Starting phenix.real_space_refine on Fri Mar 6 06:55:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ohw_20070/03_2026/6ohw_20070.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ohw_20070/03_2026/6ohw_20070.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ohw_20070/03_2026/6ohw_20070.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ohw_20070/03_2026/6ohw_20070.map" model { file = "/net/cci-nas-00/data/ceres_data/6ohw_20070/03_2026/6ohw_20070.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ohw_20070/03_2026/6ohw_20070.cif" } resolution = 2.9 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= 0.003 sd= 0.080 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 183 5.16 5 C 18222 2.51 5 N 4593 2.21 5 O 5919 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 216 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28917 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 9150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1175, 9150 Classifications: {'peptide': 1175} Link IDs: {'PCIS': 4, 'PTRANS': 46, 'TRANS': 1124} Chain breaks: 5 Chain: "B" Number of atoms: 9150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1175, 9150 Classifications: {'peptide': 1175} Link IDs: {'PCIS': 4, 'PTRANS': 46, 'TRANS': 1124} Chain breaks: 5 Chain: "C" Number of atoms: 9150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1175, 9150 Classifications: {'peptide': 1175} Link IDs: {'PCIS': 4, 'PTRANS': 46, 'TRANS': 1124} Chain breaks: 5 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 62 Classifications: {'water': 62} Link IDs: {None: 61} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 62 Classifications: {'water': 62} Link IDs: {None: 61} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 62 Classifications: {'water': 62} Link IDs: {None: 61} Time building chain proxies: 6.11, per 1000 atoms: 0.21 Number of scatterers: 28917 At special positions: 0 Unit cell: (147, 155.4, 162.75, 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 183 16.00 O 5919 8.00 N 4593 7.00 C 18222 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=63, symmetry=0 Simple disulfide: pdb=" SG CYS A 21 " - pdb=" SG CYS A 169 " distance=2.14 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS A 197 " distance=2.07 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 256 " distance=2.04 Simple disulfide: pdb=" SG CYS A 290 " - pdb=" SG CYS A 300 " distance=2.03 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 368 " distance=2.03 Simple disulfide: pdb=" SG CYS A 386 " - pdb=" SG CYS A 439 " distance=2.05 Simple disulfide: pdb=" SG CYS A 398 " - pdb=" SG CYS A 614 " distance=2.17 Simple disulfide: pdb=" SG CYS A 491 " - pdb=" SG CYS A 561 " distance=2.04 Simple disulfide: pdb=" SG CYS A 499 " - pdb=" SG CYS A 522 " distance=2.04 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=2.03 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=2.09 Simple disulfide: pdb=" SG CYS A 630 " - pdb=" SG CYS A 683 " distance=2.03 Simple disulfide: pdb=" SG CYS A 708 " - pdb=" SG CYS A 733 " distance=2.04 Simple disulfide: pdb=" SG CYS A 748 " - pdb=" SG CYS A 757 " distance=2.06 Simple disulfide: pdb=" SG CYS A 826 " - pdb=" SG CYS A 848 " distance=2.16 Simple disulfide: pdb=" SG CYS A 831 " - pdb=" SG CYS A 837 " distance=2.03 Simple disulfide: pdb=" SG CYS A 938 " - pdb=" SG CYS A 949 " distance=2.09 Simple disulfide: pdb=" SG CYS A1126 " - pdb=" SG CYS A1137 " distance=2.03 Simple disulfide: pdb=" SG CYS A1176 " - pdb=" SG CYS A1221 " distance=2.03 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 169 " distance=2.14 Simple disulfide: pdb=" SG CYS B 164 " - pdb=" SG CYS B 197 " distance=2.07 Simple disulfide: pdb=" SG CYS B 176 " - pdb=" SG CYS B 256 " distance=2.04 Simple disulfide: pdb=" SG CYS B 290 " - pdb=" SG CYS B 300 " distance=2.03 Simple disulfide: pdb=" SG CYS B 343 " - pdb=" SG CYS B 368 " distance=2.03 Simple disulfide: pdb=" SG CYS B 386 " - pdb=" SG CYS B 439 " distance=2.05 Simple disulfide: pdb=" SG CYS B 398 " - pdb=" SG CYS B 614 " distance=2.16 Simple disulfide: pdb=" SG CYS B 491 " - pdb=" SG CYS B 561 " distance=2.04 Simple disulfide: pdb=" SG CYS B 499 " - pdb=" SG CYS B 522 " distance=2.04 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=2.03 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=2.09 Simple disulfide: pdb=" SG CYS B 630 " - pdb=" SG CYS B 683 " distance=2.03 Simple disulfide: pdb=" SG CYS B 708 " - pdb=" SG CYS B 733 " distance=2.04 Simple disulfide: pdb=" SG CYS B 748 " - pdb=" SG CYS B 757 " distance=2.06 Simple disulfide: pdb=" SG CYS B 826 " - pdb=" SG CYS B 848 " distance=2.16 Simple disulfide: pdb=" SG CYS B 831 " - pdb=" SG CYS B 837 " distance=2.03 Simple disulfide: pdb=" SG CYS B 938 " - pdb=" SG CYS B 949 " distance=2.09 Simple disulfide: pdb=" SG CYS B1126 " - pdb=" SG CYS B1137 " distance=2.03 Simple disulfide: pdb=" SG CYS B1176 " - pdb=" SG CYS B1221 " distance=2.03 Simple disulfide: pdb=" SG CYS C 21 " - pdb=" SG CYS C 169 " distance=2.14 Simple disulfide: pdb=" SG CYS C 164 " - pdb=" SG CYS C 197 " distance=2.07 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 256 " distance=2.04 Simple disulfide: pdb=" SG CYS C 290 " - pdb=" SG CYS C 300 " distance=2.03 Simple disulfide: pdb=" SG CYS C 343 " - pdb=" SG CYS C 368 " distance=2.03 Simple disulfide: pdb=" SG CYS C 386 " - pdb=" SG CYS C 439 " distance=2.05 Simple disulfide: pdb=" SG CYS C 398 " - pdb=" SG CYS C 614 " distance=2.16 Simple disulfide: pdb=" SG CYS C 491 " - pdb=" SG CYS C 561 " distance=2.04 Simple disulfide: pdb=" SG CYS C 499 " - pdb=" SG CYS C 522 " distance=2.04 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS C 576 " distance=2.02 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 548 " distance=2.03 Simple disulfide: pdb=" SG CYS C 571 " - pdb=" SG CYS C 578 " distance=2.03 Simple disulfide: pdb=" SG CYS C 591 " - pdb=" SG CYS C 597 " distance=2.09 Simple disulfide: pdb=" SG CYS C 630 " - pdb=" SG CYS C 683 " distance=2.03 Simple disulfide: pdb=" SG CYS C 708 " - pdb=" SG CYS C 733 " distance=2.04 Simple disulfide: pdb=" SG CYS C 748 " - pdb=" SG CYS C 757 " distance=2.06 Simple disulfide: pdb=" SG CYS C 826 " - pdb=" SG CYS C 848 " distance=2.16 Simple disulfide: pdb=" SG CYS C 831 " - pdb=" SG CYS C 837 " distance=2.03 Simple disulfide: pdb=" SG CYS C 938 " - pdb=" SG CYS C 949 " distance=2.09 Simple disulfide: pdb=" SG CYS C1126 " - pdb=" SG CYS C1137 " distance=2.03 Simple disulfide: pdb=" SG CYS C1176 " - pdb=" SG CYS C1221 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA J 3 " - " MAN J 4 " " BMA T 3 " - " MAN T 4 " " BMA d 3 " - " MAN d 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " 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 W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " 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-ASN " NAG A1428 " - " ASN A 59 " " NAG A1429 " - " ASN A 146 " " NAG A1430 " - " ASN A 675 " " NAG A1431 " - " ASN A 695 " " NAG A1432 " - " ASN A 714 " " NAG B1428 " - " ASN B 59 " " NAG B1429 " - " ASN B 146 " " NAG B1430 " - " ASN B 675 " " NAG B1431 " - " ASN B 695 " " NAG B1432 " - " ASN B 714 " " NAG C1428 " - " ASN C 59 " " NAG C1429 " - " ASN C 146 " " NAG C1430 " - " ASN C 675 " " NAG C1431 " - " ASN C 695 " " NAG C1432 " - " ASN C 714 " " NAG D 1 " - " ASN A 133 " " NAG E 1 " - " ASN A 202 " " NAG F 1 " - " ASN A1224 " " NAG G 1 " - " ASN A 371 " " NAG H 1 " - " ASN A 449 " " NAG I 1 " - " ASN A 648 " " NAG J 1 " - " ASN A 739 " " NAG K 1 " - " ASN A 788 " " NAG L 1 " - " ASN A 937 " " NAG M 1 " - " ASN A1194 " " NAG N 1 " - " ASN B 133 " " NAG O 1 " - " ASN B 202 " " NAG P 1 " - " ASN B1224 " " NAG Q 1 " - " ASN B 371 " " NAG R 1 " - " ASN B 449 " " NAG S 1 " - " ASN B 648 " " NAG T 1 " - " ASN B 739 " " NAG U 1 " - " ASN B 788 " " NAG V 1 " - " ASN B 937 " " NAG W 1 " - " ASN B1194 " " NAG X 1 " - " ASN C 133 " " NAG Y 1 " - " ASN C 202 " " NAG Z 1 " - " ASN C1224 " " NAG a 1 " - " ASN C 371 " " NAG b 1 " - " ASN C 449 " " NAG c 1 " - " ASN C 648 " " NAG d 1 " - " ASN C 739 " " NAG e 1 " - " ASN C 788 " " NAG f 1 " - " ASN C 937 " " NAG g 1 " - " ASN C1194 " Time building additional restraints: 3.05 Conformation dependent library (CDL) restraints added in 1.4 seconds 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6588 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 66 sheets defined 25.3% alpha, 35.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 89 through 92 Processing helix chain 'A' and resid 293 through 302 Processing helix chain 'A' and resid 344 through 350 Processing helix chain 'A' and resid 371 through 379 removed outlier: 4.156A pdb=" N SER A 377 " --> pdb=" O SER A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 396 removed outlier: 4.857A pdb=" N TYR A 395 " --> pdb=" O ALA A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 418 Processing helix chain 'A' and resid 423 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 707 through 715 Processing helix chain 'A' and resid 825 through 831 Processing helix chain 'A' and resid 834 through 841 Processing helix chain 'A' and resid 844 through 874 removed outlier: 3.624A pdb=" N CYS A 848 " --> pdb=" O TYR A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 882 through 885 Processing helix chain 'A' and resid 914 through 923 removed outlier: 4.257A pdb=" N LYS A 923 " --> pdb=" O LEU A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 936 Processing helix chain 'A' and resid 946 through 954 Processing helix chain 'A' and resid 964 through 978 Processing helix chain 'A' and resid 984 through 988 Processing helix chain 'A' and resid 991 through 1002 Processing helix chain 'A' and resid 1006 through 1011 Processing helix chain 'A' and resid 1013 through 1031 Processing helix chain 'A' and resid 1036 through 1058 Processing helix chain 'A' and resid 1059 through 1062 Processing helix chain 'A' and resid 1070 through 1078 Processing helix chain 'A' and resid 1079 through 1126 removed outlier: 3.543A pdb=" N ALA A1085 " --> pdb=" O LEU A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1211 through 1213 No H-bonds generated for 'chain 'A' and resid 1211 through 1213' Processing helix chain 'B' and resid 89 through 92 Processing helix chain 'B' and resid 293 through 302 Processing helix chain 'B' and resid 344 through 350 Processing helix chain 'B' and resid 371 through 379 removed outlier: 4.156A pdb=" N SER B 377 " --> pdb=" O SER B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 396 removed outlier: 4.857A pdb=" N TYR B 395 " --> pdb=" O ALA B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 418 Processing helix chain 'B' and resid 423 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 464 Processing helix chain 'B' and resid 467 through 472 Processing helix chain 'B' and resid 707 through 715 Processing helix chain 'B' and resid 825 through 831 Processing helix chain 'B' and resid 834 through 841 Processing helix chain 'B' and resid 844 through 874 removed outlier: 3.624A pdb=" N CYS B 848 " --> pdb=" O TYR B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 882 through 885 Processing helix chain 'B' and resid 914 through 923 removed outlier: 4.256A pdb=" N LYS B 923 " --> pdb=" O LEU B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 927 through 936 Processing helix chain 'B' and resid 946 through 954 Processing helix chain 'B' and resid 964 through 978 Processing helix chain 'B' and resid 984 through 988 Processing helix chain 'B' and resid 991 through 1002 Processing helix chain 'B' and resid 1006 through 1011 Processing helix chain 'B' and resid 1013 through 1031 Processing helix chain 'B' and resid 1036 through 1058 Processing helix chain 'B' and resid 1059 through 1062 Processing helix chain 'B' and resid 1070 through 1078 Processing helix chain 'B' and resid 1079 through 1126 removed outlier: 3.543A pdb=" N ALA B1085 " --> pdb=" O LEU B1081 " (cutoff:3.500A) Processing helix chain 'B' and resid 1211 through 1213 No H-bonds generated for 'chain 'B' and resid 1211 through 1213' Processing helix chain 'C' and resid 89 through 92 Processing helix chain 'C' and resid 293 through 302 Processing helix chain 'C' and resid 344 through 350 Processing helix chain 'C' and resid 371 through 379 removed outlier: 4.156A pdb=" N SER C 377 " --> pdb=" O SER C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 396 removed outlier: 4.857A pdb=" N TYR C 395 " --> pdb=" O ALA C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'C' and resid 423 through 429 Processing helix chain 'C' and resid 448 through 450 No H-bonds generated for 'chain 'C' and resid 448 through 450' Processing helix chain 'C' and resid 458 through 464 Processing helix chain 'C' and resid 467 through 472 Processing helix chain 'C' and resid 707 through 715 Processing helix chain 'C' and resid 825 through 831 Processing helix chain 'C' and resid 834 through 841 Processing helix chain 'C' and resid 844 through 874 removed outlier: 3.625A pdb=" N CYS C 848 " --> pdb=" O TYR C 844 " (cutoff:3.500A) Processing helix chain 'C' and resid 882 through 885 Processing helix chain 'C' and resid 914 through 923 removed outlier: 4.257A pdb=" N LYS C 923 " --> pdb=" O LEU C 919 " (cutoff:3.500A) Processing helix chain 'C' and resid 927 through 936 Processing helix chain 'C' and resid 946 through 954 Processing helix chain 'C' and resid 964 through 978 Processing helix chain 'C' and resid 984 through 988 Processing helix chain 'C' and resid 991 through 1002 Processing helix chain 'C' and resid 1006 through 1011 Processing helix chain 'C' and resid 1013 through 1031 Processing helix chain 'C' and resid 1036 through 1058 Processing helix chain 'C' and resid 1059 through 1062 Processing helix chain 'C' and resid 1070 through 1078 Processing helix chain 'C' and resid 1079 through 1126 removed outlier: 3.543A pdb=" N ALA C1085 " --> pdb=" O LEU C1081 " (cutoff:3.500A) Processing helix chain 'C' and resid 1211 through 1213 No H-bonds generated for 'chain 'C' and resid 1211 through 1213' Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 27 Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 40 removed outlier: 5.271A pdb=" N TYR A 75 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N THR A 74 " --> pdb=" O PRO A 268 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLY A 102 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N PHE A 223 " --> pdb=" O ASN A 239 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ASN A 239 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ALA A 225 " --> pdb=" O LEU A 237 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 60 through 69 Processing sheet with id=AA4, first strand: chain 'A' and resid 54 through 56 removed outlier: 6.976A pdb=" N ASP A 54 " --> pdb=" O GLN C 656 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ASN C 657 " --> pdb=" O PHE C 669 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N PHE C 669 " --> pdb=" O ASN C 657 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU C 659 " --> pdb=" O TYR C 667 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N TYR C 667 " --> pdb=" O ILE C 680 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N THR C 677 " --> pdb=" O VAL C 647 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA C 331 " --> pdb=" O CYS C 630 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 81 through 82 removed outlier: 8.218A pdb=" N THR A 255 " --> pdb=" O PRO A 172 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR A 174 " --> pdb=" O THR A 255 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N TRP A 188 " --> pdb=" O CYS A 169 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.749A pdb=" N GLY A 157 " --> pdb=" O TYR A 205 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 110 through 114 Processing sheet with id=AA8, first strand: chain 'A' and resid 310 through 326 removed outlier: 4.007A pdb=" N GLY A 316 " --> pdb=" O GLY A 686 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N GLY A 686 " --> pdb=" O GLY A 316 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ARG A 687 " --> pdb=" O ARG A 704 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ARG A 704 " --> pdb=" O ARG A 687 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 331 through 335 removed outlier: 4.005A pdb=" N ALA A 331 " --> pdb=" O CYS A 630 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N THR A 677 " --> pdb=" O VAL A 647 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N TYR A 667 " --> pdb=" O ILE A 680 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU A 659 " --> pdb=" O TYR A 667 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N PHE A 669 " --> pdb=" O ASN A 657 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ASN A 657 " --> pdb=" O PHE A 669 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N GLN A 656 " --> pdb=" O ASP B 54 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL B 56 " --> pdb=" O GLN A 656 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU A 658 " --> pdb=" O VAL B 56 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 353 through 355 removed outlier: 6.836A pdb=" N VAL A 354 " --> pdb=" O SER A 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 361 through 366 removed outlier: 6.521A pdb=" N PHE A 399 " --> pdb=" O VAL A 608 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL A 608 " --> pdb=" O PHE A 399 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 380 through 387 removed outlier: 5.947A pdb=" N ALA A 381 " --> pdb=" O ASN A 444 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ASN A 444 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL A 608 " --> pdb=" O PHE A 399 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N PHE A 399 " --> pdb=" O VAL A 608 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 484 through 488 Processing sheet with id=AB5, first strand: chain 'A' and resid 492 through 493 Processing sheet with id=AB6, first strand: chain 'A' and resid 565 through 566 Processing sheet with id=AB7, first strand: chain 'A' and resid 571 through 572 Processing sheet with id=AB8, first strand: chain 'A' and resid 738 through 745 removed outlier: 6.553A pdb=" N TYR A 738 " --> pdb=" O PHE A 776 " (cutoff:3.500A) removed outlier: 8.679A pdb=" N ASN A 778 " --> pdb=" O TYR A 738 " (cutoff:3.500A) removed outlier: 9.320A pdb=" N SER A 740 " --> pdb=" O ASN A 778 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N TYR A 756 " --> pdb=" O VAL A 752 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU A 750 " --> pdb=" O VAL A 758 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 785 through 787 removed outlier: 6.049A pdb=" N ASN A 785 " --> pdb=" O LEU B 879 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 798 through 816 removed outlier: 6.714A pdb=" N GLU A 799 " --> pdb=" O ARG A1170 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ARG A1170 " --> pdb=" O GLU A 799 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLN A 801 " --> pdb=" O THR A1168 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N THR A1168 " --> pdb=" O GLN A 801 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N TYR A1166 " --> pdb=" O PRO A 803 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLU A 805 " --> pdb=" O THR A1164 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE A1144 " --> pdb=" O PHE A1159 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N TYR A1161 " --> pdb=" O HIS A1142 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N HIS A1142 " --> pdb=" O TYR A1161 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 798 through 816 removed outlier: 6.714A pdb=" N GLU A 799 " --> pdb=" O ARG A1170 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ARG A1170 " --> pdb=" O GLU A 799 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLN A 801 " --> pdb=" O THR A1168 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N THR A1168 " --> pdb=" O GLN A 801 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N TYR A1166 " --> pdb=" O PRO A 803 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLU A 805 " --> pdb=" O THR A1164 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ARG A1170 " --> pdb=" O ASN A1192 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ASN A1192 " --> pdb=" O ARG A1170 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLY A1201 " --> pdb=" O TYR A1206 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N TYR A1206 " --> pdb=" O GLY A1201 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 821 through 824 removed outlier: 4.306A pdb=" N LYS A 821 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 878 through 880 Processing sheet with id=AC5, first strand: chain 'A' and resid 890 through 891 Processing sheet with id=AC6, first strand: chain 'A' and resid 1215 through 1218 Processing sheet with id=AC7, first strand: chain 'B' and resid 26 through 27 Processing sheet with id=AC8, first strand: chain 'B' and resid 36 through 40 removed outlier: 5.271A pdb=" N TYR B 75 " --> pdb=" O SER B 37 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N THR B 74 " --> pdb=" O PRO B 268 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLY B 102 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N PHE B 223 " --> pdb=" O ASN B 239 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ASN B 239 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ALA B 225 " --> pdb=" O LEU B 237 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 60 through 69 Processing sheet with id=AD1, first strand: chain 'B' and resid 81 through 82 removed outlier: 8.219A pdb=" N THR B 255 " --> pdb=" O PRO B 172 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR B 174 " --> pdb=" O THR B 255 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N TRP B 188 " --> pdb=" O CYS B 169 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.749A pdb=" N GLY B 157 " --> pdb=" O TYR B 205 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 110 through 114 Processing sheet with id=AD4, first strand: chain 'B' and resid 310 through 326 removed outlier: 4.007A pdb=" N GLY B 316 " --> pdb=" O GLY B 686 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLY B 686 " --> pdb=" O GLY B 316 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ARG B 687 " --> pdb=" O ARG B 704 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ARG B 704 " --> pdb=" O ARG B 687 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 331 through 335 removed outlier: 4.005A pdb=" N ALA B 331 " --> pdb=" O CYS B 630 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N THR B 677 " --> pdb=" O VAL B 647 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N TYR B 667 " --> pdb=" O ILE B 680 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU B 659 " --> pdb=" O TYR B 667 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N PHE B 669 " --> pdb=" O ASN B 657 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ASN B 657 " --> pdb=" O PHE B 669 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N GLN B 656 " --> pdb=" O ASP C 54 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL C 56 " --> pdb=" O GLN B 656 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU B 658 " --> pdb=" O VAL C 56 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 353 through 355 removed outlier: 6.837A pdb=" N VAL B 354 " --> pdb=" O SER B 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 361 through 366 removed outlier: 6.521A pdb=" N PHE B 399 " --> pdb=" O VAL B 608 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL B 608 " --> pdb=" O PHE B 399 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ASN B 444 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ALA B 381 " --> pdb=" O ASN B 444 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 369 through 370 removed outlier: 3.581A pdb=" N PHE B 370 " --> pdb=" O CYS B 614 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N PHE B 399 " --> pdb=" O VAL B 608 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL B 608 " --> pdb=" O PHE B 399 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 484 through 488 Processing sheet with id=AE1, first strand: chain 'B' and resid 492 through 493 Processing sheet with id=AE2, first strand: chain 'B' and resid 565 through 566 Processing sheet with id=AE3, first strand: chain 'B' and resid 571 through 572 Processing sheet with id=AE4, first strand: chain 'B' and resid 738 through 745 removed outlier: 6.553A pdb=" N TYR B 738 " --> pdb=" O PHE B 776 " (cutoff:3.500A) removed outlier: 8.679A pdb=" N ASN B 778 " --> pdb=" O TYR B 738 " (cutoff:3.500A) removed outlier: 9.320A pdb=" N SER B 740 " --> pdb=" O ASN B 778 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N TYR B 756 " --> pdb=" O VAL B 752 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU B 750 " --> pdb=" O VAL B 758 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 785 through 787 removed outlier: 6.049A pdb=" N ASN B 785 " --> pdb=" O LEU C 879 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'B' and resid 798 through 816 removed outlier: 6.714A pdb=" N GLU B 799 " --> pdb=" O ARG B1170 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ARG B1170 " --> pdb=" O GLU B 799 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLN B 801 " --> pdb=" O THR B1168 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR B1168 " --> pdb=" O GLN B 801 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N TYR B1166 " --> pdb=" O PRO B 803 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLU B 805 " --> pdb=" O THR B1164 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE B1144 " --> pdb=" O PHE B1159 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N TYR B1161 " --> pdb=" O HIS B1142 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N HIS B1142 " --> pdb=" O TYR B1161 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 798 through 816 removed outlier: 6.714A pdb=" N GLU B 799 " --> pdb=" O ARG B1170 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ARG B1170 " --> pdb=" O GLU B 799 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLN B 801 " --> pdb=" O THR B1168 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR B1168 " --> pdb=" O GLN B 801 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N TYR B1166 " --> pdb=" O PRO B 803 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLU B 805 " --> pdb=" O THR B1164 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ARG B1170 " --> pdb=" O ASN B1192 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ASN B1192 " --> pdb=" O ARG B1170 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLY B1201 " --> pdb=" O TYR B1206 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N TYR B1206 " --> pdb=" O GLY B1201 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 821 through 824 removed outlier: 4.306A pdb=" N LYS B 821 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 890 through 891 Processing sheet with id=AF1, first strand: chain 'B' and resid 1215 through 1218 Processing sheet with id=AF2, first strand: chain 'C' and resid 26 through 27 Processing sheet with id=AF3, first strand: chain 'C' and resid 36 through 40 removed outlier: 5.271A pdb=" N TYR C 75 " --> pdb=" O SER C 37 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N THR C 74 " --> pdb=" O PRO C 268 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLY C 102 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N PHE C 223 " --> pdb=" O ASN C 239 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ASN C 239 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ALA C 225 " --> pdb=" O LEU C 237 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 60 through 69 Processing sheet with id=AF5, first strand: chain 'C' and resid 81 through 82 removed outlier: 8.218A pdb=" N THR C 255 " --> pdb=" O PRO C 172 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR C 174 " --> pdb=" O THR C 255 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N TRP C 188 " --> pdb=" O CYS C 169 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.749A pdb=" N GLY C 157 " --> pdb=" O TYR C 205 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 110 through 114 Processing sheet with id=AF8, first strand: chain 'C' and resid 310 through 326 removed outlier: 4.007A pdb=" N GLY C 316 " --> pdb=" O GLY C 686 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLY C 686 " --> pdb=" O GLY C 316 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ARG C 687 " --> pdb=" O ARG C 704 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ARG C 704 " --> pdb=" O ARG C 687 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 353 through 355 removed outlier: 6.836A pdb=" N VAL C 354 " --> pdb=" O SER C 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'C' and resid 361 through 366 removed outlier: 6.520A pdb=" N PHE C 399 " --> pdb=" O VAL C 608 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL C 608 " --> pdb=" O PHE C 399 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ASN C 444 " --> pdb=" O ALA C 381 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ALA C 381 " --> pdb=" O ASN C 444 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 369 through 370 removed outlier: 3.581A pdb=" N PHE C 370 " --> pdb=" O CYS C 614 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N PHE C 399 " --> pdb=" O VAL C 608 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL C 608 " --> pdb=" O PHE C 399 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 484 through 488 Processing sheet with id=AG4, first strand: chain 'C' and resid 492 through 493 Processing sheet with id=AG5, first strand: chain 'C' and resid 565 through 566 Processing sheet with id=AG6, first strand: chain 'C' and resid 571 through 572 Processing sheet with id=AG7, first strand: chain 'C' and resid 738 through 745 removed outlier: 6.553A pdb=" N TYR C 738 " --> pdb=" O PHE C 776 " (cutoff:3.500A) removed outlier: 8.679A pdb=" N ASN C 778 " --> pdb=" O TYR C 738 " (cutoff:3.500A) removed outlier: 9.320A pdb=" N SER C 740 " --> pdb=" O ASN C 778 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N TYR C 756 " --> pdb=" O VAL C 752 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU C 750 " --> pdb=" O VAL C 758 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 798 through 816 removed outlier: 6.715A pdb=" N GLU C 799 " --> pdb=" O ARG C1170 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ARG C1170 " --> pdb=" O GLU C 799 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLN C 801 " --> pdb=" O THR C1168 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N THR C1168 " --> pdb=" O GLN C 801 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N TYR C1166 " --> pdb=" O PRO C 803 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLU C 805 " --> pdb=" O THR C1164 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ILE C1144 " --> pdb=" O PHE C1159 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N TYR C1161 " --> pdb=" O HIS C1142 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N HIS C1142 " --> pdb=" O TYR C1161 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'C' and resid 798 through 816 removed outlier: 6.715A pdb=" N GLU C 799 " --> pdb=" O ARG C1170 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ARG C1170 " --> pdb=" O GLU C 799 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLN C 801 " --> pdb=" O THR C1168 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N THR C1168 " --> pdb=" O GLN C 801 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N TYR C1166 " --> pdb=" O PRO C 803 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLU C 805 " --> pdb=" O THR C1164 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ARG C1170 " --> pdb=" O ASN C1192 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ASN C1192 " --> pdb=" O ARG C1170 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLY C1201 " --> pdb=" O TYR C1206 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N TYR C1206 " --> pdb=" O GLY C1201 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'C' and resid 821 through 824 removed outlier: 4.306A pdb=" N LYS C 821 " --> pdb=" O LEU C 959 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'C' and resid 890 through 891 Processing sheet with id=AH3, first strand: chain 'C' and resid 1215 through 1218 1220 hydrogen bonds defined for protein. 3345 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.74 Time building geometry restraints manager: 3.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 9236 1.33 - 1.48: 9420 1.48 - 1.63: 10465 1.63 - 1.77: 101 1.77 - 1.92: 136 Bond restraints: 29358 Sorted by residual: bond pdb=" C HIS C 215 " pdb=" N PHE C 216 " ideal model delta sigma weight residual 1.331 1.204 0.128 1.29e-02 6.01e+03 9.83e+01 bond pdb=" C HIS B 215 " pdb=" N PHE B 216 " ideal model delta sigma weight residual 1.331 1.204 0.128 1.29e-02 6.01e+03 9.81e+01 bond pdb=" C HIS A 215 " pdb=" N PHE A 216 " ideal model delta sigma weight residual 1.331 1.204 0.128 1.29e-02 6.01e+03 9.78e+01 bond pdb=" CB HIS A 215 " pdb=" CG HIS A 215 " ideal model delta sigma weight residual 1.497 1.388 0.109 1.40e-02 5.10e+03 6.09e+01 bond pdb=" CB HIS C 215 " pdb=" CG HIS C 215 " ideal model delta sigma weight residual 1.497 1.388 0.109 1.40e-02 5.10e+03 6.09e+01 ... (remaining 29353 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.47: 38875 4.47 - 8.93: 1055 8.93 - 13.40: 27 13.40 - 17.86: 12 17.86 - 22.33: 3 Bond angle restraints: 39972 Sorted by residual: angle pdb=" N PHE A 399 " pdb=" CA PHE A 399 " pdb=" CB PHE A 399 " ideal model delta sigma weight residual 111.05 88.72 22.33 1.50e+00 4.44e-01 2.22e+02 angle pdb=" N PHE B 399 " pdb=" CA PHE B 399 " pdb=" CB PHE B 399 " ideal model delta sigma weight residual 111.05 88.73 22.32 1.50e+00 4.44e-01 2.21e+02 angle pdb=" N PHE C 399 " pdb=" CA PHE C 399 " pdb=" CB PHE C 399 " ideal model delta sigma weight residual 111.05 88.74 22.31 1.50e+00 4.44e-01 2.21e+02 angle pdb=" N CYS C 614 " pdb=" CA CYS C 614 " pdb=" C CYS C 614 " ideal model delta sigma weight residual 109.59 124.65 -15.06 1.61e+00 3.86e-01 8.75e+01 angle pdb=" N CYS A 614 " pdb=" CA CYS A 614 " pdb=" C CYS A 614 " ideal model delta sigma weight residual 109.59 124.64 -15.05 1.61e+00 3.86e-01 8.74e+01 ... (remaining 39967 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.00: 17898 22.00 - 43.99: 498 43.99 - 65.99: 117 65.99 - 87.99: 120 87.99 - 109.98: 75 Dihedral angle restraints: 18708 sinusoidal: 8403 harmonic: 10305 Sorted by residual: dihedral pdb=" N PHE B 399 " pdb=" C PHE B 399 " pdb=" CA PHE B 399 " pdb=" CB PHE B 399 " ideal model delta harmonic sigma weight residual 122.80 91.14 31.66 0 2.50e+00 1.60e-01 1.60e+02 dihedral pdb=" N PHE A 399 " pdb=" C PHE A 399 " pdb=" CA PHE A 399 " pdb=" CB PHE A 399 " ideal model delta harmonic sigma weight residual 122.80 91.14 31.66 0 2.50e+00 1.60e-01 1.60e+02 dihedral pdb=" N PHE C 399 " pdb=" C PHE C 399 " pdb=" CA PHE C 399 " pdb=" CB PHE C 399 " ideal model delta harmonic sigma weight residual 122.80 91.16 31.64 0 2.50e+00 1.60e-01 1.60e+02 ... (remaining 18705 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.155: 4002 0.155 - 0.310: 750 0.310 - 0.465: 39 0.465 - 0.620: 6 0.620 - 0.775: 3 Chirality restraints: 4800 Sorted by residual: chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.33e+02 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.32e+02 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.32e+02 ... (remaining 4797 not shown) Planarity restraints: 5058 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 675 " -0.054 2.00e-02 2.50e+03 5.68e-02 4.03e+01 pdb=" CG ASN A 675 " 0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN A 675 " 0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN A 675 " 0.089 2.00e-02 2.50e+03 pdb=" C1 NAG A1430 " -0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 675 " 0.054 2.00e-02 2.50e+03 5.68e-02 4.03e+01 pdb=" CG ASN B 675 " -0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN B 675 " -0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN B 675 " -0.089 2.00e-02 2.50e+03 pdb=" C1 NAG B1430 " 0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 675 " -0.054 2.00e-02 2.50e+03 5.67e-02 4.02e+01 pdb=" CG ASN C 675 " 0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN C 675 " 0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN C 675 " 0.089 2.00e-02 2.50e+03 pdb=" C1 NAG C1430 " -0.068 2.00e-02 2.50e+03 ... (remaining 5055 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 939 2.65 - 3.21: 26673 3.21 - 3.77: 47201 3.77 - 4.34: 65506 4.34 - 4.90: 106912 Nonbonded interactions: 247231 Sorted by model distance: nonbonded pdb=" O HOH A1508 " pdb=" O HOH B1516 " model vdw 2.085 3.040 nonbonded pdb=" O HOH A1516 " pdb=" O HOH C1508 " model vdw 2.085 3.040 nonbonded pdb=" O HOH B1508 " pdb=" O HOH C1516 " model vdw 2.086 3.040 nonbonded pdb=" O4 NAG I 2 " pdb=" O6 NAG I 2 " model vdw 2.368 3.040 nonbonded pdb=" O4 NAG c 2 " pdb=" O6 NAG c 2 " model vdw 2.368 3.040 ... (remaining 247226 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'g' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'b' selection = chain 'c' selection = chain 'e' selection = chain 'f' } ncs_group { reference = chain 'J' selection = chain 'T' selection = chain 'd' } 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: 4.690 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: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 29.420 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 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 : 0.026 0.169 29517 Z= 1.358 Angle : 1.823 22.328 40386 Z= 1.181 Chirality : 0.115 0.775 4800 Planarity : 0.009 0.052 5013 Dihedral : 15.316 109.983 11931 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 0.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.39 % Allowed : 0.49 % Favored : 99.12 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 8.00 % 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: 0.44 (0.13), residues: 3489 helix: -0.56 (0.16), residues: 786 sheet: 1.12 (0.16), residues: 801 loop : 0.46 (0.13), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 999 TYR 0.066 0.009 TYR B 75 PHE 0.042 0.006 PHE C 713 TRP 0.048 0.009 TRP B 655 HIS 0.009 0.003 HIS C1142 Details of bonding type rmsd covalent geometry : bond 0.02608 (29358) covalent geometry : angle 1.80070 (39972) SS BOND : bond 0.05220 ( 63) SS BOND : angle 3.44270 ( 126) hydrogen bonds : bond 0.16352 ( 1163) hydrogen bonds : angle 7.43365 ( 3345) link_ALPHA1-3 : bond 0.06522 ( 3) link_ALPHA1-3 : angle 2.20908 ( 9) link_BETA1-4 : bond 0.06111 ( 48) link_BETA1-4 : angle 3.90006 ( 144) link_NAG-ASN : bond 0.04578 ( 45) link_NAG-ASN : angle 2.52495 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 522 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.8749 (mmm) cc_final: 0.8329 (mmm) REVERT: A 376 MET cc_start: 0.8471 (mtm) cc_final: 0.8184 (mtm) REVERT: A 925 LYS cc_start: 0.7734 (tttt) cc_final: 0.7508 (mmpt) REVERT: B 168 MET cc_start: 0.8449 (mmm) cc_final: 0.8128 (mmt) REVERT: B 455 PHE cc_start: 0.8672 (m-80) cc_final: 0.8387 (m-80) REVERT: B 925 LYS cc_start: 0.7952 (tttt) cc_final: 0.7544 (mmpt) REVERT: C 78 MET cc_start: 0.8830 (mmm) cc_final: 0.8601 (mmp) REVERT: C 925 LYS cc_start: 0.7849 (tttt) cc_final: 0.7486 (mmpt) REVERT: C 1114 PHE cc_start: 0.8550 (t80) cc_final: 0.8289 (t80) outliers start: 12 outliers final: 3 residues processed: 526 average time/residue: 0.5221 time to fit residues: 333.4458 Evaluate side-chains 295 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 292 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain B residue 1224 ASN Chi-restraints excluded: chain C residue 1224 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN A 183 HIS A 444 ASN A 598 ASN A 746 GLN A1029 GLN A1036 ASN A1214 ASN B 167 ASN B 183 HIS B 286 ASN ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 746 GLN B 785 ASN B1029 GLN B1036 ASN B1213 ASN B1214 ASN C 167 ASN C 183 HIS C 444 ASN C 598 ASN C 736 ASN C 746 GLN C 895 ASN C1029 GLN C1214 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.144212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.117143 restraints weight = 34193.665| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.85 r_work: 0.3181 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 29517 Z= 0.189 Angle : 0.791 17.721 40386 Z= 0.392 Chirality : 0.055 0.670 4800 Planarity : 0.004 0.040 5013 Dihedral : 11.983 69.348 5799 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.67 % Allowed : 5.38 % Favored : 91.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.60 (0.13), residues: 3489 helix: 0.98 (0.19), residues: 783 sheet: 0.79 (0.17), residues: 777 loop : 0.09 (0.13), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 413 TYR 0.023 0.002 TYR C 738 PHE 0.027 0.002 PHE A 278 TRP 0.025 0.002 TRP A 460 HIS 0.006 0.002 HIS B 483 Details of bonding type rmsd covalent geometry : bond 0.00410 (29358) covalent geometry : angle 0.72889 (39972) SS BOND : bond 0.00237 ( 63) SS BOND : angle 1.36073 ( 126) hydrogen bonds : bond 0.05592 ( 1163) hydrogen bonds : angle 5.84350 ( 3345) link_ALPHA1-3 : bond 0.01482 ( 3) link_ALPHA1-3 : angle 2.79528 ( 9) link_BETA1-4 : bond 0.00838 ( 48) link_BETA1-4 : angle 3.22917 ( 144) link_NAG-ASN : bond 0.00909 ( 45) link_NAG-ASN : angle 4.07722 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 374 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.9057 (mmm) cc_final: 0.8765 (mmm) REVERT: A 168 MET cc_start: 0.8861 (mmm) cc_final: 0.8311 (mmt) REVERT: A 170 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7499 (mp0) REVERT: A 185 LYS cc_start: 0.7643 (mmtm) cc_final: 0.6389 (mtpm) REVERT: A 244 MET cc_start: 0.7627 (ppp) cc_final: 0.7203 (mmm) REVERT: A 252 MET cc_start: 0.8897 (mtt) cc_final: 0.8684 (mtt) REVERT: A 261 THR cc_start: 0.7761 (m) cc_final: 0.7520 (p) REVERT: A 376 MET cc_start: 0.8674 (mtm) cc_final: 0.8444 (mtm) REVERT: A 470 SER cc_start: 0.8348 (m) cc_final: 0.7892 (p) REVERT: A 593 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.7537 (mm-40) REVERT: A 925 LYS cc_start: 0.8010 (tttt) cc_final: 0.7456 (mmpt) REVERT: A 944 ILE cc_start: 0.7530 (OUTLIER) cc_final: 0.6927 (pp) REVERT: A 1051 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7693 (mm-30) REVERT: A 1084 GLU cc_start: 0.7562 (mt-10) cc_final: 0.7107 (mm-30) REVERT: A 1152 TYR cc_start: 0.8949 (m-80) cc_final: 0.7989 (m-80) REVERT: A 1165 LYS cc_start: 0.8125 (mttt) cc_final: 0.7813 (mmtt) REVERT: B 185 LYS cc_start: 0.7711 (mmtm) cc_final: 0.6552 (mtpm) REVERT: B 455 PHE cc_start: 0.8879 (m-80) cc_final: 0.8449 (m-80) REVERT: B 464 PHE cc_start: 0.7711 (m-80) cc_final: 0.7412 (m-80) REVERT: B 482 ASN cc_start: 0.7708 (m-40) cc_final: 0.7437 (m-40) REVERT: B 503 LEU cc_start: 0.7276 (OUTLIER) cc_final: 0.7002 (tt) REVERT: B 579 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.6819 (mpp-170) REVERT: B 925 LYS cc_start: 0.8178 (tttt) cc_final: 0.7491 (mmpt) REVERT: C 78 MET cc_start: 0.9043 (mmm) cc_final: 0.8773 (mmm) REVERT: C 185 LYS cc_start: 0.7656 (mmtm) cc_final: 0.6722 (mtpm) REVERT: C 240 VAL cc_start: 0.9085 (t) cc_final: 0.8845 (p) REVERT: C 261 THR cc_start: 0.7963 (m) cc_final: 0.7680 (p) REVERT: C 328 GLN cc_start: 0.8412 (mm-40) cc_final: 0.8207 (mm110) REVERT: C 536 THR cc_start: 0.6602 (OUTLIER) cc_final: 0.6359 (t) REVERT: C 707 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.8063 (mttm) REVERT: C 925 LYS cc_start: 0.8189 (tttt) cc_final: 0.7458 (mmpt) REVERT: C 1084 GLU cc_start: 0.7360 (mt-10) cc_final: 0.7005 (mm-30) REVERT: C 1089 ARG cc_start: 0.8432 (mtt-85) cc_final: 0.7935 (mtp85) outliers start: 82 outliers final: 35 residues processed: 432 average time/residue: 0.4734 time to fit residues: 251.5480 Evaluate side-chains 311 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 270 time to evaluate : 2.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 593 GLN Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 944 ILE Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 579 ARG Chi-restraints excluded: chain B residue 1176 CYS Chi-restraints excluded: chain B residue 1224 ASN Chi-restraints excluded: chain B residue 1226 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 469 ASP Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 707 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 293 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 132 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 347 optimal weight: 0.9980 chunk 181 optimal weight: 0.9990 chunk 190 optimal weight: 1.9990 chunk 73 optimal weight: 0.0980 chunk 334 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 ASN A 746 GLN A1104 GLN A1214 ASN B 444 ASN B 598 ASN B 850 ASN B 895 ASN B1104 GLN B1214 ASN C 444 ASN C 746 GLN C1214 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.144141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.117089 restraints weight = 34063.500| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.84 r_work: 0.3158 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 29517 Z= 0.156 Angle : 0.692 12.143 40386 Z= 0.338 Chirality : 0.048 0.433 4800 Planarity : 0.004 0.056 5013 Dihedral : 8.608 57.980 5797 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.39 % Allowed : 7.11 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.47 (0.14), residues: 3489 helix: 1.23 (0.19), residues: 786 sheet: 0.48 (0.18), residues: 759 loop : -0.06 (0.13), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 413 TYR 0.023 0.002 TYR A 528 PHE 0.022 0.002 PHE B 713 TRP 0.018 0.001 TRP B 460 HIS 0.004 0.001 HIS A 483 Details of bonding type rmsd covalent geometry : bond 0.00344 (29358) covalent geometry : angle 0.63259 (39972) SS BOND : bond 0.00328 ( 63) SS BOND : angle 1.23553 ( 126) hydrogen bonds : bond 0.04799 ( 1163) hydrogen bonds : angle 5.43558 ( 3345) link_ALPHA1-3 : bond 0.01491 ( 3) link_ALPHA1-3 : angle 1.73450 ( 9) link_BETA1-4 : bond 0.00967 ( 48) link_BETA1-4 : angle 2.91723 ( 144) link_NAG-ASN : bond 0.00408 ( 45) link_NAG-ASN : angle 3.73282 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 326 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.9035 (mmm) cc_final: 0.8778 (mmm) REVERT: A 168 MET cc_start: 0.8848 (mmm) cc_final: 0.8395 (mmt) REVERT: A 185 LYS cc_start: 0.7700 (mmtm) cc_final: 0.6458 (mtpm) REVERT: A 244 MET cc_start: 0.7764 (ppp) cc_final: 0.7251 (mmm) REVERT: A 261 THR cc_start: 0.7776 (m) cc_final: 0.7522 (p) REVERT: A 376 MET cc_start: 0.8638 (mtm) cc_final: 0.8348 (mtm) REVERT: A 470 SER cc_start: 0.8424 (m) cc_final: 0.7981 (p) REVERT: A 593 GLN cc_start: 0.7764 (OUTLIER) cc_final: 0.7499 (mm-40) REVERT: A 925 LYS cc_start: 0.8002 (tttt) cc_final: 0.7448 (mmpt) REVERT: A 944 ILE cc_start: 0.7699 (OUTLIER) cc_final: 0.6998 (pp) REVERT: A 1084 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7289 (mm-30) REVERT: A 1165 LYS cc_start: 0.8187 (mttt) cc_final: 0.7899 (mmtt) REVERT: B 88 ARG cc_start: 0.7755 (mtm180) cc_final: 0.7501 (mtt90) REVERT: B 118 MET cc_start: 0.6753 (OUTLIER) cc_final: 0.6494 (ttp) REVERT: B 185 LYS cc_start: 0.7671 (mmtm) cc_final: 0.6736 (mtpm) REVERT: B 455 PHE cc_start: 0.8900 (m-80) cc_final: 0.8478 (m-80) REVERT: B 503 LEU cc_start: 0.7202 (OUTLIER) cc_final: 0.6906 (tt) REVERT: B 738 TYR cc_start: 0.7873 (p90) cc_final: 0.7667 (p90) REVERT: B 866 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.8336 (tt0) REVERT: B 925 LYS cc_start: 0.8189 (tttt) cc_final: 0.7487 (mmpt) REVERT: B 1125 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8144 (mt-10) REVERT: B 1137 CYS cc_start: 0.6603 (m) cc_final: 0.6394 (m) REVERT: C 88 ARG cc_start: 0.7720 (mtt90) cc_final: 0.7490 (mtt90) REVERT: C 160 GLU cc_start: 0.7208 (tm-30) cc_final: 0.6977 (pp20) REVERT: C 185 LYS cc_start: 0.7688 (mmtm) cc_final: 0.6743 (mtpm) REVERT: C 244 MET cc_start: 0.7715 (OUTLIER) cc_final: 0.7474 (ttm) REVERT: C 261 THR cc_start: 0.7882 (m) cc_final: 0.7587 (p) REVERT: C 328 GLN cc_start: 0.8443 (mm-40) cc_final: 0.8146 (mm110) REVERT: C 536 THR cc_start: 0.6653 (OUTLIER) cc_final: 0.6377 (t) REVERT: C 747 THR cc_start: 0.8501 (t) cc_final: 0.8166 (p) REVERT: C 925 LYS cc_start: 0.8194 (tttt) cc_final: 0.7429 (mmpt) REVERT: C 1089 ARG cc_start: 0.8337 (mtt-85) cc_final: 0.7841 (mtp85) REVERT: C 1125 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8251 (mt-10) outliers start: 104 outliers final: 48 residues processed: 400 average time/residue: 0.5017 time to fit residues: 244.5470 Evaluate side-chains 335 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 278 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 548 CYS Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 593 GLN Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 944 ILE Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain A residue 1226 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 548 CYS Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 866 GLN Chi-restraints excluded: chain B residue 1125 GLU Chi-restraints excluded: chain B residue 1176 CYS Chi-restraints excluded: chain B residue 1224 ASN Chi-restraints excluded: chain B residue 1226 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain C residue 469 ASP Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 548 CYS Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 1125 GLU Chi-restraints excluded: chain C residue 1219 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 53 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 331 optimal weight: 0.9980 chunk 320 optimal weight: 0.5980 chunk 273 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 334 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 265 optimal weight: 0.0170 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 746 GLN A1214 ASN B 109 ASN B 840 GLN B1214 ASN C1104 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.143271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.115230 restraints weight = 34136.227| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.91 r_work: 0.3201 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29517 Z= 0.148 Angle : 0.642 13.174 40386 Z= 0.315 Chirality : 0.047 0.450 4800 Planarity : 0.004 0.037 5013 Dihedral : 6.897 52.659 5797 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.46 % Allowed : 8.25 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 3489 helix: 1.36 (0.19), residues: 786 sheet: 0.33 (0.17), residues: 771 loop : -0.15 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 413 TYR 0.027 0.001 TYR C 738 PHE 0.021 0.002 PHE B 278 TRP 0.016 0.001 TRP B 460 HIS 0.003 0.001 HIS A 483 Details of bonding type rmsd covalent geometry : bond 0.00331 (29358) covalent geometry : angle 0.59117 (39972) SS BOND : bond 0.00307 ( 63) SS BOND : angle 0.96587 ( 126) hydrogen bonds : bond 0.04490 ( 1163) hydrogen bonds : angle 5.30069 ( 3345) link_ALPHA1-3 : bond 0.01364 ( 3) link_ALPHA1-3 : angle 2.12448 ( 9) link_BETA1-4 : bond 0.00771 ( 48) link_BETA1-4 : angle 2.60434 ( 144) link_NAG-ASN : bond 0.00406 ( 45) link_NAG-ASN : angle 3.35652 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 302 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.7902 (mp) cc_final: 0.7506 (mt) REVERT: A 78 MET cc_start: 0.9031 (mmm) cc_final: 0.8803 (mmm) REVERT: A 168 MET cc_start: 0.8902 (mmm) cc_final: 0.8297 (mmt) REVERT: A 170 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7582 (mt-10) REVERT: A 185 LYS cc_start: 0.7670 (mmtm) cc_final: 0.6563 (mtpm) REVERT: A 252 MET cc_start: 0.8661 (mtt) cc_final: 0.8364 (mtt) REVERT: A 261 THR cc_start: 0.7841 (m) cc_final: 0.7529 (p) REVERT: A 376 MET cc_start: 0.8630 (mtm) cc_final: 0.8324 (mtm) REVERT: A 455 PHE cc_start: 0.8949 (m-80) cc_final: 0.8675 (m-10) REVERT: A 470 SER cc_start: 0.8446 (m) cc_final: 0.8022 (p) REVERT: A 866 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.8024 (mt0) REVERT: A 893 ASP cc_start: 0.8095 (t70) cc_final: 0.7516 (t0) REVERT: A 925 LYS cc_start: 0.8072 (tttt) cc_final: 0.7492 (mmpt) REVERT: A 929 VAL cc_start: 0.8313 (t) cc_final: 0.8084 (m) REVERT: A 944 ILE cc_start: 0.7765 (OUTLIER) cc_final: 0.7513 (tp) REVERT: A 1084 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7366 (mm-30) REVERT: A 1165 LYS cc_start: 0.8197 (mttt) cc_final: 0.7845 (mmtt) REVERT: B 118 MET cc_start: 0.6760 (OUTLIER) cc_final: 0.6510 (ttp) REVERT: B 185 LYS cc_start: 0.7634 (mmtm) cc_final: 0.6593 (mtpm) REVERT: B 455 PHE cc_start: 0.8899 (m-80) cc_final: 0.8409 (m-80) REVERT: B 579 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.6865 (mpp-170) REVERT: B 866 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.8297 (tt0) REVERT: B 925 LYS cc_start: 0.8221 (tttt) cc_final: 0.7511 (mmpt) REVERT: B 1125 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8290 (mt-10) REVERT: B 1137 CYS cc_start: 0.6924 (m) cc_final: 0.6690 (m) REVERT: C 22 THR cc_start: 0.6864 (t) cc_final: 0.6425 (p) REVERT: C 160 GLU cc_start: 0.7146 (tm-30) cc_final: 0.6876 (pp20) REVERT: C 170 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7446 (mt-10) REVERT: C 185 LYS cc_start: 0.7628 (mmtm) cc_final: 0.6797 (mtpm) REVERT: C 190 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7250 (tm) REVERT: C 259 LYS cc_start: 0.7228 (tptt) cc_final: 0.6924 (tptp) REVERT: C 328 GLN cc_start: 0.8354 (mm-40) cc_final: 0.8100 (mm110) REVERT: C 536 THR cc_start: 0.6948 (OUTLIER) cc_final: 0.6702 (t) REVERT: C 925 LYS cc_start: 0.8195 (tttt) cc_final: 0.7418 (mmpt) REVERT: C 944 ILE cc_start: 0.7836 (OUTLIER) cc_final: 0.7407 (tp) REVERT: C 1089 ARG cc_start: 0.8311 (mtt-85) cc_final: 0.7812 (mtp85) REVERT: C 1125 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8309 (mt-10) outliers start: 106 outliers final: 55 residues processed: 383 average time/residue: 0.4960 time to fit residues: 232.9014 Evaluate side-chains 348 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 282 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 548 CYS Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain A residue 866 GLN Chi-restraints excluded: chain A residue 944 ILE Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 1198 MET Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain A residue 1226 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 548 CYS Chi-restraints excluded: chain B residue 579 ARG Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain B residue 866 GLN Chi-restraints excluded: chain B residue 893 ASP Chi-restraints excluded: chain B residue 1125 GLU Chi-restraints excluded: chain B residue 1176 CYS Chi-restraints excluded: chain B residue 1226 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 469 ASP Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 548 CYS Chi-restraints excluded: chain C residue 944 ILE Chi-restraints excluded: chain C residue 1125 GLU Chi-restraints excluded: chain C residue 1219 SER Chi-restraints excluded: chain C residue 1224 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 267 optimal weight: 0.9980 chunk 160 optimal weight: 0.7980 chunk 15 optimal weight: 0.0270 chunk 346 optimal weight: 0.5980 chunk 196 optimal weight: 4.9990 chunk 57 optimal weight: 0.5980 chunk 145 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 262 optimal weight: 0.8980 chunk 214 optimal weight: 0.3980 chunk 227 optimal weight: 0.7980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 746 GLN A1214 ASN B 785 ASN B 850 ASN B1214 ASN C 109 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.143948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.115996 restraints weight = 34203.708| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.91 r_work: 0.3177 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29517 Z= 0.129 Angle : 0.610 9.843 40386 Z= 0.300 Chirality : 0.046 0.508 4800 Planarity : 0.003 0.041 5013 Dihedral : 6.289 47.686 5795 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.97 % Allowed : 9.85 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.41 (0.14), residues: 3489 helix: 1.49 (0.19), residues: 783 sheet: 0.24 (0.17), residues: 774 loop : -0.16 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 143 TYR 0.021 0.001 TYR B 738 PHE 0.019 0.001 PHE B 278 TRP 0.015 0.001 TRP B 460 HIS 0.003 0.001 HIS C 490 Details of bonding type rmsd covalent geometry : bond 0.00282 (29358) covalent geometry : angle 0.55893 (39972) SS BOND : bond 0.00282 ( 63) SS BOND : angle 1.05198 ( 126) hydrogen bonds : bond 0.04221 ( 1163) hydrogen bonds : angle 5.20833 ( 3345) link_ALPHA1-3 : bond 0.01326 ( 3) link_ALPHA1-3 : angle 1.84744 ( 9) link_BETA1-4 : bond 0.00773 ( 48) link_BETA1-4 : angle 2.43168 ( 144) link_NAG-ASN : bond 0.00445 ( 45) link_NAG-ASN : angle 3.37124 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 301 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.7904 (mp) cc_final: 0.7464 (mt) REVERT: A 168 MET cc_start: 0.8910 (mmm) cc_final: 0.8248 (mmt) REVERT: A 170 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7543 (mt-10) REVERT: A 185 LYS cc_start: 0.7679 (mmtm) cc_final: 0.6497 (mtpm) REVERT: A 252 MET cc_start: 0.8662 (mtt) cc_final: 0.8461 (mtt) REVERT: A 376 MET cc_start: 0.8626 (mtm) cc_final: 0.8361 (mtm) REVERT: A 470 SER cc_start: 0.8425 (m) cc_final: 0.7995 (p) REVERT: A 893 ASP cc_start: 0.8122 (t70) cc_final: 0.7493 (t0) REVERT: A 925 LYS cc_start: 0.8071 (tttt) cc_final: 0.7449 (mmpt) REVERT: A 944 ILE cc_start: 0.7704 (OUTLIER) cc_final: 0.7468 (tp) REVERT: A 1165 LYS cc_start: 0.8203 (mttt) cc_final: 0.7874 (mmtt) REVERT: B 118 MET cc_start: 0.6767 (OUTLIER) cc_final: 0.6512 (ttp) REVERT: B 185 LYS cc_start: 0.7640 (mmtm) cc_final: 0.6659 (mtpm) REVERT: B 455 PHE cc_start: 0.8914 (m-80) cc_final: 0.8388 (m-80) REVERT: B 464 PHE cc_start: 0.7744 (m-80) cc_final: 0.7505 (m-80) REVERT: B 579 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.6751 (mpp-170) REVERT: B 866 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.8281 (tt0) REVERT: B 893 ASP cc_start: 0.7902 (t0) cc_final: 0.7687 (t0) REVERT: B 925 LYS cc_start: 0.8218 (tttt) cc_final: 0.7469 (mmpt) REVERT: B 1125 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8217 (mt-10) REVERT: B 1137 CYS cc_start: 0.6950 (m) cc_final: 0.6718 (m) REVERT: B 1198 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.8492 (mtp) REVERT: C 22 THR cc_start: 0.6826 (t) cc_final: 0.6419 (p) REVERT: C 88 ARG cc_start: 0.7721 (mtt90) cc_final: 0.6800 (mpt180) REVERT: C 160 GLU cc_start: 0.7148 (tm-30) cc_final: 0.6903 (pp20) REVERT: C 170 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7452 (mt-10) REVERT: C 185 LYS cc_start: 0.7648 (mmtm) cc_final: 0.7071 (mtpm) REVERT: C 190 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.7243 (tm) REVERT: C 559 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8188 (mm-30) REVERT: C 789 ASP cc_start: 0.8284 (m-30) cc_final: 0.6973 (p0) REVERT: C 925 LYS cc_start: 0.8165 (tttt) cc_final: 0.7377 (mmpt) REVERT: C 944 ILE cc_start: 0.7855 (OUTLIER) cc_final: 0.7444 (tp) REVERT: C 1089 ARG cc_start: 0.8252 (mtt-85) cc_final: 0.7765 (mtt-85) REVERT: C 1125 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8292 (mt-10) outliers start: 91 outliers final: 47 residues processed: 370 average time/residue: 0.5086 time to fit residues: 229.3657 Evaluate side-chains 331 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 273 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 548 CYS Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 681 ARG Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 944 ILE Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 1198 MET Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 548 CYS Chi-restraints excluded: chain B residue 579 ARG Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 866 GLN Chi-restraints excluded: chain B residue 889 PHE Chi-restraints excluded: chain B residue 1125 GLU Chi-restraints excluded: chain B residue 1176 CYS Chi-restraints excluded: chain B residue 1198 MET Chi-restraints excluded: chain B residue 1224 ASN Chi-restraints excluded: chain B residue 1226 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 469 ASP Chi-restraints excluded: chain C residue 548 CYS Chi-restraints excluded: chain C residue 559 GLU Chi-restraints excluded: chain C residue 944 ILE Chi-restraints excluded: chain C residue 1125 GLU Chi-restraints excluded: chain C residue 1224 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 240 optimal weight: 3.9990 chunk 294 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 348 optimal weight: 0.0470 chunk 75 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 208 optimal weight: 4.9990 chunk 204 optimal weight: 0.9990 chunk 126 optimal weight: 0.6980 chunk 118 optimal weight: 9.9990 chunk 327 optimal weight: 1.9990 overall best weight: 1.1484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 490 HIS A 746 GLN A1214 ASN B 785 ASN B1214 ASN C 328 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.141643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.114359 restraints weight = 34267.891| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.99 r_work: 0.3116 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 29517 Z= 0.208 Angle : 0.659 11.194 40386 Z= 0.325 Chirality : 0.047 0.403 4800 Planarity : 0.004 0.043 5013 Dihedral : 6.035 43.919 5795 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.29 % Allowed : 9.88 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.31 (0.14), residues: 3489 helix: 1.30 (0.19), residues: 783 sheet: 0.31 (0.18), residues: 747 loop : -0.23 (0.14), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 76 TYR 0.026 0.002 TYR C 738 PHE 0.019 0.002 PHE A 278 TRP 0.016 0.002 TRP B 460 HIS 0.004 0.001 HIS B 483 Details of bonding type rmsd covalent geometry : bond 0.00487 (29358) covalent geometry : angle 0.61179 (39972) SS BOND : bond 0.00363 ( 63) SS BOND : angle 1.11344 ( 126) hydrogen bonds : bond 0.04735 ( 1163) hydrogen bonds : angle 5.32038 ( 3345) link_ALPHA1-3 : bond 0.01248 ( 3) link_ALPHA1-3 : angle 1.65997 ( 9) link_BETA1-4 : bond 0.00793 ( 48) link_BETA1-4 : angle 2.46892 ( 144) link_NAG-ASN : bond 0.00506 ( 45) link_NAG-ASN : angle 3.38134 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 289 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.7879 (mp) cc_final: 0.7474 (mt) REVERT: A 168 MET cc_start: 0.9003 (mmm) cc_final: 0.8248 (mmt) REVERT: A 170 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7549 (mt-10) REVERT: A 185 LYS cc_start: 0.7766 (mmtm) cc_final: 0.6642 (mtpm) REVERT: A 244 MET cc_start: 0.8039 (pmm) cc_final: 0.7114 (mmm) REVERT: A 470 SER cc_start: 0.8441 (m) cc_final: 0.8006 (p) REVERT: A 893 ASP cc_start: 0.8181 (t70) cc_final: 0.7676 (t0) REVERT: A 925 LYS cc_start: 0.8009 (tttt) cc_final: 0.7391 (mmpt) REVERT: A 944 ILE cc_start: 0.7729 (OUTLIER) cc_final: 0.7037 (pp) REVERT: A 1165 LYS cc_start: 0.8278 (mttt) cc_final: 0.7866 (mmtt) REVERT: A 1232 MET cc_start: 0.7245 (OUTLIER) cc_final: 0.6383 (mpp) REVERT: B 455 PHE cc_start: 0.8914 (m-80) cc_final: 0.8391 (m-80) REVERT: B 579 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.6799 (mpp-170) REVERT: B 889 PHE cc_start: 0.7949 (p90) cc_final: 0.6810 (m-10) REVERT: B 893 ASP cc_start: 0.7953 (t0) cc_final: 0.7719 (OUTLIER) REVERT: B 925 LYS cc_start: 0.8167 (tttt) cc_final: 0.7510 (mmpt) REVERT: B 1125 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.8428 (mt-10) REVERT: C 170 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7433 (mt-10) REVERT: C 185 LYS cc_start: 0.7730 (mmtm) cc_final: 0.7081 (mtpm) REVERT: C 244 MET cc_start: 0.7662 (ttm) cc_final: 0.7147 (mmm) REVERT: C 559 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8225 (mm-30) REVERT: C 925 LYS cc_start: 0.8152 (tttt) cc_final: 0.7345 (mmpt) REVERT: C 944 ILE cc_start: 0.7792 (OUTLIER) cc_final: 0.7467 (tp) REVERT: C 1063 ARG cc_start: 0.8437 (mtt180) cc_final: 0.8161 (mtm180) REVERT: C 1072 GLN cc_start: 0.8308 (tp40) cc_final: 0.7950 (tp40) REVERT: C 1125 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.8422 (mt-10) outliers start: 101 outliers final: 64 residues processed: 366 average time/residue: 0.5076 time to fit residues: 226.1337 Evaluate side-chains 336 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 265 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 548 CYS Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 681 ARG Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 698 GLU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 944 ILE Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1198 MET Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain A residue 1226 THR Chi-restraints excluded: chain A residue 1232 MET Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 548 CYS Chi-restraints excluded: chain B residue 579 ARG Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain B residue 840 GLN Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 1125 GLU Chi-restraints excluded: chain B residue 1176 CYS Chi-restraints excluded: chain B residue 1224 ASN Chi-restraints excluded: chain B residue 1226 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 469 ASP Chi-restraints excluded: chain C residue 548 CYS Chi-restraints excluded: chain C residue 559 GLU Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 874 MET Chi-restraints excluded: chain C residue 944 ILE Chi-restraints excluded: chain C residue 1125 GLU Chi-restraints excluded: chain C residue 1224 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 61 optimal weight: 0.9980 chunk 269 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 84 optimal weight: 0.0050 chunk 108 optimal weight: 2.9990 chunk 113 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 317 optimal weight: 1.9990 chunk 167 optimal weight: 0.2980 chunk 153 optimal weight: 0.9990 chunk 245 optimal weight: 0.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 746 GLN A 840 GLN A1214 ASN B 785 ASN B1214 ASN C 328 GLN C1062 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.143042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.114971 restraints weight = 34095.842| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.92 r_work: 0.3190 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29517 Z= 0.139 Angle : 0.630 19.120 40386 Z= 0.306 Chirality : 0.047 0.695 4800 Planarity : 0.003 0.041 5013 Dihedral : 5.761 41.974 5795 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.80 % Allowed : 10.96 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.35 (0.14), residues: 3489 helix: 1.42 (0.19), residues: 783 sheet: 0.30 (0.18), residues: 729 loop : -0.22 (0.14), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 143 TYR 0.019 0.001 TYR B 738 PHE 0.020 0.002 PHE B 278 TRP 0.016 0.001 TRP B 460 HIS 0.003 0.001 HIS A 483 Details of bonding type rmsd covalent geometry : bond 0.00310 (29358) covalent geometry : angle 0.56280 (39972) SS BOND : bond 0.00374 ( 63) SS BOND : angle 1.12496 ( 126) hydrogen bonds : bond 0.04243 ( 1163) hydrogen bonds : angle 5.23086 ( 3345) link_ALPHA1-3 : bond 0.01212 ( 3) link_ALPHA1-3 : angle 1.43114 ( 9) link_BETA1-4 : bond 0.00757 ( 48) link_BETA1-4 : angle 2.35870 ( 144) link_NAG-ASN : bond 0.00576 ( 45) link_NAG-ASN : angle 4.21696 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 281 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.7937 (mp) cc_final: 0.7557 (mt) REVERT: A 168 MET cc_start: 0.9001 (mmm) cc_final: 0.8251 (mmt) REVERT: A 170 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7596 (mt-10) REVERT: A 244 MET cc_start: 0.7855 (pmm) cc_final: 0.6896 (mmm) REVERT: A 470 SER cc_start: 0.8445 (m) cc_final: 0.8033 (p) REVERT: A 681 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.7965 (mtp-110) REVERT: A 893 ASP cc_start: 0.8159 (t70) cc_final: 0.7687 (t0) REVERT: A 944 ILE cc_start: 0.7762 (OUTLIER) cc_final: 0.7459 (tp) REVERT: A 1165 LYS cc_start: 0.8262 (mttt) cc_final: 0.7886 (mmtt) REVERT: B 455 PHE cc_start: 0.8898 (m-80) cc_final: 0.8485 (m-80) REVERT: B 579 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.6830 (mpp-170) REVERT: B 866 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.8293 (tt0) REVERT: B 889 PHE cc_start: 0.7948 (p90) cc_final: 0.6822 (m-80) REVERT: B 925 LYS cc_start: 0.8178 (tttt) cc_final: 0.7481 (mmpt) REVERT: B 1030 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7250 (tm-30) REVERT: B 1125 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8445 (mt-10) REVERT: B 1232 MET cc_start: 0.7277 (OUTLIER) cc_final: 0.6616 (mpp) REVERT: C 160 GLU cc_start: 0.7137 (tm-30) cc_final: 0.6876 (pp20) REVERT: C 170 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7508 (mt-10) REVERT: C 185 LYS cc_start: 0.7756 (mmtm) cc_final: 0.7139 (mtpm) REVERT: C 190 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7162 (tm) REVERT: C 244 MET cc_start: 0.7655 (OUTLIER) cc_final: 0.7130 (mmm) REVERT: C 470 SER cc_start: 0.8645 (m) cc_final: 0.8367 (p) REVERT: C 559 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8178 (mm-30) REVERT: C 925 LYS cc_start: 0.8178 (tttt) cc_final: 0.7366 (mmpt) REVERT: C 944 ILE cc_start: 0.7774 (OUTLIER) cc_final: 0.7425 (tp) REVERT: C 1063 ARG cc_start: 0.8448 (mtt180) cc_final: 0.8235 (mtm180) REVERT: C 1125 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8363 (mt-10) outliers start: 86 outliers final: 48 residues processed: 342 average time/residue: 0.5015 time to fit residues: 210.1167 Evaluate side-chains 333 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 272 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 548 CYS Chi-restraints excluded: chain A residue 681 ARG Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 944 ILE Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain A residue 1226 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 548 CYS Chi-restraints excluded: chain B residue 579 ARG Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain B residue 840 GLN Chi-restraints excluded: chain B residue 866 GLN Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 1030 GLU Chi-restraints excluded: chain B residue 1125 GLU Chi-restraints excluded: chain B residue 1176 CYS Chi-restraints excluded: chain B residue 1224 ASN Chi-restraints excluded: chain B residue 1226 THR Chi-restraints excluded: chain B residue 1232 MET Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 469 ASP Chi-restraints excluded: chain C residue 548 CYS Chi-restraints excluded: chain C residue 559 GLU Chi-restraints excluded: chain C residue 944 ILE Chi-restraints excluded: chain C residue 1125 GLU Chi-restraints excluded: chain C residue 1175 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 44 optimal weight: 1.9990 chunk 313 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 309 optimal weight: 3.9990 chunk 323 optimal weight: 0.2980 chunk 342 optimal weight: 2.9990 chunk 72 optimal weight: 0.2980 chunk 326 optimal weight: 1.9990 chunk 8 optimal weight: 0.4980 chunk 16 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 840 GLN A1214 ASN B 785 ASN B1214 ASN C 328 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.141792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.113580 restraints weight = 34301.380| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.93 r_work: 0.3162 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 29517 Z= 0.191 Angle : 0.671 13.265 40386 Z= 0.326 Chirality : 0.048 0.643 4800 Planarity : 0.004 0.039 5013 Dihedral : 5.869 42.048 5795 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.74 % Allowed : 11.32 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.24 (0.14), residues: 3489 helix: 1.30 (0.19), residues: 783 sheet: 0.21 (0.18), residues: 747 loop : -0.28 (0.14), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 76 TYR 0.023 0.002 TYR C 738 PHE 0.018 0.002 PHE B 278 TRP 0.016 0.001 TRP B 460 HIS 0.004 0.001 HIS B 215 Details of bonding type rmsd covalent geometry : bond 0.00444 (29358) covalent geometry : angle 0.60483 (39972) SS BOND : bond 0.00382 ( 63) SS BOND : angle 1.17417 ( 126) hydrogen bonds : bond 0.04541 ( 1163) hydrogen bonds : angle 5.26570 ( 3345) link_ALPHA1-3 : bond 0.01150 ( 3) link_ALPHA1-3 : angle 1.37366 ( 9) link_BETA1-4 : bond 0.00783 ( 48) link_BETA1-4 : angle 2.36342 ( 144) link_NAG-ASN : bond 0.00366 ( 45) link_NAG-ASN : angle 4.37497 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 274 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.7942 (mp) cc_final: 0.7563 (mt) REVERT: A 168 MET cc_start: 0.9024 (mmm) cc_final: 0.8138 (mmt) REVERT: A 170 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7636 (mt-10) REVERT: A 244 MET cc_start: 0.7939 (pmm) cc_final: 0.7051 (mmm) REVERT: A 470 SER cc_start: 0.8460 (m) cc_final: 0.8051 (p) REVERT: A 713 PHE cc_start: 0.8635 (m-10) cc_final: 0.8429 (m-10) REVERT: A 893 ASP cc_start: 0.8160 (t70) cc_final: 0.7686 (t0) REVERT: A 944 ILE cc_start: 0.7776 (OUTLIER) cc_final: 0.7030 (pp) REVERT: A 1051 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7670 (mm-30) REVERT: A 1165 LYS cc_start: 0.8228 (mttt) cc_final: 0.7832 (mmtt) REVERT: B 88 ARG cc_start: 0.7832 (mtm180) cc_final: 0.7531 (mtm180) REVERT: B 143 ARG cc_start: 0.7520 (OUTLIER) cc_final: 0.6706 (mpp80) REVERT: B 450 VAL cc_start: 0.8768 (OUTLIER) cc_final: 0.8560 (m) REVERT: B 455 PHE cc_start: 0.8938 (m-80) cc_final: 0.8423 (m-80) REVERT: B 579 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.6867 (mpp-170) REVERT: B 889 PHE cc_start: 0.7962 (p90) cc_final: 0.6857 (m-80) REVERT: B 925 LYS cc_start: 0.8166 (tttt) cc_final: 0.7501 (mmpt) REVERT: B 1125 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8460 (mt-10) REVERT: C 170 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7504 (mt-10) REVERT: C 185 LYS cc_start: 0.7800 (mmtm) cc_final: 0.7139 (mtpm) REVERT: C 190 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7167 (tm) REVERT: C 244 MET cc_start: 0.7691 (ttm) cc_final: 0.7162 (mmm) REVERT: C 470 SER cc_start: 0.8666 (m) cc_final: 0.8392 (p) REVERT: C 559 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8195 (mm-30) REVERT: C 925 LYS cc_start: 0.8172 (tttt) cc_final: 0.7354 (mmpt) REVERT: C 1063 ARG cc_start: 0.8495 (mtt180) cc_final: 0.8194 (mtm180) REVERT: C 1125 GLU cc_start: 0.8980 (OUTLIER) cc_final: 0.8434 (mt-10) outliers start: 84 outliers final: 58 residues processed: 341 average time/residue: 0.5177 time to fit residues: 214.9976 Evaluate side-chains 330 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 262 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 548 CYS Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 681 ARG Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 944 ILE Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 1051 GLU Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1198 MET Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain A residue 1226 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 548 CYS Chi-restraints excluded: chain B residue 579 ARG Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain B residue 683 CYS Chi-restraints excluded: chain B residue 840 GLN Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 1125 GLU Chi-restraints excluded: chain B residue 1132 SER Chi-restraints excluded: chain B residue 1176 CYS Chi-restraints excluded: chain B residue 1224 ASN Chi-restraints excluded: chain B residue 1226 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 469 ASP Chi-restraints excluded: chain C residue 548 CYS Chi-restraints excluded: chain C residue 559 GLU Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 944 ILE Chi-restraints excluded: chain C residue 1125 GLU Chi-restraints excluded: chain C residue 1175 LEU Chi-restraints excluded: chain C residue 1224 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 69 optimal weight: 4.9990 chunk 310 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 193 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 194 optimal weight: 3.9990 chunk 247 optimal weight: 4.9990 chunk 190 optimal weight: 0.3980 chunk 291 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 172 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1214 ASN B1214 ASN C 328 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.142635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.114585 restraints weight = 34043.163| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.92 r_work: 0.3163 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 29517 Z= 0.150 Angle : 0.643 14.106 40386 Z= 0.312 Chirality : 0.048 0.609 4800 Planarity : 0.004 0.042 5013 Dihedral : 6.375 117.954 5795 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.32 % Allowed : 11.77 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.14), residues: 3489 helix: 1.38 (0.19), residues: 783 sheet: 0.27 (0.18), residues: 729 loop : -0.29 (0.14), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 143 TYR 0.013 0.001 TYR B 217 PHE 0.020 0.002 PHE B 278 TRP 0.016 0.001 TRP B 460 HIS 0.003 0.001 HIS B 483 Details of bonding type rmsd covalent geometry : bond 0.00338 (29358) covalent geometry : angle 0.57762 (39972) SS BOND : bond 0.00275 ( 63) SS BOND : angle 0.99748 ( 126) hydrogen bonds : bond 0.04288 ( 1163) hydrogen bonds : angle 5.22200 ( 3345) link_ALPHA1-3 : bond 0.01099 ( 3) link_ALPHA1-3 : angle 1.26509 ( 9) link_BETA1-4 : bond 0.00796 ( 48) link_BETA1-4 : angle 2.29186 ( 144) link_NAG-ASN : bond 0.00493 ( 45) link_NAG-ASN : angle 4.25910 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 273 time to evaluate : 1.086 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: A 19 LEU cc_start: 0.7931 (mp) cc_final: 0.7548 (mt) REVERT: A 168 MET cc_start: 0.9015 (mmm) cc_final: 0.8106 (mmt) REVERT: A 244 MET cc_start: 0.7875 (pmm) cc_final: 0.6915 (mmm) REVERT: A 470 SER cc_start: 0.8451 (m) cc_final: 0.8054 (p) REVERT: A 593 GLN cc_start: 0.7708 (mm110) cc_final: 0.7496 (mm-40) REVERT: A 889 PHE cc_start: 0.7906 (p90) cc_final: 0.6698 (m-80) REVERT: A 893 ASP cc_start: 0.8076 (t70) cc_final: 0.7440 (t0) REVERT: A 933 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7691 (mt-10) REVERT: A 944 ILE cc_start: 0.7751 (OUTLIER) cc_final: 0.7005 (pp) REVERT: A 1165 LYS cc_start: 0.8223 (mttt) cc_final: 0.7834 (mmtt) REVERT: B 88 ARG cc_start: 0.7792 (mtm180) cc_final: 0.7498 (mtm180) REVERT: B 455 PHE cc_start: 0.8933 (m-80) cc_final: 0.8474 (m-80) REVERT: B 579 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.6866 (mpp-170) REVERT: B 889 PHE cc_start: 0.7962 (p90) cc_final: 0.6878 (m-80) REVERT: B 925 LYS cc_start: 0.8157 (tttt) cc_final: 0.7459 (mmpt) REVERT: B 1125 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8436 (mt-10) REVERT: C 170 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7496 (mt-10) REVERT: C 185 LYS cc_start: 0.7787 (mmtm) cc_final: 0.7189 (mtpm) REVERT: C 190 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7152 (tm) REVERT: C 244 MET cc_start: 0.7669 (OUTLIER) cc_final: 0.7165 (mmm) REVERT: C 470 SER cc_start: 0.8650 (m) cc_final: 0.8389 (p) REVERT: C 559 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8197 (mm-30) REVERT: C 698 GLU cc_start: 0.8290 (pt0) cc_final: 0.7986 (tt0) REVERT: C 889 PHE cc_start: 0.7917 (p90) cc_final: 0.6737 (m-80) REVERT: C 925 LYS cc_start: 0.8174 (tttt) cc_final: 0.7351 (mmpt) REVERT: C 944 ILE cc_start: 0.7734 (OUTLIER) cc_final: 0.7406 (tp) REVERT: C 1063 ARG cc_start: 0.8541 (mtt180) cc_final: 0.8206 (mtm180) REVERT: C 1125 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8392 (mt-10) outliers start: 71 outliers final: 51 residues processed: 328 average time/residue: 0.5029 time to fit residues: 201.6675 Evaluate side-chains 322 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 262 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 548 CYS Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 681 ARG Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 840 GLN Chi-restraints excluded: chain A residue 944 ILE Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain A residue 1226 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 548 CYS Chi-restraints excluded: chain B residue 579 ARG Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain B residue 683 CYS Chi-restraints excluded: chain B residue 840 GLN Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 1125 GLU Chi-restraints excluded: chain B residue 1176 CYS Chi-restraints excluded: chain B residue 1224 ASN Chi-restraints excluded: chain B residue 1226 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 469 ASP Chi-restraints excluded: chain C residue 548 CYS Chi-restraints excluded: chain C residue 559 GLU Chi-restraints excluded: chain C residue 944 ILE Chi-restraints excluded: chain C residue 1125 GLU Chi-restraints excluded: chain C residue 1175 LEU Chi-restraints excluded: chain C residue 1224 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 316 optimal weight: 0.9990 chunk 38 optimal weight: 0.0570 chunk 39 optimal weight: 0.6980 chunk 168 optimal weight: 0.5980 chunk 292 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 343 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 229 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A1214 ASN B1214 ASN C 328 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.142953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.114938 restraints weight = 33959.729| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.92 r_work: 0.3168 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29517 Z= 0.145 Angle : 0.628 11.226 40386 Z= 0.309 Chirality : 0.046 0.554 4800 Planarity : 0.004 0.041 5013 Dihedral : 6.279 117.636 5795 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.22 % Allowed : 12.20 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.26 (0.14), residues: 3489 helix: 1.41 (0.19), residues: 783 sheet: 0.24 (0.18), residues: 729 loop : -0.31 (0.14), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 76 TYR 0.017 0.001 TYR C 738 PHE 0.020 0.002 PHE B 278 TRP 0.015 0.001 TRP B 460 HIS 0.006 0.001 HIS C 560 Details of bonding type rmsd covalent geometry : bond 0.00328 (29358) covalent geometry : angle 0.57214 (39972) SS BOND : bond 0.00261 ( 63) SS BOND : angle 1.39933 ( 126) hydrogen bonds : bond 0.04216 ( 1163) hydrogen bonds : angle 5.19307 ( 3345) link_ALPHA1-3 : bond 0.01102 ( 3) link_ALPHA1-3 : angle 1.23012 ( 9) link_BETA1-4 : bond 0.00766 ( 48) link_BETA1-4 : angle 2.18159 ( 144) link_NAG-ASN : bond 0.00405 ( 45) link_NAG-ASN : angle 3.74218 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 273 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ARG cc_start: 0.7862 (mtm180) cc_final: 0.6946 (mpt180) REVERT: A 168 MET cc_start: 0.9008 (mmm) cc_final: 0.8062 (mmt) REVERT: A 244 MET cc_start: 0.7870 (pmm) cc_final: 0.6899 (mmm) REVERT: A 470 SER cc_start: 0.8449 (m) cc_final: 0.8050 (p) REVERT: A 593 GLN cc_start: 0.7683 (mm110) cc_final: 0.7471 (mm-40) REVERT: A 713 PHE cc_start: 0.8552 (m-10) cc_final: 0.8349 (m-10) REVERT: A 889 PHE cc_start: 0.7921 (p90) cc_final: 0.6705 (m-80) REVERT: A 893 ASP cc_start: 0.8121 (t70) cc_final: 0.7476 (t0) REVERT: A 933 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7721 (mt-10) REVERT: A 944 ILE cc_start: 0.7825 (OUTLIER) cc_final: 0.7074 (pp) REVERT: A 1165 LYS cc_start: 0.8220 (mttt) cc_final: 0.7831 (mmtt) REVERT: B 88 ARG cc_start: 0.7790 (mtm180) cc_final: 0.7504 (mtm180) REVERT: B 143 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.6746 (mpp80) REVERT: B 190 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.7270 (tm) REVERT: B 207 VAL cc_start: 0.8211 (m) cc_final: 0.7876 (t) REVERT: B 455 PHE cc_start: 0.8921 (m-80) cc_final: 0.8354 (m-80) REVERT: B 579 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.6849 (mpp-170) REVERT: B 889 PHE cc_start: 0.7974 (p90) cc_final: 0.6930 (m-10) REVERT: B 925 LYS cc_start: 0.8137 (tttt) cc_final: 0.7485 (mmpt) REVERT: B 1125 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.8452 (mt-10) REVERT: C 60 THR cc_start: 0.8116 (p) cc_final: 0.7910 (p) REVERT: C 170 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7552 (mt-10) REVERT: C 185 LYS cc_start: 0.7791 (mmtm) cc_final: 0.7220 (mtpm) REVERT: C 190 LEU cc_start: 0.7519 (OUTLIER) cc_final: 0.7142 (tm) REVERT: C 244 MET cc_start: 0.7690 (OUTLIER) cc_final: 0.7160 (mmm) REVERT: C 470 SER cc_start: 0.8645 (m) cc_final: 0.8388 (p) REVERT: C 698 GLU cc_start: 0.8300 (pt0) cc_final: 0.8002 (tt0) REVERT: C 889 PHE cc_start: 0.7929 (p90) cc_final: 0.6753 (m-10) REVERT: C 925 LYS cc_start: 0.8161 (tttt) cc_final: 0.7328 (mmpt) REVERT: C 944 ILE cc_start: 0.7773 (OUTLIER) cc_final: 0.7444 (tp) REVERT: C 1063 ARG cc_start: 0.8533 (mtt180) cc_final: 0.8197 (mtm180) REVERT: C 1125 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8389 (mt-10) outliers start: 68 outliers final: 48 residues processed: 325 average time/residue: 0.5118 time to fit residues: 203.2439 Evaluate side-chains 321 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 263 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 548 CYS Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 840 GLN Chi-restraints excluded: chain A residue 944 ILE Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1198 MET Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain A residue 1226 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 548 CYS Chi-restraints excluded: chain B residue 579 ARG Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain B residue 840 GLN Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 1125 GLU Chi-restraints excluded: chain B residue 1132 SER Chi-restraints excluded: chain B residue 1176 CYS Chi-restraints excluded: chain B residue 1224 ASN Chi-restraints excluded: chain B residue 1226 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 469 ASP Chi-restraints excluded: chain C residue 548 CYS Chi-restraints excluded: chain C residue 944 ILE Chi-restraints excluded: chain C residue 1125 GLU Chi-restraints excluded: chain C residue 1175 LEU Chi-restraints excluded: chain C residue 1224 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 315 optimal weight: 0.5980 chunk 222 optimal weight: 0.8980 chunk 338 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 324 optimal weight: 0.6980 chunk 343 optimal weight: 0.9980 chunk 267 optimal weight: 1.9990 chunk 295 optimal weight: 0.6980 chunk 318 optimal weight: 0.0370 chunk 333 optimal weight: 0.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1214 ASN B 444 ASN B1214 ASN C 328 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.143271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.115755 restraints weight = 34293.117| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.04 r_work: 0.3183 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29517 Z= 0.138 Angle : 0.628 15.723 40386 Z= 0.306 Chirality : 0.047 0.532 4800 Planarity : 0.003 0.043 5013 Dihedral : 6.210 109.468 5795 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.25 % Allowed : 12.36 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.28 (0.14), residues: 3489 helix: 1.45 (0.19), residues: 783 sheet: 0.25 (0.18), residues: 729 loop : -0.31 (0.14), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 143 TYR 0.013 0.001 TYR A 738 PHE 0.020 0.002 PHE B 278 TRP 0.016 0.001 TRP B 460 HIS 0.003 0.001 HIS B 483 Details of bonding type rmsd covalent geometry : bond 0.00308 (29358) covalent geometry : angle 0.56230 (39972) SS BOND : bond 0.00248 ( 63) SS BOND : angle 1.48131 ( 126) hydrogen bonds : bond 0.04144 ( 1163) hydrogen bonds : angle 5.16978 ( 3345) link_ALPHA1-3 : bond 0.01098 ( 3) link_ALPHA1-3 : angle 1.20666 ( 9) link_BETA1-4 : bond 0.00765 ( 48) link_BETA1-4 : angle 2.18671 ( 144) link_NAG-ASN : bond 0.00526 ( 45) link_NAG-ASN : angle 4.11667 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9416.16 seconds wall clock time: 160 minutes 57.47 seconds (9657.47 seconds total)