Starting phenix.real_space_refine on Sun Jul 5 22:03:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7sbw_24990/07_2026/7sbw_24990.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sbw_24990/07_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_24990/07_2026/7sbw_24990.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sbw_24990/07_2026/7sbw_24990.map" model { file = "/net/cci-nas-00/data/ceres_data/7sbw_24990/07_2026/7sbw_24990.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sbw_24990/07_2026/7sbw_24990.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7sbw_24990/07_2026/7sbw_24990.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7sbw_24990/07_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-6108/lib/python3.11/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 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 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 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 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 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 chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "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 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 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 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 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 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 chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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 chiralities: 4 Time building chain proxies: 6.90, per 1000 atoms: 0.23 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: 2.26 Conformation dependent library (CDL) restraints added in 1.1 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: 1.05 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: 8.48 Time building geometry restraints manager: 3.07 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: 17401 33.53 - 67.07: 196 67.07 - 100.60: 32 100.60 - 134.14: 3 134.14 - 167.67: 1 Dihedral angle restraints: 17633 sinusoidal: 6551 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 17630 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: 3.950 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: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 28.820 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 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 : 10.635 167.670 10342 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/Z covalent geometry : bond 0.02264 / 1.20 (30701) covalent geometry : angle 1.71932 / 1.14 (41818) SS BOND : bond 0.02521 / 1.39 ( 63) SS BOND : angle 2.84308 / 1.55 ( 126) hydrogen bonds : bond 0.16232 / 9.30 ( 1225) hydrogen bonds : angle 7.45773 / 4.76 ( 3399) link_BETA1-4 : bond 0.03594 / 2.01 ( 42) link_BETA1-4 : angle 3.28083 / 1.66 ( 126) link_NAG-ASN : bond 0.03532 / 1.93 ( 43) link_NAG-ASN : angle 3.21160 / 1.62 ( 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 : 1.091 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: 0.7493 (t) REVERT: J 371 ASN cc_start: 0.8508 (OUTLIER) cc_final: 0.8283 (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 263 ARG cc_start: 0.8024 (mtp85) cc_final: 0.7733 (mtm-85) 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: 0.5502 (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: 0.2017 time to fit residues: 122.1754 Evaluate side-chains 162 residues out of total 3105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 151 time to evaluate : 1.083 ------------------------------------------------------------------------------- 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... 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 B1057 GLN B1071 GLN B1103 GLN B1138 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.087211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.067805 restraints weight = 64551.741| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 2.77 r_work: 0.2746 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2617 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 30849 Z= 0.155 Angle : 0.681 12.792 42199 Z= 0.356 Chirality : 0.045 0.286 4997 Planarity : 0.004 0.050 5301 Dihedral : 7.429 150.379 4138 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.97 % Allowed : 3.32 % Favored : 95.72 % 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: 0.81 (0.13), residues: 3542 helix: 1.57 (0.19), residues: 801 sheet: 0.64 (0.17), residues: 795 loop : 0.14 (0.13), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J1076 TYR 0.022 0.002 TYR A 79 PHE 0.014 0.002 PHE J 428 TRP 0.026 0.002 TRP A 460 HIS 0.006 0.001 HIS A 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (30701) covalent geometry : angle 0.65652 / 0.35 (41818) SS BOND : bond 0.00280 / 0.15 ( 63) SS BOND : angle 1.48797 / 0.81 ( 126) hydrogen bonds : bond 0.05805 / 3.32 ( 1225) hydrogen bonds : angle 5.62203 / 3.66 ( 3399) link_BETA1-4 : bond 0.00463 / 0.26 ( 42) link_BETA1-4 : angle 1.97956 / 1.03 ( 126) link_NAG-ASN : bond 0.00414 / 0.23 ( 43) link_NAG-ASN : angle 2.41484 / 1.22 ( 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 245 residues out of total 3105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 215 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 117 PHE cc_start: 0.7111 (m-80) cc_final: 0.6870 (m-80) REVERT: J 121 VAL cc_start: 0.7752 (t) cc_final: 0.7507 (t) REVERT: J 372 MET cc_start: 0.9255 (mmm) cc_final: 0.9017 (mmt) REVERT: J 387 ASN cc_start: 0.8571 (t0) cc_final: 0.8357 (t0) REVERT: J 735 ASN cc_start: 0.8857 (m-40) cc_final: 0.8456 (t0) REVERT: J 1197 MET cc_start: 0.9167 (OUTLIER) cc_final: 0.8791 (mtp) REVERT: A 191 LEU cc_start: 0.8877 (tp) cc_final: 0.8588 (tp) REVERT: A 192 TRP cc_start: 0.7371 (t60) cc_final: 0.7171 (t60) REVERT: A 387 ASN cc_start: 0.8818 (t0) cc_final: 0.8538 (t0) REVERT: A 849 ASN cc_start: 0.8703 (t0) cc_final: 0.8239 (t0) REVERT: A 1194 ASN cc_start: 0.9056 (m-40) cc_final: 0.8830 (t0) REVERT: B 160 GLN cc_start: 0.8124 (tp40) cc_final: 0.7765 (tp-100) REVERT: B 256 MET cc_start: 0.9113 (mtt) cc_final: 0.8882 (mtt) REVERT: B 263 ARG cc_start: 0.7892 (mtp85) cc_final: 0.7387 (mtm-85) REVERT: B 265 ASP cc_start: 0.8153 (m-30) cc_final: 0.7927 (m-30) REVERT: B 371 ASN cc_start: 0.8024 (OUTLIER) cc_final: 0.7470 (p0) REVERT: B 943 ILE cc_start: 0.8817 (mm) cc_final: 0.8615 (mm) outliers start: 30 outliers final: 10 residues processed: 240 average time/residue: 0.1757 time to fit residues: 70.0544 Evaluate side-chains 161 residues out of total 3105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 149 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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: 0.5980 chunk 307 optimal weight: 0.9990 chunk 169 optimal weight: 5.9990 chunk 299 optimal weight: 5.9990 chunk 312 optimal weight: 9.9990 chunk 196 optimal weight: 2.9990 chunk 23 optimal weight: 0.0670 chunk 134 optimal weight: 6.9990 chunk 171 optimal weight: 3.9990 chunk 231 optimal weight: 0.0470 overall best weight: 0.9420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 532 HIS J1057 GLN A 532 HIS A 724 ASN A 839 GLN B 32 ASN B 527 ASN B1103 GLN B1138 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.086422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.066972 restraints weight = 64894.881| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 2.79 r_work: 0.2727 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2599 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30849 Z= 0.129 Angle : 0.593 14.310 42199 Z= 0.308 Chirality : 0.043 0.311 4997 Planarity : 0.004 0.042 5301 Dihedral : 6.330 130.649 4126 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.13 % Allowed : 4.22 % Favored : 94.65 % 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: 0.79 (0.14), residues: 3542 helix: 1.87 (0.19), residues: 807 sheet: 0.54 (0.17), residues: 798 loop : 0.01 (0.14), residues: 1937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 718 TYR 0.022 0.001 TYR A 79 PHE 0.015 0.001 PHE A 188 TRP 0.014 0.001 TRP A 460 HIS 0.009 0.001 HIS A 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (30701) covalent geometry : angle 0.56988 / 0.30 (41818) SS BOND : bond 0.00255 / 0.14 ( 63) SS BOND : angle 1.75355 / 1.05 ( 126) hydrogen bonds : bond 0.04955 / 2.84 ( 1225) hydrogen bonds : angle 5.12907 / 3.33 ( 3399) link_BETA1-4 : bond 0.00509 / 0.28 ( 42) link_BETA1-4 : angle 1.49838 / 0.78 ( 126) link_NAG-ASN : bond 0.00277 / 0.16 ( 43) link_NAG-ASN : angle 2.16292 / 1.10 ( 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 211 residues out of total 3105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 176 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 735 ASN cc_start: 0.8859 (m-40) cc_final: 0.8543 (t0) REVERT: J 1197 MET cc_start: 0.9217 (OUTLIER) cc_final: 0.8746 (mtp) REVERT: A 191 LEU cc_start: 0.8949 (tp) cc_final: 0.8607 (tp) REVERT: A 387 ASN cc_start: 0.8834 (t0) cc_final: 0.8608 (t0) REVERT: A 849 ASN cc_start: 0.8645 (t0) cc_final: 0.8171 (t0) REVERT: B 160 GLN cc_start: 0.8096 (tp40) cc_final: 0.7502 (tp-100) REVERT: B 263 ARG cc_start: 0.8149 (mtp85) cc_final: 0.7446 (mtm-85) REVERT: B 265 ASP cc_start: 0.8266 (m-30) cc_final: 0.7994 (m-30) REVERT: B 371 ASN cc_start: 0.8065 (OUTLIER) cc_final: 0.7683 (p0) REVERT: B 943 ILE cc_start: 0.8913 (mm) cc_final: 0.8708 (mm) outliers start: 35 outliers final: 19 residues processed: 206 average time/residue: 0.1733 time to fit residues: 60.7641 Evaluate side-chains 166 residues out of total 3105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 1.108 ------------------------------------------------------------------------------- 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 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 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 503 LEU Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 825 CYS Chi-restraints excluded: chain B residue 1138 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 310 optimal weight: 9.9990 chunk 305 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 375 optimal weight: 0.0980 chunk 47 optimal weight: 8.9990 chunk 319 optimal weight: 6.9990 chunk 241 optimal weight: 0.9990 chunk 55 optimal weight: 8.9990 chunk 376 optimal weight: 8.9990 chunk 320 optimal weight: 4.9990 chunk 185 optimal weight: 3.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 532 HIS A 186 ASN A 532 HIS A 839 GLN A 996 GLN A1011 GLN A1213 ASN B 32 ASN B 839 GLN B1103 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.084410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.064907 restraints weight = 64710.883| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 2.79 r_work: 0.2679 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2551 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 30849 Z= 0.157 Angle : 0.591 14.369 42199 Z= 0.304 Chirality : 0.044 0.305 4997 Planarity : 0.004 0.048 5301 Dihedral : 5.779 98.518 4126 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.03 % Allowed : 5.35 % Favored : 93.62 % 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: 0.66 (0.14), residues: 3542 helix: 1.85 (0.19), residues: 809 sheet: 0.54 (0.17), residues: 780 loop : -0.15 (0.14), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 718 TYR 0.020 0.001 TYR A 79 PHE 0.012 0.001 PHE B 103 TRP 0.030 0.002 TRP A 192 HIS 0.006 0.001 HIS J 532 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (30701) covalent geometry : angle 0.57064 / 0.30 (41818) SS BOND : bond 0.00408 / 0.21 ( 63) SS BOND : angle 1.43766 / 0.84 ( 126) hydrogen bonds : bond 0.04850 / 2.78 ( 1225) hydrogen bonds : angle 5.00284 / 3.23 ( 3399) link_BETA1-4 : bond 0.00435 / 0.25 ( 42) link_BETA1-4 : angle 1.41371 / 0.73 ( 126) link_NAG-ASN : bond 0.00323 / 0.18 ( 43) link_NAG-ASN : angle 2.18382 / 1.12 ( 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 189 residues out of total 3105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 157 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 735 ASN cc_start: 0.8868 (m-40) cc_final: 0.8552 (t0) REVERT: A 23 LEU cc_start: 0.6679 (mp) cc_final: 0.6225 (tp) REVERT: A 30 LEU cc_start: 0.8963 (mp) cc_final: 0.8646 (mm) REVERT: A 191 LEU cc_start: 0.9044 (tp) cc_final: 0.8776 (tp) REVERT: A 849 ASN cc_start: 0.8736 (t0) cc_final: 0.8294 (t0) REVERT: A 1072 GLU cc_start: 0.8963 (mp0) cc_final: 0.8525 (mp0) REVERT: B 160 GLN cc_start: 0.8149 (tp40) cc_final: 0.7544 (tp-100) REVERT: B 263 ARG cc_start: 0.8274 (mtp85) cc_final: 0.7542 (mtm-85) REVERT: B 265 ASP cc_start: 0.8291 (m-30) cc_final: 0.7745 (m-30) REVERT: B 371 ASN cc_start: 0.8266 (OUTLIER) cc_final: 0.7886 (p0) REVERT: B 839 GLN cc_start: 0.9035 (OUTLIER) cc_final: 0.8734 (mt0) outliers start: 32 outliers final: 24 residues processed: 185 average time/residue: 0.1570 time to fit residues: 49.6719 Evaluate side-chains 166 residues out of total 3105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 0.998 ------------------------------------------------------------------------------- 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 387 ASN Chi-restraints excluded: chain J residue 469 ASN Chi-restraints excluded: chain J residue 569 ASP 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 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 888 PHE Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 1213 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 503 LEU Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 825 CYS Chi-restraints excluded: chain B residue 839 GLN Chi-restraints excluded: chain B residue 1166 VAL Chi-restraints excluded: chain B residue 1207 GLU 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: 10.0000 chunk 201 optimal weight: 8.9990 chunk 205 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 239 optimal weight: 5.9990 chunk 362 optimal weight: 0.9990 chunk 294 optimal weight: 7.9990 chunk 314 optimal weight: 7.9990 chunk 199 optimal weight: 4.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 ASN A 532 HIS A 849 ASN B 32 ASN B 598 ASN B 839 GLN B1103 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.081752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.062451 restraints weight = 65361.724| |-----------------------------------------------------------------------------| r_work (start): 0.2739 rms_B_bonded: 2.75 r_work: 0.2614 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2485 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8991 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 30849 Z= 0.229 Angle : 0.626 14.903 42199 Z= 0.324 Chirality : 0.045 0.322 4997 Planarity : 0.004 0.055 5301 Dihedral : 5.673 67.383 4126 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.19 % Allowed : 5.73 % Favored : 93.08 % 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: 0.47 (0.14), residues: 3542 helix: 1.77 (0.19), residues: 810 sheet: 0.44 (0.18), residues: 751 loop : -0.32 (0.14), residues: 1981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J1076 TYR 0.022 0.002 TYR J 79 PHE 0.016 0.002 PHE B 103 TRP 0.013 0.002 TRP J 460 HIS 0.006 0.001 HIS J 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.23 (30701) covalent geometry : angle 0.60875 / 0.32 (41818) SS BOND : bond 0.00320 / 0.19 ( 63) SS BOND : angle 1.55345 / 0.90 ( 126) hydrogen bonds : bond 0.05221 / 3.00 ( 1225) hydrogen bonds : angle 5.09387 / 3.29 ( 3399) link_BETA1-4 : bond 0.00433 / 0.24 ( 42) link_BETA1-4 : angle 1.39979 / 0.73 ( 126) link_NAG-ASN : bond 0.00369 / 0.21 ( 43) link_NAG-ASN : angle 1.99083 / 1.02 ( 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 182 residues out of total 3105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 145 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 619 GLN cc_start: 0.7962 (pm20) cc_final: 0.7574 (pm20) REVERT: J 735 ASN cc_start: 0.8881 (m-40) cc_final: 0.8546 (t0) REVERT: J 1072 GLU cc_start: 0.8298 (tp30) cc_final: 0.8077 (mm-30) REVERT: A 191 LEU cc_start: 0.9079 (tp) cc_final: 0.8768 (tp) REVERT: A 192 TRP cc_start: 0.7431 (OUTLIER) cc_final: 0.7122 (t60) REVERT: A 849 ASN cc_start: 0.8821 (t0) cc_final: 0.8442 (t0) REVERT: A 1072 GLU cc_start: 0.9004 (mp0) cc_final: 0.8464 (mp0) REVERT: B 160 GLN cc_start: 0.8325 (tp40) cc_final: 0.7707 (tp-100) REVERT: B 263 ARG cc_start: 0.8420 (mtp85) cc_final: 0.7690 (mtm-85) REVERT: B 265 ASP cc_start: 0.8331 (m-30) cc_final: 0.7984 (m-30) REVERT: B 371 ASN cc_start: 0.8518 (OUTLIER) cc_final: 0.8185 (p0) REVERT: B 943 ILE cc_start: 0.8814 (mm) cc_final: 0.8590 (tp) outliers start: 37 outliers final: 22 residues processed: 177 average time/residue: 0.1659 time to fit residues: 49.9526 Evaluate side-chains 157 residues out of total 3105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 1.045 ------------------------------------------------------------------------------- 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 387 ASN Chi-restraints excluded: chain J residue 569 ASP Chi-restraints excluded: chain J residue 651 TYR 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 B residue 88 ASP Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 503 LEU 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: 0.8980 chunk 107 optimal weight: 10.0000 chunk 346 optimal weight: 8.9990 chunk 314 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 304 optimal weight: 0.0770 chunk 59 optimal weight: 0.9990 chunk 269 optimal weight: 5.9990 chunk 157 optimal weight: 8.9990 overall best weight: 1.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 ASN A 839 GLN A 849 ASN B 32 ASN B 849 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.083680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.064333 restraints weight = 64713.180| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 2.79 r_work: 0.2662 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2534 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8953 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 30849 Z= 0.121 Angle : 0.548 15.132 42199 Z= 0.282 Chirality : 0.042 0.288 4997 Planarity : 0.004 0.051 5301 Dihedral : 5.259 53.673 4126 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.90 % Allowed : 6.41 % Favored : 92.69 % 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: 0.51 (0.14), residues: 3542 helix: 1.86 (0.19), residues: 815 sheet: 0.47 (0.18), residues: 778 loop : -0.34 (0.14), residues: 1949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 264 TYR 0.019 0.001 TYR A 79 PHE 0.011 0.001 PHE B 980 TRP 0.015 0.001 TRP A 460 HIS 0.004 0.001 HIS B 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (30701) covalent geometry : angle 0.53123 / 0.28 (41818) SS BOND : bond 0.00210 / 0.12 ( 63) SS BOND : angle 1.38547 / 0.83 ( 126) hydrogen bonds : bond 0.04440 / 2.55 ( 1225) hydrogen bonds : angle 4.87995 / 3.15 ( 3399) link_BETA1-4 : bond 0.00447 / 0.25 ( 42) link_BETA1-4 : angle 1.28243 / 0.67 ( 126) link_NAG-ASN : bond 0.00229 / 0.12 ( 43) link_NAG-ASN : angle 1.79022 / 0.92 ( 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 178 residues out of total 3105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 619 GLN cc_start: 0.7917 (pm20) cc_final: 0.7522 (pm20) REVERT: J 735 ASN cc_start: 0.8754 (m-40) cc_final: 0.8482 (t0) REVERT: A 191 LEU cc_start: 0.9077 (tp) cc_final: 0.8771 (tp) REVERT: A 1072 GLU cc_start: 0.9027 (mp0) cc_final: 0.8455 (mp0) REVERT: B 160 GLN cc_start: 0.8312 (tp40) cc_final: 0.7701 (tp-100) REVERT: B 263 ARG cc_start: 0.8242 (mtp85) cc_final: 0.7456 (mtm-85) REVERT: B 265 ASP cc_start: 0.8237 (m-30) cc_final: 0.7789 (m-30) REVERT: B 269 THR cc_start: 0.8924 (m) cc_final: 0.8610 (p) REVERT: B 371 ASN cc_start: 0.8423 (OUTLIER) cc_final: 0.8043 (p0) REVERT: B 593 GLN cc_start: 0.8841 (mm-40) cc_final: 0.8629 (tt0) REVERT: B 943 ILE cc_start: 0.8800 (mm) cc_final: 0.8594 (tp) outliers start: 28 outliers final: 18 residues processed: 171 average time/residue: 0.1672 time to fit residues: 48.4371 Evaluate side-chains 154 residues out of total 3105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 58 ASP 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 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 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 470 SER Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 787 ASN 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: 3.9990 chunk 275 optimal weight: 10.0000 chunk 363 optimal weight: 5.9990 chunk 213 optimal weight: 0.4980 chunk 141 optimal weight: 6.9990 chunk 333 optimal weight: 7.9990 chunk 360 optimal weight: 0.6980 chunk 73 optimal weight: 4.9990 chunk 247 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 330 optimal weight: 7.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 719 GLN A 186 ASN A 849 ASN B 32 ASN B 532 HIS B 849 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.081474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.062253 restraints weight = 65316.242| |-----------------------------------------------------------------------------| r_work (start): 0.2738 rms_B_bonded: 2.76 r_work: 0.2613 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2486 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8991 moved from start: 0.3511 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= 0.210 Angle : 0.605 14.791 42199 Z= 0.310 Chirality : 0.044 0.367 4997 Planarity : 0.004 0.056 5301 Dihedral : 5.418 48.336 4126 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.10 % Allowed : 6.54 % Favored : 92.37 % 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: 0.39 (0.14), residues: 3542 helix: 1.80 (0.19), residues: 810 sheet: 0.41 (0.18), residues: 761 loop : -0.43 (0.14), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 80 TYR 0.021 0.002 TYR J 79 PHE 0.015 0.001 PHE B 103 TRP 0.011 0.001 TRP A 460 HIS 0.005 0.001 HIS J 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.21 (30701) covalent geometry : angle 0.58604 / 0.30 (41818) SS BOND : bond 0.00306 / 0.18 ( 63) SS BOND : angle 1.57408 / 0.94 ( 126) hydrogen bonds : bond 0.04980 / 2.87 ( 1225) hydrogen bonds : angle 4.98512 / 3.21 ( 3399) link_BETA1-4 : bond 0.00449 / 0.25 ( 42) link_BETA1-4 : angle 1.33635 / 0.69 ( 126) link_NAG-ASN : bond 0.00338 / 0.19 ( 43) link_NAG-ASN : angle 2.09163 / 1.07 ( 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 176 residues out of total 3105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 142 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 LEU cc_start: 0.9107 (tp) cc_final: 0.8776 (tp) REVERT: A 192 TRP cc_start: 0.7408 (OUTLIER) cc_final: 0.7054 (t60) REVERT: A 849 ASN cc_start: 0.8579 (t0) cc_final: 0.8368 (t0) REVERT: A 1072 GLU cc_start: 0.9037 (mp0) cc_final: 0.8430 (mp0) REVERT: B 160 GLN cc_start: 0.8437 (tp40) cc_final: 0.7812 (tp-100) REVERT: B 263 ARG cc_start: 0.8400 (mtp85) cc_final: 0.7745 (mtm-85) REVERT: B 265 ASP cc_start: 0.8265 (m-30) cc_final: 0.8013 (m-30) REVERT: B 371 ASN cc_start: 0.8653 (OUTLIER) cc_final: 0.8314 (p0) REVERT: B 593 GLN cc_start: 0.8865 (mm-40) cc_final: 0.8642 (tt0) REVERT: B 943 ILE cc_start: 0.8857 (mm) cc_final: 0.8574 (tp) outliers start: 34 outliers final: 27 residues processed: 171 average time/residue: 0.1703 time to fit residues: 49.7887 Evaluate side-chains 161 residues out of total 3105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 1.170 ------------------------------------------------------------------------------- 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 137 ASN Chi-restraints excluded: chain J residue 266 ILE Chi-restraints excluded: chain J residue 387 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 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 972 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 532 HIS Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 1166 VAL Chi-restraints excluded: chain B residue 1219 THR Chi-restraints excluded: chain B residue 1220 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 209 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 323 optimal weight: 0.9990 chunk 177 optimal weight: 2.9990 chunk 363 optimal weight: 5.9990 chunk 222 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 195 optimal weight: 8.9990 chunk 217 optimal weight: 3.9990 chunk 330 optimal weight: 0.0980 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 849 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.082649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.063425 restraints weight = 65446.737| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 2.76 r_work: 0.2639 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2512 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8978 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 30849 Z= 0.140 Angle : 0.564 14.815 42199 Z= 0.288 Chirality : 0.043 0.412 4997 Planarity : 0.004 0.053 5301 Dihedral : 5.261 46.387 4126 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.90 % Allowed : 7.05 % 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: 0.40 (0.14), residues: 3542 helix: 1.85 (0.19), residues: 814 sheet: 0.38 (0.18), residues: 767 loop : -0.44 (0.14), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 264 TYR 0.019 0.001 TYR A 79 PHE 0.011 0.001 PHE B 980 TRP 0.014 0.001 TRP A 460 HIS 0.012 0.001 HIS B 532 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (30701) covalent geometry : angle 0.54189 / 0.28 (41818) SS BOND : bond 0.00241 / 0.13 ( 63) SS BOND : angle 1.37443 / 0.82 ( 126) hydrogen bonds : bond 0.04601 / 2.65 ( 1225) hydrogen bonds : angle 4.89026 / 3.15 ( 3399) link_BETA1-4 : bond 0.00443 / 0.25 ( 42) link_BETA1-4 : angle 1.28587 / 0.67 ( 126) link_NAG-ASN : bond 0.00251 / 0.14 ( 43) link_NAG-ASN : angle 2.33670 / 1.17 ( 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 169 residues out of total 3105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 619 GLN cc_start: 0.7960 (pm20) cc_final: 0.7655 (pm20) REVERT: J 1179 ASP cc_start: 0.8572 (m-30) cc_final: 0.7941 (t0) REVERT: A 191 LEU cc_start: 0.9089 (tp) cc_final: 0.8769 (tp) REVERT: A 192 TRP cc_start: 0.7495 (OUTLIER) cc_final: 0.7010 (t60) REVERT: A 849 ASN cc_start: 0.8515 (t0) cc_final: 0.8295 (t0) REVERT: A 1072 GLU cc_start: 0.9036 (mp0) cc_final: 0.8428 (mp0) REVERT: B 160 GLN cc_start: 0.8383 (tp40) cc_final: 0.7754 (tp-100) REVERT: B 263 ARG cc_start: 0.8390 (mtp85) cc_final: 0.7766 (mtm-85) REVERT: B 265 ASP cc_start: 0.8259 (m-30) cc_final: 0.8014 (m-30) REVERT: B 371 ASN cc_start: 0.8587 (OUTLIER) cc_final: 0.8213 (p0) REVERT: B 873 MET cc_start: 0.9001 (mmm) cc_final: 0.8764 (mmm) REVERT: B 943 ILE cc_start: 0.8834 (mm) cc_final: 0.8564 (tp) outliers start: 28 outliers final: 23 residues processed: 163 average time/residue: 0.1709 time to fit residues: 47.0385 Evaluate side-chains 157 residues out of total 3105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 0.992 ------------------------------------------------------------------------------- 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 137 ASN Chi-restraints excluded: chain J residue 266 ILE 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 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 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 470 SER Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 1166 VAL Chi-restraints excluded: chain B residue 1220 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 252 optimal weight: 0.7980 chunk 201 optimal weight: 8.9990 chunk 74 optimal weight: 2.9990 chunk 128 optimal weight: 6.9990 chunk 136 optimal weight: 3.9990 chunk 212 optimal weight: 8.9990 chunk 205 optimal weight: 4.9990 chunk 29 optimal weight: 0.5980 chunk 313 optimal weight: 0.5980 chunk 163 optimal weight: 3.9990 chunk 241 optimal weight: 5.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 719 GLN B 849 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.082667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.063682 restraints weight = 64972.129| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 2.75 r_work: 0.2640 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2513 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8974 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 30849 Z= 0.149 Angle : 0.566 18.014 42199 Z= 0.288 Chirality : 0.044 0.678 4997 Planarity : 0.004 0.053 5301 Dihedral : 5.196 46.373 4126 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.90 % Allowed : 7.25 % Favored : 91.85 % 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: 0.38 (0.14), residues: 3542 helix: 1.88 (0.19), residues: 814 sheet: 0.33 (0.18), residues: 779 loop : -0.46 (0.14), residues: 1949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 264 TYR 0.019 0.001 TYR J 79 PHE 0.012 0.001 PHE B 980 TRP 0.013 0.001 TRP A 460 HIS 0.004 0.001 HIS B 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (30701) covalent geometry : angle 0.54425 / 0.28 (41818) SS BOND : bond 0.00249 / 0.14 ( 63) SS BOND : angle 1.31726 / 0.78 ( 126) hydrogen bonds : bond 0.04556 / 2.62 ( 1225) hydrogen bonds : angle 4.85438 / 3.12 ( 3399) link_BETA1-4 : bond 0.00444 / 0.25 ( 42) link_BETA1-4 : angle 1.27825 / 0.67 ( 126) link_NAG-ASN : bond 0.00461 / 0.23 ( 43) link_NAG-ASN : angle 2.36387 / 1.05 ( 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 165 residues out of total 3105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 619 GLN cc_start: 0.8020 (pm20) cc_final: 0.7662 (pm20) REVERT: J 1179 ASP cc_start: 0.8557 (m-30) cc_final: 0.7918 (t0) REVERT: A 191 LEU cc_start: 0.9086 (tp) cc_final: 0.8762 (tp) REVERT: A 192 TRP cc_start: 0.7513 (OUTLIER) cc_final: 0.7025 (t60) REVERT: A 849 ASN cc_start: 0.8502 (t0) cc_final: 0.8289 (t0) REVERT: A 1072 GLU cc_start: 0.9040 (mp0) cc_final: 0.8403 (mp0) REVERT: B 160 GLN cc_start: 0.8379 (tp40) cc_final: 0.7737 (tp-100) REVERT: B 263 ARG cc_start: 0.8343 (mtp85) cc_final: 0.7728 (mtm-85) REVERT: B 265 ASP cc_start: 0.8255 (m-30) cc_final: 0.8018 (m-30) REVERT: B 269 THR cc_start: 0.8956 (m) cc_final: 0.8648 (p) REVERT: B 371 ASN cc_start: 0.8630 (OUTLIER) cc_final: 0.8280 (p0) REVERT: B 873 MET cc_start: 0.8996 (mmm) cc_final: 0.8779 (mmm) REVERT: B 943 ILE cc_start: 0.8863 (mm) cc_final: 0.8582 (tp) outliers start: 28 outliers final: 24 residues processed: 159 average time/residue: 0.1524 time to fit residues: 42.0267 Evaluate side-chains 157 residues out of total 3105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.893 ------------------------------------------------------------------------------- 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 137 ASN Chi-restraints excluded: chain J residue 266 ILE Chi-restraints excluded: chain J residue 387 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 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 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 371 ASN Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 1166 VAL Chi-restraints excluded: chain B residue 1220 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 49 optimal weight: 5.9990 chunk 250 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 183 optimal weight: 0.0970 chunk 302 optimal weight: 0.8980 chunk 323 optimal weight: 4.9990 chunk 349 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 chunk 202 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 331 optimal weight: 9.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 839 GLN A1058 GLN B 849 ASN B1011 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.082734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.063822 restraints weight = 64874.325| |-----------------------------------------------------------------------------| r_work (start): 0.2765 rms_B_bonded: 2.72 r_work: 0.2641 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2515 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8975 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 30849 Z= 0.147 Angle : 0.555 15.331 42199 Z= 0.285 Chirality : 0.043 0.528 4997 Planarity : 0.004 0.054 5301 Dihedral : 5.137 46.619 4126 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.97 % Allowed : 7.41 % Favored : 91.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.14), residues: 3542 helix: 1.92 (0.19), residues: 808 sheet: 0.30 (0.18), residues: 780 loop : -0.47 (0.14), residues: 1954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J1076 TYR 0.019 0.001 TYR A 79 PHE 0.011 0.001 PHE B 980 TRP 0.013 0.001 TRP A 460 HIS 0.004 0.001 HIS B 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (30701) covalent geometry : angle 0.53783 / 0.28 (41818) SS BOND : bond 0.00240 / 0.13 ( 63) SS BOND : angle 1.26144 / 0.75 ( 126) hydrogen bonds : bond 0.04522 / 2.60 ( 1225) hydrogen bonds : angle 4.84344 / 3.11 ( 3399) link_BETA1-4 : bond 0.00446 / 0.25 ( 42) link_BETA1-4 : angle 1.27035 / 0.66 ( 126) link_NAG-ASN : bond 0.00371 / 0.19 ( 43) link_NAG-ASN : angle 1.97021 / 0.94 ( 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 165 residues out of total 3105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 135 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 619 GLN cc_start: 0.8008 (pm20) cc_final: 0.7661 (pm20) REVERT: J 1072 GLU cc_start: 0.8233 (tp30) cc_final: 0.7800 (tm-30) REVERT: J 1179 ASP cc_start: 0.8541 (m-30) cc_final: 0.7916 (t0) REVERT: A 191 LEU cc_start: 0.9106 (tp) cc_final: 0.8790 (tp) REVERT: A 192 TRP cc_start: 0.7520 (OUTLIER) cc_final: 0.7054 (t60) REVERT: B 160 GLN cc_start: 0.8351 (tp40) cc_final: 0.7715 (tp-100) REVERT: B 263 ARG cc_start: 0.8321 (mtp85) cc_final: 0.7767 (mtm-85) REVERT: B 269 THR cc_start: 0.9176 (m) cc_final: 0.8954 (p) REVERT: B 371 ASN cc_start: 0.8637 (OUTLIER) cc_final: 0.8298 (p0) REVERT: B 873 MET cc_start: 0.9000 (mmm) cc_final: 0.8765 (mmm) REVERT: B 943 ILE cc_start: 0.8873 (mm) cc_final: 0.8595 (tp) outliers start: 30 outliers final: 25 residues processed: 159 average time/residue: 0.1551 time to fit residues: 42.7231 Evaluate side-chains 156 residues out of total 3105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 1.047 ------------------------------------------------------------------------------- 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 137 ASN Chi-restraints excluded: chain J residue 266 ILE Chi-restraints excluded: chain J residue 343 CYS Chi-restraints excluded: chain J residue 387 ASN 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 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 470 SER Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 1166 VAL Chi-restraints excluded: chain B residue 1220 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 347 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 104 optimal weight: 0.7980 chunk 267 optimal weight: 7.9990 chunk 33 optimal weight: 8.9990 chunk 372 optimal weight: 7.9990 chunk 133 optimal weight: 2.9990 chunk 13 optimal weight: 20.0000 chunk 140 optimal weight: 5.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J1103 GLN A1057 GLN B 532 HIS B 849 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.082069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.063086 restraints weight = 65379.464| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 2.75 r_work: 0.2627 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2500 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8986 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 30849 Z= 0.175 Angle : 0.569 14.638 42199 Z= 0.293 Chirality : 0.044 0.436 4997 Planarity : 0.004 0.056 5301 Dihedral : 5.203 46.584 4126 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.03 % Allowed : 7.47 % Favored : 91.50 % 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: 0.35 (0.14), residues: 3542 helix: 1.98 (0.19), residues: 798 sheet: 0.31 (0.18), residues: 777 loop : -0.51 (0.14), residues: 1967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 264 TYR 0.029 0.001 TYR B 546 PHE 0.012 0.001 PHE B 103 TRP 0.011 0.001 TRP A 460 HIS 0.007 0.001 HIS B 532 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.17 (30701) covalent geometry : angle 0.55285 / 0.29 (41818) SS BOND : bond 0.00268 / 0.15 ( 63) SS BOND : angle 1.33149 / 0.79 ( 126) hydrogen bonds : bond 0.04703 / 2.71 ( 1225) hydrogen bonds : angle 4.88525 / 3.14 ( 3399) link_BETA1-4 : bond 0.00443 / 0.25 ( 42) link_BETA1-4 : angle 1.28031 / 0.67 ( 126) link_NAG-ASN : bond 0.00362 / 0.19 ( 43) link_NAG-ASN : angle 1.90126 / 0.93 ( 129) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6147.59 seconds wall clock time: 106 minutes 22.71 seconds (6382.71 seconds total)