Starting phenix.real_space_refine on Fri Mar 6 11:49:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sbw_24990/03_2026/7sbw_24990.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sbw_24990/03_2026/7sbw_24990.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sbw_24990/03_2026/7sbw_24990.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sbw_24990/03_2026/7sbw_24990.map" model { file = "/net/cci-nas-00/data/ceres_data/7sbw_24990/03_2026/7sbw_24990.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sbw_24990/03_2026/7sbw_24990.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 189 5.16 5 C 19042 2.51 5 N 4864 2.21 5 O 5966 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30061 Number of models: 1 Model: "" Number of chains: 39 Chain: "H" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 585 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 117} Link IDs: {'TRANS': 116} Unresolved non-hydrogen bonds: 234 Unresolved non-hydrogen angles: 351 Unresolved non-hydrogen dihedrals: 117 Planarities with less than four sites: {'UNK:plan-1': 117} Unresolved non-hydrogen planarities: 117 Chain: "L" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 505 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'TRANS': 100} Unresolved non-hydrogen bonds: 202 Unresolved non-hydrogen angles: 303 Unresolved non-hydrogen dihedrals: 101 Planarities with less than four sites: {'UNK:plan-1': 101} Unresolved non-hydrogen planarities: 101 Chain: "J" Number of atoms: 9260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1191, 9260 Classifications: {'peptide': 1191} Link IDs: {'PTRANS': 53, 'TRANS': 1137} Chain breaks: 4 Chain: "A" Number of atoms: 9213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1185, 9213 Classifications: {'peptide': 1185} Link IDs: {'PTRANS': 53, 'TRANS': 1131} Chain breaks: 5 Chain: "B" Number of atoms: 9287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1196, 9287 Classifications: {'peptide': 1196} Link IDs: {'PTRANS': 53, 'TRANS': 1142} Chain breaks: 3 Chain: "C" 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: "D" 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: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" 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: "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: 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: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" 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: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: 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: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 74 Unusual residues: {'8Z9': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 92 Unusual residues: {'8Z9': 2, 'NAG': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 7.81, per 1000 atoms: 0.26 Number of scatterers: 30061 At special positions: 0 Unit cell: (151.41, 150.38, 193.64, 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 189 16.00 O 5966 8.00 N 4864 7.00 C 19042 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=63, symmetry=0 Simple disulfide: pdb=" SG CYS J 21 " - pdb=" SG CYS J 173 " distance=2.02 Simple disulfide: pdb=" SG CYS J 168 " - pdb=" SG CYS J 201 " distance=2.03 Simple disulfide: pdb=" SG CYS J 180 " - pdb=" SG CYS J 260 " distance=2.03 Simple disulfide: pdb=" SG CYS J 298 " - pdb=" SG CYS J 308 " distance=2.04 Simple disulfide: pdb=" SG CYS J 343 " - pdb=" SG CYS J 368 " distance=2.10 Simple disulfide: pdb=" SG CYS J 386 " - pdb=" SG CYS J 439 " distance=2.03 Simple disulfide: pdb=" SG CYS J 398 " - pdb=" SG CYS J 614 " distance=2.06 Simple disulfide: pdb=" SG CYS J 491 " - pdb=" SG CYS J 561 " distance=2.04 Simple disulfide: pdb=" SG CYS J 499 " - pdb=" SG CYS J 522 " distance=2.04 Simple disulfide: pdb=" SG CYS J 501 " - pdb=" SG CYS J 576 " distance=2.02 Simple disulfide: pdb=" SG CYS J 535 " - pdb=" SG CYS J 548 " distance=2.03 Simple disulfide: pdb=" SG CYS J 571 " - pdb=" SG CYS J 578 " distance=2.03 Simple disulfide: pdb=" SG CYS J 591 " - pdb=" SG CYS J 597 " distance=2.04 Simple disulfide: pdb=" SG CYS J 630 " - pdb=" SG CYS J 683 " distance=2.09 Simple disulfide: pdb=" SG CYS J 708 " - pdb=" SG CYS J 732 " distance=2.04 Simple disulfide: pdb=" SG CYS J 747 " - pdb=" SG CYS J 756 " distance=2.04 Simple disulfide: pdb=" SG CYS J 825 " - pdb=" SG CYS J 847 " distance=2.02 Simple disulfide: pdb=" SG CYS J 830 " - pdb=" SG CYS J 836 " distance=2.03 Simple disulfide: pdb=" SG CYS J 937 " - pdb=" SG CYS J 948 " distance=2.05 Simple disulfide: pdb=" SG CYS J1125 " - pdb=" SG CYS J1136 " distance=2.02 Simple disulfide: pdb=" SG CYS J1175 " - pdb=" SG CYS J1220 " distance=2.03 Simple disulfide: pdb=" SG CYS A 21 " - pdb=" SG CYS A 173 " distance=2.03 Simple disulfide: pdb=" SG CYS A 168 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 260 " distance=2.04 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 368 " distance=2.10 Simple disulfide: pdb=" SG CYS A 386 " - pdb=" SG CYS A 439 " distance=2.03 Simple disulfide: pdb=" SG CYS A 398 " - pdb=" SG CYS A 614 " distance=2.04 Simple disulfide: pdb=" SG CYS A 491 " - pdb=" SG CYS A 561 " distance=2.08 Simple disulfide: pdb=" SG CYS A 499 " - pdb=" SG CYS A 522 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS A 576 " distance=2.02 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 548 " distance=2.04 Simple disulfide: pdb=" SG CYS A 571 " - pdb=" SG CYS A 578 " distance=2.03 Simple disulfide: pdb=" SG CYS A 591 " - pdb=" SG CYS A 597 " distance=2.03 Simple disulfide: pdb=" SG CYS A 630 " - pdb=" SG CYS A 683 " distance=2.06 Simple disulfide: pdb=" SG CYS A 708 " - pdb=" SG CYS A 732 " distance=2.03 Simple disulfide: pdb=" SG CYS A 747 " - pdb=" SG CYS A 756 " distance=2.03 Simple disulfide: pdb=" SG CYS A 825 " - pdb=" SG CYS A 847 " distance=2.11 Simple disulfide: pdb=" SG CYS A 830 " - pdb=" SG CYS A 836 " distance=2.03 Simple disulfide: pdb=" SG CYS A 937 " - pdb=" SG CYS A 948 " distance=2.08 Simple disulfide: pdb=" SG CYS A1125 " - pdb=" SG CYS A1136 " distance=2.02 Simple disulfide: pdb=" SG CYS A1175 " - pdb=" SG CYS A1220 " distance=2.03 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 173 " distance=2.04 Simple disulfide: pdb=" SG CYS B 168 " - pdb=" SG CYS B 201 " distance=2.04 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 260 " distance=2.04 Simple disulfide: pdb=" SG CYS B 298 " - pdb=" SG CYS B 308 " distance=2.03 Simple disulfide: pdb=" SG CYS B 343 " - pdb=" SG CYS B 368 " distance=2.12 Simple disulfide: pdb=" SG CYS B 386 " - pdb=" SG CYS B 439 " distance=2.03 Simple disulfide: pdb=" SG CYS B 398 " - pdb=" SG CYS B 614 " distance=2.05 Simple disulfide: pdb=" SG CYS B 491 " - pdb=" SG CYS B 561 " distance=2.03 Simple disulfide: pdb=" SG CYS B 499 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS B 576 " distance=2.02 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 548 " distance=2.07 Simple disulfide: pdb=" SG CYS B 571 " - pdb=" SG CYS B 578 " distance=2.03 Simple disulfide: pdb=" SG CYS B 591 " - pdb=" SG CYS B 597 " distance=2.03 Simple disulfide: pdb=" SG CYS B 630 " - pdb=" SG CYS B 683 " distance=2.04 Simple disulfide: pdb=" SG CYS B 708 " - pdb=" SG CYS B 732 " distance=2.05 Simple disulfide: pdb=" SG CYS B 747 " - pdb=" SG CYS B 756 " distance=2.03 Simple disulfide: pdb=" SG CYS B 825 " - pdb=" SG CYS B 847 " distance=2.02 Simple disulfide: pdb=" SG CYS B 830 " - pdb=" SG CYS B 836 " distance=2.04 Simple disulfide: pdb=" SG CYS B 937 " - pdb=" SG CYS B 948 " distance=2.08 Simple disulfide: pdb=" SG CYS B1125 " - pdb=" SG CYS B1136 " distance=2.02 Simple disulfide: pdb=" SG CYS B1175 " - pdb=" SG CYS B1220 " 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 BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " 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 j 1 " - " NAG j 2 " NAG-ASN " NAG A1401 " - " ASN A 212 " " NAG A1402 " - " ASN A 787 " " NAG A1403 " - " ASN A 648 " " NAG A1404 " - " ASN A 63 " " NAG B1401 " - " ASN B 713 " " NAG B1402 " - " ASN B 787 " " NAG B1403 " - " ASN B 648 " " NAG B1404 " - " ASN B 63 " " NAG C 1 " - " ASN J 137 " " NAG D 1 " - " ASN J 371 " " NAG E 1 " - " ASN J 449 " " NAG F 1 " - " ASN J 713 " " NAG G 1 " - " ASN J 738 " " NAG I 1 " - " ASN J 936 " " NAG J1401 " - " ASN J 212 " " NAG J1402 " - " ASN J 787 " " NAG J1403 " - " ASN J 648 " " NAG J1404 " - " ASN J 63 " " NAG K 1 " - " ASN J1193 " " NAG M 1 " - " ASN J 206 " " NAG N 1 " - " ASN J 675 " " NAG O 1 " - " ASN J 695 " " NAG P 1 " - " ASN A 137 " " NAG Q 1 " - " ASN A 371 " " NAG R 1 " - " ASN A 713 " " NAG S 1 " - " ASN A 738 " " NAG T 1 " - " ASN A 936 " " NAG U 1 " - " ASN A1193 " " NAG V 1 " - " ASN A 206 " " NAG W 1 " - " ASN A 675 " " NAG X 1 " - " ASN A 695 " " NAG Y 1 " - " ASN A 449 " " NAG Z 1 " - " ASN A1223 " " NAG a 1 " - " ASN B 137 " " NAG b 1 " - " ASN B 212 " " NAG c 1 " - " ASN B 371 " " NAG d 1 " - " ASN B 449 " " NAG e 1 " - " ASN B 738 " " NAG f 1 " - " ASN B 936 " " NAG g 1 " - " ASN B1193 " " NAG h 1 " - " ASN B 206 " " NAG i 1 " - " ASN B 675 " " NAG j 1 " - " ASN B 695 " Time building additional restraints: 3.14 Conformation dependent library (CDL) restraints added in 1.3 seconds 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7102 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 78 sheets defined 26.0% alpha, 31.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'H' and resid 27 through 30 removed outlier: 4.046A pdb=" N UNK H 30 " --> pdb=" O UNK H 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 27 through 30' Processing helix chain 'J' and resid 91 through 96 Processing helix chain 'J' and resid 263 through 267 Processing helix chain 'J' and resid 301 through 311 Processing helix chain 'J' and resid 344 through 350 Processing helix chain 'J' and resid 357 through 360 Processing helix chain 'J' and resid 371 through 379 Processing helix chain 'J' and resid 390 through 394 Processing helix chain 'J' and resid 413 through 418 Processing helix chain 'J' and resid 424 through 429 Processing helix chain 'J' and resid 448 through 450 No H-bonds generated for 'chain 'J' and resid 448 through 450' Processing helix chain 'J' and resid 458 through 464 Processing helix chain 'J' and resid 467 through 472 Processing helix chain 'J' and resid 530 through 534 Processing helix chain 'J' and resid 707 through 714 Processing helix chain 'J' and resid 824 through 830 Processing helix chain 'J' and resid 833 through 841 removed outlier: 3.654A pdb=" N VAL J 841 " --> pdb=" O LYS J 837 " (cutoff:3.500A) Processing helix chain 'J' and resid 843 through 874 removed outlier: 4.026A pdb=" N CYS J 847 " --> pdb=" O TYR J 843 " (cutoff:3.500A) Processing helix chain 'J' and resid 881 through 884 Processing helix chain 'J' and resid 913 through 922 removed outlier: 4.317A pdb=" N LYS J 922 " --> pdb=" O LEU J 918 " (cutoff:3.500A) Processing helix chain 'J' and resid 926 through 935 Processing helix chain 'J' and resid 945 through 953 Processing helix chain 'J' and resid 963 through 977 Processing helix chain 'J' and resid 983 through 987 Processing helix chain 'J' and resid 990 through 1001 Processing helix chain 'J' and resid 1005 through 1012 Processing helix chain 'J' and resid 1012 through 1029 Processing helix chain 'J' and resid 1035 through 1058 Processing helix chain 'J' and resid 1059 through 1061 No H-bonds generated for 'chain 'J' and resid 1059 through 1061' Processing helix chain 'J' and resid 1069 through 1077 Processing helix chain 'J' and resid 1078 through 1125 removed outlier: 4.863A pdb=" N ALA J1084 " --> pdb=" O PRO J1080 " (cutoff:3.500A) Processing helix chain 'J' and resid 1210 through 1212 No H-bonds generated for 'chain 'J' and resid 1210 through 1212' Processing helix chain 'A' and resid 117 through 121 Processing helix chain 'A' and resid 263 through 267 Processing helix chain 'A' and resid 301 through 311 Processing helix chain 'A' and resid 344 through 350 Processing helix chain 'A' and resid 357 through 360 removed outlier: 3.570A pdb=" N TRP A 360 " --> pdb=" O PRO A 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 357 through 360' Processing helix chain 'A' and resid 371 through 379 Processing helix chain 'A' and resid 390 through 394 Processing helix chain 'A' and resid 413 through 418 Processing helix chain 'A' and resid 424 through 429 Processing helix chain 'A' and resid 448 through 450 No H-bonds generated for 'chain 'A' and resid 448 through 450' Processing helix chain 'A' and resid 458 through 464 Processing helix chain 'A' and resid 467 through 472 Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 707 through 714 Processing helix chain 'A' and resid 824 through 830 Processing helix chain 'A' and resid 833 through 841 Processing helix chain 'A' and resid 843 through 874 removed outlier: 3.931A pdb=" N CYS A 847 " --> pdb=" O TYR A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 884 Processing helix chain 'A' and resid 913 through 922 removed outlier: 4.253A pdb=" N LYS A 922 " --> pdb=" O LEU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 935 Processing helix chain 'A' and resid 945 through 953 Processing helix chain 'A' and resid 963 through 977 Processing helix chain 'A' and resid 983 through 987 Processing helix chain 'A' and resid 990 through 1001 Processing helix chain 'A' and resid 1005 through 1012 Processing helix chain 'A' and resid 1012 through 1029 Processing helix chain 'A' and resid 1035 through 1059 removed outlier: 3.756A pdb=" N LEU A1059 " --> pdb=" O LEU A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1077 Processing helix chain 'A' and resid 1078 through 1125 removed outlier: 4.839A pdb=" N ALA A1084 " --> pdb=" O PRO A1080 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 310 Processing helix chain 'B' and resid 345 through 350 Processing helix chain 'B' and resid 357 through 360 Processing helix chain 'B' and resid 371 through 379 removed outlier: 4.394A pdb=" N SER B 377 " --> pdb=" O SER B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 394 Processing helix chain 'B' and resid 413 through 418 Processing helix chain 'B' and resid 424 through 429 Processing helix chain 'B' and resid 448 through 450 No H-bonds generated for 'chain 'B' and resid 448 through 450' Processing helix chain 'B' and resid 458 through 463 Processing helix chain 'B' and resid 467 through 472 Processing helix chain 'B' and resid 538 through 542 Processing helix chain 'B' and resid 707 through 714 Processing helix chain 'B' and resid 824 through 830 Processing helix chain 'B' and resid 833 through 840 Processing helix chain 'B' and resid 843 through 874 removed outlier: 3.529A pdb=" N CYS B 847 " --> pdb=" O TYR B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 881 through 885 Processing helix chain 'B' and resid 913 through 922 removed outlier: 4.359A pdb=" N LYS B 922 " --> pdb=" O LEU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 926 through 935 Processing helix chain 'B' and resid 945 through 952 Processing helix chain 'B' and resid 963 through 980 removed outlier: 4.033A pdb=" N SER B 978 " --> pdb=" O ALA B 974 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 987 removed outlier: 3.600A pdb=" N ALA B 987 " --> pdb=" O THR B 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 990 through 1001 Processing helix chain 'B' and resid 1005 through 1011 Processing helix chain 'B' and resid 1012 through 1029 Processing helix chain 'B' and resid 1035 through 1058 Processing helix chain 'B' and resid 1059 through 1061 No H-bonds generated for 'chain 'B' and resid 1059 through 1061' Processing helix chain 'B' and resid 1069 through 1077 Processing helix chain 'B' and resid 1078 through 1125 removed outlier: 4.807A pdb=" N ALA B1084 " --> pdb=" O PRO B1080 " (cutoff:3.500A) Processing helix chain 'B' and resid 1210 through 1212 No H-bonds generated for 'chain 'B' and resid 1210 through 1212' Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 56 through 58 removed outlier: 6.495A pdb=" N UNK H 35 " --> pdb=" O UNK H 46 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N UNK H 48 " --> pdb=" O UNK H 33 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N UNK H 33 " --> pdb=" O UNK H 48 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N UNK H 32 " --> pdb=" O UNK H 94 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N UNK H 91 " --> pdb=" O UNK H 110 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N UNK H 110 " --> pdb=" O UNK H 91 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N UNK H 93 " --> pdb=" O UNK H 108 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 56 through 58 removed outlier: 6.495A pdb=" N UNK H 35 " --> pdb=" O UNK H 46 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N UNK H 48 " --> pdb=" O UNK H 33 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N UNK H 33 " --> pdb=" O UNK H 48 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N UNK H 32 " --> pdb=" O UNK H 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA5, first strand: chain 'L' and resid 51 through 52 removed outlier: 4.867A pdb=" N UNK L 46 " --> pdb=" O UNK L 34 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N UNK L 34 " --> pdb=" O UNK L 46 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N UNK L 48 " --> pdb=" O UNK L 32 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N UNK L 32 " --> pdb=" O UNK L 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 51 through 52 removed outlier: 4.867A pdb=" N UNK L 46 " --> pdb=" O UNK L 34 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N UNK L 34 " --> pdb=" O UNK L 46 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N UNK L 48 " --> pdb=" O UNK L 32 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N UNK L 32 " --> pdb=" O UNK L 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 29 through 30 removed outlier: 7.063A pdb=" N SER J 29 " --> pdb=" O LEU J 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'J' and resid 42 through 44 removed outlier: 8.352A pdb=" N THR J 78 " --> pdb=" O PRO J 276 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N PHE J 227 " --> pdb=" O ASN J 243 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ASN J 243 " --> pdb=" O PHE J 227 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ALA J 229 " --> pdb=" O LEU J 241 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 59 through 60 removed outlier: 6.767A pdb=" N LEU A 659 " --> pdb=" O TYR A 667 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N TYR A 667 " --> pdb=" O ILE A 680 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 64 through 72 removed outlier: 3.603A pdb=" N ASN J 294 " --> pdb=" O ALA J 285 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 85 through 86 removed outlier: 8.393A pdb=" N THR J 259 " --> pdb=" O PRO J 176 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N THR J 178 " --> pdb=" O THR J 259 " (cutoff:3.500A) removed outlier: 9.791A pdb=" N TYR J 175 " --> pdb=" O HIS J 193 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N HIS J 193 " --> pdb=" O TYR J 175 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 100 through 102 removed outlier: 7.203A pdb=" N GLY J 161 " --> pdb=" O THR J 208 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N THR J 208 " --> pdb=" O GLY J 161 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N LEU J 163 " --> pdb=" O ASN J 206 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ASN J 206 " --> pdb=" O LEU J 163 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL J 165 " --> pdb=" O LYS J 204 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LYS J 204 " --> pdb=" O VAL J 165 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL J 167 " --> pdb=" O LEU J 202 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 116 through 118 Processing sheet with id=AB5, first strand: chain 'J' and resid 318 through 321 removed outlier: 3.502A pdb=" N CYS J 732 " --> pdb=" O PHE J 703 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 325 through 326 Processing sheet with id=AB7, first strand: chain 'J' and resid 332 through 335 removed outlier: 4.203A pdb=" N THR J 677 " --> pdb=" O VAL J 647 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N TYR J 667 " --> pdb=" O ILE J 680 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU J 659 " --> pdb=" O TYR J 667 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N PHE J 669 " --> pdb=" O ASN J 657 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ASN J 657 " --> pdb=" O PHE J 669 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N GLN J 656 " --> pdb=" O ASP B 58 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL B 60 " --> pdb=" O GLN J 656 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU J 658 " --> pdb=" O VAL B 60 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 353 through 355 removed outlier: 6.665A pdb=" N VAL J 354 " --> pdb=" O SER J 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'J' and resid 361 through 365 removed outlier: 3.609A pdb=" N SER J 401 " --> pdb=" O HIS J 606 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASN J 444 " --> pdb=" O ALA J 381 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ALA J 381 " --> pdb=" O ASN J 444 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 361 through 365 removed outlier: 3.609A pdb=" N SER J 401 " --> pdb=" O HIS J 606 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 369 through 370 Processing sheet with id=AC3, first strand: chain 'J' and resid 484 through 488 Processing sheet with id=AC4, first strand: chain 'J' and resid 491 through 493 removed outlier: 4.272A pdb=" N CYS J 491 " --> pdb=" O SER J 553 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 498 through 502 removed outlier: 3.699A pdb=" N CYS J 499 " --> pdb=" O ASN J 527 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LEU J 529 " --> pdb=" O CYS J 499 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N CYS J 501 " --> pdb=" O LEU J 529 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'J' and resid 520 through 521 Processing sheet with id=AC7, first strand: chain 'J' and resid 565 through 566 Processing sheet with id=AC8, first strand: chain 'J' and resid 737 through 744 removed outlier: 6.518A pdb=" N TYR J 737 " --> pdb=" O PHE J 775 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N ASN J 777 " --> pdb=" O TYR J 737 " (cutoff:3.500A) removed outlier: 9.463A pdb=" N SER J 739 " --> pdb=" O ASN J 777 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TYR J 755 " --> pdb=" O VAL J 751 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU J 749 " --> pdb=" O VAL J 757 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 784 through 786 removed outlier: 6.172A pdb=" N ASN J 784 " --> pdb=" O LEU B 878 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'J' and resid 797 through 815 removed outlier: 6.551A pdb=" N LYS J1164 " --> pdb=" O SER J 803 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N PHE J 805 " --> pdb=" O PRO J1162 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE J 807 " --> pdb=" O TYR J1160 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N TYR J1160 " --> pdb=" O ILE J 807 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ASN J 809 " --> pdb=" O PHE J1158 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N PHE J1158 " --> pdb=" O ASN J 809 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLU J 811 " --> pdb=" O ILE J1156 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ILE J1156 " --> pdb=" O GLU J 811 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N PHE J 813 " --> pdb=" O TYR J1154 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N TYR J1154 " --> pdb=" O PHE J 813 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLN J 815 " --> pdb=" O GLY J1152 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLY J1152 " --> pdb=" O GLN J 815 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE J1143 " --> pdb=" O PHE J1158 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N TYR J1160 " --> pdb=" O HIS J1141 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N HIS J1141 " --> pdb=" O TYR J1160 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 820 through 823 removed outlier: 4.099A pdb=" N LYS J 820 " --> pdb=" O LEU J 958 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 877 through 879 Processing sheet with id=AD4, first strand: chain 'J' and resid 889 through 890 Processing sheet with id=AD5, first strand: chain 'J' and resid 1214 through 1217 Processing sheet with id=AD6, first strand: chain 'J' and resid 1187 through 1192 Processing sheet with id=AD7, first strand: chain 'A' and resid 42 through 44 removed outlier: 8.188A pdb=" N THR A 78 " --> pdb=" O PRO A 276 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLY A 106 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N PHE A 231 " --> pdb=" O PHE A 240 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N PHE A 240 " --> pdb=" O PHE A 231 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 64 through 73 removed outlier: 3.563A pdb=" N ASN A 294 " --> pdb=" O ALA A 285 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 58 through 60 removed outlier: 6.760A pdb=" N ASP A 58 " --> pdb=" O GLN B 656 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N ASN B 657 " --> pdb=" O PHE B 669 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N PHE B 669 " --> pdb=" O ASN B 657 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LEU B 659 " --> pdb=" O TYR B 667 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N TYR B 667 " --> pdb=" O ILE B 680 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N THR B 677 " --> pdb=" O VAL B 647 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 85 through 86 removed outlier: 6.954A pdb=" N THR A 178 " --> pdb=" O THR A 259 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 101 through 102 removed outlier: 3.581A pdb=" N GLY A 161 " --> pdb=" O TYR A 209 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 114 through 116 Processing sheet with id=AE4, first strand: chain 'A' and resid 318 through 321 Processing sheet with id=AE5, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AE6, first strand: chain 'A' and resid 353 through 355 removed outlier: 6.818A pdb=" N VAL A 354 " --> pdb=" O SER A 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'A' and resid 361 through 365 removed outlier: 6.400A pdb=" N ASN A 444 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ALA A 381 " --> pdb=" O ASN A 444 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'A' and resid 361 through 365 Processing sheet with id=AE9, first strand: chain 'A' and resid 369 through 370 Processing sheet with id=AF1, first strand: chain 'A' and resid 484 through 488 Processing sheet with id=AF2, first strand: chain 'A' and resid 492 through 493 Processing sheet with id=AF3, first strand: chain 'A' and resid 565 through 566 Processing sheet with id=AF4, first strand: chain 'A' and resid 571 through 572 Processing sheet with id=AF5, first strand: chain 'A' and resid 737 through 744 removed outlier: 6.450A pdb=" N TYR A 737 " --> pdb=" O PHE A 775 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N ASN A 777 " --> pdb=" O TYR A 737 " (cutoff:3.500A) removed outlier: 9.476A pdb=" N SER A 739 " --> pdb=" O ASN A 777 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N TYR A 755 " --> pdb=" O VAL A 751 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU A 749 " --> pdb=" O VAL A 757 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'A' and resid 797 through 815 removed outlier: 6.769A pdb=" N GLU A 798 " --> pdb=" O LYS A1169 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LYS A1169 " --> pdb=" O GLU A 798 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N GLN A 800 " --> pdb=" O THR A1167 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR A1167 " --> pdb=" O GLN A 800 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N TYR A1165 " --> pdb=" O PRO A 802 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLU A 804 " --> pdb=" O THR A1163 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE A1143 " --> pdb=" O PHE A1158 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N TYR A1160 " --> pdb=" O HIS A1141 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N HIS A1141 " --> pdb=" O TYR A1160 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'A' and resid 820 through 823 removed outlier: 4.192A pdb=" N LYS A 820 " --> pdb=" O LEU A 958 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'A' and resid 877 through 879 Processing sheet with id=AF9, first strand: chain 'A' and resid 889 through 890 Processing sheet with id=AG1, first strand: chain 'A' and resid 1214 through 1217 Processing sheet with id=AG2, first strand: chain 'A' and resid 1187 through 1192 Processing sheet with id=AG3, first strand: chain 'B' and resid 29 through 31 Processing sheet with id=AG4, first strand: chain 'B' and resid 42 through 44 removed outlier: 7.893A pdb=" N THR B 78 " --> pdb=" O PRO B 276 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLY B 106 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N PHE B 227 " --> pdb=" O ASN B 243 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ASN B 243 " --> pdb=" O PHE B 227 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ALA B 229 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'B' and resid 64 through 73 removed outlier: 3.859A pdb=" N ASN B 294 " --> pdb=" O ALA B 285 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'B' and resid 101 through 102 removed outlier: 3.976A pdb=" N GLY B 161 " --> pdb=" O TYR B 209 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'B' and resid 114 through 118 Processing sheet with id=AG8, first strand: chain 'B' and resid 191 through 193 removed outlier: 7.619A pdb=" N HIS B 193 " --> pdb=" O TYR B 175 " (cutoff:3.500A) removed outlier: 9.416A pdb=" N TYR B 175 " --> pdb=" O HIS B 193 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N THR B 259 " --> pdb=" O PRO B 176 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N THR B 178 " --> pdb=" O THR B 259 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'B' and resid 318 through 321 Processing sheet with id=AH1, first strand: chain 'B' and resid 325 through 326 Processing sheet with id=AH2, first strand: chain 'B' and resid 353 through 355 removed outlier: 6.706A pdb=" N VAL B 354 " --> pdb=" O SER B 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH2 Processing sheet with id=AH3, first strand: chain 'B' and resid 361 through 365 removed outlier: 3.613A pdb=" N SER B 401 " --> pdb=" O HIS B 606 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ASN B 444 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ALA B 381 " --> pdb=" O ASN B 444 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'B' and resid 361 through 365 removed outlier: 3.613A pdb=" N SER B 401 " --> pdb=" O HIS B 606 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'B' and resid 369 through 370 Processing sheet with id=AH6, first strand: chain 'B' and resid 484 through 488 Processing sheet with id=AH7, first strand: chain 'B' and resid 492 through 493 Processing sheet with id=AH8, first strand: chain 'B' and resid 565 through 566 Processing sheet with id=AH9, first strand: chain 'B' and resid 571 through 572 Processing sheet with id=AI1, first strand: chain 'B' and resid 743 through 744 removed outlier: 6.396A pdb=" N TYR B 755 " --> pdb=" O VAL B 751 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU B 749 " --> pdb=" O VAL B 757 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'B' and resid 797 through 815 removed outlier: 6.830A pdb=" N GLU B 798 " --> pdb=" O LYS B1169 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LYS B1169 " --> pdb=" O GLU B 798 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLN B 800 " --> pdb=" O THR B1167 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR B1167 " --> pdb=" O GLN B 800 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N TYR B1165 " --> pdb=" O PRO B 802 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLU B 804 " --> pdb=" O THR B1163 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'B' and resid 820 through 823 removed outlier: 4.200A pdb=" N LYS B 820 " --> pdb=" O LEU B 958 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'B' and resid 889 through 890 Processing sheet with id=AI5, first strand: chain 'B' and resid 1214 through 1217 Processing sheet with id=AI6, first strand: chain 'B' and resid 1187 through 1192 1281 hydrogen bonds defined for protein. 3399 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: 7.24 Time building geometry restraints manager: 4.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5860 1.31 - 1.45: 10528 1.45 - 1.59: 14065 1.59 - 1.73: 14 1.73 - 1.87: 234 Bond restraints: 30701 Sorted by residual: bond pdb=" C1 NAG K 2 " pdb=" O5 NAG K 2 " ideal model delta sigma weight residual 1.406 1.555 -0.149 2.00e-02 2.50e+03 5.52e+01 bond pdb=" C1 NAG b 2 " pdb=" O5 NAG b 2 " ideal model delta sigma weight residual 1.406 1.551 -0.145 2.00e-02 2.50e+03 5.28e+01 bond pdb=" C1 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.406 1.551 -0.145 2.00e-02 2.50e+03 5.26e+01 bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.548 -0.142 2.00e-02 2.50e+03 5.07e+01 bond pdb=" C1 NAG U 2 " pdb=" O5 NAG U 2 " ideal model delta sigma weight residual 1.406 1.548 -0.142 2.00e-02 2.50e+03 5.06e+01 ... (remaining 30696 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 36005 2.37 - 4.73: 4956 4.73 - 7.10: 718 7.10 - 9.47: 123 9.47 - 11.83: 16 Bond angle restraints: 41818 Sorted by residual: angle pdb=" N PRO B 981 " pdb=" CA PRO B 981 " pdb=" C PRO B 981 " ideal model delta sigma weight residual 110.70 122.53 -11.83 1.22e+00 6.72e-01 9.41e+01 angle pdb=" N PRO J 981 " pdb=" CA PRO J 981 " pdb=" C PRO J 981 " ideal model delta sigma weight residual 110.70 122.40 -11.70 1.22e+00 6.72e-01 9.19e+01 angle pdb=" N PRO A 981 " pdb=" CA PRO A 981 " pdb=" C PRO A 981 " ideal model delta sigma weight residual 110.70 122.18 -11.48 1.22e+00 6.72e-01 8.85e+01 angle pdb=" C PRO B 959 " pdb=" N PRO B 960 " pdb=" CA PRO B 960 " ideal model delta sigma weight residual 120.03 129.00 -8.97 9.90e-01 1.02e+00 8.21e+01 angle pdb=" N VAL A 608 " pdb=" CA VAL A 608 " pdb=" C VAL A 608 " ideal model delta sigma weight residual 110.72 119.52 -8.80 1.01e+00 9.80e-01 7.60e+01 ... (remaining 41813 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.53: 18977 33.53 - 67.07: 284 67.07 - 100.60: 106 100.60 - 134.14: 28 134.14 - 167.67: 1 Dihedral angle restraints: 19396 sinusoidal: 8314 harmonic: 11082 Sorted by residual: dihedral pdb=" CB CYS A1125 " pdb=" SG CYS A1125 " pdb=" SG CYS A1136 " pdb=" CB CYS A1136 " ideal model delta sinusoidal sigma weight residual -86.00 -176.12 90.12 1 1.00e+01 1.00e-02 9.62e+01 dihedral pdb=" CB CYS B1125 " pdb=" SG CYS B1125 " pdb=" SG CYS B1136 " pdb=" CB CYS B1136 " ideal model delta sinusoidal sigma weight residual 93.00 173.47 -80.47 1 1.00e+01 1.00e-02 8.01e+01 dihedral pdb=" CB CYS B 343 " pdb=" SG CYS B 343 " pdb=" SG CYS B 368 " pdb=" CB CYS B 368 " ideal model delta sinusoidal sigma weight residual 93.00 45.80 47.20 1 1.00e+01 1.00e-02 3.08e+01 ... (remaining 19393 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 3756 0.110 - 0.220: 1082 0.220 - 0.330: 130 0.330 - 0.440: 13 0.440 - 0.550: 16 Chirality restraints: 4997 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.68 0.28 2.00e-02 2.50e+03 1.97e+02 chirality pdb=" C1 NAG a 2 " pdb=" O4 NAG a 1 " pdb=" C2 NAG a 2 " pdb=" O5 NAG a 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.67 0.27 2.00e-02 2.50e+03 1.79e+02 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.67 0.27 2.00e-02 2.50e+03 1.78e+02 ... (remaining 4994 not shown) Planarity restraints: 5344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 738 " -0.067 2.00e-02 2.50e+03 6.94e-02 6.02e+01 pdb=" CG ASN B 738 " 0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN B 738 " 0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN B 738 " 0.106 2.00e-02 2.50e+03 pdb=" C1 NAG e 1 " -0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 449 " -0.043 2.00e-02 2.50e+03 4.69e-02 2.75e+01 pdb=" CG ASN A 449 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN A 449 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN A 449 " 0.074 2.00e-02 2.50e+03 pdb=" C1 NAG Y 1 " -0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 192 " 0.062 2.00e-02 2.50e+03 3.09e-02 2.39e+01 pdb=" CG TRP A 192 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 TRP A 192 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP A 192 " -0.028 2.00e-02 2.50e+03 pdb=" NE1 TRP A 192 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TRP A 192 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 192 " -0.040 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 192 " 0.038 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 192 " -0.014 2.00e-02 2.50e+03 pdb=" CH2 TRP A 192 " 0.031 2.00e-02 2.50e+03 ... (remaining 5341 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 9768 2.82 - 3.34: 27221 3.34 - 3.86: 50346 3.86 - 4.38: 61011 4.38 - 4.90: 99321 Nonbonded interactions: 247667 Sorted by model distance: nonbonded pdb=" N ASN A 371 " pdb=" OD1 ASN A 371 " model vdw 2.302 3.120 nonbonded pdb=" O CYS J 937 " pdb=" OH TYR J 952 " model vdw 2.302 3.040 nonbonded pdb=" N ASN J 371 " pdb=" OD1 ASN J 371 " model vdw 2.326 3.120 nonbonded pdb=" OH TYR J 737 " pdb=" OG1 THR J 770 " model vdw 2.341 3.040 nonbonded pdb=" OG SER J 662 " pdb=" OG1 THR B 64 " model vdw 2.363 3.040 ... (remaining 247662 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' and resid 15 through 1404) selection = (chain 'B' and (resid 15 through 32 or resid 36 through 150 or resid 157 through \ 505 or resid 517 through 902 or resid 909 through 1404)) selection = (chain 'J' and (resid 15 through 32 or resid 36 through 505 or resid 517 through \ 762 or resid 771 through 1404)) } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'G' selection = chain 'M' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'Y' selection = chain 'c' selection = chain 'h' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'K' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'i' selection = chain 'j' } ncs_group { reference = (chain 'H' and resid 18 through 118) selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 31.590 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 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 : 0.023 0.149 30849 Z= 1.199 Angle : 1.737 11.835 42199 Z= 1.137 Chirality : 0.103 0.550 4997 Planarity : 0.009 0.038 5301 Dihedral : 13.825 167.670 12105 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.42 % Allowed : 0.16 % Favored : 99.42 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.13), residues: 3542 helix: -0.16 (0.16), residues: 820 sheet: 0.78 (0.16), residues: 848 loop : 0.46 (0.14), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 998 TYR 0.056 0.008 TYR A1154 PHE 0.030 0.005 PHE A 126 TRP 0.062 0.009 TRP A 192 HIS 0.009 0.002 HIS B 193 Details of bonding type rmsd covalent geometry : bond 0.02264 (30701) covalent geometry : angle 1.71932 (41818) SS BOND : bond 0.02521 ( 63) SS BOND : angle 2.84308 ( 126) hydrogen bonds : bond 0.16232 ( 1225) hydrogen bonds : angle 7.45773 ( 3399) link_BETA1-4 : bond 0.03594 ( 42) link_BETA1-4 : angle 3.28083 ( 126) link_NAG-ASN : bond 0.03532 ( 43) link_NAG-ASN : angle 3.21160 ( 129) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 375 time to evaluate : 1.104 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: J 20 LYS cc_start: 0.8363 (mmtt) cc_final: 0.7905 (mmmm) REVERT: J 117 PHE cc_start: 0.6724 (m-80) cc_final: 0.6426 (m-80) REVERT: J 121 VAL cc_start: 0.8023 (t) cc_final: 0.7494 (t) REVERT: J 371 ASN cc_start: 0.8508 (OUTLIER) cc_final: 0.8284 (p0) REVERT: A 192 TRP cc_start: 0.6958 (t60) cc_final: 0.6366 (t60) REVERT: A 303 MET cc_start: 0.8886 (tpt) cc_final: 0.8619 (tpt) REVERT: A 387 ASN cc_start: 0.8772 (t0) cc_final: 0.8393 (t0) REVERT: B 371 ASN cc_start: 0.8104 (OUTLIER) cc_final: 0.7871 (p0) REVERT: B 532 HIS cc_start: 0.6092 (m-70) cc_final: 0.5501 (m170) REVERT: B 546 TYR cc_start: 0.7167 (m-80) cc_final: 0.6661 (m-80) outliers start: 13 outliers final: 9 residues processed: 388 average time/residue: 0.2030 time to fit residues: 123.0428 Evaluate side-chains 160 residues out of total 3105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 149 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 137 ASN Chi-restraints excluded: chain J residue 371 ASN Chi-restraints excluded: chain J residue 695 ASN Chi-restraints excluded: chain J residue 787 ASN Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 695 ASN Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 695 ASN Chi-restraints excluded: chain B residue 787 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 0.9980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 157 ASN J 177 HIS J 219 HIS J 418 GLN J 483 HIS J 762 ASN J 849 ASN J1042 GLN J1057 GLN A 186 ASN A 252 HIS A 483 HIS A 532 HIS A 609 ASN A 619 GLN A 724 ASN A 745 GLN A 839 GLN A 849 ASN A1103 GLN B 32 ASN B 219 HIS B 252 HIS B 483 HIS ** B 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1057 GLN B1071 GLN B1103 GLN B1138 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.087125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.067770 restraints weight = 64657.409| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 2.76 r_work: 0.2743 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2615 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 30849 Z= 0.153 Angle : 0.701 12.591 42199 Z= 0.360 Chirality : 0.046 0.344 4997 Planarity : 0.004 0.049 5301 Dihedral : 10.011 150.723 5901 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.93 % Allowed : 3.29 % Favored : 95.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.13), residues: 3542 helix: 1.60 (0.19), residues: 801 sheet: 0.65 (0.17), residues: 795 loop : 0.15 (0.13), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J1076 TYR 0.023 0.002 TYR A 79 PHE 0.014 0.002 PHE J 428 TRP 0.026 0.002 TRP A 460 HIS 0.007 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00327 (30701) covalent geometry : angle 0.67311 (41818) SS BOND : bond 0.00635 ( 63) SS BOND : angle 1.49811 ( 126) hydrogen bonds : bond 0.05862 ( 1225) hydrogen bonds : angle 5.63283 ( 3399) link_BETA1-4 : bond 0.00478 ( 42) link_BETA1-4 : angle 2.40832 ( 126) link_NAG-ASN : bond 0.00403 ( 43) link_NAG-ASN : angle 2.49386 ( 129) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 3105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 212 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 117 PHE cc_start: 0.7110 (m-80) cc_final: 0.6874 (m-80) REVERT: J 121 VAL cc_start: 0.7760 (t) cc_final: 0.7514 (t) REVERT: J 372 MET cc_start: 0.9258 (mmm) cc_final: 0.9011 (mmt) REVERT: J 387 ASN cc_start: 0.8571 (t0) cc_final: 0.8356 (t0) REVERT: J 735 ASN cc_start: 0.8854 (m-40) cc_final: 0.8460 (t0) REVERT: J 1197 MET cc_start: 0.9166 (OUTLIER) cc_final: 0.8784 (mtp) REVERT: A 191 LEU cc_start: 0.8845 (tp) cc_final: 0.8556 (tp) REVERT: A 387 ASN cc_start: 0.8915 (t0) cc_final: 0.8615 (t0) REVERT: A 849 ASN cc_start: 0.8717 (t0) cc_final: 0.8256 (t0) REVERT: A 1072 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8691 (mp0) REVERT: A 1194 ASN cc_start: 0.9052 (m-40) cc_final: 0.8824 (t0) REVERT: B 160 GLN cc_start: 0.8122 (tp40) cc_final: 0.7768 (tp-100) REVERT: B 191 LEU cc_start: 0.8366 (tp) cc_final: 0.8044 (tp) REVERT: B 371 ASN cc_start: 0.8043 (OUTLIER) cc_final: 0.7590 (p0) REVERT: B 943 ILE cc_start: 0.8805 (mm) cc_final: 0.8605 (mm) outliers start: 29 outliers final: 10 residues processed: 237 average time/residue: 0.1796 time to fit residues: 70.7878 Evaluate side-chains 164 residues out of total 3105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 24 ASP Chi-restraints excluded: chain J residue 1197 MET Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 1138 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 175 optimal weight: 7.9990 chunk 235 optimal weight: 0.3980 chunk 307 optimal weight: 7.9990 chunk 169 optimal weight: 5.9990 chunk 299 optimal weight: 5.9990 chunk 312 optimal weight: 10.0000 chunk 196 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 134 optimal weight: 7.9990 chunk 171 optimal weight: 4.9990 chunk 231 optimal weight: 0.5980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 532 HIS J1057 GLN ** J1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 HIS A 724 ASN A 839 GLN A 849 ASN B 32 ASN B 527 ASN ** B 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1103 GLN B1138 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.084617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.065175 restraints weight = 65179.134| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 2.77 r_work: 0.2676 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2548 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 30849 Z= 0.174 Angle : 0.634 15.157 42199 Z= 0.327 Chirality : 0.045 0.405 4997 Planarity : 0.004 0.045 5301 Dihedral : 7.203 134.005 5889 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.10 % Allowed : 4.32 % Favored : 94.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.14), residues: 3542 helix: 1.84 (0.19), residues: 806 sheet: 0.51 (0.17), residues: 790 loop : -0.11 (0.14), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J1076 TYR 0.023 0.002 TYR A 79 PHE 0.019 0.002 PHE A 188 TRP 0.034 0.002 TRP A 192 HIS 0.009 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00395 (30701) covalent geometry : angle 0.60655 (41818) SS BOND : bond 0.00268 ( 63) SS BOND : angle 1.86758 ( 126) hydrogen bonds : bond 0.05242 ( 1225) hydrogen bonds : angle 5.17119 ( 3399) link_BETA1-4 : bond 0.00565 ( 42) link_BETA1-4 : angle 1.99190 ( 126) link_NAG-ASN : bond 0.00420 ( 43) link_NAG-ASN : angle 2.18488 ( 129) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 3105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 163 time to evaluate : 0.956 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: J 387 ASN cc_start: 0.8599 (t0) cc_final: 0.8384 (t0) REVERT: J 735 ASN cc_start: 0.8911 (m-40) cc_final: 0.8577 (t0) REVERT: J 1197 MET cc_start: 0.9251 (OUTLIER) cc_final: 0.8805 (mtp) REVERT: A 186 ASN cc_start: 0.8009 (OUTLIER) cc_final: 0.7407 (m110) REVERT: A 191 LEU cc_start: 0.9023 (tp) cc_final: 0.8687 (tp) REVERT: A 849 ASN cc_start: 0.8709 (t0) cc_final: 0.8300 (t0) REVERT: A 1072 GLU cc_start: 0.9119 (mm-30) cc_final: 0.8791 (mp0) REVERT: A 1194 ASN cc_start: 0.9071 (m-40) cc_final: 0.8848 (t0) REVERT: B 160 GLN cc_start: 0.8192 (tp40) cc_final: 0.7584 (tp-100) REVERT: B 263 ARG cc_start: 0.8605 (tpp80) cc_final: 0.8073 (mtm-85) REVERT: B 371 ASN cc_start: 0.8256 (OUTLIER) cc_final: 0.7914 (p0) outliers start: 34 outliers final: 18 residues processed: 192 average time/residue: 0.1721 time to fit residues: 56.0740 Evaluate side-chains 164 residues out of total 3105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain J residue 137 ASN Chi-restraints excluded: chain J residue 371 ASN Chi-restraints excluded: chain J residue 569 ASP Chi-restraints excluded: chain J residue 651 TYR Chi-restraints excluded: chain J residue 825 CYS Chi-restraints excluded: chain J residue 1057 GLN Chi-restraints excluded: chain J residue 1197 MET Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 825 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 310 optimal weight: 10.0000 chunk 305 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 375 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 319 optimal weight: 8.9990 chunk 241 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 376 optimal weight: 10.0000 chunk 320 optimal weight: 5.9990 chunk 185 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 532 HIS J 839 GLN ** J1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN A 532 HIS A 724 ASN A 839 GLN A 849 ASN A 874 ASN B 32 ASN B 598 ASN ** B 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1103 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.081129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.061764 restraints weight = 65115.672| |-----------------------------------------------------------------------------| r_work (start): 0.2734 rms_B_bonded: 2.75 r_work: 0.2609 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2480 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 30849 Z= 0.248 Angle : 0.667 14.601 42199 Z= 0.342 Chirality : 0.047 0.476 4997 Planarity : 0.005 0.053 5301 Dihedral : 6.637 104.168 5889 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.13 % Allowed : 5.41 % Favored : 93.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.14), residues: 3542 helix: 1.60 (0.19), residues: 817 sheet: 0.41 (0.17), residues: 753 loop : -0.33 (0.13), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 80 TYR 0.022 0.002 TYR A 79 PHE 0.018 0.002 PHE B 103 TRP 0.015 0.002 TRP J 460 HIS 0.008 0.001 HIS J 532 Details of bonding type rmsd covalent geometry : bond 0.00589 (30701) covalent geometry : angle 0.64358 (41818) SS BOND : bond 0.00333 ( 63) SS BOND : angle 1.77028 ( 126) hydrogen bonds : bond 0.05523 ( 1225) hydrogen bonds : angle 5.22779 ( 3399) link_BETA1-4 : bond 0.00491 ( 42) link_BETA1-4 : angle 1.77020 ( 126) link_NAG-ASN : bond 0.00451 ( 43) link_NAG-ASN : angle 2.23119 ( 129) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 3105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 155 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 387 ASN cc_start: 0.8618 (t0) cc_final: 0.8363 (t0) REVERT: J 619 GLN cc_start: 0.8044 (pm20) cc_final: 0.7634 (pm20) REVERT: A 191 LEU cc_start: 0.9083 (tp) cc_final: 0.8816 (tp) REVERT: A 192 TRP cc_start: 0.7561 (OUTLIER) cc_final: 0.7354 (t60) REVERT: A 849 ASN cc_start: 0.8865 (t0) cc_final: 0.8499 (t0) REVERT: A 1072 GLU cc_start: 0.9078 (mm-30) cc_final: 0.8772 (mp0) REVERT: A 1194 ASN cc_start: 0.9077 (m-40) cc_final: 0.8730 (t0) REVERT: B 160 GLN cc_start: 0.8344 (tp40) cc_final: 0.7727 (tp-100) REVERT: B 263 ARG cc_start: 0.8721 (tpp80) cc_final: 0.8483 (tpp80) REVERT: B 371 ASN cc_start: 0.8653 (OUTLIER) cc_final: 0.8331 (p0) REVERT: B 546 TYR cc_start: 0.6845 (m-80) cc_final: 0.6508 (m-80) REVERT: B 943 ILE cc_start: 0.8825 (mm) cc_final: 0.8591 (tp) outliers start: 35 outliers final: 19 residues processed: 185 average time/residue: 0.1682 time to fit residues: 53.4088 Evaluate side-chains 159 residues out of total 3105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 24 ASP Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain J residue 137 ASN Chi-restraints excluded: chain J residue 651 TYR Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 192 TRP Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 706 ILE Chi-restraints excluded: chain B residue 748 ASP Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 1166 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 306 optimal weight: 9.9990 chunk 220 optimal weight: 6.9990 chunk 201 optimal weight: 2.9990 chunk 205 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 239 optimal weight: 0.5980 chunk 362 optimal weight: 0.6980 chunk 294 optimal weight: 5.9990 chunk 314 optimal weight: 7.9990 chunk 199 optimal weight: 4.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 532 HIS A 724 ASN A 849 ASN A 996 GLN B 532 HIS ** B 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1103 GLN B1138 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.081916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.062619 restraints weight = 65321.549| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 2.76 r_work: 0.2617 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2489 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 30849 Z= 0.195 Angle : 0.605 14.036 42199 Z= 0.311 Chirality : 0.045 0.385 4997 Planarity : 0.004 0.052 5301 Dihedral : 6.213 66.984 5889 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.26 % Allowed : 6.12 % Favored : 92.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.14), residues: 3542 helix: 1.67 (0.19), residues: 815 sheet: 0.35 (0.17), residues: 765 loop : -0.41 (0.14), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 264 TYR 0.022 0.001 TYR A 79 PHE 0.012 0.001 PHE B 103 TRP 0.016 0.002 TRP A 460 HIS 0.005 0.001 HIS J 219 Details of bonding type rmsd covalent geometry : bond 0.00462 (30701) covalent geometry : angle 0.58411 (41818) SS BOND : bond 0.00274 ( 63) SS BOND : angle 1.57581 ( 126) hydrogen bonds : bond 0.05073 ( 1225) hydrogen bonds : angle 5.08642 ( 3399) link_BETA1-4 : bond 0.00485 ( 42) link_BETA1-4 : angle 1.59336 ( 126) link_NAG-ASN : bond 0.00293 ( 43) link_NAG-ASN : angle 2.05947 ( 129) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 3105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 150 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 387 ASN cc_start: 0.8567 (t0) cc_final: 0.8331 (t0) REVERT: A 191 LEU cc_start: 0.9123 (tp) cc_final: 0.8801 (tp) REVERT: A 192 TRP cc_start: 0.7442 (OUTLIER) cc_final: 0.7037 (t60) REVERT: A 849 ASN cc_start: 0.8820 (t0) cc_final: 0.8471 (t0) REVERT: A 1072 GLU cc_start: 0.9070 (mm-30) cc_final: 0.8783 (mp0) REVERT: B 160 GLN cc_start: 0.8406 (tp40) cc_final: 0.7781 (tp-100) REVERT: B 263 ARG cc_start: 0.8682 (tpp80) cc_final: 0.8102 (mtm-85) REVERT: B 371 ASN cc_start: 0.8702 (OUTLIER) cc_final: 0.8373 (p0) REVERT: B 546 TYR cc_start: 0.6858 (m-80) cc_final: 0.6479 (m-80) REVERT: B 593 GLN cc_start: 0.8844 (mm-40) cc_final: 0.8636 (tt0) REVERT: B 943 ILE cc_start: 0.8862 (mm) cc_final: 0.8576 (tp) outliers start: 39 outliers final: 28 residues processed: 179 average time/residue: 0.1672 time to fit residues: 51.3385 Evaluate side-chains 167 residues out of total 3105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 137 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 24 ASP Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain J residue 137 ASN Chi-restraints excluded: chain J residue 651 TYR Chi-restraints excluded: chain J residue 810 MET Chi-restraints excluded: chain J residue 871 SER Chi-restraints excluded: chain J residue 1101 VAL Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 192 TRP Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 891 ASP Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 532 HIS Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 706 ILE Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 946 LEU Chi-restraints excluded: chain B residue 1138 ASN Chi-restraints excluded: chain B residue 1166 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 151 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 346 optimal weight: 9.9990 chunk 314 optimal weight: 7.9990 chunk 121 optimal weight: 3.9990 chunk 129 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 304 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 269 optimal weight: 8.9990 chunk 157 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 719 GLN A 724 ASN A 849 ASN B 32 ASN B 532 HIS ** B 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1103 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.080832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.061699 restraints weight = 65147.754| |-----------------------------------------------------------------------------| r_work (start): 0.2725 rms_B_bonded: 2.74 r_work: 0.2598 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2470 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 30849 Z= 0.229 Angle : 0.627 14.120 42199 Z= 0.321 Chirality : 0.045 0.384 4997 Planarity : 0.004 0.056 5301 Dihedral : 6.198 59.343 5889 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.19 % Allowed : 6.70 % Favored : 92.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.14), residues: 3542 helix: 1.68 (0.19), residues: 809 sheet: 0.29 (0.17), residues: 758 loop : -0.52 (0.14), residues: 1975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 264 TYR 0.021 0.002 TYR A 79 PHE 0.014 0.001 PHE B 103 TRP 0.015 0.002 TRP A 460 HIS 0.025 0.001 HIS B 532 Details of bonding type rmsd covalent geometry : bond 0.00546 (30701) covalent geometry : angle 0.60548 (41818) SS BOND : bond 0.00313 ( 63) SS BOND : angle 1.76849 ( 126) hydrogen bonds : bond 0.05216 ( 1225) hydrogen bonds : angle 5.11759 ( 3399) link_BETA1-4 : bond 0.00495 ( 42) link_BETA1-4 : angle 1.60674 ( 126) link_NAG-ASN : bond 0.00342 ( 43) link_NAG-ASN : angle 2.04278 ( 129) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 3105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 140 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 619 GLN cc_start: 0.8095 (pm20) cc_final: 0.7750 (pm20) REVERT: A 191 LEU cc_start: 0.9140 (tp) cc_final: 0.8814 (tp) REVERT: A 192 TRP cc_start: 0.7432 (OUTLIER) cc_final: 0.6991 (t60) REVERT: A 849 ASN cc_start: 0.8857 (t0) cc_final: 0.8471 (t0) REVERT: A 1072 GLU cc_start: 0.9050 (mm-30) cc_final: 0.8755 (mp0) REVERT: B 160 GLN cc_start: 0.8429 (tp40) cc_final: 0.7764 (tp-100) REVERT: B 263 ARG cc_start: 0.8739 (tpp80) cc_final: 0.8182 (mtm-85) REVERT: B 371 ASN cc_start: 0.8760 (OUTLIER) cc_final: 0.8466 (p0) REVERT: B 546 TYR cc_start: 0.6924 (m-80) cc_final: 0.6573 (m-80) REVERT: B 593 GLN cc_start: 0.8835 (mm-40) cc_final: 0.8632 (tt0) REVERT: B 899 LEU cc_start: 0.9170 (mt) cc_final: 0.8942 (mt) outliers start: 37 outliers final: 29 residues processed: 170 average time/residue: 0.1744 time to fit residues: 50.2881 Evaluate side-chains 164 residues out of total 3105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 24 ASP Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain J residue 137 ASN Chi-restraints excluded: chain J residue 651 TYR Chi-restraints excluded: chain J residue 677 THR Chi-restraints excluded: chain J residue 810 MET Chi-restraints excluded: chain J residue 871 SER Chi-restraints excluded: chain J residue 1101 VAL Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 192 TRP Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 891 ASP Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain B residue 32 ASN Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 706 ILE Chi-restraints excluded: chain B residue 748 ASP Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 946 LEU Chi-restraints excluded: chain B residue 1166 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 75 optimal weight: 4.9990 chunk 275 optimal weight: 6.9990 chunk 363 optimal weight: 5.9990 chunk 213 optimal weight: 4.9990 chunk 141 optimal weight: 0.8980 chunk 333 optimal weight: 2.9990 chunk 360 optimal weight: 0.0980 chunk 73 optimal weight: 6.9990 chunk 247 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 330 optimal weight: 5.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 719 GLN A 724 ASN A 839 GLN A1058 GLN B 32 ASN ** B 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.081325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.062317 restraints weight = 65166.239| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 2.73 r_work: 0.2605 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2478 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 30849 Z= 0.170 Angle : 0.586 13.840 42199 Z= 0.300 Chirality : 0.044 0.427 4997 Planarity : 0.004 0.053 5301 Dihedral : 6.015 56.873 5889 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.10 % Allowed : 6.86 % Favored : 92.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.14), residues: 3542 helix: 1.74 (0.19), residues: 815 sheet: 0.24 (0.17), residues: 775 loop : -0.49 (0.14), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 264 TYR 0.020 0.001 TYR A 79 PHE 0.011 0.001 PHE B 103 TRP 0.015 0.001 TRP A 460 HIS 0.005 0.001 HIS B 219 Details of bonding type rmsd covalent geometry : bond 0.00400 (30701) covalent geometry : angle 0.56316 (41818) SS BOND : bond 0.00271 ( 63) SS BOND : angle 1.56071 ( 126) hydrogen bonds : bond 0.04889 ( 1225) hydrogen bonds : angle 5.01939 ( 3399) link_BETA1-4 : bond 0.00463 ( 42) link_BETA1-4 : angle 1.55083 ( 126) link_NAG-ASN : bond 0.00269 ( 43) link_NAG-ASN : angle 2.14808 ( 129) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 3105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 619 GLN cc_start: 0.8001 (pm20) cc_final: 0.7644 (pm20) REVERT: A 191 LEU cc_start: 0.9135 (tp) cc_final: 0.8812 (tp) REVERT: A 192 TRP cc_start: 0.7379 (OUTLIER) cc_final: 0.6993 (t60) REVERT: A 849 ASN cc_start: 0.8753 (t0) cc_final: 0.8432 (t0) REVERT: A 1072 GLU cc_start: 0.9067 (mm-30) cc_final: 0.8788 (mp0) REVERT: B 160 GLN cc_start: 0.8406 (tp40) cc_final: 0.7730 (tp-100) REVERT: B 263 ARG cc_start: 0.8733 (tpp80) cc_final: 0.8186 (mtm-85) REVERT: B 303 MET cc_start: 0.9231 (tpt) cc_final: 0.8982 (tpt) REVERT: B 371 ASN cc_start: 0.8731 (OUTLIER) cc_final: 0.8422 (p0) REVERT: B 546 TYR cc_start: 0.7018 (m-80) cc_final: 0.6610 (m-80) REVERT: B 593 GLN cc_start: 0.8841 (mm-40) cc_final: 0.8626 (tt0) REVERT: B 873 MET cc_start: 0.9057 (mmm) cc_final: 0.8837 (mmm) REVERT: B 943 ILE cc_start: 0.8844 (mm) cc_final: 0.8615 (tp) outliers start: 34 outliers final: 28 residues processed: 172 average time/residue: 0.1611 time to fit residues: 47.6528 Evaluate side-chains 163 residues out of total 3105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 133 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 24 ASP Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain J residue 137 ASN Chi-restraints excluded: chain J residue 343 CYS Chi-restraints excluded: chain J residue 651 TYR Chi-restraints excluded: chain J residue 810 MET Chi-restraints excluded: chain J residue 871 SER Chi-restraints excluded: chain J residue 1101 VAL Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 192 TRP Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 891 ASP Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 1231 MET Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 706 ILE Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 946 LEU Chi-restraints excluded: chain B residue 1166 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 209 optimal weight: 6.9990 chunk 109 optimal weight: 0.0570 chunk 323 optimal weight: 0.9990 chunk 177 optimal weight: 0.8980 chunk 363 optimal weight: 4.9990 chunk 222 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 195 optimal weight: 0.9980 chunk 217 optimal weight: 1.9990 chunk 330 optimal weight: 7.9990 overall best weight: 0.7902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 719 GLN A 724 ASN A 849 ASN A1057 GLN B 839 GLN B 849 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.084146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.065249 restraints weight = 65409.450| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 2.76 r_work: 0.2677 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2548 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 30849 Z= 0.105 Angle : 0.530 14.329 42199 Z= 0.271 Chirality : 0.042 0.369 4997 Planarity : 0.004 0.052 5301 Dihedral : 5.488 54.621 5889 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.68 % Allowed : 7.25 % Favored : 92.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.14), residues: 3542 helix: 1.97 (0.19), residues: 807 sheet: 0.32 (0.18), residues: 776 loop : -0.43 (0.14), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 264 TYR 0.018 0.001 TYR A 79 PHE 0.012 0.001 PHE B 980 TRP 0.016 0.001 TRP A 460 HIS 0.003 0.001 HIS B 219 Details of bonding type rmsd covalent geometry : bond 0.00228 (30701) covalent geometry : angle 0.50889 (41818) SS BOND : bond 0.00258 ( 63) SS BOND : angle 1.13828 ( 126) hydrogen bonds : bond 0.04052 ( 1225) hydrogen bonds : angle 4.76869 ( 3399) link_BETA1-4 : bond 0.00486 ( 42) link_BETA1-4 : angle 1.46772 ( 126) link_NAG-ASN : bond 0.00272 ( 43) link_NAG-ASN : angle 2.17718 ( 129) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 3105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 161 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 223 GLU cc_start: 0.9089 (tt0) cc_final: 0.8877 (tt0) REVERT: J 619 GLN cc_start: 0.7882 (pm20) cc_final: 0.7457 (pm20) REVERT: J 1179 ASP cc_start: 0.8557 (m-30) cc_final: 0.7867 (t0) REVERT: A 191 LEU cc_start: 0.9168 (tp) cc_final: 0.8853 (tp) REVERT: A 849 ASN cc_start: 0.8571 (t0) cc_final: 0.8289 (t0) REVERT: A 1072 GLU cc_start: 0.9066 (mm-30) cc_final: 0.8821 (mp0) REVERT: B 160 GLN cc_start: 0.8326 (tp40) cc_final: 0.7688 (tp-100) REVERT: B 263 ARG cc_start: 0.8642 (tpp80) cc_final: 0.8232 (mtm-85) REVERT: B 371 ASN cc_start: 0.8583 (OUTLIER) cc_final: 0.8253 (p0) REVERT: B 546 TYR cc_start: 0.6899 (m-80) cc_final: 0.6525 (m-80) REVERT: B 873 MET cc_start: 0.8809 (mmm) cc_final: 0.8598 (mmm) REVERT: B 899 LEU cc_start: 0.9226 (mt) cc_final: 0.8953 (mt) REVERT: B 943 ILE cc_start: 0.8818 (mm) cc_final: 0.8617 (tp) outliers start: 21 outliers final: 13 residues processed: 176 average time/residue: 0.1644 time to fit residues: 50.1430 Evaluate side-chains 151 residues out of total 3105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 343 CYS Chi-restraints excluded: chain J residue 810 MET Chi-restraints excluded: chain J residue 1101 VAL Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 1166 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 252 optimal weight: 10.0000 chunk 201 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 128 optimal weight: 7.9990 chunk 136 optimal weight: 0.9990 chunk 212 optimal weight: 9.9990 chunk 205 optimal weight: 8.9990 chunk 29 optimal weight: 4.9990 chunk 313 optimal weight: 10.0000 chunk 163 optimal weight: 3.9990 chunk 241 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 719 GLN A 849 ASN B1011 GLN B1103 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.079760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.060771 restraints weight = 65708.492| |-----------------------------------------------------------------------------| r_work (start): 0.2700 rms_B_bonded: 2.74 r_work: 0.2574 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2448 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.097 30849 Z= 0.290 Angle : 0.675 21.318 42199 Z= 0.341 Chirality : 0.047 0.414 4997 Planarity : 0.005 0.061 5301 Dihedral : 6.197 58.491 5889 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.97 % Allowed : 7.34 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.14), residues: 3542 helix: 1.71 (0.19), residues: 803 sheet: 0.26 (0.18), residues: 761 loop : -0.57 (0.14), residues: 1978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 80 TYR 0.022 0.002 TYR J 79 PHE 0.019 0.002 PHE B 103 TRP 0.011 0.002 TRP A 460 HIS 0.005 0.001 HIS J 219 Details of bonding type rmsd covalent geometry : bond 0.00695 (30701) covalent geometry : angle 0.64271 (41818) SS BOND : bond 0.00464 ( 63) SS BOND : angle 1.66831 ( 126) hydrogen bonds : bond 0.05417 ( 1225) hydrogen bonds : angle 5.11295 ( 3399) link_BETA1-4 : bond 0.00506 ( 42) link_BETA1-4 : angle 1.61097 ( 126) link_NAG-ASN : bond 0.00443 ( 43) link_NAG-ASN : angle 3.14780 ( 129) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 3105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 133 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 619 GLN cc_start: 0.7897 (pm20) cc_final: 0.7476 (pm20) REVERT: J 1179 ASP cc_start: 0.8601 (m-30) cc_final: 0.7891 (t0) REVERT: A 191 LEU cc_start: 0.9158 (tp) cc_final: 0.8789 (tp) REVERT: A 192 TRP cc_start: 0.7419 (OUTLIER) cc_final: 0.7071 (t60) REVERT: A 849 ASN cc_start: 0.8884 (t0) cc_final: 0.8522 (t0) REVERT: A 1072 GLU cc_start: 0.9118 (mm-30) cc_final: 0.8812 (mp0) REVERT: B 160 GLN cc_start: 0.8445 (tp40) cc_final: 0.8038 (tp-100) REVERT: B 263 ARG cc_start: 0.8704 (tpp80) cc_final: 0.8210 (mtm-85) REVERT: B 269 THR cc_start: 0.9144 (m) cc_final: 0.8843 (p) REVERT: B 371 ASN cc_start: 0.8815 (OUTLIER) cc_final: 0.8558 (p0) REVERT: B 546 TYR cc_start: 0.7061 (m-80) cc_final: 0.6631 (m-80) outliers start: 30 outliers final: 25 residues processed: 157 average time/residue: 0.1580 time to fit residues: 43.1747 Evaluate side-chains 155 residues out of total 3105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 137 ASN Chi-restraints excluded: chain J residue 343 CYS Chi-restraints excluded: chain J residue 387 ASN Chi-restraints excluded: chain J residue 651 TYR Chi-restraints excluded: chain J residue 677 THR Chi-restraints excluded: chain J residue 810 MET Chi-restraints excluded: chain J residue 1101 VAL Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 192 TRP Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 533 ASN Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 1231 MET Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 387 ASN Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 1166 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 49 optimal weight: 0.8980 chunk 250 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 183 optimal weight: 1.9990 chunk 302 optimal weight: 0.7980 chunk 323 optimal weight: 5.9990 chunk 349 optimal weight: 0.9990 chunk 200 optimal weight: 4.9990 chunk 202 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 331 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 663 ASN J 719 GLN A 724 ASN A1057 GLN B1103 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.082649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.064081 restraints weight = 64838.270| |-----------------------------------------------------------------------------| r_work (start): 0.2765 rms_B_bonded: 2.66 r_work: 0.2641 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2515 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 30849 Z= 0.112 Angle : 0.545 13.855 42199 Z= 0.279 Chirality : 0.043 0.349 4997 Planarity : 0.004 0.053 5301 Dihedral : 5.719 59.268 5889 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.55 % Allowed : 7.76 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.14), residues: 3542 helix: 1.96 (0.19), residues: 802 sheet: 0.29 (0.18), residues: 791 loop : -0.49 (0.14), residues: 1949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 264 TYR 0.018 0.001 TYR J 79 PHE 0.010 0.001 PHE B 980 TRP 0.016 0.001 TRP A 460 HIS 0.003 0.001 HIS B 219 Details of bonding type rmsd covalent geometry : bond 0.00247 (30701) covalent geometry : angle 0.52226 (41818) SS BOND : bond 0.00243 ( 63) SS BOND : angle 1.17778 ( 126) hydrogen bonds : bond 0.04344 ( 1225) hydrogen bonds : angle 4.85341 ( 3399) link_BETA1-4 : bond 0.00482 ( 42) link_BETA1-4 : angle 1.46519 ( 126) link_NAG-ASN : bond 0.00294 ( 43) link_NAG-ASN : angle 2.29259 ( 129) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 3105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 619 GLN cc_start: 0.7807 (pm20) cc_final: 0.7406 (pm20) REVERT: J 1179 ASP cc_start: 0.8508 (m-30) cc_final: 0.7918 (t0) REVERT: A 191 LEU cc_start: 0.9102 (tp) cc_final: 0.8781 (tp) REVERT: A 849 ASN cc_start: 0.8732 (t0) cc_final: 0.8391 (t0) REVERT: B 160 GLN cc_start: 0.8366 (tp40) cc_final: 0.7710 (tp-100) REVERT: B 263 ARG cc_start: 0.8606 (tpp80) cc_final: 0.8196 (mtm-85) REVERT: B 371 ASN cc_start: 0.8706 (OUTLIER) cc_final: 0.8414 (p0) REVERT: B 546 TYR cc_start: 0.6875 (m-80) cc_final: 0.6505 (m-80) outliers start: 17 outliers final: 14 residues processed: 151 average time/residue: 0.1650 time to fit residues: 43.2767 Evaluate side-chains 148 residues out of total 3105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 343 CYS Chi-restraints excluded: chain J residue 1101 VAL Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 533 ASN Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 1166 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 347 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 200 optimal weight: 1.9990 chunk 128 optimal weight: 6.9990 chunk 104 optimal weight: 0.9980 chunk 267 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 372 optimal weight: 8.9990 chunk 133 optimal weight: 5.9990 chunk 13 optimal weight: 20.0000 chunk 140 optimal weight: 1.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 663 ASN J 719 GLN B 849 ASN B1103 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.081241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.062435 restraints weight = 65744.960| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 2.70 r_work: 0.2608 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2481 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 30849 Z= 0.178 Angle : 0.569 13.554 42199 Z= 0.293 Chirality : 0.044 0.374 4997 Planarity : 0.004 0.054 5301 Dihedral : 5.729 56.901 5889 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.71 % Allowed : 7.60 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.14), residues: 3542 helix: 1.90 (0.19), residues: 802 sheet: 0.26 (0.18), residues: 779 loop : -0.56 (0.14), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 264 TYR 0.020 0.001 TYR J 79 PHE 0.013 0.001 PHE B 103 TRP 0.012 0.001 TRP A 460 HIS 0.004 0.001 HIS J 219 Details of bonding type rmsd covalent geometry : bond 0.00419 (30701) covalent geometry : angle 0.54820 (41818) SS BOND : bond 0.00297 ( 63) SS BOND : angle 1.33409 ( 126) hydrogen bonds : bond 0.04735 ( 1225) hydrogen bonds : angle 4.90127 ( 3399) link_BETA1-4 : bond 0.00466 ( 42) link_BETA1-4 : angle 1.50574 ( 126) link_NAG-ASN : bond 0.00297 ( 43) link_NAG-ASN : angle 2.15812 ( 129) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6185.64 seconds wall clock time: 107 minutes 3.51 seconds (6423.51 seconds total)