Starting phenix.real_space_refine on Fri Sep 19 08:57:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6bfu_7094/09_2025/6bfu_7094.cif Found real_map, /net/cci-nas-00/data/ceres_data/6bfu_7094/09_2025/6bfu_7094.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6bfu_7094/09_2025/6bfu_7094.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6bfu_7094/09_2025/6bfu_7094.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6bfu_7094/09_2025/6bfu_7094.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6bfu_7094/09_2025/6bfu_7094.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 129 5.16 5 C 15255 2.51 5 N 3864 2.21 5 O 5232 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 86 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24480 Number of models: 1 Model: "" Number of chains: 45 Chain: "A" Number of atoms: 7442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 964, 7442 Classifications: {'peptide': 964} Link IDs: {'PTRANS': 34, 'TRANS': 929} Chain breaks: 1 Chain: "B" Number of atoms: 7442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 964, 7442 Classifications: {'peptide': 964} Link IDs: {'PTRANS': 34, 'TRANS': 929} Chain breaks: 1 Chain: "C" Number of atoms: 7442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 964, 7442 Classifications: {'peptide': 964} Link IDs: {'PTRANS': 34, 'TRANS': 929} Chain breaks: 1 Chain: "D" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "i" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "l" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "m" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "o" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 5.52, per 1000 atoms: 0.23 Number of scatterers: 24480 At special positions: 0 Unit cell: (122.36, 125.02, 159.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 129 16.00 O 5232 8.00 N 3864 7.00 C 15255 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 93 " - pdb=" SG CYS A 116 " distance=2.04 Simple disulfide: pdb=" SG CYS A 157 " - pdb=" SG CYS A 181 " distance=2.05 Simple disulfide: pdb=" SG CYS A 260 " - pdb=" SG CYS A 270 " distance=2.03 Simple disulfide: pdb=" SG CYS A 335 " - pdb=" SG CYS A 378 " distance=2.04 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 352 " distance=2.01 Simple disulfide: pdb=" SG CYS A 361 " - pdb=" SG CYS A 386 " distance=2.03 Simple disulfide: pdb=" SG CYS A 433 " - pdb=" SG CYS A 484 " distance=2.04 Simple disulfide: pdb=" SG CYS A 532 " - pdb=" SG CYS A 545 " distance=2.03 Simple disulfide: pdb=" SG CYS A 597 " - pdb=" SG CYS A 619 " distance=2.08 Simple disulfide: pdb=" SG CYS A 602 " - pdb=" SG CYS A 608 " distance=2.04 Simple disulfide: pdb=" SG CYS A 699 " - pdb=" SG CYS A 710 " distance=2.04 Simple disulfide: pdb=" SG CYS A 901 " - pdb=" SG CYS A 912 " distance=2.01 Simple disulfide: pdb=" SG CYS A 951 " - pdb=" SG CYS A 997 " distance=2.03 Simple disulfide: pdb=" SG CYS B 93 " - pdb=" SG CYS B 116 " distance=2.03 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 181 " distance=2.05 Simple disulfide: pdb=" SG CYS B 260 " - pdb=" SG CYS B 270 " distance=2.03 Simple disulfide: pdb=" SG CYS B 335 " - pdb=" SG CYS B 378 " distance=2.05 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 352 " distance=2.01 Simple disulfide: pdb=" SG CYS B 361 " - pdb=" SG CYS B 386 " distance=2.03 Simple disulfide: pdb=" SG CYS B 433 " - pdb=" SG CYS B 484 " distance=2.04 Simple disulfide: pdb=" SG CYS B 532 " - pdb=" SG CYS B 545 " distance=2.03 Simple disulfide: pdb=" SG CYS B 597 " - pdb=" SG CYS B 619 " distance=2.08 Simple disulfide: pdb=" SG CYS B 602 " - pdb=" SG CYS B 608 " distance=2.05 Simple disulfide: pdb=" SG CYS B 699 " - pdb=" SG CYS B 710 " distance=2.04 Simple disulfide: pdb=" SG CYS B 901 " - pdb=" SG CYS B 912 " distance=2.01 Simple disulfide: pdb=" SG CYS B 951 " - pdb=" SG CYS B 997 " distance=2.03 Simple disulfide: pdb=" SG CYS C 93 " - pdb=" SG CYS C 116 " distance=2.03 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 181 " distance=2.05 Simple disulfide: pdb=" SG CYS C 260 " - pdb=" SG CYS C 270 " distance=2.03 Simple disulfide: pdb=" SG CYS C 335 " - pdb=" SG CYS C 378 " distance=2.04 Simple disulfide: pdb=" SG CYS C 349 " - pdb=" SG CYS C 352 " distance=2.01 Simple disulfide: pdb=" SG CYS C 361 " - pdb=" SG CYS C 386 " distance=2.03 Simple disulfide: pdb=" SG CYS C 433 " - pdb=" SG CYS C 484 " distance=2.04 Simple disulfide: pdb=" SG CYS C 532 " - pdb=" SG CYS C 545 " distance=2.03 Simple disulfide: pdb=" SG CYS C 597 " - pdb=" SG CYS C 619 " distance=2.08 Simple disulfide: pdb=" SG CYS C 602 " - pdb=" SG CYS C 608 " distance=2.04 Simple disulfide: pdb=" SG CYS C 699 " - pdb=" SG CYS C 710 " distance=2.04 Simple disulfide: pdb=" SG CYS C 901 " - pdb=" SG CYS C 912 " distance=2.01 Simple disulfide: pdb=" SG CYS C 951 " - pdb=" SG CYS C 997 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN D 4 " - " MAN D 5 " " MAN F 4 " - " MAN F 5 " " MAN O 4 " - " MAN O 5 " " MAN Q 4 " - " MAN Q 5 " " MAN S 4 " - " MAN S 5 " " MAN b 4 " - " MAN b 5 " " MAN d 4 " - " MAN d 5 " " MAN f 4 " - " MAN f 5 " " MAN o 4 " - " MAN o 5 " ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA F 3 " - " MAN F 4 " " BMA I 3 " - " MAN I 4 " " BMA O 3 " - " MAN O 4 " " BMA Q 3 " - " MAN Q 4 " " BMA S 3 " - " MAN S 4 " " BMA V 3 " - " MAN V 4 " " BMA b 3 " - " MAN b 4 " " BMA d 3 " - " MAN d 4 " " BMA f 3 " - " MAN f 4 " " BMA i 3 " - " MAN i 4 " " BMA o 3 " - " MAN o 4 " ALPHA1-6 " BMA D 3 " - " MAN D 6 " " BMA F 3 " - " MAN F 6 " " BMA I 3 " - " MAN I 5 " " BMA O 3 " - " MAN O 6 " " BMA Q 3 " - " MAN Q 6 " " BMA S 3 " - " MAN S 6 " " BMA V 3 " - " MAN V 5 " " BMA b 3 " - " MAN b 6 " " BMA d 3 " - " MAN d 6 " " BMA f 3 " - " MAN f 6 " " BMA i 3 " - " MAN i 5 " " BMA o 3 " - " MAN o 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " NAG-ASN " NAG A1099 " - " ASN A 99 " " NAG A1162 " - " ASN A 162 " " NAG A1169 " - " ASN A 169 " " NAG A1331 " - " ASN A 331 " " NAG A1505 " - " ASN A 505 " " NAG A1531 " - " ASN A 531 " " NAG A1945 " - " ASN A 945 " " NAG A1970 " - " ASN A 970 " " NAG B1099 " - " ASN B 99 " " NAG B1162 " - " ASN B 162 " " NAG B1169 " - " ASN B 169 " " NAG B1331 " - " ASN B 331 " " NAG B1505 " - " ASN B 505 " " NAG B1531 " - " ASN B 531 " " NAG B1945 " - " ASN B 945 " " NAG B1970 " - " ASN B 970 " " NAG C1099 " - " ASN C 99 " " NAG C1162 " - " ASN C 162 " " NAG C1169 " - " ASN C 169 " " NAG C1331 " - " ASN C 331 " " NAG C1505 " - " ASN C 505 " " NAG C1531 " - " ASN C 531 " " NAG C1945 " - " ASN C 945 " " NAG C1970 " - " ASN C 970 " " NAG D 1 " - " ASN A 74 " " NAG E 1 " - " ASN A 184 " " NAG F 1 " - " ASN A 241 " " NAG G 1 " - " ASN A 251 " " NAG H 1 " - " ASN A 311 " " NAG I 1 " - " ASN A 472 " " NAG J 1 " - " ASN A 494 " " NAG K 1 " - " ASN A 526 " " NAG L 1 " - " ASN A 652 " " NAG M 1 " - " ASN A 661 " " NAG N 1 " - " ASN A 788 " " NAG O 1 " - " ASN A 914 " " NAG P 1 " - " ASN A1003 " " NAG Q 1 " - " ASN B 74 " " NAG R 1 " - " ASN B 184 " " NAG S 1 " - " ASN B 241 " " NAG T 1 " - " ASN B 251 " " NAG U 1 " - " ASN B 311 " " NAG V 1 " - " ASN B 472 " " NAG W 1 " - " ASN B 494 " " NAG X 1 " - " ASN B 526 " " NAG Y 1 " - " ASN B 652 " " NAG Z 1 " - " ASN B 661 " " NAG a 1 " - " ASN B 788 " " NAG b 1 " - " ASN B 914 " " NAG c 1 " - " ASN B1003 " " NAG d 1 " - " ASN C 74 " " NAG e 1 " - " ASN C 184 " " NAG f 1 " - " ASN C 241 " " NAG g 1 " - " ASN C 251 " " NAG h 1 " - " ASN C 311 " " NAG i 1 " - " ASN C 472 " " NAG j 1 " - " ASN C 494 " " NAG k 1 " - " ASN C 526 " " NAG l 1 " - " ASN C 652 " " NAG m 1 " - " ASN C 661 " " NAG n 1 " - " ASN C 788 " " NAG o 1 " - " ASN C 914 " " NAG p 1 " - " ASN C1003 " Time building additional restraints: 2.07 Conformation dependent library (CDL) restraints added in 976.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5484 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 48 sheets defined 28.5% alpha, 38.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 118 through 123 Processing helix chain 'A' and resid 162 through 169 Processing helix chain 'A' and resid 263 through 272 Processing helix chain 'A' and resid 285 through 288 Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.560A pdb=" N VAL A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASN A 369 " --> pdb=" O LEU A 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 364 through 369' Processing helix chain 'A' and resid 504 through 508 removed outlier: 4.040A pdb=" N THR A 507 " --> pdb=" O SER A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 603 Processing helix chain 'A' and resid 605 through 613 Processing helix chain 'A' and resid 617 through 641 Processing helix chain 'A' and resid 645 through 651 Processing helix chain 'A' and resid 652 through 657 removed outlier: 3.808A pdb=" N LYS A 657 " --> pdb=" O THR A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 683 Processing helix chain 'A' and resid 695 through 701 Processing helix chain 'A' and resid 703 through 706 Processing helix chain 'A' and resid 707 through 714 Processing helix chain 'A' and resid 725 through 739 Processing helix chain 'A' and resid 740 through 742 No H-bonds generated for 'chain 'A' and resid 740 through 742' Processing helix chain 'A' and resid 752 through 765 Processing helix chain 'A' and resid 774 through 795 Processing helix chain 'A' and resid 804 through 823 Processing helix chain 'A' and resid 825 through 834 Processing helix chain 'A' and resid 835 through 837 No H-bonds generated for 'chain 'A' and resid 835 through 837' Processing helix chain 'A' and resid 845 through 853 Processing helix chain 'A' and resid 854 through 901 removed outlier: 3.721A pdb=" N GLN A 860 " --> pdb=" O VAL A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 989 No H-bonds generated for 'chain 'A' and resid 987 through 989' Processing helix chain 'A' and resid 1008 through 1012 Processing helix chain 'B' and resid 118 through 123 Processing helix chain 'B' and resid 162 through 169 Processing helix chain 'B' and resid 263 through 272 Processing helix chain 'B' and resid 285 through 288 Processing helix chain 'B' and resid 364 through 369 removed outlier: 3.560A pdb=" N VAL B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASN B 369 " --> pdb=" O LEU B 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 364 through 369' Processing helix chain 'B' and resid 504 through 508 removed outlier: 4.039A pdb=" N THR B 507 " --> pdb=" O SER B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 603 Processing helix chain 'B' and resid 605 through 613 Processing helix chain 'B' and resid 617 through 641 Processing helix chain 'B' and resid 645 through 651 Processing helix chain 'B' and resid 652 through 657 removed outlier: 3.808A pdb=" N LYS B 657 " --> pdb=" O THR B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 683 Processing helix chain 'B' and resid 695 through 701 Processing helix chain 'B' and resid 703 through 706 Processing helix chain 'B' and resid 707 through 714 Processing helix chain 'B' and resid 725 through 739 Processing helix chain 'B' and resid 740 through 742 No H-bonds generated for 'chain 'B' and resid 740 through 742' Processing helix chain 'B' and resid 752 through 765 Processing helix chain 'B' and resid 774 through 795 Processing helix chain 'B' and resid 804 through 823 Processing helix chain 'B' and resid 825 through 834 Processing helix chain 'B' and resid 835 through 837 No H-bonds generated for 'chain 'B' and resid 835 through 837' Processing helix chain 'B' and resid 845 through 853 Processing helix chain 'B' and resid 854 through 901 removed outlier: 3.719A pdb=" N GLN B 860 " --> pdb=" O VAL B 856 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 989 No H-bonds generated for 'chain 'B' and resid 987 through 989' Processing helix chain 'B' and resid 1008 through 1012 Processing helix chain 'C' and resid 118 through 123 Processing helix chain 'C' and resid 162 through 169 Processing helix chain 'C' and resid 263 through 272 Processing helix chain 'C' and resid 285 through 288 Processing helix chain 'C' and resid 364 through 369 removed outlier: 3.560A pdb=" N VAL C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASN C 369 " --> pdb=" O LEU C 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 364 through 369' Processing helix chain 'C' and resid 504 through 508 removed outlier: 4.040A pdb=" N THR C 507 " --> pdb=" O SER C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 603 Processing helix chain 'C' and resid 605 through 613 Processing helix chain 'C' and resid 617 through 641 Processing helix chain 'C' and resid 645 through 651 Processing helix chain 'C' and resid 652 through 657 removed outlier: 3.806A pdb=" N LYS C 657 " --> pdb=" O THR C 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 674 through 683 Processing helix chain 'C' and resid 695 through 701 Processing helix chain 'C' and resid 703 through 706 Processing helix chain 'C' and resid 707 through 714 Processing helix chain 'C' and resid 725 through 739 Processing helix chain 'C' and resid 740 through 742 No H-bonds generated for 'chain 'C' and resid 740 through 742' Processing helix chain 'C' and resid 752 through 765 Processing helix chain 'C' and resid 774 through 795 Processing helix chain 'C' and resid 804 through 823 Processing helix chain 'C' and resid 825 through 834 Processing helix chain 'C' and resid 835 through 837 No H-bonds generated for 'chain 'C' and resid 835 through 837' Processing helix chain 'C' and resid 845 through 853 Processing helix chain 'C' and resid 854 through 901 removed outlier: 3.720A pdb=" N GLN C 860 " --> pdb=" O VAL C 856 " (cutoff:3.500A) Processing helix chain 'C' and resid 987 through 989 No H-bonds generated for 'chain 'C' and resid 987 through 989' Processing helix chain 'C' and resid 1008 through 1012 Processing sheet with id=AA1, first strand: chain 'A' and resid 81 through 91 removed outlier: 3.542A pdb=" N LEU A 89 " --> pdb=" O ASN A 241 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASN A 241 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LEU A 91 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU A 239 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLN A 205 " --> pdb=" O TYR A 201 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N PHE A 206 " --> pdb=" O LEU A 213 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 95 through 96 removed outlier: 7.375A pdb=" N ASP A 244 " --> pdb=" O TYR A 259 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N TYR A 259 " --> pdb=" O ASP A 244 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU A 246 " --> pdb=" O ILE A 257 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE A 257 " --> pdb=" O LEU A 246 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR A 248 " --> pdb=" O SER A 255 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 105 removed outlier: 3.531A pdb=" N GLY A 189 " --> pdb=" O CYS A 181 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N THR A 183 " --> pdb=" O TYR A 187 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N TYR A 187 " --> pdb=" O THR A 183 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 280 through 283 removed outlier: 3.595A pdb=" N GLY A 499 " --> pdb=" O ILE A 491 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ILE A 493 " --> pdb=" O VAL A 497 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N VAL A 497 " --> pdb=" O ILE A 493 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 293 through 297 removed outlier: 3.658A pdb=" N GLN A 293 " --> pdb=" O CYS A 433 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N TYR A 468 " --> pdb=" O VAL A 481 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N PHE A 460 " --> pdb=" O TYR A 468 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 349 through 350 removed outlier: 7.247A pdb=" N THR A 350 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ALA A 314 " --> pdb=" O THR A 350 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLN A 309 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ILE A 328 " --> pdb=" O GLN A 309 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ASN A 311 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL A 326 " --> pdb=" O ASN A 311 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N SER A 313 " --> pdb=" O ASP A 324 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 320 through 328 removed outlier: 6.494A pdb=" N SER A 313 " --> pdb=" O ASP A 324 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL A 326 " --> pdb=" O ASN A 311 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ASN A 311 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ILE A 328 " --> pdb=" O GLN A 309 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLN A 309 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N TYR A 405 " --> pdb=" O LEU A 379 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N LEU A 379 " --> pdb=" O TYR A 405 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N THR A 407 " --> pdb=" O PHE A 377 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE A 377 " --> pdb=" O THR A 407 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL A 409 " --> pdb=" O SER A 375 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N SER A 373 " --> pdb=" O GLY A 411 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 333 through 335 removed outlier: 4.692A pdb=" N SER A 373 " --> pdb=" O GLY A 411 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL A 409 " --> pdb=" O SER A 375 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE A 377 " --> pdb=" O THR A 407 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N THR A 407 " --> pdb=" O PHE A 377 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N LEU A 379 " --> pdb=" O TYR A 405 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N TYR A 405 " --> pdb=" O LEU A 379 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 397 through 399 Processing sheet with id=AB1, first strand: chain 'A' and resid 353 through 358 removed outlier: 7.247A pdb=" N THR A 350 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ALA A 314 " --> pdb=" O THR A 350 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 537 through 539 Processing sheet with id=AB3, first strand: chain 'A' and resid 556 through 557 Processing sheet with id=AB4, first strand: chain 'A' and resid 571 through 587 removed outlier: 6.946A pdb=" N GLU A 572 " --> pdb=" O ARG A 943 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ARG A 943 " --> pdb=" O GLU A 572 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N PHE A 941 " --> pdb=" O PRO A 574 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ALA A 576 " --> pdb=" O ASN A 939 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLY A 928 " --> pdb=" O THR A 924 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N THR A 924 " --> pdb=" O GLY A 928 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N PHE A 930 " --> pdb=" O THR A 922 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N THR A 922 " --> pdb=" O PHE A 930 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N MET A 932 " --> pdb=" O SER A 920 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N SER A 920 " --> pdb=" O MET A 932 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ALA A 934 " --> pdb=" O ILE A 918 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 592 through 595 removed outlier: 4.173A pdb=" N GLN A 592 " --> pdb=" O LEU A 720 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 643 through 644 removed outlier: 5.865A pdb=" N THR A 643 " --> pdb=" O GLN B 557 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 991 through 994 Processing sheet with id=AB8, first strand: chain 'A' and resid 964 through 969 Processing sheet with id=AB9, first strand: chain 'B' and resid 81 through 91 removed outlier: 3.543A pdb=" N LEU B 89 " --> pdb=" O ASN B 241 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ASN B 241 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N LEU B 91 " --> pdb=" O LEU B 239 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU B 239 " --> pdb=" O LEU B 91 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLN B 205 " --> pdb=" O TYR B 201 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N PHE B 206 " --> pdb=" O LEU B 213 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 95 through 96 removed outlier: 7.377A pdb=" N ASP B 244 " --> pdb=" O TYR B 259 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N TYR B 259 " --> pdb=" O ASP B 244 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU B 246 " --> pdb=" O ILE B 257 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE B 257 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR B 248 " --> pdb=" O SER B 255 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 101 through 105 removed outlier: 3.532A pdb=" N GLY B 189 " --> pdb=" O CYS B 181 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N THR B 183 " --> pdb=" O TYR B 187 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N TYR B 187 " --> pdb=" O THR B 183 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 280 through 283 removed outlier: 3.594A pdb=" N GLY B 499 " --> pdb=" O ILE B 491 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ILE B 493 " --> pdb=" O VAL B 497 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N VAL B 497 " --> pdb=" O ILE B 493 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 293 through 297 removed outlier: 3.658A pdb=" N GLN B 293 " --> pdb=" O CYS B 433 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N TYR B 468 " --> pdb=" O VAL B 481 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N PHE B 460 " --> pdb=" O TYR B 468 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 349 through 350 removed outlier: 7.246A pdb=" N THR B 350 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA B 314 " --> pdb=" O THR B 350 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLN B 309 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ILE B 328 " --> pdb=" O GLN B 309 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ASN B 311 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL B 326 " --> pdb=" O ASN B 311 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N SER B 313 " --> pdb=" O ASP B 324 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 320 through 328 removed outlier: 6.494A pdb=" N SER B 313 " --> pdb=" O ASP B 324 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL B 326 " --> pdb=" O ASN B 311 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ASN B 311 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ILE B 328 " --> pdb=" O GLN B 309 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLN B 309 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N TYR B 405 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N LEU B 379 " --> pdb=" O TYR B 405 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR B 407 " --> pdb=" O PHE B 377 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N PHE B 377 " --> pdb=" O THR B 407 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL B 409 " --> pdb=" O SER B 375 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N SER B 373 " --> pdb=" O GLY B 411 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 333 through 335 removed outlier: 4.691A pdb=" N SER B 373 " --> pdb=" O GLY B 411 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL B 409 " --> pdb=" O SER B 375 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N PHE B 377 " --> pdb=" O THR B 407 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR B 407 " --> pdb=" O PHE B 377 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N LEU B 379 " --> pdb=" O TYR B 405 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N TYR B 405 " --> pdb=" O LEU B 379 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 397 through 399 Processing sheet with id=AC9, first strand: chain 'B' and resid 353 through 358 removed outlier: 7.246A pdb=" N THR B 350 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA B 314 " --> pdb=" O THR B 350 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 537 through 539 Processing sheet with id=AD2, first strand: chain 'B' and resid 571 through 587 removed outlier: 6.944A pdb=" N GLU B 572 " --> pdb=" O ARG B 943 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ARG B 943 " --> pdb=" O GLU B 572 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N PHE B 941 " --> pdb=" O PRO B 574 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ALA B 576 " --> pdb=" O ASN B 939 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLY B 928 " --> pdb=" O THR B 924 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N THR B 924 " --> pdb=" O GLY B 928 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N PHE B 930 " --> pdb=" O THR B 922 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N THR B 922 " --> pdb=" O PHE B 930 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N MET B 932 " --> pdb=" O SER B 920 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N SER B 920 " --> pdb=" O MET B 932 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ALA B 934 " --> pdb=" O ILE B 918 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 592 through 595 removed outlier: 4.172A pdb=" N GLN B 592 " --> pdb=" O LEU B 720 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 643 through 644 removed outlier: 5.865A pdb=" N THR B 643 " --> pdb=" O GLN C 557 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 991 through 994 Processing sheet with id=AD6, first strand: chain 'B' and resid 964 through 969 Processing sheet with id=AD7, first strand: chain 'C' and resid 81 through 91 removed outlier: 3.541A pdb=" N LEU C 89 " --> pdb=" O ASN C 241 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASN C 241 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N LEU C 91 " --> pdb=" O LEU C 239 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU C 239 " --> pdb=" O LEU C 91 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLN C 205 " --> pdb=" O TYR C 201 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N PHE C 206 " --> pdb=" O LEU C 213 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 95 through 96 removed outlier: 7.377A pdb=" N ASP C 244 " --> pdb=" O TYR C 259 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N TYR C 259 " --> pdb=" O ASP C 244 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU C 246 " --> pdb=" O ILE C 257 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE C 257 " --> pdb=" O LEU C 246 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR C 248 " --> pdb=" O SER C 255 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 101 through 105 removed outlier: 3.531A pdb=" N GLY C 189 " --> pdb=" O CYS C 181 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N THR C 183 " --> pdb=" O TYR C 187 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N TYR C 187 " --> pdb=" O THR C 183 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 280 through 283 removed outlier: 3.594A pdb=" N GLY C 499 " --> pdb=" O ILE C 491 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE C 493 " --> pdb=" O VAL C 497 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N VAL C 497 " --> pdb=" O ILE C 493 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 293 through 297 removed outlier: 3.659A pdb=" N GLN C 293 " --> pdb=" O CYS C 433 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N TYR C 468 " --> pdb=" O VAL C 481 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N PHE C 460 " --> pdb=" O TYR C 468 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 349 through 350 removed outlier: 7.247A pdb=" N THR C 350 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA C 314 " --> pdb=" O THR C 350 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLN C 309 " --> pdb=" O ILE C 328 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ILE C 328 " --> pdb=" O GLN C 309 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ASN C 311 " --> pdb=" O VAL C 326 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL C 326 " --> pdb=" O ASN C 311 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N SER C 313 " --> pdb=" O ASP C 324 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 320 through 328 removed outlier: 6.494A pdb=" N SER C 313 " --> pdb=" O ASP C 324 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL C 326 " --> pdb=" O ASN C 311 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ASN C 311 " --> pdb=" O VAL C 326 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ILE C 328 " --> pdb=" O GLN C 309 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLN C 309 " --> pdb=" O ILE C 328 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N TYR C 405 " --> pdb=" O LEU C 379 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LEU C 379 " --> pdb=" O TYR C 405 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR C 407 " --> pdb=" O PHE C 377 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE C 377 " --> pdb=" O THR C 407 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL C 409 " --> pdb=" O SER C 375 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N SER C 373 " --> pdb=" O GLY C 411 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 333 through 335 removed outlier: 4.691A pdb=" N SER C 373 " --> pdb=" O GLY C 411 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL C 409 " --> pdb=" O SER C 375 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE C 377 " --> pdb=" O THR C 407 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR C 407 " --> pdb=" O PHE C 377 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LEU C 379 " --> pdb=" O TYR C 405 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N TYR C 405 " --> pdb=" O LEU C 379 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 397 through 399 Processing sheet with id=AE7, first strand: chain 'C' and resid 353 through 358 removed outlier: 7.247A pdb=" N THR C 350 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA C 314 " --> pdb=" O THR C 350 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 537 through 539 Processing sheet with id=AE9, first strand: chain 'C' and resid 571 through 587 removed outlier: 6.946A pdb=" N GLU C 572 " --> pdb=" O ARG C 943 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ARG C 943 " --> pdb=" O GLU C 572 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N PHE C 941 " --> pdb=" O PRO C 574 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ALA C 576 " --> pdb=" O ASN C 939 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLY C 928 " --> pdb=" O THR C 924 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N THR C 924 " --> pdb=" O GLY C 928 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N PHE C 930 " --> pdb=" O THR C 922 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N THR C 922 " --> pdb=" O PHE C 930 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N MET C 932 " --> pdb=" O SER C 920 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N SER C 920 " --> pdb=" O MET C 932 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ALA C 934 " --> pdb=" O ILE C 918 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 592 through 595 removed outlier: 4.173A pdb=" N GLN C 592 " --> pdb=" O LEU C 720 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 991 through 994 Processing sheet with id=AF3, first strand: chain 'C' and resid 964 through 969 1078 hydrogen bonds defined for protein. 2874 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: 5.37 Time building geometry restraints manager: 2.55 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: 5199 1.32 - 1.45: 6468 1.45 - 1.58: 12897 1.58 - 1.71: 144 1.71 - 1.83: 180 Bond restraints: 24888 Sorted by residual: bond pdb=" N PRO C 59 " pdb=" CA PRO C 59 " ideal model delta sigma weight residual 1.474 1.438 0.036 7.40e-03 1.83e+04 2.31e+01 bond pdb=" N PRO B 59 " pdb=" CA PRO B 59 " ideal model delta sigma weight residual 1.474 1.439 0.035 7.40e-03 1.83e+04 2.26e+01 bond pdb=" N PRO A 59 " pdb=" CA PRO A 59 " ideal model delta sigma weight residual 1.474 1.439 0.035 7.40e-03 1.83e+04 2.25e+01 bond pdb=" C2 NAG D 2 " pdb=" N2 NAG D 2 " ideal model delta sigma weight residual 1.439 1.353 0.086 2.00e-02 2.50e+03 1.87e+01 bond pdb=" C2 NAG d 2 " pdb=" N2 NAG d 2 " ideal model delta sigma weight residual 1.439 1.353 0.086 2.00e-02 2.50e+03 1.87e+01 ... (remaining 24883 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.24: 33225 4.24 - 8.49: 711 8.49 - 12.73: 0 12.73 - 16.98: 0 16.98 - 21.22: 3 Bond angle restraints: 33939 Sorted by residual: angle pdb=" CD1 LEU B 453 " pdb=" CG LEU B 453 " pdb=" CD2 LEU B 453 " ideal model delta sigma weight residual 110.80 132.02 -21.22 2.20e+00 2.07e-01 9.31e+01 angle pdb=" CD1 LEU A 453 " pdb=" CG LEU A 453 " pdb=" CD2 LEU A 453 " ideal model delta sigma weight residual 110.80 131.99 -21.19 2.20e+00 2.07e-01 9.28e+01 angle pdb=" CD1 LEU C 453 " pdb=" CG LEU C 453 " pdb=" CD2 LEU C 453 " ideal model delta sigma weight residual 110.80 131.96 -21.16 2.20e+00 2.07e-01 9.25e+01 angle pdb=" C LYS B 338 " pdb=" N PRO B 339 " pdb=" CA PRO B 339 " ideal model delta sigma weight residual 119.32 127.75 -8.43 1.14e+00 7.69e-01 5.46e+01 angle pdb=" C LYS A 338 " pdb=" N PRO A 339 " pdb=" CA PRO A 339 " ideal model delta sigma weight residual 119.32 127.71 -8.39 1.14e+00 7.69e-01 5.42e+01 ... (remaining 33934 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.43: 16035 21.43 - 42.87: 624 42.87 - 64.30: 108 64.30 - 85.74: 213 85.74 - 107.17: 138 Dihedral angle restraints: 17118 sinusoidal: 8619 harmonic: 8499 Sorted by residual: dihedral pdb=" CB CYS C 433 " pdb=" SG CYS C 433 " pdb=" SG CYS C 484 " pdb=" CB CYS C 484 " ideal model delta sinusoidal sigma weight residual -86.00 -164.50 78.50 1 1.00e+01 1.00e-02 7.69e+01 dihedral pdb=" CB CYS A 433 " pdb=" SG CYS A 433 " pdb=" SG CYS A 484 " pdb=" CB CYS A 484 " ideal model delta sinusoidal sigma weight residual -86.00 -164.50 78.50 1 1.00e+01 1.00e-02 7.69e+01 dihedral pdb=" CB CYS B 433 " pdb=" SG CYS B 433 " pdb=" SG CYS B 484 " pdb=" CB CYS B 484 " ideal model delta sinusoidal sigma weight residual -86.00 -164.48 78.48 1 1.00e+01 1.00e-02 7.68e+01 ... (remaining 17115 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.153: 4244 0.153 - 0.306: 151 0.306 - 0.458: 123 0.458 - 0.611: 45 0.611 - 0.764: 3 Chirality restraints: 4566 Sorted by residual: chirality pdb=" C1 BMA m 3 " pdb=" O4 NAG m 2 " pdb=" C2 BMA m 3 " pdb=" O5 BMA m 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.22e+02 chirality pdb=" C1 BMA Z 3 " pdb=" O4 NAG Z 2 " pdb=" C2 BMA Z 3 " pdb=" O5 BMA Z 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.19e+02 chirality pdb=" C1 BMA M 3 " pdb=" O4 NAG M 2 " pdb=" C2 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.15e+02 ... (remaining 4563 not shown) Planarity restraints: 4167 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 114 " 0.064 2.00e-02 2.50e+03 3.42e-02 2.34e+01 pdb=" CG TYR A 114 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR A 114 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR A 114 " -0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR A 114 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR A 114 " -0.019 2.00e-02 2.50e+03 pdb=" CZ TYR A 114 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 114 " 0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 114 " 0.064 2.00e-02 2.50e+03 3.41e-02 2.32e+01 pdb=" CG TYR B 114 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR B 114 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR B 114 " -0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR B 114 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR B 114 " -0.019 2.00e-02 2.50e+03 pdb=" CZ TYR B 114 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 114 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 114 " -0.064 2.00e-02 2.50e+03 3.40e-02 2.32e+01 pdb=" CG TYR C 114 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR C 114 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR C 114 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR C 114 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR C 114 " 0.019 2.00e-02 2.50e+03 pdb=" CZ TYR C 114 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR C 114 " -0.051 2.00e-02 2.50e+03 ... (remaining 4164 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 90 2.58 - 3.16: 22370 3.16 - 3.74: 36760 3.74 - 4.32: 54914 4.32 - 4.90: 87383 Nonbonded interactions: 201517 Sorted by model distance: nonbonded pdb=" O ASN A 169 " pdb=" OD1 ASN A 169 " model vdw 2.005 3.040 nonbonded pdb=" O ASN B 169 " pdb=" OD1 ASN B 169 " model vdw 2.006 3.040 nonbonded pdb=" O ASN C 169 " pdb=" OD1 ASN C 169 " model vdw 2.007 3.040 nonbonded pdb=" O ASN B 914 " pdb=" OD1 ASN B 914 " model vdw 2.060 3.040 nonbonded pdb=" O ASN A 914 " pdb=" OD1 ASN A 914 " model vdw 2.060 3.040 ... (remaining 201512 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'b' selection = chain 'd' selection = chain 'f' selection = chain 'o' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'R' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'e' selection = chain 'h' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' } ncs_group { reference = chain 'G' selection = chain 'P' selection = chain 'T' selection = chain 'c' selection = chain 'g' selection = chain 'p' } ncs_group { reference = chain 'I' selection = chain 'V' selection = chain 'i' } 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: 1.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 22.570 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.080 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: 0.000 Load rotamer database and sin/cos tables:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 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 : 0.019 0.086 25095 Z= 0.974 Angle : 1.413 21.223 34521 Z= 0.815 Chirality : 0.108 0.764 4566 Planarity : 0.006 0.034 4104 Dihedral : 18.523 107.169 11517 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.23 % Favored : 96.56 % Rotamer: Outliers : 0.35 % Allowed : 0.94 % Favored : 98.70 % 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 aren not related in a simple way. whole: 0.52 (0.16), residues: 2880 helix: 1.17 (0.19), residues: 693 sheet: 0.14 (0.18), residues: 675 loop : 0.18 (0.17), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 130 TYR 0.064 0.006 TYR A 114 PHE 0.024 0.004 PHE A 460 TRP 0.008 0.003 TRP C 396 HIS 0.006 0.001 HIS A 236 Details of bonding type rmsd covalent geometry : bond 0.01842 (24888) covalent geometry : angle 1.39130 (33939) SS BOND : bond 0.01835 ( 39) SS BOND : angle 3.07283 ( 78) hydrogen bonds : bond 0.16328 ( 991) hydrogen bonds : angle 7.96012 ( 2874) link_ALPHA1-2 : bond 0.04011 ( 9) link_ALPHA1-2 : angle 1.46917 ( 27) link_ALPHA1-3 : bond 0.03458 ( 12) link_ALPHA1-3 : angle 1.20073 ( 36) link_ALPHA1-6 : bond 0.03131 ( 12) link_ALPHA1-6 : angle 2.06955 ( 36) link_BETA1-4 : bond 0.03634 ( 72) link_BETA1-4 : angle 2.65821 ( 216) link_NAG-ASN : bond 0.02263 ( 63) link_NAG-ASN : angle 1.98873 ( 189) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 529 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 PHE cc_start: 0.7994 (m-80) cc_final: 0.7721 (m-80) REVERT: A 252 THR cc_start: 0.8447 (p) cc_final: 0.8124 (p) REVERT: A 621 ASN cc_start: 0.8192 (m-40) cc_final: 0.7989 (m110) REVERT: A 886 GLN cc_start: 0.8275 (mt0) cc_final: 0.8069 (mt0) REVERT: B 76 THR cc_start: 0.8874 (p) cc_final: 0.8617 (p) REVERT: B 770 VAL cc_start: 0.9263 (m) cc_final: 0.8898 (p) REVERT: C 76 THR cc_start: 0.9135 (p) cc_final: 0.8915 (p) REVERT: C 770 VAL cc_start: 0.9224 (m) cc_final: 0.8985 (p) outliers start: 9 outliers final: 7 residues processed: 538 average time/residue: 0.1684 time to fit residues: 141.8924 Evaluate side-chains 236 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 229 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 531 ASN Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 531 ASN Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain C residue 531 ASN Chi-restraints excluded: chain C residue 914 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 197 optimal weight: 0.2980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.6980 chunk 111 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 HIS A 589 GLN A 627 HIS A 712 GLN A 830 HIS A 895 GLN B 168 HIS B 712 GLN ** B 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 830 HIS B 961 GLN C 168 HIS C 589 GLN C 712 GLN C 808 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.117087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.088377 restraints weight = 41995.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.092432 restraints weight = 19387.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.094989 restraints weight = 12450.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.096492 restraints weight = 9607.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.097375 restraints weight = 8275.324| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 25095 Z= 0.179 Angle : 0.771 8.613 34521 Z= 0.369 Chirality : 0.047 0.188 4566 Planarity : 0.005 0.084 4104 Dihedral : 14.395 86.092 6527 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.71 % Favored : 97.26 % Rotamer: Outliers : 1.73 % Allowed : 7.52 % Favored : 90.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.16), residues: 2880 helix: 2.64 (0.20), residues: 669 sheet: 0.16 (0.19), residues: 669 loop : 0.30 (0.17), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 701 TYR 0.015 0.001 TYR A 468 PHE 0.017 0.002 PHE A 930 TRP 0.008 0.001 TRP C 396 HIS 0.009 0.001 HIS C 100 Details of bonding type rmsd covalent geometry : bond 0.00394 (24888) covalent geometry : angle 0.71742 (33939) SS BOND : bond 0.00259 ( 39) SS BOND : angle 0.78842 ( 78) hydrogen bonds : bond 0.05054 ( 991) hydrogen bonds : angle 5.63645 ( 2874) link_ALPHA1-2 : bond 0.00323 ( 9) link_ALPHA1-2 : angle 1.50458 ( 27) link_ALPHA1-3 : bond 0.00989 ( 12) link_ALPHA1-3 : angle 2.35329 ( 36) link_ALPHA1-6 : bond 0.00681 ( 12) link_ALPHA1-6 : angle 2.21978 ( 36) link_BETA1-4 : bond 0.01202 ( 72) link_BETA1-4 : angle 3.03746 ( 216) link_NAG-ASN : bond 0.00402 ( 63) link_NAG-ASN : angle 1.77335 ( 189) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 282 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 PHE cc_start: 0.8696 (m-80) cc_final: 0.8257 (m-80) REVERT: A 292 ARG cc_start: 0.7772 (mpt180) cc_final: 0.7231 (mmt-90) REVERT: A 388 MET cc_start: 0.8355 (mtt) cc_final: 0.7946 (mtt) REVERT: A 607 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.8637 (mpp80) REVERT: A 640 MET cc_start: 0.8857 (ttt) cc_final: 0.8598 (ttt) REVERT: A 884 MET cc_start: 0.8547 (mmt) cc_final: 0.7986 (mmt) REVERT: B 388 MET cc_start: 0.8529 (mtp) cc_final: 0.8320 (mtt) REVERT: B 607 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.8503 (mpp80) REVERT: B 1011 ASN cc_start: 0.8281 (t0) cc_final: 0.7970 (t0) REVERT: C 372 MET cc_start: 0.8226 (mtm) cc_final: 0.7957 (mtp) REVERT: C 388 MET cc_start: 0.8605 (mtp) cc_final: 0.8356 (mtt) REVERT: C 607 ARG cc_start: 0.8983 (OUTLIER) cc_final: 0.8482 (mpp80) REVERT: C 780 GLU cc_start: 0.7493 (tp30) cc_final: 0.6841 (tp30) outliers start: 44 outliers final: 22 residues processed: 315 average time/residue: 0.1600 time to fit residues: 79.8101 Evaluate side-chains 223 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 198 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 607 ARG Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 904 SER Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain B residue 607 ARG Chi-restraints excluded: chain B residue 836 SER Chi-restraints excluded: chain B residue 843 SER Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain B residue 904 SER Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain C residue 477 LYS Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 607 ARG Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 904 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 50 optimal weight: 2.9990 chunk 148 optimal weight: 0.6980 chunk 202 optimal weight: 0.9990 chunk 222 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 151 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 255 optimal weight: 1.9990 chunk 224 optimal weight: 0.6980 chunk 121 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 621 ASN A 772 GLN ** B 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 923 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.109741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.080183 restraints weight = 43143.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.083864 restraints weight = 20832.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.086206 restraints weight = 13611.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.087637 restraints weight = 10598.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.088478 restraints weight = 9149.455| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25095 Z= 0.181 Angle : 0.721 11.163 34521 Z= 0.339 Chirality : 0.046 0.253 4566 Planarity : 0.005 0.079 4104 Dihedral : 10.904 77.907 6515 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.09 % Allowed : 8.74 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.16), residues: 2880 helix: 2.84 (0.20), residues: 672 sheet: 0.02 (0.20), residues: 639 loop : 0.18 (0.16), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 84 TYR 0.014 0.001 TYR B 468 PHE 0.017 0.002 PHE B 930 TRP 0.004 0.001 TRP C 396 HIS 0.006 0.001 HIS A 100 Details of bonding type rmsd covalent geometry : bond 0.00394 (24888) covalent geometry : angle 0.66773 (33939) SS BOND : bond 0.00364 ( 39) SS BOND : angle 0.98411 ( 78) hydrogen bonds : bond 0.04589 ( 991) hydrogen bonds : angle 5.23117 ( 2874) link_ALPHA1-2 : bond 0.00343 ( 9) link_ALPHA1-2 : angle 1.42150 ( 27) link_ALPHA1-3 : bond 0.00998 ( 12) link_ALPHA1-3 : angle 2.00277 ( 36) link_ALPHA1-6 : bond 0.00881 ( 12) link_ALPHA1-6 : angle 1.61780 ( 36) link_BETA1-4 : bond 0.01163 ( 72) link_BETA1-4 : angle 2.80862 ( 216) link_NAG-ASN : bond 0.00459 ( 63) link_NAG-ASN : angle 2.01060 ( 189) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 223 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 607 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.8606 (mpp80) REVERT: A 727 GLU cc_start: 0.7760 (tm-30) cc_final: 0.7417 (tm-30) REVERT: A 798 ASP cc_start: 0.7743 (t0) cc_final: 0.7497 (t0) REVERT: A 884 MET cc_start: 0.8736 (mmt) cc_final: 0.8492 (mmt) REVERT: B 191 LEU cc_start: 0.9132 (tp) cc_final: 0.8539 (mp) REVERT: B 399 LEU cc_start: 0.9210 (tp) cc_final: 0.8952 (tt) REVERT: B 701 ARG cc_start: 0.8525 (ttp80) cc_final: 0.8153 (ttp80) REVERT: B 718 MET cc_start: 0.7361 (ptm) cc_final: 0.7072 (ptp) REVERT: B 1011 ASN cc_start: 0.8491 (t0) cc_final: 0.8151 (t0) REVERT: C 372 MET cc_start: 0.8257 (mtm) cc_final: 0.7985 (mtp) REVERT: C 607 ARG cc_start: 0.9055 (OUTLIER) cc_final: 0.8142 (mpp80) REVERT: C 701 ARG cc_start: 0.8546 (ttp80) cc_final: 0.8218 (ttp80) REVERT: C 1011 ASN cc_start: 0.8427 (t0) cc_final: 0.8189 (t0) outliers start: 53 outliers final: 26 residues processed: 262 average time/residue: 0.1548 time to fit residues: 66.1914 Evaluate side-chains 211 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 183 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 607 ARG Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain B residue 836 SER Chi-restraints excluded: chain B residue 843 SER Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 477 LYS Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 559 THR Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 607 ARG Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 904 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 270 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 218 optimal weight: 4.9990 chunk 148 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 95 optimal weight: 0.3980 chunk 110 optimal weight: 0.0170 chunk 231 optimal weight: 0.7980 chunk 73 optimal weight: 0.0980 chunk 87 optimal weight: 1.9990 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 621 ASN B 627 HIS C 883 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.110459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.081126 restraints weight = 43122.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.084752 restraints weight = 21311.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.087058 restraints weight = 14078.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.088459 restraints weight = 11032.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.089290 restraints weight = 9564.362| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25095 Z= 0.136 Angle : 0.662 9.846 34521 Z= 0.311 Chirality : 0.045 0.263 4566 Planarity : 0.004 0.082 4104 Dihedral : 9.242 71.358 6513 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.53 % Allowed : 10.35 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.16), residues: 2880 helix: 2.66 (0.20), residues: 690 sheet: 0.01 (0.20), residues: 654 loop : 0.17 (0.17), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 84 TYR 0.011 0.001 TYR A 222 PHE 0.013 0.001 PHE A 930 TRP 0.004 0.001 TRP C 396 HIS 0.003 0.001 HIS C 236 Details of bonding type rmsd covalent geometry : bond 0.00287 (24888) covalent geometry : angle 0.60422 (33939) SS BOND : bond 0.00264 ( 39) SS BOND : angle 0.82774 ( 78) hydrogen bonds : bond 0.04117 ( 991) hydrogen bonds : angle 4.95574 ( 2874) link_ALPHA1-2 : bond 0.00387 ( 9) link_ALPHA1-2 : angle 1.43497 ( 27) link_ALPHA1-3 : bond 0.01006 ( 12) link_ALPHA1-3 : angle 2.19999 ( 36) link_ALPHA1-6 : bond 0.00874 ( 12) link_ALPHA1-6 : angle 1.50635 ( 36) link_BETA1-4 : bond 0.01136 ( 72) link_BETA1-4 : angle 2.63222 ( 216) link_NAG-ASN : bond 0.00394 ( 63) link_NAG-ASN : angle 2.17984 ( 189) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 213 time to evaluate : 0.746 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 159 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7552 (mt-10) REVERT: A 292 ARG cc_start: 0.7463 (mmt-90) cc_final: 0.7033 (mmt-90) REVERT: A 545 CYS cc_start: 0.6131 (m) cc_final: 0.5909 (m) REVERT: A 607 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.8630 (mpp80) REVERT: A 701 ARG cc_start: 0.8194 (ttp80) cc_final: 0.7867 (ttp80) REVERT: A 703 MET cc_start: 0.9221 (tpp) cc_final: 0.8889 (tpp) REVERT: A 798 ASP cc_start: 0.7779 (t0) cc_final: 0.7506 (t0) REVERT: A 884 MET cc_start: 0.8826 (mmt) cc_final: 0.8587 (mmt) REVERT: A 1011 ASN cc_start: 0.8402 (t0) cc_final: 0.8009 (t0) REVERT: B 607 ARG cc_start: 0.9019 (OUTLIER) cc_final: 0.8632 (mpp80) REVERT: B 701 ARG cc_start: 0.8473 (ttp80) cc_final: 0.8103 (ttp80) REVERT: B 718 MET cc_start: 0.7241 (ptm) cc_final: 0.6974 (ptp) REVERT: B 1011 ASN cc_start: 0.8479 (t0) cc_final: 0.8173 (t0) REVERT: C 372 MET cc_start: 0.8250 (mtm) cc_final: 0.8001 (mtp) REVERT: C 607 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.8446 (mpp80) REVERT: C 701 ARG cc_start: 0.8512 (ttp80) cc_final: 0.8179 (ttp80) REVERT: C 854 GLU cc_start: 0.7511 (pm20) cc_final: 0.7203 (pm20) REVERT: C 884 MET cc_start: 0.8941 (tpp) cc_final: 0.8683 (mmt) outliers start: 39 outliers final: 24 residues processed: 242 average time/residue: 0.1500 time to fit residues: 58.6202 Evaluate side-chains 205 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 177 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 607 ARG Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain B residue 607 ARG Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain B residue 836 SER Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 477 LYS Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 559 THR Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 607 ARG Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 904 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 32 optimal weight: 2.9990 chunk 242 optimal weight: 0.0060 chunk 80 optimal weight: 0.9990 chunk 185 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 257 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 5 optimal weight: 8.9990 chunk 220 optimal weight: 2.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 621 ASN B 589 GLN C1011 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.109207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.079987 restraints weight = 43129.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.083546 restraints weight = 21358.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.085818 restraints weight = 14151.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.087188 restraints weight = 11119.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.087973 restraints weight = 9646.636| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 25095 Z= 0.159 Angle : 0.654 10.724 34521 Z= 0.307 Chirality : 0.044 0.265 4566 Planarity : 0.004 0.084 4104 Dihedral : 8.444 65.036 6513 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.97 % Allowed : 10.70 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.16), residues: 2880 helix: 2.63 (0.20), residues: 693 sheet: -0.02 (0.20), residues: 657 loop : 0.13 (0.17), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 84 TYR 0.010 0.001 TYR A 222 PHE 0.013 0.001 PHE A 930 TRP 0.004 0.001 TRP C 973 HIS 0.003 0.001 HIS A 933 Details of bonding type rmsd covalent geometry : bond 0.00351 (24888) covalent geometry : angle 0.59710 (33939) SS BOND : bond 0.00293 ( 39) SS BOND : angle 0.83288 ( 78) hydrogen bonds : bond 0.04064 ( 991) hydrogen bonds : angle 4.89926 ( 2874) link_ALPHA1-2 : bond 0.00408 ( 9) link_ALPHA1-2 : angle 1.38780 ( 27) link_ALPHA1-3 : bond 0.01004 ( 12) link_ALPHA1-3 : angle 2.33214 ( 36) link_ALPHA1-6 : bond 0.00823 ( 12) link_ALPHA1-6 : angle 1.49714 ( 36) link_BETA1-4 : bond 0.01110 ( 72) link_BETA1-4 : angle 2.62032 ( 216) link_NAG-ASN : bond 0.00320 ( 63) link_NAG-ASN : angle 2.08015 ( 189) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 192 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7419 (mt-10) REVERT: A 191 LEU cc_start: 0.9180 (tp) cc_final: 0.8682 (mp) REVERT: A 607 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.8565 (mpp80) REVERT: A 701 ARG cc_start: 0.8241 (ttp80) cc_final: 0.7889 (ttp80) REVERT: A 703 MET cc_start: 0.9204 (tpp) cc_final: 0.8840 (tpp) REVERT: A 798 ASP cc_start: 0.7768 (t0) cc_final: 0.7489 (t0) REVERT: A 1011 ASN cc_start: 0.8346 (t0) cc_final: 0.8104 (t0) REVERT: B 191 LEU cc_start: 0.9180 (tp) cc_final: 0.8741 (mp) REVERT: B 607 ARG cc_start: 0.9050 (OUTLIER) cc_final: 0.8831 (mmm-85) REVERT: B 701 ARG cc_start: 0.8481 (ttp80) cc_final: 0.8124 (ttp80) REVERT: B 718 MET cc_start: 0.7224 (ptm) cc_final: 0.6934 (ptp) REVERT: B 1011 ASN cc_start: 0.8459 (t0) cc_final: 0.8160 (t0) REVERT: C 372 MET cc_start: 0.8288 (mtm) cc_final: 0.8016 (mtp) REVERT: C 607 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8495 (mpp80) REVERT: C 701 ARG cc_start: 0.8527 (ttp80) cc_final: 0.8211 (ttp80) REVERT: C 854 GLU cc_start: 0.7452 (pm20) cc_final: 0.7001 (pm20) REVERT: C 884 MET cc_start: 0.8984 (tpp) cc_final: 0.8710 (mmt) outliers start: 50 outliers final: 35 residues processed: 233 average time/residue: 0.1505 time to fit residues: 57.5237 Evaluate side-chains 204 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 165 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 607 ARG Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain B residue 607 ARG Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain B residue 836 SER Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 477 LYS Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 559 THR Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 607 ARG Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 904 SER Chi-restraints excluded: chain C residue 985 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 40 optimal weight: 0.0000 chunk 269 optimal weight: 0.9990 chunk 216 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 211 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 621 ASN B 823 GLN C 847 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.108641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.079278 restraints weight = 43314.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.082923 restraints weight = 21003.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.085244 restraints weight = 13737.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.086653 restraints weight = 10712.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.087479 restraints weight = 9269.544| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25095 Z= 0.155 Angle : 0.645 9.062 34521 Z= 0.303 Chirality : 0.045 0.269 4566 Planarity : 0.004 0.083 4104 Dihedral : 7.783 57.713 6513 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.36 % Allowed : 10.86 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.16), residues: 2880 helix: 2.59 (0.20), residues: 696 sheet: -0.09 (0.21), residues: 597 loop : 0.11 (0.16), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 84 TYR 0.013 0.001 TYR C 222 PHE 0.012 0.001 PHE C 237 TRP 0.004 0.001 TRP C 973 HIS 0.003 0.001 HIS A 933 Details of bonding type rmsd covalent geometry : bond 0.00340 (24888) covalent geometry : angle 0.58905 (33939) SS BOND : bond 0.00315 ( 39) SS BOND : angle 0.80245 ( 78) hydrogen bonds : bond 0.03962 ( 991) hydrogen bonds : angle 4.82148 ( 2874) link_ALPHA1-2 : bond 0.00468 ( 9) link_ALPHA1-2 : angle 1.36911 ( 27) link_ALPHA1-3 : bond 0.01031 ( 12) link_ALPHA1-3 : angle 2.41540 ( 36) link_ALPHA1-6 : bond 0.00823 ( 12) link_ALPHA1-6 : angle 1.47111 ( 36) link_BETA1-4 : bond 0.01107 ( 72) link_BETA1-4 : angle 2.57196 ( 216) link_NAG-ASN : bond 0.00357 ( 63) link_NAG-ASN : angle 2.02149 ( 189) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 184 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7412 (mt-10) REVERT: A 701 ARG cc_start: 0.8281 (ttp80) cc_final: 0.7959 (ttp80) REVERT: A 703 MET cc_start: 0.9196 (tpp) cc_final: 0.8776 (tpp) REVERT: A 884 MET cc_start: 0.9009 (tpp) cc_final: 0.8692 (mmt) REVERT: A 936 LEU cc_start: 0.8744 (tt) cc_final: 0.8348 (mt) REVERT: B 607 ARG cc_start: 0.9056 (OUTLIER) cc_final: 0.8814 (mmm-85) REVERT: B 701 ARG cc_start: 0.8490 (ttp80) cc_final: 0.8113 (ttp80) REVERT: B 718 MET cc_start: 0.7252 (ptm) cc_final: 0.6949 (ptp) REVERT: B 780 GLU cc_start: 0.7847 (tp30) cc_final: 0.7157 (tp30) REVERT: B 987 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.7952 (ptm-80) REVERT: B 1011 ASN cc_start: 0.8525 (t0) cc_final: 0.8245 (t0) REVERT: C 59 PRO cc_start: 0.8170 (Cg_exo) cc_final: 0.7947 (Cg_endo) REVERT: C 372 MET cc_start: 0.8282 (mtm) cc_final: 0.7998 (mtp) REVERT: C 607 ARG cc_start: 0.9084 (OUTLIER) cc_final: 0.8681 (mpp80) REVERT: C 701 ARG cc_start: 0.8531 (ttp80) cc_final: 0.8228 (ttp80) REVERT: C 854 GLU cc_start: 0.7170 (pm20) cc_final: 0.6844 (pm20) REVERT: C 884 MET cc_start: 0.8998 (tpp) cc_final: 0.8712 (mmt) outliers start: 60 outliers final: 37 residues processed: 232 average time/residue: 0.1567 time to fit residues: 59.2750 Evaluate side-chains 202 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 161 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 286 LYS Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain B residue 607 ARG Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 727 GLU Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain B residue 836 SER Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain B residue 987 ARG Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 477 LYS Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 559 THR Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 607 ARG Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 985 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 191 optimal weight: 0.8980 chunk 138 optimal weight: 1.9990 chunk 263 optimal weight: 0.9990 chunk 221 optimal weight: 0.7980 chunk 215 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 73 optimal weight: 0.5980 chunk 113 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 621 ASN A1011 ASN B 823 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.108046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.078851 restraints weight = 43144.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.082366 restraints weight = 21484.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.084610 restraints weight = 14258.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.085966 restraints weight = 11199.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.086799 restraints weight = 9740.983| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 25095 Z= 0.169 Angle : 0.651 8.853 34521 Z= 0.307 Chirality : 0.045 0.269 4566 Planarity : 0.004 0.073 4104 Dihedral : 7.255 50.608 6513 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.28 % Allowed : 11.41 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.16), residues: 2880 helix: 2.41 (0.20), residues: 711 sheet: -0.08 (0.21), residues: 621 loop : 0.06 (0.17), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 943 TYR 0.011 0.001 TYR B 222 PHE 0.014 0.001 PHE B 742 TRP 0.006 0.001 TRP C 973 HIS 0.005 0.001 HIS C 100 Details of bonding type rmsd covalent geometry : bond 0.00377 (24888) covalent geometry : angle 0.59614 (33939) SS BOND : bond 0.00353 ( 39) SS BOND : angle 0.79322 ( 78) hydrogen bonds : bond 0.03979 ( 991) hydrogen bonds : angle 4.82251 ( 2874) link_ALPHA1-2 : bond 0.00477 ( 9) link_ALPHA1-2 : angle 1.36781 ( 27) link_ALPHA1-3 : bond 0.01026 ( 12) link_ALPHA1-3 : angle 2.49455 ( 36) link_ALPHA1-6 : bond 0.00799 ( 12) link_ALPHA1-6 : angle 1.47139 ( 36) link_BETA1-4 : bond 0.01075 ( 72) link_BETA1-4 : angle 2.57254 ( 216) link_NAG-ASN : bond 0.00377 ( 63) link_NAG-ASN : angle 1.95446 ( 189) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 170 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7602 (mt-10) REVERT: A 191 LEU cc_start: 0.9176 (tp) cc_final: 0.8832 (mp) REVERT: A 316 MET cc_start: 0.8603 (mmm) cc_final: 0.8340 (mmm) REVERT: A 701 ARG cc_start: 0.8297 (ttp80) cc_final: 0.7981 (ttp80) REVERT: A 703 MET cc_start: 0.9133 (tpp) cc_final: 0.8671 (tpp) REVERT: A 884 MET cc_start: 0.9017 (tpp) cc_final: 0.8652 (mmt) REVERT: A 936 LEU cc_start: 0.8755 (tt) cc_final: 0.8386 (mt) REVERT: B 104 MET cc_start: 0.8232 (mtm) cc_final: 0.7799 (mtt) REVERT: B 191 LEU cc_start: 0.9125 (tp) cc_final: 0.8821 (mp) REVERT: B 701 ARG cc_start: 0.8393 (ttp80) cc_final: 0.8025 (ttp80) REVERT: B 718 MET cc_start: 0.7296 (ptm) cc_final: 0.6978 (ptp) REVERT: B 780 GLU cc_start: 0.7836 (tp30) cc_final: 0.7225 (tp30) REVERT: B 987 ARG cc_start: 0.9100 (OUTLIER) cc_final: 0.8003 (ptm-80) REVERT: B 1011 ASN cc_start: 0.8513 (t0) cc_final: 0.8246 (t0) REVERT: C 372 MET cc_start: 0.8290 (mtm) cc_final: 0.8020 (mtp) REVERT: C 607 ARG cc_start: 0.9032 (OUTLIER) cc_final: 0.8611 (mpp80) REVERT: C 701 ARG cc_start: 0.8590 (ttp80) cc_final: 0.8297 (ttp80) REVERT: C 703 MET cc_start: 0.9152 (tpp) cc_final: 0.8945 (tpp) REVERT: C 854 GLU cc_start: 0.7130 (pm20) cc_final: 0.6851 (pm20) REVERT: C 884 MET cc_start: 0.9007 (tpp) cc_final: 0.8716 (mmt) outliers start: 58 outliers final: 38 residues processed: 220 average time/residue: 0.1459 time to fit residues: 52.4573 Evaluate side-chains 202 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 161 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain B residue 836 SER Chi-restraints excluded: chain B residue 843 SER Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain B residue 987 ARG Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 477 LYS Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 559 THR Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 607 ARG Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain C residue 985 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 202 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 197 optimal weight: 0.7980 chunk 209 optimal weight: 0.8980 chunk 215 optimal weight: 2.9990 chunk 263 optimal weight: 0.8980 chunk 51 optimal weight: 0.4980 chunk 225 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 621 ASN B 823 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.108054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.078867 restraints weight = 43212.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.082480 restraints weight = 20705.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.084770 restraints weight = 13464.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.086191 restraints weight = 10468.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.087019 restraints weight = 9030.433| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 25095 Z= 0.157 Angle : 0.641 10.374 34521 Z= 0.303 Chirality : 0.045 0.263 4566 Planarity : 0.004 0.069 4104 Dihedral : 6.967 47.849 6513 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.05 % Allowed : 11.73 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.16), residues: 2880 helix: 2.35 (0.20), residues: 711 sheet: -0.10 (0.21), residues: 621 loop : 0.04 (0.17), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 84 TYR 0.011 0.001 TYR B 222 PHE 0.012 0.001 PHE A 930 TRP 0.006 0.001 TRP C 973 HIS 0.003 0.001 HIS A 100 Details of bonding type rmsd covalent geometry : bond 0.00348 (24888) covalent geometry : angle 0.58803 (33939) SS BOND : bond 0.00319 ( 39) SS BOND : angle 0.80200 ( 78) hydrogen bonds : bond 0.03885 ( 991) hydrogen bonds : angle 4.77799 ( 2874) link_ALPHA1-2 : bond 0.00485 ( 9) link_ALPHA1-2 : angle 1.35540 ( 27) link_ALPHA1-3 : bond 0.01056 ( 12) link_ALPHA1-3 : angle 2.44250 ( 36) link_ALPHA1-6 : bond 0.00805 ( 12) link_ALPHA1-6 : angle 1.43842 ( 36) link_BETA1-4 : bond 0.01094 ( 72) link_BETA1-4 : angle 2.54174 ( 216) link_NAG-ASN : bond 0.00393 ( 63) link_NAG-ASN : angle 1.89000 ( 189) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 180 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7465 (mt-10) REVERT: A 191 LEU cc_start: 0.9161 (tp) cc_final: 0.8725 (mp) REVERT: A 316 MET cc_start: 0.8645 (mmm) cc_final: 0.8359 (mmm) REVERT: A 701 ARG cc_start: 0.8347 (ttp80) cc_final: 0.8058 (ttp80) REVERT: A 703 MET cc_start: 0.9202 (tpp) cc_final: 0.8721 (tpp) REVERT: A 884 MET cc_start: 0.9014 (tpp) cc_final: 0.8673 (mmt) REVERT: A 936 LEU cc_start: 0.8698 (tt) cc_final: 0.8369 (mt) REVERT: B 104 MET cc_start: 0.8244 (mtm) cc_final: 0.7797 (mtt) REVERT: B 568 ASP cc_start: 0.8650 (m-30) cc_final: 0.8337 (m-30) REVERT: B 607 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.8843 (mmm-85) REVERT: B 701 ARG cc_start: 0.8296 (ttp80) cc_final: 0.7913 (ttp80) REVERT: B 718 MET cc_start: 0.7218 (ptm) cc_final: 0.6905 (ptp) REVERT: B 780 GLU cc_start: 0.7907 (tp30) cc_final: 0.7299 (tp30) REVERT: B 987 ARG cc_start: 0.9109 (OUTLIER) cc_final: 0.7956 (ptm-80) REVERT: B 1011 ASN cc_start: 0.8568 (t0) cc_final: 0.8324 (t0) REVERT: C 372 MET cc_start: 0.8267 (mtm) cc_final: 0.7984 (mtp) REVERT: C 607 ARG cc_start: 0.9077 (OUTLIER) cc_final: 0.8643 (mpp80) REVERT: C 640 MET cc_start: 0.9077 (ttp) cc_final: 0.8836 (tmm) REVERT: C 701 ARG cc_start: 0.8583 (ttp80) cc_final: 0.8278 (ttp80) REVERT: C 731 MET cc_start: 0.8359 (mtp) cc_final: 0.8015 (mtm) REVERT: C 740 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.8278 (mtt) REVERT: C 854 GLU cc_start: 0.7086 (pm20) cc_final: 0.6836 (pm20) REVERT: C 884 MET cc_start: 0.9002 (tpp) cc_final: 0.8738 (mmt) outliers start: 52 outliers final: 36 residues processed: 225 average time/residue: 0.1596 time to fit residues: 58.0119 Evaluate side-chains 204 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 163 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain B residue 607 ARG Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain B residue 836 SER Chi-restraints excluded: chain B residue 843 SER Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain B residue 987 ARG Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 477 LYS Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 559 THR Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 607 ARG Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 985 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 150 optimal weight: 0.5980 chunk 262 optimal weight: 0.9990 chunk 280 optimal weight: 0.8980 chunk 139 optimal weight: 3.9990 chunk 97 optimal weight: 0.5980 chunk 5 optimal weight: 0.2980 chunk 25 optimal weight: 3.9990 chunk 164 optimal weight: 0.9980 chunk 159 optimal weight: 3.9990 chunk 208 optimal weight: 0.9980 chunk 95 optimal weight: 0.0870 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 621 ASN A 824 GLN B 772 GLN B 823 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.110429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.080911 restraints weight = 43248.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.084595 restraints weight = 20984.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.086964 restraints weight = 13720.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.088441 restraints weight = 10679.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.089266 restraints weight = 9203.192| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25095 Z= 0.134 Angle : 0.626 12.365 34521 Z= 0.294 Chirality : 0.044 0.251 4566 Planarity : 0.004 0.065 4104 Dihedral : 6.686 47.615 6513 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.73 % Allowed : 12.16 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.16), residues: 2880 helix: 2.42 (0.20), residues: 711 sheet: -0.08 (0.21), residues: 618 loop : 0.05 (0.17), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 84 TYR 0.009 0.001 TYR A 222 PHE 0.012 0.001 PHE C 206 TRP 0.006 0.001 TRP A 973 HIS 0.004 0.001 HIS C 100 Details of bonding type rmsd covalent geometry : bond 0.00292 (24888) covalent geometry : angle 0.57404 (33939) SS BOND : bond 0.00256 ( 39) SS BOND : angle 0.75878 ( 78) hydrogen bonds : bond 0.03746 ( 991) hydrogen bonds : angle 4.72438 ( 2874) link_ALPHA1-2 : bond 0.00549 ( 9) link_ALPHA1-2 : angle 1.37043 ( 27) link_ALPHA1-3 : bond 0.01071 ( 12) link_ALPHA1-3 : angle 2.36118 ( 36) link_ALPHA1-6 : bond 0.00822 ( 12) link_ALPHA1-6 : angle 1.40187 ( 36) link_BETA1-4 : bond 0.01101 ( 72) link_BETA1-4 : angle 2.51884 ( 216) link_NAG-ASN : bond 0.00402 ( 63) link_NAG-ASN : angle 1.80237 ( 189) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 184 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 TYR cc_start: 0.7478 (m-80) cc_final: 0.7040 (m-80) REVERT: A 159 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7401 (mt-10) REVERT: A 191 LEU cc_start: 0.9155 (tp) cc_final: 0.8668 (mp) REVERT: A 701 ARG cc_start: 0.8369 (ttp80) cc_final: 0.8086 (ttp80) REVERT: A 703 MET cc_start: 0.9174 (tpp) cc_final: 0.8675 (tpp) REVERT: A 884 MET cc_start: 0.9001 (tpp) cc_final: 0.8553 (mmt) REVERT: A 936 LEU cc_start: 0.8661 (tt) cc_final: 0.8364 (mt) REVERT: B 104 MET cc_start: 0.8252 (mtm) cc_final: 0.7881 (mtm) REVERT: B 568 ASP cc_start: 0.8666 (m-30) cc_final: 0.8378 (m-30) REVERT: B 701 ARG cc_start: 0.8277 (ttp80) cc_final: 0.7900 (ttp80) REVERT: B 718 MET cc_start: 0.7165 (ptm) cc_final: 0.6860 (ptp) REVERT: B 780 GLU cc_start: 0.7851 (tp30) cc_final: 0.6872 (tp30) REVERT: B 980 MET cc_start: 0.8175 (mtp) cc_final: 0.7966 (mtm) REVERT: B 987 ARG cc_start: 0.9118 (OUTLIER) cc_final: 0.7948 (ptm-80) REVERT: C 252 THR cc_start: 0.9497 (OUTLIER) cc_final: 0.9270 (t) REVERT: C 372 MET cc_start: 0.8267 (mtm) cc_final: 0.8000 (mtp) REVERT: C 461 THR cc_start: 0.8801 (p) cc_final: 0.8573 (t) REVERT: C 607 ARG cc_start: 0.9091 (OUTLIER) cc_final: 0.8672 (mpp80) REVERT: C 640 MET cc_start: 0.9208 (ttp) cc_final: 0.8937 (tmm) REVERT: C 701 ARG cc_start: 0.8532 (ttp80) cc_final: 0.8229 (ttp80) REVERT: C 740 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.8292 (mtt) REVERT: C 854 GLU cc_start: 0.7068 (pm20) cc_final: 0.6841 (pm20) REVERT: C 884 MET cc_start: 0.9022 (tpp) cc_final: 0.8783 (mmt) outliers start: 44 outliers final: 34 residues processed: 221 average time/residue: 0.1476 time to fit residues: 53.5219 Evaluate side-chains 207 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 168 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain B residue 836 SER Chi-restraints excluded: chain B residue 843 SER Chi-restraints excluded: chain B residue 987 ARG Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 477 LYS Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 559 THR Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 607 ARG Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 985 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 180 optimal weight: 0.9990 chunk 82 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 118 optimal weight: 0.5980 chunk 246 optimal weight: 0.7980 chunk 191 optimal weight: 0.0870 chunk 69 optimal weight: 1.9990 chunk 148 optimal weight: 0.6980 chunk 235 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 621 ASN B 823 GLN B1011 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.108724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.079560 restraints weight = 43006.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.083168 restraints weight = 20656.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.085487 restraints weight = 13438.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.086917 restraints weight = 10446.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.087772 restraints weight = 8991.877| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25095 Z= 0.141 Angle : 0.632 13.851 34521 Z= 0.298 Chirality : 0.044 0.241 4566 Planarity : 0.004 0.064 4104 Dihedral : 6.544 47.242 6513 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.73 % Allowed : 12.16 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.16), residues: 2880 helix: 2.58 (0.20), residues: 693 sheet: -0.12 (0.21), residues: 627 loop : 0.01 (0.17), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 84 TYR 0.010 0.001 TYR C 259 PHE 0.012 0.001 PHE C 641 TRP 0.007 0.001 TRP A 973 HIS 0.004 0.001 HIS C 100 Details of bonding type rmsd covalent geometry : bond 0.00309 (24888) covalent geometry : angle 0.58063 (33939) SS BOND : bond 0.00257 ( 39) SS BOND : angle 0.76659 ( 78) hydrogen bonds : bond 0.03729 ( 991) hydrogen bonds : angle 4.71399 ( 2874) link_ALPHA1-2 : bond 0.00562 ( 9) link_ALPHA1-2 : angle 1.38089 ( 27) link_ALPHA1-3 : bond 0.01052 ( 12) link_ALPHA1-3 : angle 2.35425 ( 36) link_ALPHA1-6 : bond 0.00809 ( 12) link_ALPHA1-6 : angle 1.39859 ( 36) link_BETA1-4 : bond 0.01090 ( 72) link_BETA1-4 : angle 2.51447 ( 216) link_NAG-ASN : bond 0.00387 ( 63) link_NAG-ASN : angle 1.78103 ( 189) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 172 time to evaluate : 0.805 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 123 TYR cc_start: 0.7544 (m-80) cc_final: 0.7119 (m-80) REVERT: A 159 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7406 (mt-10) REVERT: A 701 ARG cc_start: 0.8370 (ttp80) cc_final: 0.8142 (ttp80) REVERT: A 703 MET cc_start: 0.9183 (tpp) cc_final: 0.8672 (tpp) REVERT: A 884 MET cc_start: 0.9001 (tpp) cc_final: 0.8545 (mmt) REVERT: A 936 LEU cc_start: 0.8642 (tt) cc_final: 0.8336 (mt) REVERT: B 104 MET cc_start: 0.8270 (mtm) cc_final: 0.7825 (mtt) REVERT: B 568 ASP cc_start: 0.8628 (m-30) cc_final: 0.8343 (m-30) REVERT: B 701 ARG cc_start: 0.8242 (ttp80) cc_final: 0.7839 (ttp80) REVERT: B 718 MET cc_start: 0.7174 (ptm) cc_final: 0.6874 (ptp) REVERT: B 780 GLU cc_start: 0.7882 (tp30) cc_final: 0.6883 (tp30) REVERT: B 980 MET cc_start: 0.8198 (mtp) cc_final: 0.7981 (mtm) REVERT: B 987 ARG cc_start: 0.9123 (OUTLIER) cc_final: 0.7976 (ptm-80) REVERT: C 252 THR cc_start: 0.9510 (OUTLIER) cc_final: 0.9302 (t) REVERT: C 372 MET cc_start: 0.8274 (mtm) cc_final: 0.7853 (mtp) REVERT: C 461 THR cc_start: 0.8819 (p) cc_final: 0.8587 (t) REVERT: C 607 ARG cc_start: 0.9101 (OUTLIER) cc_final: 0.8665 (mpp80) REVERT: C 640 MET cc_start: 0.9256 (ttp) cc_final: 0.8980 (tmm) REVERT: C 701 ARG cc_start: 0.8499 (ttp80) cc_final: 0.8210 (ttp80) REVERT: C 731 MET cc_start: 0.8345 (mtp) cc_final: 0.8017 (mtm) REVERT: C 740 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.8321 (mtt) REVERT: C 854 GLU cc_start: 0.7037 (pm20) cc_final: 0.6805 (pm20) REVERT: C 884 MET cc_start: 0.9023 (tpp) cc_final: 0.8775 (mmt) outliers start: 44 outliers final: 34 residues processed: 209 average time/residue: 0.1463 time to fit residues: 50.5684 Evaluate side-chains 204 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 165 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain B residue 836 SER Chi-restraints excluded: chain B residue 843 SER Chi-restraints excluded: chain B residue 987 ARG Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 559 THR Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 607 ARG Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 985 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 40 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 145 optimal weight: 0.8980 chunk 131 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 89 optimal weight: 0.0980 chunk 284 optimal weight: 0.9990 chunk 143 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 ASN B 823 GLN C 954 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.109663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.080625 restraints weight = 43131.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.084207 restraints weight = 20764.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.086534 restraints weight = 13563.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.087955 restraints weight = 10537.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.088788 restraints weight = 9078.537| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 25095 Z= 0.159 Angle : 0.639 13.995 34521 Z= 0.301 Chirality : 0.044 0.238 4566 Planarity : 0.004 0.064 4104 Dihedral : 6.437 47.905 6513 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.93 % Allowed : 12.28 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.16), residues: 2880 helix: 2.59 (0.20), residues: 690 sheet: -0.20 (0.21), residues: 642 loop : -0.07 (0.17), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 84 TYR 0.011 0.001 TYR C 259 PHE 0.012 0.001 PHE A 930 TRP 0.008 0.001 TRP C 973 HIS 0.004 0.001 HIS C 100 Details of bonding type rmsd covalent geometry : bond 0.00356 (24888) covalent geometry : angle 0.58823 (33939) SS BOND : bond 0.00296 ( 39) SS BOND : angle 0.74431 ( 78) hydrogen bonds : bond 0.03800 ( 991) hydrogen bonds : angle 4.75234 ( 2874) link_ALPHA1-2 : bond 0.00558 ( 9) link_ALPHA1-2 : angle 1.38795 ( 27) link_ALPHA1-3 : bond 0.01024 ( 12) link_ALPHA1-3 : angle 2.38037 ( 36) link_ALPHA1-6 : bond 0.00785 ( 12) link_ALPHA1-6 : angle 1.39905 ( 36) link_BETA1-4 : bond 0.01074 ( 72) link_BETA1-4 : angle 2.52721 ( 216) link_NAG-ASN : bond 0.00385 ( 63) link_NAG-ASN : angle 1.78536 ( 189) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3528.43 seconds wall clock time: 62 minutes 24.22 seconds (3744.22 seconds total)