 18.017 37550 Z= 0.320 Chirality : 0.043 0.229 4457 Planarity : 0.005 0.061 4677 Dihedral : 4.607 26.987 3584 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.62 % Favored : 97.35 % Rotamer: Outliers : 2.58 % Allowed : 11.21 % Favored : 86.21 % 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: 0.15 (0.14), residues: 3277 helix: 1.68 (0.20), residues: 679 sheet: 0.46 (0.18), residues: 742 loop : -0.64 (0.13), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1113 TYR 0.016 0.001 TYR A1141 PHE 0.017 0.002 PHE B 239 TRP 0.016 0.001 TRP H 117 HIS 0.008 0.001 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (27273) covalent geometry : angle 0.61566 / 0.31 (37121) SS BOND : bond 0.00358 / 0.21 ( 45) SS BOND : angle 2.32692 / 1.75 ( 90) hydrogen bonds : bond 0.05607 / 3.89 ( 1031) hydrogen bonds : angle 5.29858 / 3.67 ( 2802) link_ALPHA1-2 : bond 0.00504 / 0.27 ( 1) link_ALPHA1-2 : angle 1.29092 / 0.69 ( 3) link_ALPHA1-3 : bond 0.00468 / 0.30 ( 9) link_ALPHA1-3 : angle 1.47106 / 0.93 ( 27) link_ALPHA1-6 : bond 0.00420 / 0.23 ( 7) link_ALPHA1-6 : angle 1.38977 / 0.96 ( 21) link_BETA1-4 : bond 0.01035 / 0.68 ( 49) link_BETA1-4 : angle 1.84464 / 1.28 ( 147) link_NAG-ASN : bond 0.00322 / 0.20 ( 47) link_NAG-ASN : angle 1.76697 / 1.24 ( 141) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 218 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 467 PHE cc_start: 0.6337 (m-10) cc_final: 0.5956 (m-10) REVERT: A 473 PHE cc_start: 0.7984 (p90) cc_final: 0.7748 (p90) REVERT: A 729 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8372 (pp) REVERT: A 1153 TYR cc_start: 0.7642 (m-80) cc_final: 0.7259 (m-80) REVERT: B 261 GLN cc_start: 0.7677 (tm-30) cc_final: 0.7431 (tm-30) REVERT: B 686 MET cc_start: 0.7613 (mmm) cc_final: 0.7398 (tpp) REVERT: B 725 GLU cc_start: 0.7458 (mt-10) cc_final: 0.7150 (mm-30) REVERT: B 726 ASP cc_start: 0.7779 (m-30) cc_final: 0.7087 (p0) REVERT: B 1056 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7893 (pp30) REVERT: B 1204 TYR cc_start: 0.8189 (m-80) cc_final: 0.7913 (m-10) REVERT: C 31 ILE cc_start: 0.8090 (mm) cc_final: 0.7800 (tp) REVERT: C 147 PHE cc_start: 0.7745 (m-80) cc_final: 0.7509 (m-10) REVERT: C 1035 LYS cc_start: 0.8008 (tppt) cc_final: 0.7805 (tptp) REVERT: H 33 TRP cc_start: 0.4152 (m-10) cc_final: 0.3941 (m-10) outliers start: 69 outliers final: 47 residues processed: 275 average time/residue: 0.1432 time to fit residues: 67.0937 Evaluate side-chains 237 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 188 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 502 LYS Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 540 TYR Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 772 GLN Chi-restraints excluded: chain A residue 806 CYS Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain B residue 859 SER Chi-restraints excluded: chain B residue 966 SER Chi-restraints excluded: chain B residue 1020 GLN Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1056 GLN Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 592 ASN Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 986 THR Chi-restraints excluded: chain C residue 1041 SER Chi-restraints excluded: chain C residue 1042 ASN Chi-restraints excluded: chain C residue 1087 VAL Chi-restraints excluded: chain C residue 1094 LEU Chi-restraints excluded: chain C residue 1121 THR Chi-restraints excluded: chain C residue 1205 VAL Chi-restraints excluded: chain C residue 1210 THR Chi-restraints excluded: chain H residue 62 TYR Chi-restraints excluded: chain L residue 33 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 287 optimal weight: 0.9980 chunk 307 optimal weight: 10.0000 chunk 172 optimal weight: 2.9990 chunk 168 optimal weight: 0.6980 chunk 145 optimal weight: 0.9990 chunk 139 optimal weight: 0.8980 chunk 230 optimal weight: 0.0980 chunk 237 optimal weight: 0.9980 chunk 136 optimal weight: 3.9990 chunk 187 optimal weight: 0.5980 chunk 177 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 421 ASN ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1122 HIS B 636 GLN B 812 ASN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1056 GLN B1066 GLN C 618 GLN C 812 ASN C 836 HIS C1042 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.149821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.123344 restraints weight = 48380.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.122527 restraints weight = 42620.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.123448 restraints weight = 39240.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.123794 restraints weight = 32472.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.124037 restraints weight = 30325.325| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.135 27431 Z= 0.149 Angle : 0.643 19.007 37550 Z= 0.316 Chirality : 0.043 0.247 4457 Planarity : 0.004 0.066 4677 Dihedral : 4.499 24.651 3584 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.69 % Allowed : 12.29 % Favored : 85.01 % 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: 0.13 (0.14), residues: 3277 helix: 1.74 (0.21), residues: 676 sheet: 0.44 (0.18), residues: 751 loop : -0.69 (0.13), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 269 TYR 0.015 0.001 TYR A1141 PHE 0.015 0.002 PHE B 266 TRP 0.018 0.001 TRP H 117 HIS 0.007 0.001 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (27273) covalent geometry : angle 0.61529 / 0.31 (37121) SS BOND : bond 0.00327 / 0.19 ( 45) SS BOND : angle 2.34806 / 1.92 ( 90) hydrogen bonds : bond 0.05450 / 3.77 ( 1031) hydrogen bonds : angle 5.17149 / 3.58 ( 2802) link_ALPHA1-2 : bond 0.00514 / 0.27 ( 1) link_ALPHA1-2 : angle 1.30413 / 0.70 ( 3) link_ALPHA1-3 : bond 0.00512 / 0.33 ( 9) link_ALPHA1-3 : angle 1.42522 / 0.91 ( 27) link_ALPHA1-6 : bond 0.00393 / 0.20 ( 7) link_ALPHA1-6 : angle 1.41644 / 0.97 ( 21) link_BETA1-4 : bond 0.01015 / 0.65 ( 49) link_BETA1-4 : angle 1.86467 / 1.30 ( 147) link_NAG-ASN : bond 0.00341 / 0.23 ( 47) link_NAG-ASN : angle 1.64287 / 1.16 ( 141) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 203 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 GLU cc_start: 0.7471 (pp20) cc_final: 0.7228 (tm-30) REVERT: A 467 PHE cc_start: 0.6357 (m-10) cc_final: 0.6008 (m-10) REVERT: A 473 PHE cc_start: 0.7910 (p90) cc_final: 0.7697 (p90) REVERT: A 474 SER cc_start: 0.8641 (OUTLIER) cc_final: 0.8008 (t) REVERT: A 674 PHE cc_start: 0.8819 (m-80) cc_final: 0.8493 (m-10) REVERT: A 729 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8506 (pp) REVERT: A 915 GLN cc_start: 0.7311 (tm-30) cc_final: 0.7095 (tt0) REVERT: A 1153 TYR cc_start: 0.7709 (m-80) cc_final: 0.7318 (m-80) REVERT: B 686 MET cc_start: 0.7676 (mmm) cc_final: 0.7418 (tpp) REVERT: B 725 GLU cc_start: 0.7502 (mt-10) cc_final: 0.7079 (mm-30) REVERT: B 726 ASP cc_start: 0.7798 (m-30) cc_final: 0.7020 (p0) REVERT: B 1056 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.7809 (pp30) REVERT: C 31 ILE cc_start: 0.8116 (mm) cc_final: 0.7820 (tp) REVERT: C 240 MET cc_start: 0.7843 (tpp) cc_final: 0.7259 (mmm) REVERT: H 33 TRP cc_start: 0.4412 (m-10) cc_final: 0.4193 (m-10) outliers start: 72 outliers final: 54 residues processed: 263 average time/residue: 0.1472 time to fit residues: 65.2893 Evaluate side-chains 238 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 181 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 438 TYR Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 540 TYR Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 772 GLN Chi-restraints excluded: chain A residue 806 CYS Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 819 GLN Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain A residue 1042 ASN Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1190 SER Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 258 GLN Chi-restraints excluded: chain B residue 355 ASP Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain B residue 859 SER Chi-restraints excluded: chain B residue 1020 GLN Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1055 ILE Chi-restraints excluded: chain B residue 1056 GLN Chi-restraints excluded: chain B residue 1210 THR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 986 THR Chi-restraints excluded: chain C residue 1087 VAL Chi-restraints excluded: chain C residue 1094 LEU Chi-restraints excluded: chain C residue 1205 VAL Chi-restraints excluded: chain C residue 1210 THR Chi-restraints excluded: chain H residue 62 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 209 optimal weight: 0.1980 chunk 196 optimal weight: 0.6980 chunk 78 optimal weight: 0.0970 chunk 173 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 309 optimal weight: 20.0000 chunk 39 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 chunk 100 optimal weight: 0.9990 chunk 304 optimal weight: 0.0980 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 636 GLN B 812 ASN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 812 ASN C1042 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.151743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.125377 restraints weight = 48647.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.126094 restraints weight = 41698.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.126879 restraints weight = 36565.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.127563 restraints weight = 28781.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.127753 restraints weight = 26659.256| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27431 Z= 0.118 Angle : 0.599 19.802 37550 Z= 0.293 Chirality : 0.042 0.206 4457 Planarity : 0.004 0.063 4677 Dihedral : 4.276 23.381 3584 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.65 % Allowed : 12.86 % Favored : 84.49 % 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 (0.14), residues: 3277 helix: 1.88 (0.21), residues: 672 sheet: 0.50 (0.18), residues: 744 loop : -0.64 (0.14), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1057 TYR 0.032 0.001 TYR B 649 PHE 0.014 0.001 PHE A 778 TRP 0.021 0.001 TRP H 117 HIS 0.007 0.001 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (27273) covalent geometry : angle 0.57713 / 0.29 (37121) SS BOND : bond 0.00686 / 0.25 ( 45) SS BOND : angle 1.25458 / 0.91 ( 90) hydrogen bonds : bond 0.04829 / 3.34 ( 1031) hydrogen bonds : angle 4.98648 / 3.45 ( 2802) link_ALPHA1-2 : bond 0.00497 / 0.26 ( 1) link_ALPHA1-2 : angle 1.31410 / 0.71 ( 3) link_ALPHA1-3 : bond 0.00482 / 0.30 ( 9) link_ALPHA1-3 : angle 1.39859 / 0.90 ( 27) link_ALPHA1-6 : bond 0.00502 / 0.24 ( 7) link_ALPHA1-6 : angle 1.33575 / 0.90 ( 21) link_BETA1-4 : bond 0.01021 / 0.66 ( 49) link_BETA1-4 : angle 1.83171 / 1.28 ( 147) link_NAG-ASN : bond 0.00218 / 0.15 ( 47) link_NAG-ASN : angle 1.59143 / 1.10 ( 141) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 210 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 467 PHE cc_start: 0.6274 (m-10) cc_final: 0.5841 (m-10) REVERT: A 474 SER cc_start: 0.8556 (OUTLIER) cc_final: 0.7878 (t) REVERT: A 674 PHE cc_start: 0.8754 (m-80) cc_final: 0.8459 (m-10) REVERT: A 729 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8345 (pp) REVERT: A 819 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7962 (mm-40) REVERT: A 1153 TYR cc_start: 0.7726 (m-80) cc_final: 0.7374 (m-80) REVERT: B 686 MET cc_start: 0.7554 (mmm) cc_final: 0.7340 (tpp) REVERT: B 725 GLU cc_start: 0.7399 (mt-10) cc_final: 0.7033 (mm-30) REVERT: B 726 ASP cc_start: 0.7748 (m-30) cc_final: 0.6971 (p0) REVERT: B 871 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7925 (pp) REVERT: B 1020 GLN cc_start: 0.7776 (OUTLIER) cc_final: 0.7480 (mp10) REVERT: B 1204 TYR cc_start: 0.8150 (m-80) cc_final: 0.7887 (m-10) REVERT: C 31 ILE cc_start: 0.7900 (mm) cc_final: 0.7700 (tp) REVERT: C 147 PHE cc_start: 0.7616 (m-80) cc_final: 0.7358 (m-10) REVERT: C 240 MET cc_start: 0.7875 (tpp) cc_final: 0.7285 (mmm) REVERT: C 964 LEU cc_start: 0.7968 (mm) cc_final: 0.7705 (mp) REVERT: C 1035 LYS cc_start: 0.8123 (tppt) cc_final: 0.7766 (tptp) REVERT: H 33 TRP cc_start: 0.4398 (m-10) cc_final: 0.4190 (m-10) outliers start: 71 outliers final: 49 residues processed: 268 average time/residue: 0.1510 time to fit residues: 68.9557 Evaluate side-chains 234 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 180 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 438 TYR Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 540 TYR Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 772 GLN Chi-restraints excluded: chain A residue 806 CYS Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 819 GLN Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain A residue 1042 ASN Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 258 GLN Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain B residue 859 SER Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 966 SER Chi-restraints excluded: chain B residue 1020 GLN Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1055 ILE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 592 ASN Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 986 THR Chi-restraints excluded: chain C residue 1042 ASN Chi-restraints excluded: chain C residue 1087 VAL Chi-restraints excluded: chain C residue 1094 LEU Chi-restraints excluded: chain C residue 1205 VAL Chi-restraints excluded: chain C residue 1210 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 186 optimal weight: 2.9990 chunk 247 optimal weight: 0.0670 chunk 124 optimal weight: 0.0070 chunk 130 optimal weight: 0.1980 chunk 264 optimal weight: 0.9980 chunk 281 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 206 optimal weight: 0.9990 chunk 259 optimal weight: 1.9990 chunk 209 optimal weight: 0.6980 chunk 115 optimal weight: 0.2980 overall best weight: 0.2536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 636 GLN B 812 ASN B1056 GLN B1085 GLN C 812 ASN C1042 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.151427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.125016 restraints weight = 48027.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.124897 restraints weight = 38735.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.125790 restraints weight = 34505.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.126413 restraints weight = 27832.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.126603 restraints weight = 24771.918| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 27431 Z= 0.110 Angle : 0.589 19.544 37550 Z= 0.288 Chirality : 0.042 0.208 4457 Planarity : 0.004 0.063 4677 Dihedral : 4.152 22.572 3584 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.28 % Allowed : 13.53 % Favored : 84.19 % 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 (0.14), residues: 3277 helix: 1.95 (0.21), residues: 674 sheet: 0.54 (0.18), residues: 731 loop : -0.60 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1113 TYR 0.014 0.001 TYR A1141 PHE 0.014 0.001 PHE A 778 TRP 0.024 0.001 TRP H 117 HIS 0.007 0.001 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (27273) covalent geometry : angle 0.56712 / 0.28 (37121) SS BOND : bond 0.00282 / 0.15 ( 45) SS BOND : angle 1.47251 / 1.10 ( 90) hydrogen bonds : bond 0.04522 / 3.14 ( 1031) hydrogen bonds : angle 4.88374 / 3.38 ( 2802) link_ALPHA1-2 : bond 0.00488 / 0.26 ( 1) link_ALPHA1-2 : angle 1.33153 / 0.72 ( 3) link_ALPHA1-3 : bond 0.00459 / 0.29 ( 9) link_ALPHA1-3 : angle 1.39978 / 0.91 ( 27) link_ALPHA1-6 : bond 0.00475 / 0.24 ( 7) link_ALPHA1-6 : angle 1.34825 / 0.92 ( 21) link_BETA1-4 : bond 0.01022 / 0.65 ( 49) link_BETA1-4 : angle 1.82028 / 1.28 ( 147) link_NAG-ASN : bond 0.00279 / 0.19 ( 47) link_NAG-ASN : angle 1.47573 / 1.01 ( 141) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 191 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 467 PHE cc_start: 0.6283 (m-10) cc_final: 0.6023 (m-10) REVERT: A 474 SER cc_start: 0.8526 (OUTLIER) cc_final: 0.7921 (t) REVERT: A 674 PHE cc_start: 0.8699 (m-80) cc_final: 0.8388 (m-10) REVERT: A 729 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8447 (pp) REVERT: A 1153 TYR cc_start: 0.7802 (m-80) cc_final: 0.7436 (m-80) REVERT: B 185 CYS cc_start: 0.3896 (OUTLIER) cc_final: 0.3168 (m) REVERT: B 686 MET cc_start: 0.7614 (mmm) cc_final: 0.7380 (tpp) REVERT: B 725 GLU cc_start: 0.7522 (mt-10) cc_final: 0.7080 (mm-30) REVERT: B 726 ASP cc_start: 0.7810 (m-30) cc_final: 0.6975 (p0) REVERT: B 871 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8086 (pp) REVERT: B 1020 GLN cc_start: 0.7735 (OUTLIER) cc_final: 0.7443 (mp10) REVERT: B 1056 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.8015 (pp30) REVERT: B 1204 TYR cc_start: 0.8121 (m-80) cc_final: 0.7788 (m-10) REVERT: C 31 ILE cc_start: 0.7928 (mm) cc_final: 0.7685 (tp) REVERT: C 147 PHE cc_start: 0.7624 (m-80) cc_final: 0.7250 (m-10) REVERT: C 240 MET cc_start: 0.7934 (tpp) cc_final: 0.7374 (mmm) REVERT: C 964 LEU cc_start: 0.7969 (mm) cc_final: 0.7704 (mp) REVERT: C 1035 LYS cc_start: 0.8083 (tppt) cc_final: 0.7672 (tptp) REVERT: H 33 TRP cc_start: 0.4411 (m-10) cc_final: 0.4186 (m-10) outliers start: 61 outliers final: 41 residues processed: 239 average time/residue: 0.1535 time to fit residues: 62.8721 Evaluate side-chains 228 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 181 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 438 TYR Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 540 TYR Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 772 GLN Chi-restraints excluded: chain A residue 806 CYS Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain A residue 1042 ASN Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain B residue 859 SER Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 966 SER Chi-restraints excluded: chain B residue 1020 GLN Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1056 GLN Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 592 ASN Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 986 THR Chi-restraints excluded: chain C residue 1094 LEU Chi-restraints excluded: chain C residue 1205 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 234 optimal weight: 2.9990 chunk 259 optimal weight: 1.9990 chunk 298 optimal weight: 0.6980 chunk 265 optimal weight: 0.7980 chunk 201 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 327 optimal weight: 8.9990 chunk 278 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 131 optimal weight: 0.6980 chunk 241 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 81 HIS B 636 GLN B1056 GLN C 277 ASN C 812 ASN C1042 ASN C1122 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.149138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.122283 restraints weight = 48789.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.123349 restraints weight = 41663.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.124215 restraints weight = 33378.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.124794 restraints weight = 26852.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.124950 restraints weight = 25534.712| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.4587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 27431 Z= 0.160 Angle : 0.636 20.004 37550 Z= 0.312 Chirality : 0.043 0.213 4457 Planarity : 0.004 0.066 4677 Dihedral : 4.315 23.464 3584 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.73 % Allowed : 13.27 % Favored : 84.01 % 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 (0.14), residues: 3277 helix: 1.82 (0.20), residues: 682 sheet: 0.49 (0.18), residues: 750 loop : -0.67 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B1113 TYR 0.017 0.001 TYR B 635 PHE 0.015 0.002 PHE A 850 TRP 0.021 0.001 TRP H 117 HIS 0.008 0.001 HIS A1138 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (27273) covalent geometry : angle 0.61141 / 0.31 (37121) SS BOND : bond 0.00316 / 0.18 ( 45) SS BOND : angle 1.86940 / 1.35 ( 90) hydrogen bonds : bond 0.05175 / 3.56 ( 1031) hydrogen bonds : angle 5.01538 / 3.47 ( 2802) link_ALPHA1-2 : bond 0.00511 / 0.27 ( 1) link_ALPHA1-2 : angle 1.34839 / 0.73 ( 3) link_ALPHA1-3 : bond 0.00486 / 0.31 ( 9) link_ALPHA1-3 : angle 1.43731 / 0.92 ( 27) link_ALPHA1-6 : bond 0.00416 / 0.22 ( 7) link_ALPHA1-6 : angle 1.42677 / 1.00 ( 21) link_BETA1-4 : bond 0.00991 / 0.63 ( 49) link_BETA1-4 : angle 1.88919 / 1.32 ( 147) link_NAG-ASN : bond 0.00393 / 0.29 ( 47) link_NAG-ASN : angle 1.61687 / 1.12 ( 141) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 200 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 LEU cc_start: 0.6132 (mt) cc_final: 0.5759 (mt) REVERT: A 467 PHE cc_start: 0.6272 (m-10) cc_final: 0.6033 (m-10) REVERT: A 576 GLN cc_start: 0.8129 (mm-40) cc_final: 0.7799 (mm-40) REVERT: A 674 PHE cc_start: 0.8840 (m-80) cc_final: 0.8472 (m-10) REVERT: A 729 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8492 (pp) REVERT: B 185 CYS cc_start: 0.3984 (OUTLIER) cc_final: 0.3236 (m) REVERT: B 686 MET cc_start: 0.7639 (mmm) cc_final: 0.7376 (tpp) REVERT: B 725 GLU cc_start: 0.7543 (mt-10) cc_final: 0.7079 (mm-30) REVERT: B 726 ASP cc_start: 0.7821 (m-30) cc_final: 0.7009 (p0) REVERT: B 871 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8148 (pp) REVERT: B 1020 GLN cc_start: 0.7858 (OUTLIER) cc_final: 0.7545 (mp10) REVERT: B 1056 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.7768 (pp30) REVERT: C 31 ILE cc_start: 0.7932 (mm) cc_final: 0.7692 (tp) REVERT: C 240 MET cc_start: 0.7917 (tpp) cc_final: 0.7368 (mmm) REVERT: C 805 ASP cc_start: 0.7444 (OUTLIER) cc_final: 0.7064 (p0) REVERT: C 964 LEU cc_start: 0.8004 (mm) cc_final: 0.7754 (mp) REVERT: C 1035 LYS cc_start: 0.8160 (tppt) cc_final: 0.7723 (tptp) outliers start: 73 outliers final: 52 residues processed: 263 average time/residue: 0.1474 time to fit residues: 66.2236 Evaluate side-chains 240 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 182 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 438 TYR Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 540 TYR Chi-restraints excluded: chain A residue 541 TYR Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain A residue 1042 ASN Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1190 SER Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 258 GLN Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain B residue 859 SER Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 966 SER Chi-restraints excluded: chain B residue 1020 GLN Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1056 GLN Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 592 ASN Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 805 ASP Chi-restraints excluded: chain C residue 853 VAL Chi-restraints excluded: chain C residue 928 TYR Chi-restraints excluded: chain C residue 986 THR Chi-restraints excluded: chain C residue 1042 ASN Chi-restraints excluded: chain C residue 1087 VAL Chi-restraints excluded: chain C residue 1094 LEU Chi-restraints excluded: chain C residue 1205 VAL Chi-restraints excluded: chain C residue 1210 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 43 optimal weight: 0.9990 chunk 200 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 33 optimal weight: 0.4980 chunk 152 optimal weight: 5.9990 chunk 278 optimal weight: 0.9990 chunk 172 optimal weight: 0.9990 chunk 229 optimal weight: 6.9990 chunk 80 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 466 GLN ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN B 812 ASN ** B1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 812 ASN C1042 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.147936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.121246 restraints weight = 48262.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.122756 restraints weight = 38810.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.123514 restraints weight = 31293.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.123772 restraints weight = 24633.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.123893 restraints weight = 23162.317| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.4731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 27431 Z= 0.158 Angle : 0.639 20.397 37550 Z= 0.313 Chirality : 0.043 0.204 4457 Planarity : 0.005 0.065 4677 Dihedral : 4.385 28.342 3584 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.62 % Allowed : 13.83 % Favored : 83.56 % 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: 0.15 (0.14), residues: 3277 helix: 1.76 (0.21), residues: 674 sheet: 0.48 (0.18), residues: 758 loop : -0.70 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 181 TYR 0.015 0.001 TYR A1141 PHE 0.018 0.002 PHE C1044 TRP 0.021 0.001 TRP H 117 HIS 0.007 0.001 HIS A1138 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (27273) covalent geometry : angle 0.61506 / 0.31 (37121) SS BOND : bond 0.00321 / 0.19 ( 45) SS BOND : angle 1.83509 / 1.24 ( 90) hydrogen bonds : bond 0.05193 / 3.57 ( 1031) hydrogen bonds : angle 5.04158 / 3.49 ( 2802) link_ALPHA1-2 : bond 0.00533 / 0.28 ( 1) link_ALPHA1-2 : angle 1.32728 / 0.72 ( 3) link_ALPHA1-3 : bond 0.00491 / 0.31 ( 9) link_ALPHA1-3 : angle 1.41639 / 0.91 ( 27) link_ALPHA1-6 : bond 0.00397 / 0.21 ( 7) link_ALPHA1-6 : angle 1.41144 / 0.98 ( 21) link_BETA1-4 : bond 0.01012 / 0.65 ( 49) link_BETA1-4 : angle 1.88688 / 1.32 ( 147) link_NAG-ASN : bond 0.00318 / 0.22 ( 47) link_NAG-ASN : angle 1.61427 / 1.12 ( 141) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 189 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 LEU cc_start: 0.5944 (mt) cc_final: 0.5544 (mt) REVERT: A 467 PHE cc_start: 0.6113 (m-10) cc_final: 0.5897 (m-10) REVERT: A 576 GLN cc_start: 0.8169 (mm-40) cc_final: 0.7826 (mm-40) REVERT: A 674 PHE cc_start: 0.8760 (m-80) cc_final: 0.8413 (m-10) REVERT: A 707 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7423 (pt) REVERT: A 729 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8484 (pp) REVERT: B 261 GLN cc_start: 0.7992 (tm-30) cc_final: 0.7778 (tm-30) REVERT: B 686 MET cc_start: 0.7627 (mmm) cc_final: 0.7375 (tpp) REVERT: B 725 GLU cc_start: 0.7521 (mt-10) cc_final: 0.7064 (mm-30) REVERT: B 726 ASP cc_start: 0.7838 (m-30) cc_final: 0.7006 (p0) REVERT: B 871 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8173 (pp) REVERT: B 1020 GLN cc_start: 0.7849 (OUTLIER) cc_final: 0.7537 (mp10) REVERT: C 31 ILE cc_start: 0.7927 (mm) cc_final: 0.7671 (tp) REVERT: C 240 MET cc_start: 0.7958 (tpp) cc_final: 0.7399 (mmm) REVERT: C 272 ASP cc_start: 0.6913 (t70) cc_final: 0.6283 (t0) REVERT: C 805 ASP cc_start: 0.7336 (OUTLIER) cc_final: 0.7031 (p0) REVERT: C 964 LEU cc_start: 0.7900 (mm) cc_final: 0.7662 (mp) REVERT: C 1035 LYS cc_start: 0.8157 (tppt) cc_final: 0.7689 (tptp) outliers start: 70 outliers final: 59 residues processed: 247 average time/residue: 0.1494 time to fit residues: 63.3118 Evaluate side-chains 247 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 183 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 438 TYR Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 540 TYR Chi-restraints excluded: chain A residue 541 TYR Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 772 GLN Chi-restraints excluded: chain A residue 806 CYS Chi-restraints excluded: chain A residue 817 CYS Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain A residue 1042 ASN Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1190 SER Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 258 GLN Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain B residue 859 SER Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 966 SER Chi-restraints excluded: chain B residue 1020 GLN Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 592 ASN Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 805 ASP Chi-restraints excluded: chain C residue 812 ASN Chi-restraints excluded: chain C residue 853 VAL Chi-restraints excluded: chain C residue 913 MET Chi-restraints excluded: chain C residue 928 TYR Chi-restraints excluded: chain C residue 986 THR Chi-restraints excluded: chain C residue 1042 ASN Chi-restraints excluded: chain C residue 1087 VAL Chi-restraints excluded: chain C residue 1094 LEU Chi-restraints excluded: chain C residue 1205 VAL Chi-restraints excluded: chain C residue 1210 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 326 optimal weight: 7.9990 chunk 186 optimal weight: 4.9990 chunk 321 optimal weight: 0.3980 chunk 1 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 179 optimal weight: 0.9990 chunk 268 optimal weight: 0.0270 chunk 166 optimal weight: 0.0770 chunk 118 optimal weight: 0.5980 chunk 163 optimal weight: 1.9990 chunk 265 optimal weight: 0.2980 overall best weight: 0.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 466 GLN ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1020 GLN B 636 GLN B1056 GLN C 812 ASN C1042 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.150574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.124146 restraints weight = 48118.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.123720 restraints weight = 39111.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.124381 restraints weight = 37917.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.124945 restraints weight = 31376.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.125231 restraints weight = 26842.307| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.4804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 27431 Z= 0.112 Angle : 0.619 20.324 37550 Z= 0.300 Chirality : 0.042 0.239 4457 Planarity : 0.004 0.060 4677 Dihedral : 4.238 24.441 3584 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.20 % Allowed : 14.39 % Favored : 83.41 % 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: 0.29 (0.14), residues: 3277 helix: 1.97 (0.21), residues: 674 sheet: 0.53 (0.18), residues: 758 loop : -0.63 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1113 TYR 0.016 0.001 TYR A1141 PHE 0.017 0.001 PHE C 40 TRP 0.019 0.001 TRP H 117 HIS 0.007 0.001 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (27273) covalent geometry : angle 0.59645 / 0.29 (37121) SS BOND : bond 0.00283 / 0.15 ( 45) SS BOND : angle 1.69350 / 1.15 ( 90) hydrogen bonds : bond 0.04652 / 3.21 ( 1031) hydrogen bonds : angle 4.89964 / 3.39 ( 2802) link_ALPHA1-2 : bond 0.00519 / 0.27 ( 1) link_ALPHA1-2 : angle 1.32359 / 0.72 ( 3) link_ALPHA1-3 : bond 0.00467 / 0.29 ( 9) link_ALPHA1-3 : angle 1.39968 / 0.92 ( 27) link_ALPHA1-6 : bond 0.00461 / 0.24 ( 7) link_ALPHA1-6 : angle 1.34038 / 0.91 ( 21) link_BETA1-4 : bond 0.01012 / 0.65 ( 49) link_BETA1-4 : angle 1.83113 / 1.28 ( 147) link_NAG-ASN : bond 0.00284 / 0.19 ( 47) link_NAG-ASN : angle 1.51655 / 1.05 ( 141) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 202 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 LEU cc_start: 0.5760 (mt) cc_final: 0.5346 (mt) REVERT: A 486 HIS cc_start: 0.7196 (m90) cc_final: 0.6873 (m-70) REVERT: A 576 GLN cc_start: 0.8129 (mm-40) cc_final: 0.7718 (mm-40) REVERT: A 674 PHE cc_start: 0.8678 (m-80) cc_final: 0.8338 (m-10) REVERT: A 729 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8491 (pp) REVERT: B 686 MET cc_start: 0.7614 (mmm) cc_final: 0.7388 (tpp) REVERT: B 725 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7074 (mm-30) REVERT: B 726 ASP cc_start: 0.7832 (m-30) cc_final: 0.7018 (p0) REVERT: B 871 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8182 (pp) REVERT: B 1020 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.7445 (mp10) REVERT: B 1056 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8141 (pp30) REVERT: C 31 ILE cc_start: 0.7934 (mm) cc_final: 0.7639 (tp) REVERT: C 147 PHE cc_start: 0.7586 (m-80) cc_final: 0.7257 (m-10) REVERT: C 240 MET cc_start: 0.7948 (tpp) cc_final: 0.7388 (mmm) REVERT: C 805 ASP cc_start: 0.7632 (OUTLIER) cc_final: 0.7110 (p0) REVERT: C 964 LEU cc_start: 0.7958 (mm) cc_final: 0.7710 (mp) REVERT: C 1035 LYS cc_start: 0.8145 (tppt) cc_final: 0.7701 (tptp) outliers start: 59 outliers final: 50 residues processed: 250 average time/residue: 0.1538 time to fit residues: 66.0183 Evaluate side-chains 245 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 190 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 438 TYR Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 540 TYR Chi-restraints excluded: chain A residue 541 TYR Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 772 GLN Chi-restraints excluded: chain A residue 817 CYS Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain A residue 1042 ASN Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 258 GLN Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain B residue 859 SER Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 912 CYS Chi-restraints excluded: chain B residue 966 SER Chi-restraints excluded: chain B residue 1020 GLN Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1056 GLN Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 805 ASP Chi-restraints excluded: chain C residue 853 VAL Chi-restraints excluded: chain C residue 913 MET Chi-restraints excluded: chain C residue 928 TYR Chi-restraints excluded: chain C residue 986 THR Chi-restraints excluded: chain C residue 1087 VAL Chi-restraints excluded: chain C residue 1094 LEU Chi-restraints excluded: chain C residue 1205 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 7 optimal weight: 6.9990 chunk 178 optimal weight: 1.9990 chunk 290 optimal weight: 0.7980 chunk 150 optimal weight: 1.9990 chunk 269 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 167 optimal weight: 1.9990 chunk 234 optimal weight: 0.9980 chunk 245 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN C 812 ASN C1042 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.149867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.123133 restraints weight = 48117.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.124105 restraints weight = 38622.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.124877 restraints weight = 32162.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.125669 restraints weight = 26181.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.125649 restraints weight = 24153.464| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.4800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.154 27431 Z= 0.179 Angle : 0.762 59.143 37550 Z= 0.399 Chirality : 0.044 0.809 4457 Planarity : 0.004 0.060 4677 Dihedral : 4.237 24.297 3584 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.28 % Allowed : 14.31 % Favored : 83.41 % Cbeta Deviations : 0.03 % 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 (0.14), residues: 3277 helix: 1.95 (0.21), residues: 674 sheet: 0.53 (0.18), residues: 758 loop : -0.63 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1113 TYR 0.019 0.001 TYR C 332 PHE 0.015 0.001 PHE A 232 TRP 0.017 0.001 TRP H 117 HIS 0.006 0.001 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.18 (27273) covalent geometry : angle 0.74564 / 0.40 (37121) SS BOND : bond 0.00300 / 0.17 ( 45) SS BOND : angle 1.61768 / 1.09 ( 90) hydrogen bonds : bond 0.04820 / 3.32 ( 1031) hydrogen bonds : angle 4.90315 / 3.40 ( 2802) link_ALPHA1-2 : bond 0.00606 / 0.32 ( 1) link_ALPHA1-2 : angle 1.30809 / 0.71 ( 3) link_ALPHA1-3 : bond 0.00501 / 0.32 ( 9) link_ALPHA1-3 : angle 1.37722 / 0.90 ( 27) link_ALPHA1-6 : bond 0.00460 / 0.23 ( 7) link_ALPHA1-6 : angle 1.37179 / 0.93 ( 21) link_BETA1-4 : bond 0.01041 / 0.66 ( 49) link_BETA1-4 : angle 1.84887 / 1.30 ( 147) link_NAG-ASN : bond 0.00307 / 0.21 ( 47) link_NAG-ASN : angle 1.51300 / 1.04 ( 141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3890.60 seconds wall clock time: 84 minutes 2.44 seconds (5042.44 seconds total)