Starting phenix.real_space_refine on Sat Jun 21 09:07:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6bfu_7094/06_2025/6bfu_7094.cif Found real_map, /net/cci-nas-00/data/ceres_data/6bfu_7094/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6bfu_7094/06_2025/6bfu_7094.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6bfu_7094/06_2025/6bfu_7094.map" model { file = "/net/cci-nas-00/data/ceres_data/6bfu_7094/06_2025/6bfu_7094.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6bfu_7094/06_2025/6bfu_7094.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 15.16, per 1000 atoms: 0.62 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: 8.27 Conformation dependent library (CDL) restraints added in 2.9 seconds 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: 3.98 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: 10.94 Time building geometry restraints manager: 9.40 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: 0.00 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: 1.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.830 Check model and map are aligned: 0.170 Set scattering table: 0.230 Process input model: 60.110 Find NCS groups from input model: 1.420 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.730 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.008 0.003 TRP C 396 HIS 0.006 0.001 HIS A 236 PHE 0.024 0.004 PHE A 460 TYR 0.064 0.006 TYR A 114 ARG 0.006 0.001 ARG C 130 Details of bonding type rmsd link_NAG-ASN : bond 0.02263 ( 63) link_NAG-ASN : angle 1.98873 ( 189) 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_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) hydrogen bonds : bond 0.16328 ( 991) hydrogen bonds : angle 7.96012 ( 2874) SS BOND : bond 0.01835 ( 39) SS BOND : angle 3.07283 ( 78) covalent geometry : bond 0.01842 (24888) covalent geometry : angle 1.39130 (33939) *********************** 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 : 2.592 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: 0.8984 (p) outliers start: 9 outliers final: 7 residues processed: 538 average time/residue: 0.3704 time to fit residues: 313.2501 Evaluate side-chains 238 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 231 time to evaluate : 2.877 ------------------------------------------------------------------------------- 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 243 optimal weight: 0.8980 chunk 218 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 147 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 chunk 225 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 137 optimal weight: 0.7980 chunk 168 optimal weight: 0.6980 chunk 261 optimal weight: 4.9990 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 168 HIS A 589 GLN A 627 HIS A 712 GLN A 772 GLN A 830 HIS 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 = 0.3605 r_free = 0.3605 target = 0.116346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.087657 restraints weight = 41741.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.091667 restraints weight = 19370.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.094172 restraints weight = 12493.344| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25095 Z= 0.192 Angle : 0.773 8.500 34521 Z= 0.369 Chirality : 0.048 0.199 4566 Planarity : 0.005 0.084 4104 Dihedral : 14.092 85.879 6527 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.71 % Favored : 97.26 % Rotamer: Outliers : 1.85 % Allowed : 7.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.16), residues: 2880 helix: 2.74 (0.20), residues: 669 sheet: 0.17 (0.19), residues: 669 loop : 0.33 (0.17), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 396 HIS 0.009 0.001 HIS C 100 PHE 0.019 0.002 PHE A 930 TYR 0.012 0.001 TYR A 763 ARG 0.007 0.001 ARG A 292 Details of bonding type rmsd link_NAG-ASN : bond 0.00309 ( 63) link_NAG-ASN : angle 1.75060 ( 189) link_ALPHA1-6 : bond 0.00660 ( 12) link_ALPHA1-6 : angle 2.20040 ( 36) link_BETA1-4 : bond 0.01175 ( 72) link_BETA1-4 : angle 3.01516 ( 216) link_ALPHA1-2 : bond 0.00364 ( 9) link_ALPHA1-2 : angle 1.63259 ( 27) link_ALPHA1-3 : bond 0.01002 ( 12) link_ALPHA1-3 : angle 2.09621 ( 36) hydrogen bonds : bond 0.05111 ( 991) hydrogen bonds : angle 5.62783 ( 2874) SS BOND : bond 0.00292 ( 39) SS BOND : angle 0.78735 ( 78) covalent geometry : bond 0.00422 (24888) covalent geometry : angle 0.72036 (33939) *********************** 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 327 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 280 time to evaluate : 2.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 PHE cc_start: 0.8743 (m-80) cc_final: 0.8291 (m-80) REVERT: A 292 ARG cc_start: 0.7858 (mpt180) cc_final: 0.7573 (mmt-90) REVERT: A 388 MET cc_start: 0.8368 (mtt) cc_final: 0.7977 (mtt) REVERT: A 607 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.8690 (mpp80) REVERT: A 640 MET cc_start: 0.8865 (ttt) cc_final: 0.8612 (ttt) REVERT: A 884 MET cc_start: 0.8642 (mmt) cc_final: 0.8112 (mmt) REVERT: B 191 LEU cc_start: 0.9151 (tp) cc_final: 0.8570 (mp) REVERT: B 388 MET cc_start: 0.8554 (mtp) cc_final: 0.8343 (mtt) REVERT: B 1011 ASN cc_start: 0.8300 (t0) cc_final: 0.8040 (t0) REVERT: C 372 MET cc_start: 0.8237 (mtm) cc_final: 0.7993 (mtp) REVERT: C 388 MET cc_start: 0.8675 (mtp) cc_final: 0.8445 (mtt) REVERT: C 607 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.8495 (mpp80) REVERT: C 780 GLU cc_start: 0.7551 (tp30) cc_final: 0.6869 (tp30) outliers start: 47 outliers final: 26 residues processed: 316 average time/residue: 0.3634 time to fit residues: 182.0857 Evaluate side-chains 220 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 192 time to evaluate : 2.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 245 THR 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 99 ASN Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 245 THR 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 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 245 THR 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 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 906 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 52 optimal weight: 0.9980 chunk 120 optimal weight: 0.0980 chunk 60 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 chunk 204 optimal weight: 0.6980 chunk 105 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 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 621 ASN ** B 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 961 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.110082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.080800 restraints weight = 42839.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.084397 restraints weight = 21137.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.086702 restraints weight = 13984.710| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25095 Z= 0.169 Angle : 0.720 11.912 34521 Z= 0.338 Chirality : 0.047 0.332 4566 Planarity : 0.005 0.079 4104 Dihedral : 10.700 77.250 6515 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.13 % Allowed : 8.74 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.16), residues: 2880 helix: 2.87 (0.20), residues: 672 sheet: 0.07 (0.20), residues: 654 loop : 0.23 (0.17), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP C 396 HIS 0.005 0.001 HIS A 100 PHE 0.016 0.002 PHE B 930 TYR 0.013 0.001 TYR B 259 ARG 0.011 0.001 ARG C 84 Details of bonding type rmsd link_NAG-ASN : bond 0.00374 ( 63) link_NAG-ASN : angle 2.04231 ( 189) link_ALPHA1-6 : bond 0.00915 ( 12) link_ALPHA1-6 : angle 1.62910 ( 36) link_BETA1-4 : bond 0.01176 ( 72) link_BETA1-4 : angle 2.78577 ( 216) link_ALPHA1-2 : bond 0.00365 ( 9) link_ALPHA1-2 : angle 1.40271 ( 27) link_ALPHA1-3 : bond 0.01011 ( 12) link_ALPHA1-3 : angle 2.00636 ( 36) hydrogen bonds : bond 0.04585 ( 991) hydrogen bonds : angle 5.19991 ( 2874) SS BOND : bond 0.00322 ( 39) SS BOND : angle 1.03613 ( 78) covalent geometry : bond 0.00364 (24888) covalent geometry : angle 0.66550 (33939) *********************** 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 286 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 232 time to evaluate : 2.507 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: 0.8999 (OUTLIER) cc_final: 0.8578 (mpp80) REVERT: A 727 GLU cc_start: 0.7727 (tm-30) cc_final: 0.7353 (tm-30) REVERT: A 798 ASP cc_start: 0.7806 (t0) cc_final: 0.7583 (t0) REVERT: A 884 MET cc_start: 0.8758 (mmt) cc_final: 0.8389 (mmt) REVERT: A 1011 ASN cc_start: 0.8464 (t0) cc_final: 0.8183 (t0) REVERT: B 104 MET cc_start: 0.8550 (mtm) cc_final: 0.8316 (mtm) REVERT: B 607 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.8625 (mpp80) REVERT: B 701 ARG cc_start: 0.8532 (ttp80) cc_final: 0.8140 (ttp80) REVERT: B 718 MET cc_start: 0.7455 (ptm) cc_final: 0.7150 (ptp) REVERT: B 1011 ASN cc_start: 0.8551 (t0) cc_final: 0.8213 (t0) REVERT: C 372 MET cc_start: 0.8271 (mtm) cc_final: 0.8023 (mtp) REVERT: C 388 MET cc_start: 0.8597 (mtp) cc_final: 0.8389 (mtt) REVERT: C 607 ARG cc_start: 0.9057 (OUTLIER) cc_final: 0.8159 (mpp80) REVERT: C 622 ILE cc_start: 0.9136 (OUTLIER) cc_final: 0.8928 (mp) REVERT: C 701 ARG cc_start: 0.8512 (ttp80) cc_final: 0.8149 (ttp80) REVERT: C 884 MET cc_start: 0.8912 (tpp) cc_final: 0.8652 (mmt) REVERT: C 971 ASN cc_start: 0.8081 (t0) cc_final: 0.7875 (t0) REVERT: C 1011 ASN cc_start: 0.8464 (t0) cc_final: 0.8222 (t0) outliers start: 54 outliers final: 25 residues processed: 270 average time/residue: 0.3467 time to fit residues: 151.5162 Evaluate side-chains 212 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 183 time to evaluate : 2.540 ------------------------------------------------------------------------------- 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 620 SER 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 607 ARG 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 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 622 ILE 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 232 optimal weight: 0.9990 chunk 139 optimal weight: 0.9980 chunk 126 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 248 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 123 optimal weight: 0.9980 chunk 86 optimal weight: 0.3980 chunk 7 optimal weight: 0.8980 chunk 61 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 627 HIS C 883 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.109721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.080355 restraints weight = 43405.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.083962 restraints weight = 21422.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.086263 restraints weight = 14166.254| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 25095 Z= 0.150 Angle : 0.666 10.119 34521 Z= 0.314 Chirality : 0.045 0.266 4566 Planarity : 0.004 0.083 4104 Dihedral : 8.976 70.190 6513 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.65 % Allowed : 10.43 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.16), residues: 2880 helix: 2.66 (0.20), residues: 693 sheet: -0.01 (0.20), residues: 657 loop : 0.15 (0.17), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 973 HIS 0.006 0.001 HIS C 100 PHE 0.014 0.001 PHE A 930 TYR 0.011 0.001 TYR A 696 ARG 0.006 0.000 ARG C 84 Details of bonding type rmsd link_NAG-ASN : bond 0.00390 ( 63) link_NAG-ASN : angle 2.22681 ( 189) link_ALPHA1-6 : bond 0.00855 ( 12) link_ALPHA1-6 : angle 1.50862 ( 36) link_BETA1-4 : bond 0.01111 ( 72) link_BETA1-4 : angle 2.62172 ( 216) link_ALPHA1-2 : bond 0.00366 ( 9) link_ALPHA1-2 : angle 1.42551 ( 27) link_ALPHA1-3 : bond 0.01000 ( 12) link_ALPHA1-3 : angle 2.27976 ( 36) hydrogen bonds : bond 0.04140 ( 991) hydrogen bonds : angle 4.94775 ( 2874) SS BOND : bond 0.00297 ( 39) SS BOND : angle 0.84832 ( 78) covalent geometry : bond 0.00325 (24888) covalent geometry : angle 0.60673 (33939) *********************** 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 243 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 201 time to evaluate : 2.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8638 (mtm) cc_final: 0.8393 (mtm) REVERT: A 159 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7451 (mt-10) REVERT: A 292 ARG cc_start: 0.7540 (mmt-90) cc_final: 0.7191 (mmt-90) REVERT: A 607 ARG cc_start: 0.9029 (OUTLIER) cc_final: 0.8342 (mpp80) REVERT: A 701 ARG cc_start: 0.8195 (ttp80) cc_final: 0.7839 (ttp80) REVERT: A 703 MET cc_start: 0.9273 (tpp) cc_final: 0.8932 (tpp) REVERT: A 798 ASP cc_start: 0.7834 (t0) cc_final: 0.7578 (t0) REVERT: A 855 GLU cc_start: 0.6933 (mp0) cc_final: 0.6662 (mp0) REVERT: A 1011 ASN cc_start: 0.8456 (t0) cc_final: 0.8058 (t0) REVERT: B 607 ARG cc_start: 0.9042 (OUTLIER) cc_final: 0.8666 (mpp80) REVERT: B 701 ARG cc_start: 0.8492 (ttp80) cc_final: 0.8107 (ttp80) REVERT: B 718 MET cc_start: 0.7325 (ptm) cc_final: 0.7014 (ptp) REVERT: B 1011 ASN cc_start: 0.8524 (t0) cc_final: 0.8204 (t0) REVERT: C 372 MET cc_start: 0.8306 (mtm) cc_final: 0.8050 (mtp) REVERT: C 701 ARG cc_start: 0.8519 (ttp80) cc_final: 0.8162 (ttp80) REVERT: C 884 MET cc_start: 0.8955 (tpp) cc_final: 0.8683 (mmt) REVERT: C 971 ASN cc_start: 0.8135 (t0) cc_final: 0.7872 (t0) REVERT: C 1011 ASN cc_start: 0.8398 (t0) cc_final: 0.8165 (t0) outliers start: 42 outliers final: 25 residues processed: 232 average time/residue: 0.3210 time to fit residues: 122.0382 Evaluate side-chains 204 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 176 time to evaluate : 2.387 ------------------------------------------------------------------------------- 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 617 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 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 836 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 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 164 optimal weight: 0.9990 chunk 234 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 238 optimal weight: 0.0570 chunk 110 optimal weight: 3.9990 chunk 254 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 chunk 224 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 3 optimal weight: 0.3980 chunk 160 optimal weight: 1.9990 overall best weight: 0.6702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 589 GLN ** B 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 627 HIS C 847 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.109014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.079719 restraints weight = 43293.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.083261 restraints weight = 21426.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.085531 restraints weight = 14194.573| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 25095 Z= 0.156 Angle : 0.649 9.711 34521 Z= 0.306 Chirality : 0.045 0.269 4566 Planarity : 0.004 0.081 4104 Dihedral : 8.181 62.624 6513 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.05 % Allowed : 10.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.16), residues: 2880 helix: 2.49 (0.20), residues: 711 sheet: 0.10 (0.20), residues: 642 loop : 0.08 (0.17), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 973 HIS 0.004 0.001 HIS A 933 PHE 0.014 0.001 PHE A 460 TYR 0.012 0.001 TYR C 222 ARG 0.006 0.000 ARG C 84 Details of bonding type rmsd link_NAG-ASN : bond 0.00345 ( 63) link_NAG-ASN : angle 2.11150 ( 189) link_ALPHA1-6 : bond 0.00825 ( 12) link_ALPHA1-6 : angle 1.49325 ( 36) link_BETA1-4 : bond 0.01114 ( 72) link_BETA1-4 : angle 2.61179 ( 216) link_ALPHA1-2 : bond 0.00426 ( 9) link_ALPHA1-2 : angle 1.36626 ( 27) link_ALPHA1-3 : bond 0.01022 ( 12) link_ALPHA1-3 : angle 2.34891 ( 36) hydrogen bonds : bond 0.04028 ( 991) hydrogen bonds : angle 4.85812 ( 2874) SS BOND : bond 0.00307 ( 39) SS BOND : angle 0.79172 ( 78) covalent geometry : bond 0.00341 (24888) covalent geometry : angle 0.59074 (33939) *********************** 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 238 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 186 time to evaluate : 2.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7437 (mt-10) REVERT: A 191 LEU cc_start: 0.9199 (tp) cc_final: 0.8769 (mp) REVERT: A 292 ARG cc_start: 0.7576 (mmt-90) cc_final: 0.7283 (mmt-90) REVERT: A 607 ARG cc_start: 0.9077 (OUTLIER) cc_final: 0.8821 (mpp80) REVERT: A 701 ARG cc_start: 0.8232 (ttp80) cc_final: 0.7847 (ttp80) REVERT: A 703 MET cc_start: 0.9268 (tpp) cc_final: 0.8872 (tpp) REVERT: A 798 ASP cc_start: 0.7743 (t0) cc_final: 0.7531 (t0) REVERT: A 884 MET cc_start: 0.9011 (tpp) cc_final: 0.8689 (mmt) REVERT: A 1011 ASN cc_start: 0.8369 (t0) cc_final: 0.8084 (t0) REVERT: B 191 LEU cc_start: 0.9183 (tp) cc_final: 0.8759 (mp) REVERT: B 607 ARG cc_start: 0.9042 (OUTLIER) cc_final: 0.8815 (mmm-85) REVERT: B 701 ARG cc_start: 0.8503 (ttp80) cc_final: 0.8123 (ttp80) REVERT: B 780 GLU cc_start: 0.7870 (tp30) cc_final: 0.7243 (tp30) REVERT: B 1011 ASN cc_start: 0.8546 (t0) cc_final: 0.8246 (t0) REVERT: C 372 MET cc_start: 0.8297 (mtm) cc_final: 0.8029 (mtp) REVERT: C 607 ARG cc_start: 0.9026 (OUTLIER) cc_final: 0.8627 (mpp80) REVERT: C 701 ARG cc_start: 0.8531 (ttp80) cc_final: 0.8193 (ttp80) REVERT: C 884 MET cc_start: 0.8990 (tpp) cc_final: 0.8700 (mmt) REVERT: C 971 ASN cc_start: 0.8165 (t0) cc_final: 0.7957 (t0) outliers start: 52 outliers final: 36 residues processed: 230 average time/residue: 0.3422 time to fit residues: 127.2452 Evaluate side-chains 198 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 158 time to evaluate : 2.422 ------------------------------------------------------------------------------- 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 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 620 SER 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 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 843 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 531 ASN 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 985 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 253 optimal weight: 0.5980 chunk 228 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 104 optimal weight: 0.8980 chunk 270 optimal weight: 0.4980 chunk 197 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 180 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 824 GLN ** B 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1011 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.108454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.079111 restraints weight = 43408.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.082616 restraints weight = 21567.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.084870 restraints weight = 14357.634| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 25095 Z= 0.164 Angle : 0.651 8.732 34521 Z= 0.307 Chirality : 0.045 0.270 4566 Planarity : 0.004 0.081 4104 Dihedral : 7.562 55.343 6513 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.36 % Allowed : 11.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.16), residues: 2880 helix: 2.61 (0.20), residues: 693 sheet: 0.00 (0.20), residues: 657 loop : 0.08 (0.17), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 973 HIS 0.003 0.001 HIS A 933 PHE 0.013 0.001 PHE B 577 TYR 0.010 0.001 TYR C 876 ARG 0.007 0.000 ARG B 888 Details of bonding type rmsd link_NAG-ASN : bond 0.00448 ( 63) link_NAG-ASN : angle 2.00832 ( 189) link_ALPHA1-6 : bond 0.00812 ( 12) link_ALPHA1-6 : angle 1.47344 ( 36) link_BETA1-4 : bond 0.01088 ( 72) link_BETA1-4 : angle 2.56473 ( 216) link_ALPHA1-2 : bond 0.00467 ( 9) link_ALPHA1-2 : angle 1.37071 ( 27) link_ALPHA1-3 : bond 0.01007 ( 12) link_ALPHA1-3 : angle 2.45492 ( 36) hydrogen bonds : bond 0.03985 ( 991) hydrogen bonds : angle 4.82050 ( 2874) SS BOND : bond 0.00294 ( 39) SS BOND : angle 0.76276 ( 78) covalent geometry : bond 0.00366 (24888) covalent geometry : angle 0.59573 (33939) *********************** 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 246 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 186 time to evaluate : 2.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7583 (mt-10) REVERT: A 701 ARG cc_start: 0.8265 (ttp80) cc_final: 0.7920 (ttp80) REVERT: A 703 MET cc_start: 0.9261 (tpp) cc_final: 0.8829 (tpp) REVERT: A 884 MET cc_start: 0.9020 (tpp) cc_final: 0.8660 (mmt) REVERT: A 936 LEU cc_start: 0.8761 (tt) cc_final: 0.8395 (mt) REVERT: B 607 ARG cc_start: 0.9071 (OUTLIER) cc_final: 0.8811 (mmm-85) REVERT: B 701 ARG cc_start: 0.8384 (ttp80) cc_final: 0.8030 (ttp80) REVERT: B 780 GLU cc_start: 0.7917 (tp30) cc_final: 0.7275 (tp30) REVERT: B 860 GLN cc_start: 0.8085 (tt0) cc_final: 0.7867 (tt0) REVERT: B 987 ARG cc_start: 0.9110 (OUTLIER) cc_final: 0.7979 (ptm-80) REVERT: B 1011 ASN cc_start: 0.8511 (t0) cc_final: 0.8231 (t0) REVERT: C 59 PRO cc_start: 0.8151 (Cg_exo) cc_final: 0.7933 (Cg_endo) REVERT: C 372 MET cc_start: 0.8305 (mtm) cc_final: 0.8044 (mtp) REVERT: C 387 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7505 (mt-10) REVERT: C 607 ARG cc_start: 0.9075 (OUTLIER) cc_final: 0.8706 (mpp80) REVERT: C 701 ARG cc_start: 0.8540 (ttp80) cc_final: 0.8217 (ttp80) REVERT: C 884 MET cc_start: 0.8995 (tpp) cc_final: 0.8709 (mmt) outliers start: 60 outliers final: 39 residues processed: 235 average time/residue: 0.3395 time to fit residues: 129.7563 Evaluate side-chains 202 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 159 time to evaluate : 2.420 ------------------------------------------------------------------------------- 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 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 620 SER Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 975 VAL 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 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 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 531 ASN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 235 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 241 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 217 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 173 optimal weight: 0.5980 chunk 238 optimal weight: 0.2980 chunk 145 optimal weight: 0.9980 chunk 250 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1011 ASN ** B 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.108192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.078962 restraints weight = 43403.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.082492 restraints weight = 21499.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.084747 restraints weight = 14243.906| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25095 Z= 0.162 Angle : 0.644 9.466 34521 Z= 0.304 Chirality : 0.045 0.268 4566 Planarity : 0.004 0.072 4104 Dihedral : 7.200 50.136 6513 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.16 % Allowed : 11.85 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.16), residues: 2880 helix: 2.57 (0.20), residues: 690 sheet: -0.09 (0.20), residues: 666 loop : 0.05 (0.17), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 973 HIS 0.005 0.001 HIS C 100 PHE 0.012 0.001 PHE A 930 TYR 0.010 0.001 TYR A 222 ARG 0.006 0.000 ARG C 943 Details of bonding type rmsd link_NAG-ASN : bond 0.00422 ( 63) link_NAG-ASN : angle 1.91983 ( 189) link_ALPHA1-6 : bond 0.00805 ( 12) link_ALPHA1-6 : angle 1.45547 ( 36) link_BETA1-4 : bond 0.01090 ( 72) link_BETA1-4 : angle 2.56088 ( 216) link_ALPHA1-2 : bond 0.00496 ( 9) link_ALPHA1-2 : angle 1.37487 ( 27) link_ALPHA1-3 : bond 0.01039 ( 12) link_ALPHA1-3 : angle 2.47398 ( 36) hydrogen bonds : bond 0.03905 ( 991) hydrogen bonds : angle 4.78908 ( 2874) SS BOND : bond 0.00313 ( 39) SS BOND : angle 0.78487 ( 78) covalent geometry : bond 0.00359 (24888) covalent geometry : angle 0.59038 (33939) *********************** 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 222 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 167 time to evaluate : 2.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7599 (mt-10) REVERT: A 191 LEU cc_start: 0.9181 (tp) cc_final: 0.8856 (mp) REVERT: A 701 ARG cc_start: 0.8279 (ttp80) cc_final: 0.7929 (ttp80) REVERT: A 703 MET cc_start: 0.9245 (tpp) cc_final: 0.8782 (tpp) REVERT: A 884 MET cc_start: 0.9047 (tpp) cc_final: 0.8696 (mmt) REVERT: A 936 LEU cc_start: 0.8741 (tt) cc_final: 0.8375 (mt) REVERT: B 191 LEU cc_start: 0.9138 (tp) cc_final: 0.8857 (mp) REVERT: B 607 ARG cc_start: 0.9054 (OUTLIER) cc_final: 0.8822 (mmm-85) REVERT: B 701 ARG cc_start: 0.8374 (ttp80) cc_final: 0.8015 (ttp80) REVERT: B 729 MET cc_start: 0.8473 (mtm) cc_final: 0.8255 (ttm) REVERT: B 780 GLU cc_start: 0.7929 (tp30) cc_final: 0.7320 (tp30) REVERT: B 987 ARG cc_start: 0.9124 (OUTLIER) cc_final: 0.8023 (ptm-80) REVERT: B 1011 ASN cc_start: 0.8518 (t0) cc_final: 0.8255 (t0) REVERT: C 372 MET cc_start: 0.8290 (mtm) cc_final: 0.7890 (mtp) REVERT: C 607 ARG cc_start: 0.9099 (OUTLIER) cc_final: 0.8753 (mpp80) REVERT: C 701 ARG cc_start: 0.8543 (ttp80) cc_final: 0.8225 (ttp80) REVERT: C 884 MET cc_start: 0.8996 (tpp) cc_final: 0.8701 (mmt) outliers start: 55 outliers final: 38 residues processed: 213 average time/residue: 0.3513 time to fit residues: 120.5436 Evaluate side-chains 194 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 152 time to evaluate : 2.441 ------------------------------------------------------------------------------- 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 343 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 975 VAL 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 444 THR 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 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 157 CYS Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 477 LYS Chi-restraints excluded: chain C residue 531 ASN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 283 optimal weight: 0.9980 chunk 173 optimal weight: 0.6980 chunk 96 optimal weight: 5.9990 chunk 272 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 0.9980 chunk 126 optimal weight: 0.5980 chunk 257 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 823 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.107681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.078078 restraints weight = 43284.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.081592 restraints weight = 21718.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.083841 restraints weight = 14490.778| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25095 Z= 0.171 Angle : 0.650 10.659 34521 Z= 0.306 Chirality : 0.045 0.263 4566 Planarity : 0.004 0.069 4104 Dihedral : 6.927 47.811 6513 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.89 % Allowed : 12.59 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.16), residues: 2880 helix: 2.57 (0.20), residues: 690 sheet: -0.14 (0.20), residues: 672 loop : 0.00 (0.17), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 973 HIS 0.003 0.001 HIS C 100 PHE 0.013 0.001 PHE C 641 TYR 0.011 0.001 TYR B 222 ARG 0.006 0.000 ARG B 943 Details of bonding type rmsd link_NAG-ASN : bond 0.00402 ( 63) link_NAG-ASN : angle 1.92901 ( 189) link_ALPHA1-6 : bond 0.00808 ( 12) link_ALPHA1-6 : angle 1.45065 ( 36) link_BETA1-4 : bond 0.01078 ( 72) link_BETA1-4 : angle 2.55636 ( 216) link_ALPHA1-2 : bond 0.00524 ( 9) link_ALPHA1-2 : angle 1.38400 ( 27) link_ALPHA1-3 : bond 0.00977 ( 12) link_ALPHA1-3 : angle 2.45088 ( 36) hydrogen bonds : bond 0.03912 ( 991) hydrogen bonds : angle 4.80624 ( 2874) SS BOND : bond 0.00354 ( 39) SS BOND : angle 0.79730 ( 78) covalent geometry : bond 0.00382 (24888) covalent geometry : angle 0.59648 (33939) *********************** 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 218 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 170 time to evaluate : 2.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7459 (mt-10) REVERT: A 191 LEU cc_start: 0.9180 (tp) cc_final: 0.8766 (mp) REVERT: A 701 ARG cc_start: 0.8352 (ttp80) cc_final: 0.8050 (ttp80) REVERT: A 703 MET cc_start: 0.9229 (tpp) cc_final: 0.8733 (tpp) REVERT: A 884 MET cc_start: 0.9055 (tpp) cc_final: 0.8693 (mmt) REVERT: A 936 LEU cc_start: 0.8742 (tt) cc_final: 0.8418 (mt) REVERT: B 104 MET cc_start: 0.8316 (mtm) cc_final: 0.7937 (mtm) REVERT: B 568 ASP cc_start: 0.8629 (m-30) cc_final: 0.8337 (m-30) REVERT: B 607 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.8850 (mmm-85) REVERT: B 701 ARG cc_start: 0.8296 (ttp80) cc_final: 0.7919 (ttp80) REVERT: B 780 GLU cc_start: 0.7944 (tp30) cc_final: 0.7373 (tp30) REVERT: B 860 GLN cc_start: 0.8073 (tt0) cc_final: 0.7840 (tt0) REVERT: B 987 ARG cc_start: 0.9138 (OUTLIER) cc_final: 0.8018 (ptm-80) REVERT: B 1011 ASN cc_start: 0.8560 (t0) cc_final: 0.8294 (t0) REVERT: C 252 THR cc_start: 0.9513 (OUTLIER) cc_final: 0.9284 (t) REVERT: C 372 MET cc_start: 0.8283 (mtm) cc_final: 0.7859 (mtp) REVERT: C 461 THR cc_start: 0.8831 (p) cc_final: 0.8614 (t) REVERT: C 607 ARG cc_start: 0.9109 (OUTLIER) cc_final: 0.8800 (mpp80) REVERT: C 640 MET cc_start: 0.9202 (ttp) cc_final: 0.8968 (tmm) REVERT: C 701 ARG cc_start: 0.8554 (ttp80) cc_final: 0.8229 (ttp80) REVERT: C 740 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.8250 (mtt) REVERT: C 884 MET cc_start: 0.8993 (tpp) cc_final: 0.8723 (mmt) outliers start: 48 outliers final: 37 residues processed: 210 average time/residue: 0.3553 time to fit residues: 120.4153 Evaluate side-chains 201 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 158 time to evaluate : 2.712 ------------------------------------------------------------------------------- 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 171 THR 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 708 LEU Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 975 VAL 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 444 THR 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 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 531 ASN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 260 optimal weight: 1.9990 chunk 216 optimal weight: 0.3980 chunk 254 optimal weight: 1.9990 chunk 215 optimal weight: 0.8980 chunk 253 optimal weight: 0.5980 chunk 147 optimal weight: 0.8980 chunk 274 optimal weight: 0.6980 chunk 243 optimal weight: 0.0770 chunk 2 optimal weight: 0.6980 chunk 212 optimal weight: 0.7980 chunk 248 optimal weight: 0.8980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 823 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.108786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.079476 restraints weight = 43350.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.083031 restraints weight = 21475.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.085312 restraints weight = 14235.522| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 25095 Z= 0.133 Angle : 0.627 12.173 34521 Z= 0.296 Chirality : 0.045 0.250 4566 Planarity : 0.004 0.065 4104 Dihedral : 6.646 47.631 6513 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.65 % Allowed : 12.87 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.16), residues: 2880 helix: 2.56 (0.20), residues: 690 sheet: -0.19 (0.21), residues: 642 loop : 0.02 (0.17), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 973 HIS 0.004 0.001 HIS C 100 PHE 0.014 0.001 PHE C 641 TYR 0.009 0.001 TYR A 222 ARG 0.007 0.000 ARG A 943 Details of bonding type rmsd link_NAG-ASN : bond 0.00461 ( 63) link_NAG-ASN : angle 1.81222 ( 189) link_ALPHA1-6 : bond 0.00830 ( 12) link_ALPHA1-6 : angle 1.39278 ( 36) link_BETA1-4 : bond 0.01101 ( 72) link_BETA1-4 : angle 2.51315 ( 216) link_ALPHA1-2 : bond 0.00558 ( 9) link_ALPHA1-2 : angle 1.37108 ( 27) link_ALPHA1-3 : bond 0.01076 ( 12) link_ALPHA1-3 : angle 2.32870 ( 36) hydrogen bonds : bond 0.03751 ( 991) hydrogen bonds : angle 4.72987 ( 2874) SS BOND : bond 0.00245 ( 39) SS BOND : angle 0.76147 ( 78) covalent geometry : bond 0.00291 (24888) covalent geometry : angle 0.57545 (33939) *********************** 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 229 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 187 time to evaluate : 2.661 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: 0.7442 (m-80) cc_final: 0.6975 (m-80) REVERT: A 159 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7248 (mt-10) REVERT: A 191 LEU cc_start: 0.9173 (tp) cc_final: 0.8709 (mp) REVERT: A 701 ARG cc_start: 0.8369 (ttp80) cc_final: 0.8133 (ttp80) REVERT: A 703 MET cc_start: 0.9206 (tpp) cc_final: 0.8695 (tpp) REVERT: A 884 MET cc_start: 0.9020 (tpp) cc_final: 0.8697 (mmt) REVERT: A 936 LEU cc_start: 0.8667 (tt) cc_final: 0.8389 (mt) REVERT: B 104 MET cc_start: 0.8307 (mtm) cc_final: 0.7936 (mtm) REVERT: B 607 ARG cc_start: 0.9047 (OUTLIER) cc_final: 0.8846 (mmm-85) REVERT: B 701 ARG cc_start: 0.8245 (ttp80) cc_final: 0.7863 (ttp80) REVERT: B 729 MET cc_start: 0.8355 (mtm) cc_final: 0.8138 (ttm) REVERT: B 987 ARG cc_start: 0.9139 (OUTLIER) cc_final: 0.7981 (ptm-80) REVERT: C 252 THR cc_start: 0.9517 (OUTLIER) cc_final: 0.9302 (t) REVERT: C 372 MET cc_start: 0.8261 (mtm) cc_final: 0.7887 (mtp) REVERT: C 607 ARG cc_start: 0.9082 (OUTLIER) cc_final: 0.8821 (mpp80) REVERT: C 640 MET cc_start: 0.9212 (ttp) cc_final: 0.8975 (tmm) REVERT: C 701 ARG cc_start: 0.8550 (ttp80) cc_final: 0.8239 (ttp80) REVERT: C 740 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.8286 (mtt) REVERT: C 884 MET cc_start: 0.9015 (tpp) cc_final: 0.8777 (mmt) outliers start: 42 outliers final: 30 residues processed: 222 average time/residue: 0.4216 time to fit residues: 149.9831 Evaluate side-chains 203 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 167 time to evaluate : 3.403 ------------------------------------------------------------------------------- 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 343 LEU Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 975 VAL 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 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 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 252 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 477 LYS Chi-restraints excluded: chain C residue 531 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 168 optimal weight: 0.9990 chunk 216 optimal weight: 0.5980 chunk 276 optimal weight: 0.5980 chunk 122 optimal weight: 0.9990 chunk 223 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 262 optimal weight: 0.9990 chunk 34 optimal weight: 0.2980 chunk 116 optimal weight: 1.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 823 GLN B1011 ASN C 823 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.109778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.080780 restraints weight = 43203.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.084405 restraints weight = 20741.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.086731 restraints weight = 13482.920| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 25095 Z= 0.152 Angle : 0.642 13.991 34521 Z= 0.303 Chirality : 0.045 0.243 4566 Planarity : 0.004 0.064 4104 Dihedral : 6.534 47.326 6513 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.69 % Allowed : 13.14 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.16), residues: 2880 helix: 2.73 (0.20), residues: 672 sheet: -0.19 (0.21), residues: 642 loop : -0.01 (0.17), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 973 HIS 0.004 0.001 HIS C 100 PHE 0.014 0.001 PHE C 641 TYR 0.010 0.001 TYR C 259 ARG 0.005 0.000 ARG C 84 Details of bonding type rmsd link_NAG-ASN : bond 0.00452 ( 63) link_NAG-ASN : angle 1.84301 ( 189) link_ALPHA1-6 : bond 0.00802 ( 12) link_ALPHA1-6 : angle 1.40227 ( 36) link_BETA1-4 : bond 0.01086 ( 72) link_BETA1-4 : angle 2.52569 ( 216) link_ALPHA1-2 : bond 0.00562 ( 9) link_ALPHA1-2 : angle 1.38694 ( 27) link_ALPHA1-3 : bond 0.01038 ( 12) link_ALPHA1-3 : angle 2.37038 ( 36) hydrogen bonds : bond 0.03779 ( 991) hydrogen bonds : angle 4.74395 ( 2874) SS BOND : bond 0.00310 ( 39) SS BOND : angle 0.81495 ( 78) covalent geometry : bond 0.00341 (24888) covalent geometry : angle 0.59091 (33939) ********************** 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 215 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 172 time to evaluate : 4.062 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: 0.7560 (m-80) cc_final: 0.7077 (m-80) REVERT: A 159 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7405 (mt-10) REVERT: A 191 LEU cc_start: 0.9178 (tp) cc_final: 0.8708 (mp) REVERT: A 701 ARG cc_start: 0.8367 (ttp80) cc_final: 0.8126 (ttp80) REVERT: A 703 MET cc_start: 0.9218 (tpp) cc_final: 0.8697 (tpp) REVERT: A 884 MET cc_start: 0.9034 (tpp) cc_final: 0.8704 (mmt) REVERT: A 936 LEU cc_start: 0.8678 (tt) cc_final: 0.8383 (mt) REVERT: B 104 MET cc_start: 0.8315 (mtm) cc_final: 0.7902 (mtm) REVERT: B 568 ASP cc_start: 0.8643 (m-30) cc_final: 0.8346 (m-30) REVERT: B 607 ARG cc_start: 0.9054 (OUTLIER) cc_final: 0.8850 (mmm-85) REVERT: B 701 ARG cc_start: 0.8215 (ttp80) cc_final: 0.7819 (ttp80) REVERT: B 727 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7571 (tm-30) REVERT: B 729 MET cc_start: 0.8387 (mtm) cc_final: 0.8143 (ttm) REVERT: B 780 GLU cc_start: 0.7943 (tp30) cc_final: 0.6906 (tp30) REVERT: B 987 ARG cc_start: 0.9144 (OUTLIER) cc_final: 0.7969 (ptm-80) REVERT: C 252 THR cc_start: 0.9513 (OUTLIER) cc_final: 0.9310 (t) REVERT: C 372 MET cc_start: 0.8271 (mtm) cc_final: 0.7895 (mtp) REVERT: C 640 MET cc_start: 0.9244 (ttp) cc_final: 0.9035 (tmm) REVERT: C 701 ARG cc_start: 0.8510 (ttp80) cc_final: 0.8213 (ttp80) REVERT: C 740 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.8310 (mtt) REVERT: C 884 MET cc_start: 0.9015 (tpp) cc_final: 0.8770 (mmt) outliers start: 43 outliers final: 35 residues processed: 206 average time/residue: 0.3445 time to fit residues: 116.1435 Evaluate side-chains 202 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 162 time to evaluate : 2.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 171 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 975 VAL 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 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 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 99 ASN Chi-restraints excluded: chain C residue 157 CYS 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 531 ASN 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 729 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 22 optimal weight: 5.9990 chunk 286 optimal weight: 0.5980 chunk 73 optimal weight: 0.7980 chunk 169 optimal weight: 0.7980 chunk 186 optimal weight: 0.4980 chunk 24 optimal weight: 0.8980 chunk 168 optimal weight: 0.7980 chunk 75 optimal weight: 0.5980 chunk 61 optimal weight: 0.2980 chunk 68 optimal weight: 1.9990 chunk 239 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 823 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.108709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.079568 restraints weight = 43215.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.083192 restraints weight = 20732.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.085537 restraints weight = 13474.399| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 25095 Z= 0.140 Angle : 0.631 13.753 34521 Z= 0.298 Chirality : 0.044 0.242 4566 Planarity : 0.004 0.063 4104 Dihedral : 6.370 47.557 6513 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.69 % Allowed : 13.58 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.16), residues: 2880 helix: 2.59 (0.20), residues: 690 sheet: -0.15 (0.21), residues: 627 loop : -0.05 (0.17), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 973 HIS 0.004 0.001 HIS C 100 PHE 0.013 0.001 PHE C 641 TYR 0.009 0.001 TYR A 114 ARG 0.005 0.000 ARG A 943 Details of bonding type rmsd link_NAG-ASN : bond 0.00442 ( 63) link_NAG-ASN : angle 1.80454 ( 189) link_ALPHA1-6 : bond 0.00804 ( 12) link_ALPHA1-6 : angle 1.37283 ( 36) link_BETA1-4 : bond 0.01093 ( 72) link_BETA1-4 : angle 2.50284 ( 216) link_ALPHA1-2 : bond 0.00587 ( 9) link_ALPHA1-2 : angle 1.38594 ( 27) link_ALPHA1-3 : bond 0.01041 ( 12) link_ALPHA1-3 : angle 2.29195 ( 36) hydrogen bonds : bond 0.03702 ( 991) hydrogen bonds : angle 4.70346 ( 2874) SS BOND : bond 0.00250 ( 39) SS BOND : angle 0.76330 ( 78) covalent geometry : bond 0.00309 (24888) covalent geometry : angle 0.58051 (33939) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7178.26 seconds wall clock time: 128 minutes 56.55 seconds (7736.55 seconds total)