Starting phenix.real_space_refine on Sun Jul 5 19:53:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7k9j_22750/07_2026/7k9j_22750.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k9j_22750/07_2026/7k9j_22750.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7k9j_22750/07_2026/7k9j_22750.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k9j_22750/07_2026/7k9j_22750.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7k9j_22750/07_2026/7k9j_22750.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7k9j_22750/07_2026/7k9j_22750.cif" model { file = "/net/cci-nas-00/data/ceres_data/7k9j_22750/07_2026/7k9j_22750.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k9j_22750/07_2026/7k9j_22750.cif" } resolution = 3.0 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= 0.091 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 117 5.16 5 C 18876 2.51 5 N 4779 2.21 5 O 5994 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 93 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29766 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 7680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 982, 7680 Classifications: {'peptide': 982} Link IDs: {'PTRANS': 48, 'TRANS': 933} Chain breaks: 8 Chain: "B" Number of atoms: 7680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 982, 7680 Classifications: {'peptide': 982} Link IDs: {'PTRANS': 48, 'TRANS': 933} Chain breaks: 8 Chain: "C" Number of atoms: 7680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 982, 7680 Classifications: {'peptide': 982} Link IDs: {'PTRANS': 48, 'TRANS': 933} Chain breaks: 8 Chain: "H" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 947 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "I" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 947 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "J" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 947 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "L" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 806 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "M" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 806 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "N" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 806 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "O" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 chiralities: 2 Chain: "S" 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 chiralities: 4 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "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 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 chiralities: 3 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "c" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 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 chiralities: 4 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 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 chiralities: 2 Chain: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "l" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "m" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "q" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 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 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 chiralities: 2 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "u" 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 chiralities: 4 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 chiralities: 2 Chain: "w" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "x" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.33, per 1000 atoms: 0.21 Number of scatterers: 29766 At special positions: 0 Unit cell: (133.1, 147.4, 192.5, 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 117 16.00 O 5994 8.00 N 4779 7.00 C 18876 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 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 ALPHA1-6 " BMA S 3 " - " MAN S 4 " " BMA g 3 " - " MAN g 4 " " BMA u 3 " - " MAN u 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 G 1 " - " NAG G 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG 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 k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " BETA1-6 " NAG K 1 " - " FUC K 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG O 1 " - " FUC O 2 " " NAG b 1 " - " FUC b 4 " " NAG c 1 " - " FUC c 2 " " NAG p 1 " - " FUC p 4 " " NAG q 1 " - " FUC q 2 " NAG-ASN " NAG A1300 " - " ASN A 61 " " NAG B1300 " - " ASN B 61 " " NAG C1300 " - " ASN C 61 " " NAG D 1 " - " ASN A 165 " " NAG E 1 " - " ASN A 234 " " NAG F 1 " - " ASN A 282 " " NAG G 1 " - " ASN A 331 " " NAG K 1 " - " ASN A 343 " " NAG O 1 " - " ASN A 603 " " NAG P 1 " - " ASN A 616 " " NAG Q 1 " - " ASN A 657 " " NAG R 1 " - " ASN A 709 " " NAG S 1 " - " ASN A 717 " " NAG T 1 " - " ASN A 801 " " NAG U 1 " - " ASN A1074 " " NAG V 1 " - " ASN A1098 " " NAG W 1 " - " ASN A1134 " " NAG X 1 " - " ASN B 165 " " NAG Y 1 " - " ASN B 234 " " NAG Z 1 " - " ASN B 282 " " NAG a 1 " - " ASN B 331 " " NAG b 1 " - " ASN B 343 " " NAG c 1 " - " ASN B 603 " " NAG d 1 " - " ASN B 616 " " NAG e 1 " - " ASN B 657 " " NAG f 1 " - " ASN B 709 " " NAG g 1 " - " ASN B 717 " " NAG h 1 " - " ASN B 801 " " NAG i 1 " - " ASN B1074 " " NAG j 1 " - " ASN B1098 " " NAG k 1 " - " ASN B1134 " " NAG l 1 " - " ASN C 165 " " NAG m 1 " - " ASN C 234 " " NAG n 1 " - " ASN C 282 " " NAG o 1 " - " ASN C 331 " " NAG p 1 " - " ASN C 343 " " NAG q 1 " - " ASN C 603 " " NAG r 1 " - " ASN C 616 " " NAG s 1 " - " ASN C 657 " " NAG t 1 " - " ASN C 709 " " NAG u 1 " - " ASN C 717 " " NAG v 1 " - " ASN C 801 " " NAG w 1 " - " ASN C1074 " " NAG x 1 " - " ASN C1098 " " NAG y 1 " - " ASN C1134 " Time building additional restraints: 2.66 Conformation dependent library (CDL) restraints added in 1.2 seconds 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6774 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 66 sheets defined 22.5% alpha, 31.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.669A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 385 through 389 removed outlier: 3.836A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.442A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.694A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 759 through 783 removed outlier: 3.888A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.919A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.696A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.555A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.537A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.019A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.769A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.605A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.180A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.669A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 385 through 389 removed outlier: 3.836A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.443A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.694A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 759 through 783 removed outlier: 3.888A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.920A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.696A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.555A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.536A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER B 940 " --> pdb=" O ASP B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.018A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.768A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.605A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.181A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.669A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 385 through 389 removed outlier: 3.836A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.442A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.693A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 759 through 783 removed outlier: 3.889A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.920A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.695A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.555A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.536A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER C 940 " --> pdb=" O ASP C 936 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.019A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.768A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.606A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.180A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'I' and resid 62 through 65 Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'J' and resid 62 through 65 Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'M' and resid 79 through 83 Processing helix chain 'N' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.783A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.019A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 52 removed outlier: 7.201A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.686A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 118 through 121 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.204A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 595 " --> pdb=" O SER A 316 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.078A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N THR A 430 " --> pdb=" O PHE A 515 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 3.593A pdb=" N CYS A 525 " --> pdb=" O CYS A 361 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.544A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 702 removed outlier: 7.014A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.553A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.553A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.606A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1123 removed outlier: 3.939A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.783A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.019A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 52 removed outlier: 7.201A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.685A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC4, first strand: chain 'B' and resid 118 through 121 Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.204A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL B 595 " --> pdb=" O SER B 316 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.078A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N THR B 430 " --> pdb=" O PHE B 515 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N ASN B 437 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N PHE B 374 " --> pdb=" O ASN B 437 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 3.593A pdb=" N CYS B 525 " --> pdb=" O CYS B 361 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.544A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.981A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.553A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.553A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.606A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1123 removed outlier: 3.938A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.784A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.019A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 48 through 52 removed outlier: 7.200A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.686A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE2, first strand: chain 'C' and resid 118 through 121 Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.203A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL C 595 " --> pdb=" O SER C 316 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 325 through 328 Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.079A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N THR C 430 " --> pdb=" O PHE C 515 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N ASN C 437 " --> pdb=" O PHE C 374 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N PHE C 374 " --> pdb=" O ASN C 437 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 361 through 362 removed outlier: 3.593A pdb=" N CYS C 525 " --> pdb=" O CYS C 361 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.543A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.553A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.553A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.606A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1123 removed outlier: 3.938A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AF5, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.082A pdb=" N VAL H 12 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE H 34 " --> pdb=" O ASP H 50 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ASP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS H 59 " --> pdb=" O ASP H 50 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.082A pdb=" N VAL H 12 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N TYR H 109 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AF8, first strand: chain 'I' and resid 11 through 12 removed outlier: 4.081A pdb=" N VAL I 12 " --> pdb=" O THR I 117 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE I 34 " --> pdb=" O ASP I 50 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ASP I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS I 59 " --> pdb=" O ASP I 50 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 11 through 12 removed outlier: 4.081A pdb=" N VAL I 12 " --> pdb=" O THR I 117 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N TYR I 109 " --> pdb=" O ARG I 98 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AG2, first strand: chain 'J' and resid 11 through 12 removed outlier: 4.081A pdb=" N VAL J 12 " --> pdb=" O THR J 117 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE J 34 " --> pdb=" O ASP J 50 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ASP J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS J 59 " --> pdb=" O ASP J 50 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 11 through 12 removed outlier: 4.081A pdb=" N VAL J 12 " --> pdb=" O THR J 117 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N TYR J 109 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.961A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER L 63 " --> pdb=" O SER L 74 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.537A pdb=" N LEU L 11 " --> pdb=" O LYS L 103 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'L' and resid 44 through 48 removed outlier: 3.512A pdb=" N ARG L 45 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN L 37 " --> pdb=" O ARG L 45 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR L 36 " --> pdb=" O TYR L 87 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'M' and resid 5 through 6 removed outlier: 3.961A pdb=" N VAL M 19 " --> pdb=" O ILE M 75 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER M 63 " --> pdb=" O SER M 74 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'M' and resid 10 through 12 removed outlier: 3.537A pdb=" N LEU M 11 " --> pdb=" O LYS M 103 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU M 105 " --> pdb=" O LEU M 11 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'M' and resid 44 through 48 removed outlier: 3.511A pdb=" N ARG M 45 " --> pdb=" O GLN M 37 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN M 37 " --> pdb=" O ARG M 45 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR M 36 " --> pdb=" O TYR M 87 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'N' and resid 5 through 6 removed outlier: 3.961A pdb=" N VAL N 19 " --> pdb=" O ILE N 75 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER N 63 " --> pdb=" O SER N 74 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.536A pdb=" N LEU N 11 " --> pdb=" O LYS N 103 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU N 105 " --> pdb=" O LEU N 11 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH2 Processing sheet with id=AH3, first strand: chain 'N' and resid 44 through 48 removed outlier: 3.511A pdb=" N ARG N 45 " --> pdb=" O GLN N 37 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN N 37 " --> pdb=" O ARG N 45 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR N 36 " --> pdb=" O TYR N 87 " (cutoff:3.500A) 1093 hydrogen bonds defined for protein. 2943 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: 6.46 Time building geometry restraints manager: 3.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4774 1.32 - 1.45: 8759 1.45 - 1.57: 16725 1.57 - 1.70: 3 1.70 - 1.82: 147 Bond restraints: 30408 Sorted by residual: bond pdb=" C PHE A 377 " pdb=" O PHE A 377 " ideal model delta sigma weight residual 1.236 1.194 0.042 1.14e-02 7.69e+03 1.37e+01 bond pdb=" C PRO B 384 " pdb=" O PRO B 384 " ideal model delta sigma weight residual 1.238 1.194 0.044 1.33e-02 5.65e+03 1.11e+01 bond pdb=" C1 NAG X 2 " pdb=" O5 NAG X 2 " ideal model delta sigma weight residual 1.406 1.473 -0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.472 -0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" C1 NAG l 2 " pdb=" O5 NAG l 2 " ideal model delta sigma weight residual 1.406 1.472 -0.066 2.00e-02 2.50e+03 1.09e+01 ... (remaining 30403 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 40231 2.26 - 4.52: 943 4.52 - 6.78: 159 6.78 - 9.04: 23 9.04 - 11.30: 5 Bond angle restraints: 41361 Sorted by residual: angle pdb=" CA ALA C 520 " pdb=" C ALA C 520 " pdb=" N PRO C 521 " ideal model delta sigma weight residual 117.96 122.84 -4.88 8.10e-01 1.52e+00 3.63e+01 angle pdb=" CA ALA B 520 " pdb=" C ALA B 520 " pdb=" N PRO B 521 " ideal model delta sigma weight residual 117.96 122.64 -4.68 8.10e-01 1.52e+00 3.34e+01 angle pdb=" N ALA C 520 " pdb=" CA ALA C 520 " pdb=" C ALA C 520 " ideal model delta sigma weight residual 108.22 103.06 5.16 9.00e-01 1.23e+00 3.29e+01 angle pdb=" CA ALA A 520 " pdb=" C ALA A 520 " pdb=" N PRO A 521 " ideal model delta sigma weight residual 117.96 122.47 -4.51 8.10e-01 1.52e+00 3.10e+01 angle pdb=" N ILE C 434 " pdb=" CA ILE C 434 " pdb=" CB ILE C 434 " ideal model delta sigma weight residual 111.90 105.73 6.17 1.26e+00 6.30e-01 2.40e+01 ... (remaining 41356 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 15912 18.00 - 36.00: 1008 36.00 - 54.00: 199 54.00 - 72.00: 50 72.00 - 90.00: 27 Dihedral angle restraints: 17196 sinusoidal: 6663 harmonic: 10533 Sorted by residual: dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual -86.00 -176.00 90.00 1 1.00e+01 1.00e-02 9.60e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual -86.00 -175.99 89.99 1 1.00e+01 1.00e-02 9.60e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual -86.00 -175.96 89.96 1 1.00e+01 1.00e-02 9.59e+01 ... (remaining 17193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 4494 0.090 - 0.180: 467 0.180 - 0.270: 32 0.270 - 0.360: 19 0.360 - 0.451: 10 Chirality restraints: 5022 Sorted by residual: chirality pdb=" C1 NAG A1300 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG A1300 " pdb=" O5 NAG A1300 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.08e+00 chirality pdb=" C1 NAG B1300 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B1300 " pdb=" O5 NAG B1300 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.02e+00 chirality pdb=" C1 NAG C1300 " pdb=" ND2 ASN C 61 " pdb=" C2 NAG C1300 " pdb=" O5 NAG C1300 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 4.99e+00 ... (remaining 5019 not shown) Planarity restraints: 5202 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 81 " -0.055 5.00e-02 4.00e+02 8.40e-02 1.13e+01 pdb=" N PRO C 82 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO C 82 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 82 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 81 " 0.055 5.00e-02 4.00e+02 8.40e-02 1.13e+01 pdb=" N PRO A 82 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 82 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 82 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 81 " -0.055 5.00e-02 4.00e+02 8.38e-02 1.12e+01 pdb=" N PRO B 82 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO B 82 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 82 " -0.046 5.00e-02 4.00e+02 ... (remaining 5199 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 526 2.65 - 3.21: 27487 3.21 - 3.77: 43017 3.77 - 4.34: 61555 4.34 - 4.90: 100880 Nonbonded interactions: 233465 Sorted by model distance: nonbonded pdb=" O ARG J 105 " pdb=" NE2 HIS N 34 " model vdw 2.084 3.120 nonbonded pdb=" OG1 THR A 29 " pdb=" OD2 ASP A 215 " model vdw 2.154 3.040 nonbonded pdb=" OG1 THR B 29 " pdb=" OD2 ASP B 215 " model vdw 2.154 3.040 nonbonded pdb=" OG1 THR C 29 " pdb=" OD2 ASP C 215 " model vdw 2.155 3.040 nonbonded pdb=" OD1 ASP I 90 " pdb=" OH TYR I 94 " model vdw 2.162 3.040 ... (remaining 233460 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'x' selection = chain 'y' } ncs_group { reference = (chain 'F' and resid 1) selection = (chain 'G' and resid 1) selection = (chain 'O' and resid 1) selection = (chain 'P' and resid 1) selection = (chain 'Q' and resid 1) selection = (chain 'R' and resid 1) selection = (chain 'T' and resid 1) selection = (chain 'U' and resid 1) selection = (chain 'Z' and resid 1) selection = (chain 'a' and resid 1) selection = (chain 'c' and resid 1) selection = (chain 'd' and resid 1) selection = (chain 'e' and resid 1) selection = (chain 'f' and resid 1) selection = (chain 'h' and resid 1) selection = (chain 'i' and resid 1) selection = (chain 'n' and resid 1) selection = (chain 'o' and resid 1) selection = (chain 'q' and resid 1) selection = (chain 'r' and resid 1) selection = (chain 's' and resid 1) selection = (chain 't' and resid 1) selection = (chain 'v' and resid 1) selection = (chain 'w' and resid 1) } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = (chain 'K' and resid 1 through 3) selection = (chain 'S' and resid 1 through 3) selection = (chain 'b' and resid 1 through 3) selection = (chain 'g' and resid 1 through 3) selection = (chain 'p' and resid 1 through 3) selection = (chain 'u' and resid 1 through 3) } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 2.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 26.790 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 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 : 0.005 0.067 30561 Z= 0.259 Angle : 0.877 12.254 41778 Z= 0.451 Chirality : 0.058 0.451 5022 Planarity : 0.005 0.084 5157 Dihedral : 13.021 86.891 10296 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.57 % Allowed : 0.54 % Favored : 98.89 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.79 % 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: -0.88 (0.13), residues: 3561 helix: -0.06 (0.18), residues: 648 sheet: 0.40 (0.16), residues: 942 loop : -1.29 (0.13), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.054 0.002 ARG A 355 TYR 0.030 0.002 TYR A 904 PHE 0.029 0.002 PHE C 58 TRP 0.016 0.002 TRP A 353 HIS 0.006 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.26 (30408) covalent geometry : angle 0.84449 / 0.44 (41361) SS BOND : bond 0.00377 / 0.22 ( 42) SS BOND : angle 2.07292 / 1.18 ( 84) hydrogen bonds : bond 0.26096 / 17.13 ( 1063) hydrogen bonds : angle 9.68528 / 6.77 ( 2943) link_ALPHA1-6 : bond 0.00218 / 0.10 ( 3) link_ALPHA1-6 : angle 1.73772 / 0.95 ( 9) link_BETA1-4 : bond 0.00774 / 0.49 ( 57) link_BETA1-4 : angle 1.89616 / 1.29 ( 171) link_BETA1-6 : bond 0.00350 / 0.22 ( 6) link_BETA1-6 : angle 1.64095 / 0.91 ( 18) link_NAG-ASN : bond 0.00533 / 0.29 ( 45) link_NAG-ASN : angle 3.42742 / 2.22 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 268 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 231 ILE cc_start: 0.7751 (mm) cc_final: 0.7537 (pp) REVERT: A 365 TYR cc_start: 0.8032 (m-80) cc_final: 0.7663 (m-80) REVERT: B 988 GLU cc_start: 0.7362 (mp0) cc_final: 0.6995 (mp0) REVERT: C 306 PHE cc_start: 0.8426 (m-10) cc_final: 0.8062 (m-10) REVERT: C 902 MET cc_start: 0.8180 (mmm) cc_final: 0.7957 (mmt) REVERT: H 10 GLU cc_start: 0.5054 (OUTLIER) cc_final: 0.3902 (tm-30) REVERT: I 50 ASP cc_start: 0.7790 (p0) cc_final: 0.7535 (p0) REVERT: J 50 ASP cc_start: 0.7445 (p0) cc_final: 0.7211 (p0) REVERT: J 81 MET cc_start: 0.5790 (tmm) cc_final: 0.5477 (tmm) REVERT: M 3 VAL cc_start: 0.8740 (t) cc_final: 0.8506 (p) outliers start: 18 outliers final: 6 residues processed: 282 average time/residue: 0.4593 time to fit residues: 159.2029 Evaluate side-chains 206 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 199 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain J residue 10 GLU Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain M residue 13 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.0370 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 20.0000 overall best weight: 0.9262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 GLN A 675 GLN A 762 GLN A 804 GLN A 935 GLN B 196 ASN B 239 GLN B 804 GLN B 935 GLN C 239 GLN L 27 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.205318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.140686 restraints weight = 38627.151| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 3.43 r_work: 0.3631 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30561 Z= 0.150 Angle : 0.683 10.413 41778 Z= 0.343 Chirality : 0.047 0.409 5022 Planarity : 0.005 0.057 5157 Dihedral : 5.159 23.945 3897 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.79 % Allowed : 6.26 % Favored : 92.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -0.48 (0.14), residues: 3561 helix: 1.19 (0.20), residues: 669 sheet: 0.28 (0.16), residues: 966 loop : -1.22 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 98 TYR 0.023 0.001 TYR B 265 PHE 0.024 0.001 PHE I 64 TRP 0.015 0.002 TRP C 104 HIS 0.006 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (30408) covalent geometry : angle 0.65428 / 0.34 (41361) SS BOND : bond 0.00706 / 0.38 ( 42) SS BOND : angle 1.46251 / 0.81 ( 84) hydrogen bonds : bond 0.05761 / 3.78 ( 1063) hydrogen bonds : angle 6.80806 / 4.76 ( 2943) link_ALPHA1-6 : bond 0.00507 / 0.23 ( 3) link_ALPHA1-6 : angle 1.56141 / 0.91 ( 9) link_BETA1-4 : bond 0.00789 / 0.50 ( 57) link_BETA1-4 : angle 1.75407 / 1.20 ( 171) link_BETA1-6 : bond 0.00459 / 0.27 ( 6) link_BETA1-6 : angle 1.59955 / 0.91 ( 18) link_NAG-ASN : bond 0.00471 / 0.28 ( 45) link_NAG-ASN : angle 2.71863 / 1.72 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 231 time to evaluate : 1.062 Fit side-chains revert: symmetry clash REVERT: A 99 ASN cc_start: 0.7617 (t0) cc_final: 0.7213 (t0) REVERT: A 170 TYR cc_start: 0.6966 (t80) cc_final: 0.6583 (t80) REVERT: A 237 ARG cc_start: 0.7615 (tmt170) cc_final: 0.7107 (tmt-80) REVERT: A 571 ASP cc_start: 0.8215 (t0) cc_final: 0.7850 (t0) REVERT: A 902 MET cc_start: 0.8481 (mmt) cc_final: 0.8234 (tpt) REVERT: A 988 GLU cc_start: 0.8052 (mp0) cc_final: 0.7706 (mp0) REVERT: B 99 ASN cc_start: 0.8052 (t0) cc_final: 0.7787 (t0) REVERT: B 170 TYR cc_start: 0.6859 (t80) cc_final: 0.6438 (t80) REVERT: B 237 ARG cc_start: 0.7591 (tmt170) cc_final: 0.6785 (tmt-80) REVERT: B 571 ASP cc_start: 0.8352 (t0) cc_final: 0.8012 (t0) REVERT: B 646 ARG cc_start: 0.7882 (tmt170) cc_final: 0.7468 (tpt170) REVERT: B 804 GLN cc_start: 0.8728 (mm-40) cc_final: 0.8299 (mt0) REVERT: B 988 GLU cc_start: 0.7965 (mp0) cc_final: 0.7304 (mp0) REVERT: B 1107 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7501 (mmt-90) REVERT: C 99 ASN cc_start: 0.7865 (t0) cc_final: 0.7604 (t0) REVERT: C 237 ARG cc_start: 0.7532 (tmt170) cc_final: 0.6885 (tmt-80) REVERT: C 306 PHE cc_start: 0.8483 (m-10) cc_final: 0.8120 (m-10) REVERT: C 571 ASP cc_start: 0.8339 (t0) cc_final: 0.7966 (t0) REVERT: C 578 ASP cc_start: 0.8242 (t0) cc_final: 0.7883 (t0) REVERT: C 936 ASP cc_start: 0.8534 (t0) cc_final: 0.8175 (t0) REVERT: H 99 TRP cc_start: 0.5543 (t60) cc_final: 0.5317 (t60) REVERT: H 100 ASP cc_start: 0.6157 (t0) cc_final: 0.5934 (p0) REVERT: I 50 ASP cc_start: 0.7993 (p0) cc_final: 0.7739 (p0) REVERT: J 81 MET cc_start: 0.5953 (tmm) cc_final: 0.5604 (tmm) REVERT: M 3 VAL cc_start: 0.8471 (t) cc_final: 0.8220 (p) REVERT: N 37 GLN cc_start: 0.6395 (pm20) cc_final: 0.5852 (pm20) REVERT: N 90 GLN cc_start: 0.7527 (pp30) cc_final: 0.6933 (pp30) outliers start: 25 outliers final: 13 residues processed: 248 average time/residue: 0.4068 time to fit residues: 127.0026 Evaluate side-chains 216 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 202 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 29 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 295 optimal weight: 8.9990 chunk 282 optimal weight: 0.5980 chunk 146 optimal weight: 0.0000 chunk 240 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 313 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 265 optimal weight: 9.9990 chunk 339 optimal weight: 9.9990 chunk 315 optimal weight: 6.9990 overall best weight: 3.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN A1002 GLN B 196 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.200670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.133543 restraints weight = 38723.082| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 2.82 r_work: 0.3626 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 30561 Z= 0.275 Angle : 0.723 10.933 41778 Z= 0.363 Chirality : 0.050 0.412 5022 Planarity : 0.005 0.060 5157 Dihedral : 5.214 25.189 3886 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.33 % Allowed : 8.89 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -0.78 (0.14), residues: 3561 helix: 0.89 (0.20), residues: 675 sheet: -0.00 (0.16), residues: 987 loop : -1.34 (0.14), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B1107 TYR 0.032 0.002 TYR B 265 PHE 0.020 0.002 PHE B1103 TRP 0.015 0.002 TRP C 436 HIS 0.008 0.002 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00677 / 0.27 (30408) covalent geometry : angle 0.69381 / 0.36 (41361) SS BOND : bond 0.00497 / 0.31 ( 42) SS BOND : angle 1.58757 / 0.88 ( 84) hydrogen bonds : bond 0.06279 / 4.19 ( 1063) hydrogen bonds : angle 6.42358 / 4.48 ( 2943) link_ALPHA1-6 : bond 0.00490 / 0.22 ( 3) link_ALPHA1-6 : angle 1.45919 / 0.81 ( 9) link_BETA1-4 : bond 0.00657 / 0.42 ( 57) link_BETA1-4 : angle 1.73481 / 1.20 ( 171) link_BETA1-6 : bond 0.00283 / 0.17 ( 6) link_BETA1-6 : angle 1.60882 / 0.91 ( 18) link_NAG-ASN : bond 0.00458 / 0.26 ( 45) link_NAG-ASN : angle 2.86973 / 1.85 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 216 time to evaluate : 0.942 Fit side-chains REVERT: A 99 ASN cc_start: 0.7735 (t0) cc_final: 0.7271 (t0) REVERT: A 237 ARG cc_start: 0.7866 (tmt170) cc_final: 0.7554 (tmt170) REVERT: A 571 ASP cc_start: 0.8543 (t0) cc_final: 0.8139 (t0) REVERT: A 574 ASP cc_start: 0.8122 (t0) cc_final: 0.7839 (t0) REVERT: A 988 GLU cc_start: 0.8294 (mp0) cc_final: 0.7955 (mp0) REVERT: B 99 ASN cc_start: 0.8155 (t0) cc_final: 0.7947 (t0) REVERT: B 571 ASP cc_start: 0.8501 (t0) cc_final: 0.8189 (t0) REVERT: B 988 GLU cc_start: 0.8219 (mp0) cc_final: 0.7605 (mp0) REVERT: B 995 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.8015 (mtt-85) REVERT: B 1107 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7633 (mmt-90) REVERT: C 99 ASN cc_start: 0.7985 (t0) cc_final: 0.7770 (t0) REVERT: C 306 PHE cc_start: 0.8570 (m-80) cc_final: 0.8203 (m-10) REVERT: C 571 ASP cc_start: 0.8435 (t0) cc_final: 0.7982 (t0) REVERT: C 574 ASP cc_start: 0.8033 (t0) cc_final: 0.7688 (t0) REVERT: C 578 ASP cc_start: 0.8438 (t0) cc_final: 0.8113 (t0) REVERT: C 882 ILE cc_start: 0.8820 (OUTLIER) cc_final: 0.8541 (mt) REVERT: C 995 ARG cc_start: 0.8526 (mtt-85) cc_final: 0.8274 (mtt180) REVERT: H 100 ASP cc_start: 0.6064 (t0) cc_final: 0.5852 (p0) REVERT: I 100 ASP cc_start: 0.6316 (p0) cc_final: 0.5949 (t70) REVERT: I 108 ASP cc_start: 0.7385 (m-30) cc_final: 0.6636 (p0) REVERT: I 109 TYR cc_start: 0.6720 (m-80) cc_final: 0.5985 (m-80) REVERT: J 81 MET cc_start: 0.5836 (tmm) cc_final: 0.5414 (tmm) REVERT: J 108 ASP cc_start: 0.7476 (m-30) cc_final: 0.6599 (p0) REVERT: M 3 VAL cc_start: 0.8681 (t) cc_final: 0.8414 (p) REVERT: N 37 GLN cc_start: 0.6631 (pm20) cc_final: 0.6068 (pm20) REVERT: N 90 GLN cc_start: 0.7901 (pp30) cc_final: 0.7681 (pp30) outliers start: 42 outliers final: 18 residues processed: 240 average time/residue: 0.4392 time to fit residues: 131.8429 Evaluate side-chains 216 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 195 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 29 ILE Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 29 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 119 optimal weight: 0.8980 chunk 225 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 239 optimal weight: 1.9990 chunk 108 optimal weight: 8.9990 chunk 169 optimal weight: 0.7980 chunk 230 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 171 optimal weight: 0.2980 chunk 320 optimal weight: 2.9990 chunk 270 optimal weight: 0.5980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN B 49 HIS B 196 ASN B 762 GLN C 196 ASN L 6 GLN M 6 GLN N 6 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.204866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.139450 restraints weight = 38393.405| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 3.32 r_work: 0.3673 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30561 Z= 0.128 Angle : 0.609 10.567 41778 Z= 0.301 Chirality : 0.045 0.401 5022 Planarity : 0.004 0.057 5157 Dihedral : 4.750 22.669 3886 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.04 % Allowed : 11.39 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.14), residues: 3561 helix: 1.45 (0.21), residues: 669 sheet: 0.04 (0.16), residues: 987 loop : -1.17 (0.14), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 357 TYR 0.019 0.001 TYR A 170 PHE 0.023 0.001 PHE B 140 TRP 0.015 0.001 TRP C 104 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (30408) covalent geometry : angle 0.58056 / 0.29 (41361) SS BOND : bond 0.00334 / 0.21 ( 42) SS BOND : angle 1.38865 / 0.77 ( 84) hydrogen bonds : bond 0.04692 / 3.11 ( 1063) hydrogen bonds : angle 5.94508 / 4.15 ( 2943) link_ALPHA1-6 : bond 0.00463 / 0.20 ( 3) link_ALPHA1-6 : angle 1.45576 / 0.81 ( 9) link_BETA1-4 : bond 0.00688 / 0.44 ( 57) link_BETA1-4 : angle 1.65453 / 1.14 ( 171) link_BETA1-6 : bond 0.00487 / 0.27 ( 6) link_BETA1-6 : angle 1.53848 / 0.86 ( 18) link_NAG-ASN : bond 0.00396 / 0.23 ( 45) link_NAG-ASN : angle 2.50641 / 1.59 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 214 time to evaluate : 0.785 Fit side-chains revert: symmetry clash REVERT: A 99 ASN cc_start: 0.7466 (t0) cc_final: 0.6957 (t0) REVERT: A 170 TYR cc_start: 0.7067 (t80) cc_final: 0.6728 (t80) REVERT: A 196 ASN cc_start: 0.5971 (OUTLIER) cc_final: 0.5653 (m-40) REVERT: A 512 VAL cc_start: 0.8387 (OUTLIER) cc_final: 0.8135 (m) REVERT: A 571 ASP cc_start: 0.8544 (t0) cc_final: 0.8117 (t0) REVERT: A 574 ASP cc_start: 0.8103 (t0) cc_final: 0.7799 (t0) REVERT: A 904 TYR cc_start: 0.7736 (m-80) cc_final: 0.7449 (m-80) REVERT: A 988 GLU cc_start: 0.8310 (mp0) cc_final: 0.7885 (mp0) REVERT: B 99 ASN cc_start: 0.8200 (t0) cc_final: 0.7899 (t0) REVERT: B 170 TYR cc_start: 0.6986 (t80) cc_final: 0.6704 (t80) REVERT: B 571 ASP cc_start: 0.8455 (t0) cc_final: 0.8140 (t0) REVERT: B 988 GLU cc_start: 0.8264 (mp0) cc_final: 0.7605 (mp0) REVERT: B 1107 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7698 (mmt-90) REVERT: C 99 ASN cc_start: 0.8069 (t0) cc_final: 0.7758 (t0) REVERT: C 306 PHE cc_start: 0.8512 (m-80) cc_final: 0.8122 (m-10) REVERT: C 571 ASP cc_start: 0.8439 (t0) cc_final: 0.8007 (t0) REVERT: C 574 ASP cc_start: 0.7961 (t0) cc_final: 0.7593 (t0) REVERT: C 578 ASP cc_start: 0.8415 (t0) cc_final: 0.8059 (t0) REVERT: C 936 ASP cc_start: 0.8565 (t0) cc_final: 0.8289 (t0) REVERT: C 995 ARG cc_start: 0.8411 (mtt-85) cc_final: 0.8143 (mtt180) REVERT: C 1002 GLN cc_start: 0.8372 (tp40) cc_final: 0.7911 (tt0) REVERT: H 99 TRP cc_start: 0.5535 (t60) cc_final: 0.5331 (t60) REVERT: H 100 ASP cc_start: 0.6201 (t0) cc_final: 0.5943 (p0) REVERT: I 100 ASP cc_start: 0.6566 (p0) cc_final: 0.6321 (t70) REVERT: I 108 ASP cc_start: 0.7136 (m-30) cc_final: 0.6487 (p0) REVERT: I 109 TYR cc_start: 0.6534 (m-80) cc_final: 0.5897 (m-80) REVERT: J 48 ILE cc_start: 0.7720 (OUTLIER) cc_final: 0.7425 (pp) REVERT: J 81 MET cc_start: 0.5713 (tmm) cc_final: 0.5278 (tmm) REVERT: J 108 ASP cc_start: 0.7581 (m-30) cc_final: 0.6516 (p0) REVERT: J 109 TYR cc_start: 0.6419 (m-80) cc_final: 0.5747 (m-80) REVERT: M 3 VAL cc_start: 0.8561 (t) cc_final: 0.8300 (p) REVERT: M 90 GLN cc_start: 0.7576 (pp30) cc_final: 0.7235 (pp30) REVERT: N 37 GLN cc_start: 0.6582 (pm20) cc_final: 0.5994 (pm20) REVERT: N 90 GLN cc_start: 0.7798 (pp30) cc_final: 0.7511 (pp30) outliers start: 33 outliers final: 9 residues processed: 240 average time/residue: 0.3998 time to fit residues: 122.4690 Evaluate side-chains 210 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 197 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 80 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 179 optimal weight: 3.9990 chunk 313 optimal weight: 9.9990 chunk 93 optimal weight: 0.5980 chunk 177 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 212 optimal weight: 1.9990 chunk 166 optimal weight: 0.0670 chunk 24 optimal weight: 5.9990 chunk 160 optimal weight: 2.9990 chunk 254 optimal weight: 1.9990 overall best weight: 0.8922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN A 121 ASN B 196 ASN C 99 ASN C 121 ASN C 762 GLN M 28 ASN ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.205538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.140868 restraints weight = 38438.055| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 3.20 r_work: 0.3704 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3545 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30561 Z= 0.122 Angle : 0.584 10.542 41778 Z= 0.289 Chirality : 0.045 0.389 5022 Planarity : 0.004 0.053 5157 Dihedral : 4.527 22.330 3884 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.23 % Allowed : 12.21 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.14), residues: 3561 helix: 1.71 (0.21), residues: 669 sheet: 0.00 (0.16), residues: 996 loop : -1.08 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 357 TYR 0.025 0.001 TYR C 453 PHE 0.020 0.001 PHE A 140 TRP 0.016 0.001 TRP J 99 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (30408) covalent geometry : angle 0.55799 / 0.28 (41361) SS BOND : bond 0.00340 / 0.21 ( 42) SS BOND : angle 1.22209 / 0.69 ( 84) hydrogen bonds : bond 0.04347 / 2.87 ( 1063) hydrogen bonds : angle 5.58351 / 3.89 ( 2943) link_ALPHA1-6 : bond 0.00454 / 0.20 ( 3) link_ALPHA1-6 : angle 1.43451 / 0.80 ( 9) link_BETA1-4 : bond 0.00669 / 0.42 ( 57) link_BETA1-4 : angle 1.60762 / 1.11 ( 171) link_BETA1-6 : bond 0.00352 / 0.21 ( 6) link_BETA1-6 : angle 1.51264 / 0.85 ( 18) link_NAG-ASN : bond 0.00379 / 0.21 ( 45) link_NAG-ASN : angle 2.36816 / 1.51 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 213 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.7519 (t0) cc_final: 0.7030 (t0) REVERT: A 170 TYR cc_start: 0.7175 (t80) cc_final: 0.6823 (t80) REVERT: A 196 ASN cc_start: 0.6065 (OUTLIER) cc_final: 0.5715 (m-40) REVERT: A 357 ARG cc_start: 0.7597 (tpp80) cc_final: 0.7333 (ttm-80) REVERT: A 512 VAL cc_start: 0.8418 (OUTLIER) cc_final: 0.8178 (m) REVERT: A 532 ASN cc_start: 0.7976 (t0) cc_final: 0.7738 (t0) REVERT: A 571 ASP cc_start: 0.8559 (t0) cc_final: 0.8225 (t0) REVERT: A 904 TYR cc_start: 0.7659 (m-80) cc_final: 0.7415 (m-80) REVERT: A 936 ASP cc_start: 0.8342 (t0) cc_final: 0.8086 (t0) REVERT: A 988 GLU cc_start: 0.8304 (mp0) cc_final: 0.7912 (mp0) REVERT: B 99 ASN cc_start: 0.7856 (t0) cc_final: 0.7423 (t0) REVERT: B 571 ASP cc_start: 0.8483 (t0) cc_final: 0.8149 (t0) REVERT: B 988 GLU cc_start: 0.8285 (mp0) cc_final: 0.7714 (mp0) REVERT: C 99 ASN cc_start: 0.7722 (t0) cc_final: 0.7310 (t0) REVERT: C 571 ASP cc_start: 0.8425 (t0) cc_final: 0.7963 (t0) REVERT: C 574 ASP cc_start: 0.7997 (t0) cc_final: 0.7695 (t0) REVERT: C 578 ASP cc_start: 0.8329 (t0) cc_final: 0.8012 (t0) REVERT: C 646 ARG cc_start: 0.7793 (tmt170) cc_final: 0.7522 (tmt170) REVERT: C 904 TYR cc_start: 0.7329 (m-10) cc_final: 0.7100 (m-10) REVERT: C 995 ARG cc_start: 0.8376 (mtt-85) cc_final: 0.8137 (mtt180) REVERT: C 1002 GLN cc_start: 0.8372 (tp40) cc_final: 0.7910 (tt0) REVERT: H 100 ASP cc_start: 0.6150 (t0) cc_final: 0.5866 (p0) REVERT: I 50 ASP cc_start: 0.7747 (p0) cc_final: 0.7295 (t0) REVERT: I 100 ASP cc_start: 0.6547 (p0) cc_final: 0.6206 (t70) REVERT: I 108 ASP cc_start: 0.7131 (m-30) cc_final: 0.6438 (p0) REVERT: I 109 TYR cc_start: 0.6625 (m-80) cc_final: 0.5945 (m-80) REVERT: J 108 ASP cc_start: 0.7438 (m-30) cc_final: 0.6347 (p0) REVERT: J 109 TYR cc_start: 0.6531 (m-80) cc_final: 0.5843 (m-80) REVERT: M 3 VAL cc_start: 0.8691 (t) cc_final: 0.8440 (p) REVERT: N 37 GLN cc_start: 0.6536 (pm20) cc_final: 0.5846 (pm20) REVERT: N 90 GLN cc_start: 0.7921 (pp30) cc_final: 0.7619 (pp30) outliers start: 39 outliers final: 12 residues processed: 242 average time/residue: 0.4021 time to fit residues: 123.8744 Evaluate side-chains 212 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 198 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 80 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 70 optimal weight: 2.9990 chunk 200 optimal weight: 2.9990 chunk 351 optimal weight: 0.1980 chunk 83 optimal weight: 2.9990 chunk 215 optimal weight: 0.8980 chunk 253 optimal weight: 0.9980 chunk 210 optimal weight: 0.0040 chunk 309 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 68 optimal weight: 0.0060 chunk 105 optimal weight: 7.9990 overall best weight: 0.4208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 99 ASN B 121 ASN B 196 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.207491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.144509 restraints weight = 38369.262| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 3.29 r_work: 0.3732 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3567 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 30561 Z= 0.103 Angle : 0.568 11.254 41778 Z= 0.279 Chirality : 0.044 0.379 5022 Planarity : 0.004 0.056 5157 Dihedral : 4.338 22.955 3884 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.95 % Allowed : 13.19 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -0.20 (0.14), residues: 3561 helix: 1.93 (0.22), residues: 672 sheet: 0.04 (0.16), residues: 999 loop : -1.00 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1107 TYR 0.024 0.001 TYR B 453 PHE 0.024 0.001 PHE A 201 TRP 0.021 0.001 TRP H 99 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (30408) covalent geometry : angle 0.54364 / 0.27 (41361) SS BOND : bond 0.00315 / 0.19 ( 42) SS BOND : angle 0.95564 / 0.56 ( 84) hydrogen bonds : bond 0.03842 / 2.53 ( 1063) hydrogen bonds : angle 5.34106 / 3.72 ( 2943) link_ALPHA1-6 : bond 0.00444 / 0.20 ( 3) link_ALPHA1-6 : angle 1.42580 / 0.79 ( 9) link_BETA1-4 : bond 0.00682 / 0.43 ( 57) link_BETA1-4 : angle 1.60284 / 1.11 ( 171) link_BETA1-6 : bond 0.00365 / 0.21 ( 6) link_BETA1-6 : angle 1.47134 / 0.83 ( 18) link_NAG-ASN : bond 0.00405 / 0.23 ( 45) link_NAG-ASN : angle 2.23318 / 1.42 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 233 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.7437 (t0) cc_final: 0.6955 (t0) REVERT: A 196 ASN cc_start: 0.6050 (OUTLIER) cc_final: 0.5736 (m-40) REVERT: A 360 ASN cc_start: 0.7930 (t0) cc_final: 0.7643 (t0) REVERT: A 512 VAL cc_start: 0.8362 (OUTLIER) cc_final: 0.8133 (m) REVERT: A 532 ASN cc_start: 0.7984 (t0) cc_final: 0.7722 (t0) REVERT: A 571 ASP cc_start: 0.8546 (t0) cc_final: 0.8226 (t0) REVERT: A 904 TYR cc_start: 0.7637 (m-80) cc_final: 0.7429 (m-80) REVERT: A 936 ASP cc_start: 0.8419 (t0) cc_final: 0.8215 (t0) REVERT: A 988 GLU cc_start: 0.8370 (mp0) cc_final: 0.7961 (mp0) REVERT: A 1119 ASN cc_start: 0.8332 (m-40) cc_final: 0.8034 (m110) REVERT: B 571 ASP cc_start: 0.8465 (t0) cc_final: 0.8159 (t0) REVERT: B 583 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7281 (pm20) REVERT: B 882 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8546 (mp) REVERT: B 936 ASP cc_start: 0.8368 (t0) cc_final: 0.8137 (t0) REVERT: B 988 GLU cc_start: 0.8335 (mp0) cc_final: 0.7755 (mp0) REVERT: C 99 ASN cc_start: 0.7654 (t0) cc_final: 0.7167 (t0) REVERT: C 571 ASP cc_start: 0.8415 (t0) cc_final: 0.7960 (t0) REVERT: C 574 ASP cc_start: 0.8032 (t0) cc_final: 0.7677 (t0) REVERT: C 578 ASP cc_start: 0.8300 (t0) cc_final: 0.7978 (t0) REVERT: C 583 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7537 (pm20) REVERT: C 902 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7883 (mmp) REVERT: C 988 GLU cc_start: 0.7891 (mp0) cc_final: 0.7654 (mp0) REVERT: C 995 ARG cc_start: 0.8309 (mtt-85) cc_final: 0.8075 (mtt180) REVERT: C 1002 GLN cc_start: 0.8361 (tp40) cc_final: 0.7835 (tt0) REVERT: H 100 ASP cc_start: 0.6116 (t0) cc_final: 0.5835 (p0) REVERT: I 50 ASP cc_start: 0.7793 (p0) cc_final: 0.7304 (t0) REVERT: I 100 ASP cc_start: 0.6599 (p0) cc_final: 0.6214 (t70) REVERT: I 108 ASP cc_start: 0.7288 (m-30) cc_final: 0.6586 (p0) REVERT: I 109 TYR cc_start: 0.6611 (m-80) cc_final: 0.5921 (m-80) REVERT: J 48 ILE cc_start: 0.7791 (OUTLIER) cc_final: 0.7479 (pp) REVERT: J 81 MET cc_start: 0.5154 (tmm) cc_final: 0.4770 (tmm) REVERT: M 3 VAL cc_start: 0.8717 (t) cc_final: 0.8473 (p) REVERT: M 90 GLN cc_start: 0.7710 (pp30) cc_final: 0.7074 (pp30) REVERT: N 90 GLN cc_start: 0.7946 (pp30) cc_final: 0.7615 (pp30) outliers start: 30 outliers final: 11 residues processed: 252 average time/residue: 0.3783 time to fit residues: 121.8070 Evaluate side-chains 216 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 198 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain M residue 29 ILE Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 80 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 115 optimal weight: 10.0000 chunk 334 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 241 optimal weight: 4.9990 chunk 270 optimal weight: 2.9990 chunk 127 optimal weight: 0.0970 chunk 15 optimal weight: 4.9990 chunk 181 optimal weight: 2.9990 chunk 359 optimal weight: 8.9990 chunk 288 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 935 GLN B 196 ASN B1119 ASN C 394 ASN C 804 GLN C 957 GLN L 27 GLN M 28 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.201725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.134988 restraints weight = 38655.253| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 3.28 r_work: 0.3632 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3469 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 30561 Z= 0.246 Angle : 0.663 10.974 41778 Z= 0.332 Chirality : 0.048 0.377 5022 Planarity : 0.005 0.065 5157 Dihedral : 4.717 27.465 3884 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.61 % Allowed : 13.41 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -0.56 (0.14), residues: 3561 helix: 1.47 (0.21), residues: 666 sheet: -0.19 (0.17), residues: 960 loop : -1.14 (0.14), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 357 TYR 0.031 0.002 TYR A 265 PHE 0.025 0.002 PHE B 201 TRP 0.024 0.002 TRP H 99 HIS 0.008 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00605 / 0.25 (30408) covalent geometry : angle 0.63733 / 0.33 (41361) SS BOND : bond 0.00410 / 0.26 ( 42) SS BOND : angle 1.48175 / 0.82 ( 84) hydrogen bonds : bond 0.05384 / 3.61 ( 1063) hydrogen bonds : angle 5.56732 / 3.86 ( 2943) link_ALPHA1-6 : bond 0.00430 / 0.19 ( 3) link_ALPHA1-6 : angle 1.43987 / 0.79 ( 9) link_BETA1-4 : bond 0.00645 / 0.41 ( 57) link_BETA1-4 : angle 1.61801 / 1.11 ( 171) link_BETA1-6 : bond 0.00255 / 0.15 ( 6) link_BETA1-6 : angle 1.60708 / 0.91 ( 18) link_NAG-ASN : bond 0.00437 / 0.24 ( 45) link_NAG-ASN : angle 2.51549 / 1.62 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 214 time to evaluate : 1.085 Fit side-chains REVERT: A 58 PHE cc_start: 0.6755 (OUTLIER) cc_final: 0.5119 (m-80) REVERT: A 99 ASN cc_start: 0.7446 (t0) cc_final: 0.6968 (t0) REVERT: A 170 TYR cc_start: 0.7180 (t80) cc_final: 0.6969 (t80) REVERT: A 196 ASN cc_start: 0.6330 (OUTLIER) cc_final: 0.5871 (m-40) REVERT: A 233 ILE cc_start: 0.2644 (OUTLIER) cc_final: 0.1930 (mt) REVERT: A 237 ARG cc_start: 0.7774 (tmt-80) cc_final: 0.7315 (tmt-80) REVERT: A 357 ARG cc_start: 0.7722 (tpp80) cc_final: 0.7408 (ttm-80) REVERT: A 360 ASN cc_start: 0.7969 (t0) cc_final: 0.7641 (t0) REVERT: A 532 ASN cc_start: 0.8109 (t0) cc_final: 0.7876 (t0) REVERT: A 571 ASP cc_start: 0.8559 (t0) cc_final: 0.8234 (t0) REVERT: A 574 ASP cc_start: 0.8068 (t0) cc_final: 0.7784 (t0) REVERT: A 583 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7750 (pm20) REVERT: A 651 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8602 (mt) REVERT: A 904 TYR cc_start: 0.7873 (m-80) cc_final: 0.7549 (m-80) REVERT: A 988 GLU cc_start: 0.8398 (mp0) cc_final: 0.7951 (mp0) REVERT: B 571 ASP cc_start: 0.8516 (t0) cc_final: 0.8178 (t0) REVERT: B 583 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7399 (pm20) REVERT: B 882 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8644 (mp) REVERT: B 904 TYR cc_start: 0.7752 (m-80) cc_final: 0.7079 (m-80) REVERT: B 936 ASP cc_start: 0.8509 (t0) cc_final: 0.8211 (t0) REVERT: B 988 GLU cc_start: 0.8365 (mp0) cc_final: 0.7744 (mp0) REVERT: C 99 ASN cc_start: 0.7735 (t0) cc_final: 0.7308 (t0) REVERT: C 237 ARG cc_start: 0.7688 (tmt-80) cc_final: 0.7251 (tmt-80) REVERT: C 571 ASP cc_start: 0.8433 (t0) cc_final: 0.8015 (t0) REVERT: C 574 ASP cc_start: 0.8063 (t0) cc_final: 0.7651 (t0) REVERT: C 578 ASP cc_start: 0.8366 (t0) cc_final: 0.8012 (t0) REVERT: C 583 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7614 (pm20) REVERT: C 995 ARG cc_start: 0.8424 (mtt-85) cc_final: 0.8192 (mtt180) REVERT: C 1002 GLN cc_start: 0.8456 (tp40) cc_final: 0.7984 (tt0) REVERT: I 50 ASP cc_start: 0.7932 (p0) cc_final: 0.7484 (t0) REVERT: I 100 ASP cc_start: 0.6629 (p0) cc_final: 0.6142 (t0) REVERT: I 108 ASP cc_start: 0.7503 (m-30) cc_final: 0.6747 (p0) REVERT: J 48 ILE cc_start: 0.7810 (OUTLIER) cc_final: 0.7504 (pp) REVERT: J 50 ASP cc_start: 0.8003 (p0) cc_final: 0.7098 (t0) REVERT: J 81 MET cc_start: 0.5194 (tmm) cc_final: 0.4789 (tmm) REVERT: J 108 ASP cc_start: 0.7299 (m-30) cc_final: 0.6482 (p0) REVERT: M 3 VAL cc_start: 0.8672 (t) cc_final: 0.8415 (p) REVERT: M 90 GLN cc_start: 0.7717 (pp30) cc_final: 0.7209 (pp30) REVERT: N 37 GLN cc_start: 0.6634 (pm20) cc_final: 0.5952 (pm20) REVERT: N 90 GLN cc_start: 0.8006 (pp30) cc_final: 0.7655 (pp30) outliers start: 51 outliers final: 16 residues processed: 250 average time/residue: 0.4040 time to fit residues: 127.5578 Evaluate side-chains 234 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 209 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain M residue 29 ILE Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 80 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 262 optimal weight: 0.6980 chunk 23 optimal weight: 20.0000 chunk 123 optimal weight: 0.9990 chunk 171 optimal weight: 0.5980 chunk 177 optimal weight: 1.9990 chunk 339 optimal weight: 0.0670 chunk 273 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 344 optimal weight: 0.0670 chunk 318 optimal weight: 6.9990 chunk 232 optimal weight: 9.9990 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 196 ASN B1002 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 804 GLN C 935 GLN L 27 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.206456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.143214 restraints weight = 38516.590| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 3.41 r_work: 0.3695 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 30561 Z= 0.110 Angle : 0.583 11.170 41778 Z= 0.289 Chirality : 0.044 0.369 5022 Planarity : 0.004 0.059 5157 Dihedral : 4.376 22.665 3884 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.98 % Allowed : 14.52 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -0.30 (0.14), residues: 3561 helix: 1.82 (0.21), residues: 672 sheet: -0.08 (0.16), residues: 1005 loop : -1.02 (0.14), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 357 TYR 0.025 0.001 TYR B 453 PHE 0.026 0.001 PHE C 201 TRP 0.030 0.001 TRP H 99 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (30408) covalent geometry : angle 0.55891 / 0.28 (41361) SS BOND : bond 0.00355 / 0.21 ( 42) SS BOND : angle 1.20100 / 0.68 ( 84) hydrogen bonds : bond 0.03995 / 2.65 ( 1063) hydrogen bonds : angle 5.28384 / 3.68 ( 2943) link_ALPHA1-6 : bond 0.00439 / 0.19 ( 3) link_ALPHA1-6 : angle 1.43799 / 0.80 ( 9) link_BETA1-4 : bond 0.00661 / 0.41 ( 57) link_BETA1-4 : angle 1.57788 / 1.08 ( 171) link_BETA1-6 : bond 0.00346 / 0.20 ( 6) link_BETA1-6 : angle 1.44894 / 0.81 ( 18) link_NAG-ASN : bond 0.00393 / 0.22 ( 45) link_NAG-ASN : angle 2.22709 / 1.41 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 221 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.6489 (OUTLIER) cc_final: 0.4988 (m-80) REVERT: A 99 ASN cc_start: 0.7389 (t0) cc_final: 0.7022 (t0) REVERT: A 170 TYR cc_start: 0.7107 (t80) cc_final: 0.6844 (t80) REVERT: A 196 ASN cc_start: 0.6279 (OUTLIER) cc_final: 0.5837 (m-40) REVERT: A 237 ARG cc_start: 0.7334 (tmt-80) cc_final: 0.6962 (tmt-80) REVERT: A 357 ARG cc_start: 0.7637 (tpp80) cc_final: 0.7320 (ttm-80) REVERT: A 360 ASN cc_start: 0.7850 (t0) cc_final: 0.7567 (t0) REVERT: A 532 ASN cc_start: 0.7993 (t0) cc_final: 0.7745 (t0) REVERT: A 571 ASP cc_start: 0.8475 (t0) cc_final: 0.8174 (t0) REVERT: A 574 ASP cc_start: 0.7854 (t0) cc_final: 0.7594 (t0) REVERT: A 583 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7745 (pm20) REVERT: A 988 GLU cc_start: 0.8183 (mp0) cc_final: 0.7782 (mp0) REVERT: B 277 LEU cc_start: 0.8052 (mp) cc_final: 0.7848 (mp) REVERT: B 571 ASP cc_start: 0.8376 (t0) cc_final: 0.8087 (t0) REVERT: B 583 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7461 (pm20) REVERT: B 882 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8510 (mp) REVERT: B 936 ASP cc_start: 0.8356 (t0) cc_final: 0.8071 (t0) REVERT: B 988 GLU cc_start: 0.8120 (mp0) cc_final: 0.7578 (mp0) REVERT: C 99 ASN cc_start: 0.7586 (t0) cc_final: 0.7248 (t0) REVERT: C 571 ASP cc_start: 0.8320 (t0) cc_final: 0.7801 (t0) REVERT: C 574 ASP cc_start: 0.7820 (t0) cc_final: 0.7471 (t0) REVERT: C 578 ASP cc_start: 0.8153 (t0) cc_final: 0.7902 (t0) REVERT: C 988 GLU cc_start: 0.7675 (mp0) cc_final: 0.7413 (mp0) REVERT: C 995 ARG cc_start: 0.8120 (mtt-85) cc_final: 0.7883 (mtt180) REVERT: C 1002 GLN cc_start: 0.8136 (tp40) cc_final: 0.7614 (tt0) REVERT: H 99 TRP cc_start: 0.5350 (t60) cc_final: 0.5130 (t60) REVERT: I 50 ASP cc_start: 0.7871 (p0) cc_final: 0.7324 (t0) REVERT: I 100 ASP cc_start: 0.6670 (p0) cc_final: 0.6074 (t0) REVERT: I 108 ASP cc_start: 0.7382 (m-30) cc_final: 0.6792 (p0) REVERT: J 48 ILE cc_start: 0.7785 (OUTLIER) cc_final: 0.7507 (pp) REVERT: J 50 ASP cc_start: 0.8010 (p0) cc_final: 0.7026 (t0) REVERT: J 81 MET cc_start: 0.5168 (tmm) cc_final: 0.4746 (tmm) REVERT: M 3 VAL cc_start: 0.8668 (t) cc_final: 0.8423 (p) REVERT: M 90 GLN cc_start: 0.7704 (pp30) cc_final: 0.7068 (pp30) REVERT: N 37 GLN cc_start: 0.6549 (pm20) cc_final: 0.5925 (pm20) REVERT: N 90 GLN cc_start: 0.7934 (pp30) cc_final: 0.7599 (pp30) outliers start: 31 outliers final: 20 residues processed: 245 average time/residue: 0.3873 time to fit residues: 121.0718 Evaluate side-chains 236 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 210 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain M residue 29 ILE Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 80 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 269 optimal weight: 0.6980 chunk 136 optimal weight: 20.0000 chunk 276 optimal weight: 3.9990 chunk 249 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 92 optimal weight: 0.9990 chunk 321 optimal weight: 20.0000 chunk 320 optimal weight: 6.9990 chunk 346 optimal weight: 40.0000 chunk 93 optimal weight: 0.5980 chunk 11 optimal weight: 7.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 ASN A 957 GLN A1119 ASN B 196 ASN B 957 GLN B1002 GLN B1119 ASN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 27 GLN M 28 ASN ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.206199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.141723 restraints weight = 38418.350| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 3.23 r_work: 0.3719 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3559 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30561 Z= 0.118 Angle : 0.584 16.473 41778 Z= 0.288 Chirality : 0.044 0.366 5022 Planarity : 0.005 0.061 5157 Dihedral : 4.346 24.193 3884 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.08 % Allowed : 14.67 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -0.22 (0.14), residues: 3561 helix: 2.06 (0.22), residues: 654 sheet: -0.09 (0.16), residues: 1005 loop : -0.97 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 357 TYR 0.023 0.001 TYR H 102 PHE 0.033 0.001 PHE B 192 TRP 0.023 0.001 TRP H 99 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (30408) covalent geometry : angle 0.56061 / 0.28 (41361) SS BOND : bond 0.00310 / 0.19 ( 42) SS BOND : angle 1.14961 / 0.65 ( 84) hydrogen bonds : bond 0.04006 / 2.66 ( 1063) hydrogen bonds : angle 5.21248 / 3.63 ( 2943) link_ALPHA1-6 : bond 0.00429 / 0.19 ( 3) link_ALPHA1-6 : angle 1.43274 / 0.79 ( 9) link_BETA1-4 : bond 0.00661 / 0.42 ( 57) link_BETA1-4 : angle 1.57036 / 1.08 ( 171) link_BETA1-6 : bond 0.00325 / 0.19 ( 6) link_BETA1-6 : angle 1.48659 / 0.84 ( 18) link_NAG-ASN : bond 0.00388 / 0.21 ( 45) link_NAG-ASN : angle 2.21088 / 1.41 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 218 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.6563 (OUTLIER) cc_final: 0.5006 (m-80) REVERT: A 99 ASN cc_start: 0.7424 (t0) cc_final: 0.6975 (t0) REVERT: A 170 TYR cc_start: 0.7227 (t80) cc_final: 0.6959 (t80) REVERT: A 196 ASN cc_start: 0.6205 (OUTLIER) cc_final: 0.5797 (m-40) REVERT: A 233 ILE cc_start: 0.2196 (OUTLIER) cc_final: 0.1586 (mt) REVERT: A 237 ARG cc_start: 0.7608 (tmt-80) cc_final: 0.7129 (tmt-80) REVERT: A 357 ARG cc_start: 0.7663 (tpp80) cc_final: 0.7372 (ttm-80) REVERT: A 360 ASN cc_start: 0.7886 (t0) cc_final: 0.7608 (t0) REVERT: A 532 ASN cc_start: 0.8103 (t0) cc_final: 0.7807 (t0) REVERT: A 571 ASP cc_start: 0.8545 (t0) cc_final: 0.8229 (t0) REVERT: A 574 ASP cc_start: 0.7971 (t0) cc_final: 0.7693 (t0) REVERT: A 583 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7802 (pm20) REVERT: A 988 GLU cc_start: 0.8405 (mp0) cc_final: 0.7928 (mp0) REVERT: B 277 LEU cc_start: 0.8057 (mp) cc_final: 0.7846 (mp) REVERT: B 571 ASP cc_start: 0.8472 (t0) cc_final: 0.8174 (t0) REVERT: B 583 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7349 (pm20) REVERT: B 882 ILE cc_start: 0.8862 (OUTLIER) cc_final: 0.8556 (mp) REVERT: B 936 ASP cc_start: 0.8426 (t0) cc_final: 0.8185 (t0) REVERT: B 988 GLU cc_start: 0.8338 (mp0) cc_final: 0.7711 (mp0) REVERT: C 99 ASN cc_start: 0.7645 (t0) cc_final: 0.7215 (t0) REVERT: C 571 ASP cc_start: 0.8402 (t0) cc_final: 0.7954 (t0) REVERT: C 578 ASP cc_start: 0.8262 (t0) cc_final: 0.7984 (t0) REVERT: C 988 GLU cc_start: 0.7891 (mp0) cc_final: 0.7602 (mp0) REVERT: C 995 ARG cc_start: 0.8300 (mtt-85) cc_final: 0.8068 (mtt180) REVERT: C 1002 GLN cc_start: 0.8381 (tp40) cc_final: 0.7843 (tt0) REVERT: H 99 TRP cc_start: 0.5234 (t60) cc_final: 0.5028 (t60) REVERT: I 50 ASP cc_start: 0.7862 (p0) cc_final: 0.7326 (t0) REVERT: I 100 ASP cc_start: 0.6669 (p0) cc_final: 0.6169 (t70) REVERT: I 108 ASP cc_start: 0.7389 (m-30) cc_final: 0.6797 (p0) REVERT: J 48 ILE cc_start: 0.7813 (OUTLIER) cc_final: 0.7533 (pp) REVERT: J 50 ASP cc_start: 0.8079 (p0) cc_final: 0.7049 (t0) REVERT: J 81 MET cc_start: 0.5111 (tmm) cc_final: 0.4690 (tmm) REVERT: J 108 ASP cc_start: 0.7132 (m-30) cc_final: 0.6338 (p0) REVERT: M 3 VAL cc_start: 0.8693 (t) cc_final: 0.8446 (p) REVERT: M 90 GLN cc_start: 0.7702 (pp30) cc_final: 0.7340 (pp30) REVERT: N 37 GLN cc_start: 0.6555 (pm20) cc_final: 0.5956 (pm20) REVERT: N 90 GLN cc_start: 0.7963 (pp30) cc_final: 0.7614 (pp30) outliers start: 34 outliers final: 17 residues processed: 243 average time/residue: 0.3829 time to fit residues: 118.9709 Evaluate side-chains 231 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 207 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain M residue 29 ILE Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 80 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 333 optimal weight: 10.0000 chunk 255 optimal weight: 0.0470 chunk 205 optimal weight: 9.9990 chunk 105 optimal weight: 6.9990 chunk 138 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 157 optimal weight: 2.9990 chunk 217 optimal weight: 4.9990 chunk 126 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 overall best weight: 1.9684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 ASN B 196 ASN B 239 GLN B 519 HIS B 957 GLN B1002 GLN L 27 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.203602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.140738 restraints weight = 38349.359| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 3.18 r_work: 0.3663 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 30561 Z= 0.187 Angle : 0.626 15.452 41778 Z= 0.310 Chirality : 0.046 0.364 5022 Planarity : 0.005 0.062 5157 Dihedral : 4.510 25.386 3884 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.11 % Allowed : 14.96 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -0.36 (0.14), residues: 3561 helix: 1.87 (0.21), residues: 651 sheet: -0.13 (0.16), residues: 1020 loop : -1.07 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 357 TYR 0.027 0.001 TYR B 453 PHE 0.042 0.002 PHE B 192 TRP 0.019 0.002 TRP H 99 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.19 (30408) covalent geometry : angle 0.60119 / 0.31 (41361) SS BOND : bond 0.00368 / 0.23 ( 42) SS BOND : angle 1.48310 / 0.83 ( 84) hydrogen bonds : bond 0.04721 / 3.16 ( 1063) hydrogen bonds : angle 5.31644 / 3.70 ( 2943) link_ALPHA1-6 : bond 0.00426 / 0.19 ( 3) link_ALPHA1-6 : angle 1.43199 / 0.79 ( 9) link_BETA1-4 : bond 0.00653 / 0.41 ( 57) link_BETA1-4 : angle 1.57872 / 1.08 ( 171) link_BETA1-6 : bond 0.00230 / 0.14 ( 6) link_BETA1-6 : angle 1.54809 / 0.87 ( 18) link_NAG-ASN : bond 0.00409 / 0.22 ( 45) link_NAG-ASN : angle 2.32997 / 1.49 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 212 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.6691 (OUTLIER) cc_final: 0.5117 (m-80) REVERT: A 99 ASN cc_start: 0.7439 (t0) cc_final: 0.6992 (t0) REVERT: A 170 TYR cc_start: 0.7312 (t80) cc_final: 0.7104 (t80) REVERT: A 196 ASN cc_start: 0.6337 (OUTLIER) cc_final: 0.5903 (m-40) REVERT: A 233 ILE cc_start: 0.2407 (OUTLIER) cc_final: 0.1740 (mt) REVERT: A 237 ARG cc_start: 0.7689 (tmt-80) cc_final: 0.7258 (tmt-80) REVERT: A 357 ARG cc_start: 0.7760 (tpp80) cc_final: 0.7471 (ttm-80) REVERT: A 360 ASN cc_start: 0.7926 (t0) cc_final: 0.7617 (t0) REVERT: A 532 ASN cc_start: 0.8183 (t0) cc_final: 0.7905 (t0) REVERT: A 571 ASP cc_start: 0.8573 (t0) cc_final: 0.8280 (t0) REVERT: A 574 ASP cc_start: 0.8048 (t0) cc_final: 0.7750 (t0) REVERT: A 583 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7830 (pm20) REVERT: A 988 GLU cc_start: 0.8392 (mp0) cc_final: 0.7899 (mp0) REVERT: B 571 ASP cc_start: 0.8500 (t0) cc_final: 0.8202 (t0) REVERT: B 583 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7366 (pm20) REVERT: B 882 ILE cc_start: 0.8856 (OUTLIER) cc_final: 0.8638 (mp) REVERT: B 904 TYR cc_start: 0.7296 (t80) cc_final: 0.6496 (t80) REVERT: B 988 GLU cc_start: 0.8358 (mp0) cc_final: 0.7694 (mp0) REVERT: C 99 ASN cc_start: 0.7705 (t0) cc_final: 0.7293 (t0) REVERT: C 571 ASP cc_start: 0.8417 (t0) cc_final: 0.7971 (t0) REVERT: C 574 ASP cc_start: 0.7953 (t0) cc_final: 0.7594 (t0) REVERT: C 578 ASP cc_start: 0.8297 (t0) cc_final: 0.8001 (t0) REVERT: C 988 GLU cc_start: 0.7909 (mp0) cc_final: 0.7620 (mp0) REVERT: C 995 ARG cc_start: 0.8369 (mtt-85) cc_final: 0.8144 (mtt180) REVERT: C 1002 GLN cc_start: 0.8421 (tp40) cc_final: 0.7938 (tt0) REVERT: H 99 TRP cc_start: 0.5206 (t60) cc_final: 0.4993 (t60) REVERT: I 50 ASP cc_start: 0.7829 (p0) cc_final: 0.7296 (t0) REVERT: I 100 ASP cc_start: 0.6700 (p0) cc_final: 0.6087 (t0) REVERT: I 108 ASP cc_start: 0.7622 (m-30) cc_final: 0.6939 (p0) REVERT: J 48 ILE cc_start: 0.7781 (OUTLIER) cc_final: 0.7478 (pp) REVERT: J 50 ASP cc_start: 0.8082 (p0) cc_final: 0.7080 (t0) REVERT: J 81 MET cc_start: 0.5253 (tmm) cc_final: 0.4856 (tmm) REVERT: J 108 ASP cc_start: 0.7257 (m-30) cc_final: 0.6467 (p0) REVERT: M 3 VAL cc_start: 0.8697 (t) cc_final: 0.8450 (p) REVERT: M 90 GLN cc_start: 0.7761 (pp30) cc_final: 0.7537 (pp30) REVERT: N 37 GLN cc_start: 0.6561 (pm20) cc_final: 0.5961 (pm20) REVERT: N 90 GLN cc_start: 0.7981 (pp30) cc_final: 0.7606 (pp30) outliers start: 35 outliers final: 19 residues processed: 238 average time/residue: 0.3967 time to fit residues: 120.6923 Evaluate side-chains 232 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 206 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain M residue 29 ILE Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 80 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 119 optimal weight: 1.9990 chunk 243 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 224 optimal weight: 8.9990 chunk 19 optimal weight: 0.0870 chunk 291 optimal weight: 0.9980 chunk 123 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 chunk 213 optimal weight: 10.0000 chunk 271 optimal weight: 1.9990 chunk 164 optimal weight: 0.3980 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 ASN B 196 ASN B 935 GLN B1002 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 28 ASN ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.205515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.140809 restraints weight = 38518.875| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 3.16 r_work: 0.3710 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3549 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30561 Z= 0.122 Angle : 0.588 14.411 41778 Z= 0.290 Chirality : 0.045 0.360 5022 Planarity : 0.005 0.062 5157 Dihedral : 4.388 23.415 3884 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.92 % Allowed : 15.37 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.14), residues: 3561 helix: 2.01 (0.21), residues: 651 sheet: -0.09 (0.16), residues: 1041 loop : -0.98 (0.14), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 357 TYR 0.028 0.001 TYR C 453 PHE 0.033 0.001 PHE B 192 TRP 0.019 0.002 TRP H 99 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (30408) covalent geometry : angle 0.56424 / 0.29 (41361) SS BOND : bond 0.00304 / 0.19 ( 42) SS BOND : angle 1.15610 / 0.65 ( 84) hydrogen bonds : bond 0.04187 / 2.79 ( 1063) hydrogen bonds : angle 5.20628 / 3.62 ( 2943) link_ALPHA1-6 : bond 0.00443 / 0.20 ( 3) link_ALPHA1-6 : angle 1.41924 / 0.79 ( 9) link_BETA1-4 : bond 0.00657 / 0.41 ( 57) link_BETA1-4 : angle 1.55594 / 1.07 ( 171) link_BETA1-6 : bond 0.00317 / 0.19 ( 6) link_BETA1-6 : angle 1.50134 / 0.84 ( 18) link_NAG-ASN : bond 0.00395 / 0.21 ( 45) link_NAG-ASN : angle 2.22808 / 1.42 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9875.82 seconds wall clock time: 168 minutes 50.60 seconds (10130.60 seconds total)