Starting phenix.real_space_refine on Fri Mar 6 09:50:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k9j_22750/03_2026/7k9j_22750.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k9j_22750/03_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_22750/03_2026/7k9j_22750.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k9j_22750/03_2026/7k9j_22750.map" model { file = "/net/cci-nas-00/data/ceres_data/7k9j_22750/03_2026/7k9j_22750.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k9j_22750/03_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-5986/lib/python3.9/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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 12 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 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 dihedrals: 12 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "l" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "m" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 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 dihedrals: 12 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "x" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.08, per 1000 atoms: 0.24 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: 3.01 Conformation dependent library (CDL) restraints added in 1.4 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: 1.20 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: 8.29 Time building geometry restraints manager: 3.89 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 - 22.69: 17874 22.69 - 45.39: 960 45.39 - 68.08: 249 68.08 - 90.77: 192 90.77 - 113.46: 186 Dihedral angle restraints: 19461 sinusoidal: 8928 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 19458 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: 0.06 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: 2.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 30.750 Find NCS groups from input model: 0.960 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: 0.010 Load rotamer database and sin/cos tables:6.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 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 : 20.825 113.464 12561 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 covalent geometry : bond 0.00521 (30408) covalent geometry : angle 0.84449 (41361) SS BOND : bond 0.00377 ( 42) SS BOND : angle 2.07292 ( 84) hydrogen bonds : bond 0.26096 ( 1063) hydrogen bonds : angle 9.68528 ( 2943) link_ALPHA1-6 : bond 0.00218 ( 3) link_ALPHA1-6 : angle 1.73772 ( 9) link_BETA1-4 : bond 0.00774 ( 57) link_BETA1-4 : angle 1.89616 ( 171) link_BETA1-6 : bond 0.00350 ( 6) link_BETA1-6 : angle 1.64095 ( 18) link_NAG-ASN : bond 0.00533 ( 45) link_NAG-ASN : angle 3.42742 ( 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 : 1.173 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: 0.5252 time to fit residues: 180.6209 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 : 1.042 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 675 GLN A 762 GLN A 804 GLN A 935 GLN B 196 ASN B 804 GLN B 935 GLN L 27 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.205348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.142991 restraints weight = 38561.642| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 3.25 r_work: 0.3655 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30561 Z= 0.152 Angle : 0.737 10.752 41778 Z= 0.355 Chirality : 0.050 0.429 5022 Planarity : 0.005 0.056 5157 Dihedral : 18.140 93.855 6162 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.73 % Allowed : 6.23 % Favored : 93.04 % 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: 1.20 (0.20), residues: 651 sheet: 0.27 (0.16), residues: 966 loop : -1.19 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 273 TYR 0.022 0.001 TYR B 265 PHE 0.024 0.001 PHE I 64 TRP 0.014 0.002 TRP B 436 HIS 0.007 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00343 (30408) covalent geometry : angle 0.70016 (41361) SS BOND : bond 0.00410 ( 42) SS BOND : angle 1.44822 ( 84) hydrogen bonds : bond 0.05870 ( 1063) hydrogen bonds : angle 6.80233 ( 2943) link_ALPHA1-6 : bond 0.00530 ( 3) link_ALPHA1-6 : angle 1.80783 ( 9) link_BETA1-4 : bond 0.00714 ( 57) link_BETA1-4 : angle 2.51189 ( 171) link_BETA1-6 : bond 0.00327 ( 6) link_BETA1-6 : angle 1.67009 ( 18) link_NAG-ASN : bond 0.00474 ( 45) link_NAG-ASN : angle 2.85184 ( 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: 23 poor density : 233 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.7611 (t0) cc_final: 0.7235 (t0) REVERT: A 170 TYR cc_start: 0.6960 (t80) cc_final: 0.6588 (t80) REVERT: A 239 GLN cc_start: 0.7704 (tt0) cc_final: 0.7457 (tt0) REVERT: A 571 ASP cc_start: 0.8184 (t0) cc_final: 0.7817 (t0) REVERT: A 902 MET cc_start: 0.8451 (mmt) cc_final: 0.8191 (tpt) REVERT: A 988 GLU cc_start: 0.8075 (mp0) cc_final: 0.7764 (mp0) REVERT: B 99 ASN cc_start: 0.8120 (t0) cc_final: 0.7883 (t0) REVERT: B 170 TYR cc_start: 0.6847 (t80) cc_final: 0.6446 (t80) REVERT: B 571 ASP cc_start: 0.8335 (t0) cc_final: 0.7990 (t0) REVERT: B 646 ARG cc_start: 0.7868 (tmt170) cc_final: 0.7522 (tpt170) REVERT: B 988 GLU cc_start: 0.7953 (mp0) cc_final: 0.7303 (mp0) REVERT: B 1107 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.7475 (mmt-90) REVERT: C 99 ASN cc_start: 0.7838 (t0) cc_final: 0.7586 (t0) REVERT: C 237 ARG cc_start: 0.7530 (tmt170) cc_final: 0.6871 (tmt-80) REVERT: C 306 PHE cc_start: 0.8484 (m-10) cc_final: 0.8120 (m-10) REVERT: C 571 ASP cc_start: 0.8262 (t0) cc_final: 0.7917 (t0) REVERT: C 578 ASP cc_start: 0.8234 (t0) cc_final: 0.7890 (t0) REVERT: C 936 ASP cc_start: 0.8513 (t0) cc_final: 0.8157 (t0) REVERT: I 50 ASP cc_start: 0.7997 (p0) cc_final: 0.7721 (p0) REVERT: J 81 MET cc_start: 0.5933 (tmm) cc_final: 0.5588 (tmm) REVERT: M 3 VAL cc_start: 0.8447 (t) cc_final: 0.8197 (p) REVERT: N 37 GLN cc_start: 0.6397 (pm20) cc_final: 0.5859 (pm20) REVERT: N 90 GLN cc_start: 0.7520 (pp30) cc_final: 0.6934 (pp30) outliers start: 23 outliers final: 10 residues processed: 248 average time/residue: 0.4689 time to fit residues: 144.4380 Evaluate side-chains 216 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 205 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 551 VAL 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 L residue 13 VAL Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain N residue 3 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 295 optimal weight: 5.9990 chunk 282 optimal weight: 0.5980 chunk 146 optimal weight: 0.0870 chunk 240 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 313 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 265 optimal weight: 9.9990 chunk 339 optimal weight: 20.0000 chunk 315 optimal weight: 7.9990 overall best weight: 1.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN B 196 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 GLN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.204031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.138752 restraints weight = 38567.838| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 3.18 r_work: 0.3664 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3502 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 30561 Z= 0.182 Angle : 0.711 11.079 41778 Z= 0.338 Chirality : 0.049 0.423 5022 Planarity : 0.005 0.056 5157 Dihedral : 13.777 87.674 6151 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.04 % Allowed : 9.08 % Favored : 89.88 % 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: -0.50 (0.14), residues: 3561 helix: 1.26 (0.20), residues: 672 sheet: 0.13 (0.16), residues: 987 loop : -1.19 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B1107 TYR 0.027 0.002 TYR A 453 PHE 0.020 0.002 PHE C 192 TRP 0.016 0.002 TRP H 99 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00434 (30408) covalent geometry : angle 0.67218 (41361) SS BOND : bond 0.00740 ( 42) SS BOND : angle 1.35391 ( 84) hydrogen bonds : bond 0.05445 ( 1063) hydrogen bonds : angle 6.18887 ( 2943) link_ALPHA1-6 : bond 0.00700 ( 3) link_ALPHA1-6 : angle 1.72115 ( 9) link_BETA1-4 : bond 0.00800 ( 57) link_BETA1-4 : angle 2.62653 ( 171) link_BETA1-6 : bond 0.00313 ( 6) link_BETA1-6 : angle 1.61233 ( 18) link_NAG-ASN : bond 0.00456 ( 45) link_NAG-ASN : angle 2.76277 ( 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 254 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 221 time to evaluate : 0.897 Fit side-chains revert: symmetry clash REVERT: A 99 ASN cc_start: 0.7682 (t0) cc_final: 0.7179 (t0) REVERT: A 170 TYR cc_start: 0.7230 (t80) cc_final: 0.6805 (t80) REVERT: A 571 ASP cc_start: 0.8512 (t0) cc_final: 0.8131 (t0) REVERT: A 904 TYR cc_start: 0.7887 (m-80) cc_final: 0.7600 (m-80) REVERT: A 988 GLU cc_start: 0.8305 (mp0) cc_final: 0.7937 (mp0) REVERT: B 99 ASN cc_start: 0.8168 (t0) cc_final: 0.7875 (t0) REVERT: B 170 TYR cc_start: 0.7025 (t80) cc_final: 0.6690 (t80) REVERT: B 433 VAL cc_start: 0.8140 (t) cc_final: 0.7937 (m) REVERT: B 571 ASP cc_start: 0.8491 (t0) cc_final: 0.8115 (t0) REVERT: B 988 GLU cc_start: 0.8236 (mp0) cc_final: 0.7645 (mp0) REVERT: B 995 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.8237 (mtp180) REVERT: B 1107 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7550 (mmt-90) REVERT: C 99 ASN cc_start: 0.7978 (t0) cc_final: 0.7714 (t0) REVERT: C 306 PHE cc_start: 0.8539 (m-10) cc_final: 0.8201 (m-10) REVERT: C 571 ASP cc_start: 0.8448 (t0) cc_final: 0.8034 (t0) REVERT: C 574 ASP cc_start: 0.8041 (t0) cc_final: 0.7741 (t0) REVERT: C 578 ASP cc_start: 0.8386 (t0) cc_final: 0.8045 (t0) REVERT: C 936 ASP cc_start: 0.8608 (t0) cc_final: 0.8306 (t0) REVERT: C 995 ARG cc_start: 0.8459 (mtt-85) cc_final: 0.8216 (mtt180) REVERT: C 1029 MET cc_start: 0.9232 (tpp) cc_final: 0.9026 (tpp) REVERT: H 99 TRP cc_start: 0.5682 (t60) cc_final: 0.5424 (t60) REVERT: I 100 ASP cc_start: 0.6434 (p0) cc_final: 0.6127 (t70) REVERT: I 108 ASP cc_start: 0.7233 (m-30) cc_final: 0.6566 (p0) REVERT: I 109 TYR cc_start: 0.6563 (m-80) cc_final: 0.6079 (m-80) REVERT: J 81 MET cc_start: 0.5957 (tmm) cc_final: 0.5524 (tmm) REVERT: J 108 ASP cc_start: 0.7541 (m-30) cc_final: 0.6522 (p0) REVERT: J 109 TYR cc_start: 0.6521 (m-80) cc_final: 0.5871 (m-80) REVERT: M 3 VAL cc_start: 0.8637 (t) cc_final: 0.8376 (p) REVERT: M 90 GLN cc_start: 0.7740 (pp30) cc_final: 0.7217 (pp30) REVERT: N 37 GLN cc_start: 0.6614 (pm20) cc_final: 0.6060 (pm20) REVERT: N 90 GLN cc_start: 0.7837 (pp30) cc_final: 0.7618 (pp30) outliers start: 33 outliers final: 13 residues processed: 239 average time/residue: 0.4525 time to fit residues: 135.2812 Evaluate side-chains 210 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 195 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 395 VAL 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 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: 2.9990 chunk 225 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 239 optimal weight: 0.9980 chunk 108 optimal weight: 10.0000 chunk 169 optimal weight: 1.9990 chunk 230 optimal weight: 6.9990 chunk 8 optimal weight: 0.8980 chunk 171 optimal weight: 1.9990 chunk 320 optimal weight: 7.9990 chunk 270 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 99 ASN B 49 HIS B 196 ASN C 49 HIS ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN M 28 ASN N 6 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.205914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.145279 restraints weight = 38281.099| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 3.37 r_work: 0.3666 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30561 Z= 0.139 Angle : 0.667 11.360 41778 Z= 0.313 Chirality : 0.047 0.416 5022 Planarity : 0.004 0.058 5157 Dihedral : 11.843 83.455 6151 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.17 % Allowed : 10.63 % Favored : 88.20 % 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: -0.38 (0.14), residues: 3561 helix: 1.53 (0.21), residues: 669 sheet: 0.07 (0.16), residues: 999 loop : -1.11 (0.14), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 357 TYR 0.020 0.001 TYR B 265 PHE 0.025 0.001 PHE B 140 TRP 0.014 0.001 TRP C 104 HIS 0.005 0.001 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00320 (30408) covalent geometry : angle 0.62561 (41361) SS BOND : bond 0.00313 ( 42) SS BOND : angle 1.38784 ( 84) hydrogen bonds : bond 0.04708 ( 1063) hydrogen bonds : angle 5.87972 ( 2943) link_ALPHA1-6 : bond 0.00765 ( 3) link_ALPHA1-6 : angle 1.96040 ( 9) link_BETA1-4 : bond 0.00805 ( 57) link_BETA1-4 : angle 2.64757 ( 171) link_BETA1-6 : bond 0.00330 ( 6) link_BETA1-6 : angle 1.61357 ( 18) link_NAG-ASN : bond 0.00447 ( 45) link_NAG-ASN : angle 2.62384 ( 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 242 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 205 time to evaluate : 0.988 Fit side-chains REVERT: A 99 ASN cc_start: 0.7479 (t0) cc_final: 0.7051 (t0) REVERT: A 170 TYR cc_start: 0.7110 (t80) cc_final: 0.6756 (t80) REVERT: A 196 ASN cc_start: 0.6033 (OUTLIER) cc_final: 0.5700 (m-40) REVERT: A 237 ARG cc_start: 0.7514 (tmt-80) cc_final: 0.7106 (tmt-80) REVERT: A 512 VAL cc_start: 0.8159 (OUTLIER) cc_final: 0.7925 (m) REVERT: A 571 ASP cc_start: 0.8375 (t0) cc_final: 0.8039 (t0) REVERT: A 574 ASP cc_start: 0.7922 (t0) cc_final: 0.7633 (t0) REVERT: A 936 ASP cc_start: 0.8258 (t0) cc_final: 0.7964 (t0) REVERT: A 988 GLU cc_start: 0.8107 (mp0) cc_final: 0.7825 (mp0) REVERT: B 99 ASN cc_start: 0.7784 (t0) cc_final: 0.7568 (t0) REVERT: B 571 ASP cc_start: 0.8418 (t0) cc_final: 0.8109 (t0) REVERT: B 988 GLU cc_start: 0.8127 (mp0) cc_final: 0.7542 (mp0) REVERT: C 99 ASN cc_start: 0.8025 (t0) cc_final: 0.7736 (t0) REVERT: C 306 PHE cc_start: 0.8471 (m-80) cc_final: 0.8105 (m-10) REVERT: C 571 ASP cc_start: 0.8370 (t0) cc_final: 0.7949 (t0) REVERT: C 578 ASP cc_start: 0.8264 (t0) cc_final: 0.7976 (t0) REVERT: C 740 MET cc_start: 0.8019 (tpt) cc_final: 0.7653 (tpt) REVERT: C 995 ARG cc_start: 0.8229 (mtt-85) cc_final: 0.7992 (mtt180) REVERT: H 99 TRP cc_start: 0.5421 (t60) cc_final: 0.5208 (t60) REVERT: I 50 ASP cc_start: 0.7625 (p0) cc_final: 0.7244 (t0) REVERT: I 100 ASP cc_start: 0.6523 (p0) cc_final: 0.6251 (t70) REVERT: I 108 ASP cc_start: 0.7253 (m-30) cc_final: 0.6546 (p0) REVERT: I 109 TYR cc_start: 0.6663 (m-80) cc_final: 0.6041 (m-80) REVERT: J 81 MET cc_start: 0.5847 (tmm) cc_final: 0.5398 (tmm) REVERT: J 108 ASP cc_start: 0.7597 (m-30) cc_final: 0.6543 (p0) REVERT: J 109 TYR cc_start: 0.6480 (m-80) cc_final: 0.5796 (m-80) REVERT: M 3 VAL cc_start: 0.8615 (t) cc_final: 0.8375 (p) REVERT: M 90 GLN cc_start: 0.7762 (pp30) cc_final: 0.7367 (pp30) REVERT: N 37 GLN cc_start: 0.6547 (pm20) cc_final: 0.5897 (pm20) REVERT: N 90 GLN cc_start: 0.7835 (pp30) cc_final: 0.7567 (pp30) outliers start: 37 outliers final: 10 residues processed: 232 average time/residue: 0.4157 time to fit residues: 123.1009 Evaluate side-chains 200 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 188 time to evaluate : 1.013 ------------------------------------------------------------------------------- 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 196 ASN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 240 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 179 optimal weight: 0.6980 chunk 313 optimal weight: 9.9990 chunk 93 optimal weight: 0.9990 chunk 177 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 212 optimal weight: 0.8980 chunk 166 optimal weight: 0.0970 chunk 24 optimal weight: 2.9990 chunk 160 optimal weight: 0.8980 chunk 254 optimal weight: 2.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN B 196 ASN C 99 ASN C 121 ASN C 196 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.206499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.142516 restraints weight = 38417.939| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 3.21 r_work: 0.3695 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3533 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 30561 Z= 0.118 Angle : 0.632 10.492 41778 Z= 0.298 Chirality : 0.046 0.404 5022 Planarity : 0.004 0.055 5157 Dihedral : 10.353 79.017 6149 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.20 % Allowed : 11.10 % Favored : 87.70 % 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: 1.78 (0.21), residues: 669 sheet: 0.11 (0.16), residues: 1002 loop : -1.02 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 357 TYR 0.020 0.001 TYR I 102 PHE 0.025 0.001 PHE J 64 TRP 0.014 0.001 TRP J 99 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00263 (30408) covalent geometry : angle 0.59307 (41361) SS BOND : bond 0.00384 ( 42) SS BOND : angle 1.15161 ( 84) hydrogen bonds : bond 0.04221 ( 1063) hydrogen bonds : angle 5.58973 ( 2943) link_ALPHA1-6 : bond 0.00817 ( 3) link_ALPHA1-6 : angle 1.50391 ( 9) link_BETA1-4 : bond 0.00798 ( 57) link_BETA1-4 : angle 2.58554 ( 171) link_BETA1-6 : bond 0.00331 ( 6) link_BETA1-6 : angle 1.56473 ( 18) link_NAG-ASN : bond 0.00450 ( 45) link_NAG-ASN : angle 2.49541 ( 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 258 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 220 time to evaluate : 0.783 Fit side-chains revert: symmetry clash REVERT: A 99 ASN cc_start: 0.7512 (t0) cc_final: 0.7012 (t0) REVERT: A 196 ASN cc_start: 0.5984 (OUTLIER) cc_final: 0.5715 (m-40) REVERT: A 512 VAL cc_start: 0.8328 (OUTLIER) cc_final: 0.8099 (m) REVERT: A 532 ASN cc_start: 0.7962 (t0) cc_final: 0.7746 (t0) REVERT: A 571 ASP cc_start: 0.8543 (t0) cc_final: 0.8209 (t0) REVERT: A 936 ASP cc_start: 0.8438 (t0) cc_final: 0.8223 (t0) REVERT: A 988 GLU cc_start: 0.8348 (mp0) cc_final: 0.7969 (mp0) REVERT: A 1119 ASN cc_start: 0.8454 (m-40) cc_final: 0.8133 (m110) REVERT: B 99 ASN cc_start: 0.7778 (t0) cc_final: 0.7516 (t0) REVERT: B 170 TYR cc_start: 0.7033 (t80) cc_final: 0.6692 (t80) REVERT: B 277 LEU cc_start: 0.7977 (mp) cc_final: 0.7766 (mp) REVERT: B 571 ASP cc_start: 0.8510 (t0) cc_final: 0.8178 (t0) REVERT: B 936 ASP cc_start: 0.8432 (t0) cc_final: 0.8191 (t0) REVERT: B 988 GLU cc_start: 0.8318 (mp0) cc_final: 0.7763 (mp0) REVERT: C 99 ASN cc_start: 0.7735 (t0) cc_final: 0.7311 (t0) REVERT: C 231 ILE cc_start: 0.7898 (OUTLIER) cc_final: 0.7413 (tp) REVERT: C 306 PHE cc_start: 0.8516 (m-80) cc_final: 0.8143 (m-10) REVERT: C 571 ASP cc_start: 0.8430 (t0) cc_final: 0.7938 (t0) REVERT: C 578 ASP cc_start: 0.8343 (t0) cc_final: 0.7971 (t0) REVERT: C 583 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7492 (pm20) REVERT: C 936 ASP cc_start: 0.8503 (t0) cc_final: 0.8303 (t0) REVERT: C 995 ARG cc_start: 0.8343 (mtt-85) cc_final: 0.8097 (mtt180) REVERT: I 50 ASP cc_start: 0.7700 (p0) cc_final: 0.7181 (t0) REVERT: I 100 ASP cc_start: 0.6547 (p0) cc_final: 0.6231 (t70) REVERT: I 108 ASP cc_start: 0.7234 (m-30) cc_final: 0.6536 (p0) REVERT: I 109 TYR cc_start: 0.6655 (m-80) cc_final: 0.6022 (m-80) REVERT: J 108 ASP cc_start: 0.7387 (m-30) cc_final: 0.6338 (p0) REVERT: J 109 TYR cc_start: 0.6538 (m-80) cc_final: 0.5876 (m-80) REVERT: M 3 VAL cc_start: 0.8673 (t) cc_final: 0.8426 (p) REVERT: M 90 GLN cc_start: 0.7802 (pp30) cc_final: 0.7528 (pp30) REVERT: N 37 GLN cc_start: 0.6524 (pm20) cc_final: 0.5858 (pm20) REVERT: N 90 GLN cc_start: 0.7897 (pp30) cc_final: 0.7592 (pp30) outliers start: 38 outliers final: 10 residues processed: 247 average time/residue: 0.4396 time to fit residues: 137.9324 Evaluate side-chains 208 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 194 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 100 ILE Chi-restraints excluded: chain B residue 697 MET 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 1032 CYS Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain M residue 29 ILE Chi-restraints excluded: chain N residue 3 VAL 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: 6.9990 chunk 351 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 215 optimal weight: 0.8980 chunk 253 optimal weight: 0.4980 chunk 210 optimal weight: 0.0370 chunk 309 optimal weight: 6.9990 chunk 88 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 ASN B1119 ASN C 957 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.207091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.146908 restraints weight = 38370.446| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 3.46 r_work: 0.3699 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 30561 Z= 0.113 Angle : 0.627 11.431 41778 Z= 0.294 Chirality : 0.045 0.394 5022 Planarity : 0.004 0.055 5157 Dihedral : 9.399 74.055 6149 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.79 % Allowed : 12.49 % Favored : 86.72 % 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: -0.14 (0.14), residues: 3561 helix: 1.89 (0.21), residues: 672 sheet: 0.13 (0.16), residues: 996 loop : -0.95 (0.14), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 357 TYR 0.022 0.001 TYR A 170 PHE 0.023 0.001 PHE B 201 TRP 0.019 0.001 TRP H 99 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00253 (30408) covalent geometry : angle 0.58899 (41361) SS BOND : bond 0.00290 ( 42) SS BOND : angle 0.98183 ( 84) hydrogen bonds : bond 0.04005 ( 1063) hydrogen bonds : angle 5.41611 ( 2943) link_ALPHA1-6 : bond 0.00640 ( 3) link_ALPHA1-6 : angle 1.52388 ( 9) link_BETA1-4 : bond 0.00788 ( 57) link_BETA1-4 : angle 2.54425 ( 171) link_BETA1-6 : bond 0.00343 ( 6) link_BETA1-6 : angle 1.54588 ( 18) link_NAG-ASN : bond 0.00427 ( 45) link_NAG-ASN : angle 2.43095 ( 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 247 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 222 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.7426 (t0) cc_final: 0.7015 (t0) REVERT: A 196 ASN cc_start: 0.6088 (OUTLIER) cc_final: 0.5694 (m-40) REVERT: A 360 ASN cc_start: 0.7897 (t0) cc_final: 0.7599 (t0) REVERT: A 512 VAL cc_start: 0.8089 (OUTLIER) cc_final: 0.7871 (m) REVERT: A 532 ASN cc_start: 0.7884 (t0) cc_final: 0.7657 (t0) REVERT: A 571 ASP cc_start: 0.8448 (t0) cc_final: 0.8095 (t0) REVERT: A 988 GLU cc_start: 0.8169 (mp0) cc_final: 0.7819 (mp0) REVERT: B 99 ASN cc_start: 0.7719 (t0) cc_final: 0.7499 (t0) REVERT: B 277 LEU cc_start: 0.7905 (mp) cc_final: 0.7687 (mp) REVERT: B 571 ASP cc_start: 0.8369 (t0) cc_final: 0.8062 (t0) REVERT: B 936 ASP cc_start: 0.8252 (t0) cc_final: 0.8023 (t0) REVERT: B 988 GLU cc_start: 0.8192 (mp0) cc_final: 0.7661 (mp0) REVERT: C 99 ASN cc_start: 0.7629 (t0) cc_final: 0.7204 (t0) REVERT: C 231 ILE cc_start: 0.7886 (OUTLIER) cc_final: 0.7402 (tp) REVERT: C 306 PHE cc_start: 0.8468 (m-80) cc_final: 0.8082 (m-10) REVERT: C 571 ASP cc_start: 0.8341 (t0) cc_final: 0.7874 (t0) REVERT: C 578 ASP cc_start: 0.8160 (t0) cc_final: 0.7871 (t0) REVERT: C 995 ARG cc_start: 0.8154 (mtt-85) cc_final: 0.7920 (mtt180) REVERT: I 100 ASP cc_start: 0.6574 (p0) cc_final: 0.6213 (t70) REVERT: I 108 ASP cc_start: 0.7114 (m-30) cc_final: 0.6456 (p0) REVERT: I 109 TYR cc_start: 0.6625 (m-80) cc_final: 0.5958 (m-80) REVERT: J 108 ASP cc_start: 0.7208 (m-30) cc_final: 0.6268 (p0) REVERT: J 109 TYR cc_start: 0.6560 (m-80) cc_final: 0.5893 (m-80) REVERT: M 3 VAL cc_start: 0.8640 (t) cc_final: 0.8405 (p) REVERT: M 90 GLN cc_start: 0.7838 (pp30) cc_final: 0.7506 (pp30) REVERT: N 90 GLN cc_start: 0.7859 (pp30) cc_final: 0.7533 (pp30) outliers start: 25 outliers final: 10 residues processed: 239 average time/residue: 0.3963 time to fit residues: 122.3627 Evaluate side-chains 209 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 196 time to evaluate : 1.038 ------------------------------------------------------------------------------- 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 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 231 ILE Chi-restraints excluded: chain C residue 350 VAL 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 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: 0.6980 chunk 68 optimal weight: 2.9990 chunk 241 optimal weight: 0.8980 chunk 270 optimal weight: 2.9990 chunk 127 optimal weight: 0.0870 chunk 15 optimal weight: 10.0000 chunk 181 optimal weight: 3.9990 chunk 359 optimal weight: 9.9990 chunk 288 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 overall best weight: 1.5362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 GLN A1119 ASN B 196 ASN B1119 ASN C 394 ASN L 27 GLN ** 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 = 0.4588 r_free = 0.4588 target = 0.204946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.143354 restraints weight = 38610.020| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 3.45 r_work: 0.3661 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 30561 Z= 0.162 Angle : 0.649 10.232 41778 Z= 0.308 Chirality : 0.046 0.387 5022 Planarity : 0.005 0.056 5157 Dihedral : 8.823 69.081 6149 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.11 % Allowed : 13.06 % Favored : 85.83 % 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: -0.26 (0.14), residues: 3561 helix: 1.76 (0.21), residues: 672 sheet: 0.03 (0.16), residues: 996 loop : -1.01 (0.14), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1107 TYR 0.024 0.001 TYR C 453 PHE 0.029 0.002 PHE J 64 TRP 0.022 0.001 TRP H 99 HIS 0.006 0.001 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00391 (30408) covalent geometry : angle 0.61236 (41361) SS BOND : bond 0.00327 ( 42) SS BOND : angle 1.19121 ( 84) hydrogen bonds : bond 0.04507 ( 1063) hydrogen bonds : angle 5.40631 ( 2943) link_ALPHA1-6 : bond 0.00601 ( 3) link_ALPHA1-6 : angle 1.44470 ( 9) link_BETA1-4 : bond 0.00758 ( 57) link_BETA1-4 : angle 2.50826 ( 171) link_BETA1-6 : bond 0.00428 ( 6) link_BETA1-6 : angle 1.59656 ( 18) link_NAG-ASN : bond 0.00414 ( 45) link_NAG-ASN : angle 2.51025 ( 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 246 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 211 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7658 (OUTLIER) cc_final: 0.7438 (mmtt) REVERT: A 99 ASN cc_start: 0.7455 (t0) cc_final: 0.7055 (t0) REVERT: A 196 ASN cc_start: 0.6193 (OUTLIER) cc_final: 0.5802 (m-40) REVERT: A 360 ASN cc_start: 0.7889 (t0) cc_final: 0.7590 (t0) REVERT: A 512 VAL cc_start: 0.8207 (OUTLIER) cc_final: 0.7966 (m) REVERT: A 532 ASN cc_start: 0.7963 (t0) cc_final: 0.7728 (t0) REVERT: A 571 ASP cc_start: 0.8438 (t0) cc_final: 0.8111 (t0) REVERT: A 651 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8418 (mt) REVERT: A 988 GLU cc_start: 0.8185 (mp0) cc_final: 0.7789 (mp0) REVERT: B 277 LEU cc_start: 0.8001 (mp) cc_final: 0.7798 (mp) REVERT: B 571 ASP cc_start: 0.8410 (t0) cc_final: 0.8101 (t0) REVERT: B 581 THR cc_start: 0.8496 (OUTLIER) cc_final: 0.8291 (p) REVERT: B 936 ASP cc_start: 0.8396 (t0) cc_final: 0.8125 (t0) REVERT: B 988 GLU cc_start: 0.8160 (mp0) cc_final: 0.7563 (mp0) REVERT: C 99 ASN cc_start: 0.7630 (t0) cc_final: 0.7246 (t0) REVERT: C 306 PHE cc_start: 0.8489 (m-80) cc_final: 0.8077 (m-10) REVERT: C 571 ASP cc_start: 0.8332 (t0) cc_final: 0.7877 (t0) REVERT: C 574 ASP cc_start: 0.7849 (t0) cc_final: 0.7535 (t0) REVERT: C 578 ASP cc_start: 0.8115 (t0) cc_final: 0.7871 (t0) REVERT: C 995 ARG cc_start: 0.8214 (mtt-85) cc_final: 0.7985 (mtt180) REVERT: I 50 ASP cc_start: 0.7852 (p0) cc_final: 0.7379 (t0) REVERT: I 100 ASP cc_start: 0.6613 (p0) cc_final: 0.6155 (t70) REVERT: I 108 ASP cc_start: 0.7240 (m-30) cc_final: 0.6575 (p0) REVERT: I 109 TYR cc_start: 0.6687 (m-80) cc_final: 0.6020 (m-80) REVERT: J 50 ASP cc_start: 0.7940 (p0) cc_final: 0.7004 (t0) REVERT: J 108 ASP cc_start: 0.7253 (m-30) cc_final: 0.6296 (p0) REVERT: J 109 TYR cc_start: 0.6540 (m-80) cc_final: 0.5899 (m-80) REVERT: M 3 VAL cc_start: 0.8650 (t) cc_final: 0.8412 (p) REVERT: M 90 GLN cc_start: 0.7845 (pp30) cc_final: 0.7483 (pp30) REVERT: N 37 GLN cc_start: 0.6589 (pm20) cc_final: 0.5929 (pm20) REVERT: N 90 GLN cc_start: 0.7889 (pp30) cc_final: 0.7558 (pp30) outliers start: 35 outliers final: 18 residues processed: 234 average time/residue: 0.3932 time to fit residues: 119.3086 Evaluate side-chains 224 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 201 time to evaluate : 0.835 ------------------------------------------------------------------------------- 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 196 ASN Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 785 VAL 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 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: 1.9990 chunk 23 optimal weight: 20.0000 chunk 123 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 177 optimal weight: 0.6980 chunk 339 optimal weight: 9.9990 chunk 273 optimal weight: 5.9990 chunk 94 optimal weight: 0.7980 chunk 344 optimal weight: 0.0470 chunk 318 optimal weight: 8.9990 chunk 232 optimal weight: 8.9990 overall best weight: 1.1082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN B 121 ASN B 196 ASN C 394 ASN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.205812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.142856 restraints weight = 38536.664| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 3.45 r_work: 0.3656 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30561 Z= 0.134 Angle : 0.630 11.963 41778 Z= 0.299 Chirality : 0.045 0.381 5022 Planarity : 0.004 0.057 5157 Dihedral : 8.311 65.357 6149 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.17 % Allowed : 13.63 % Favored : 85.20 % 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: 1.81 (0.21), residues: 672 sheet: 0.02 (0.16), residues: 999 loop : -0.98 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 357 TYR 0.022 0.001 TYR A 170 PHE 0.028 0.001 PHE J 64 TRP 0.025 0.001 TRP H 99 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00314 (30408) covalent geometry : angle 0.59421 (41361) SS BOND : bond 0.00304 ( 42) SS BOND : angle 1.08962 ( 84) hydrogen bonds : bond 0.04236 ( 1063) hydrogen bonds : angle 5.28539 ( 2943) link_ALPHA1-6 : bond 0.00554 ( 3) link_ALPHA1-6 : angle 1.44571 ( 9) link_BETA1-4 : bond 0.00765 ( 57) link_BETA1-4 : angle 2.46115 ( 171) link_BETA1-6 : bond 0.00289 ( 6) link_BETA1-6 : angle 1.54895 ( 18) link_NAG-ASN : bond 0.00398 ( 45) link_NAG-ASN : angle 2.44055 ( 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 253 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 216 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7646 (OUTLIER) cc_final: 0.7401 (mmtt) REVERT: A 58 PHE cc_start: 0.6480 (OUTLIER) cc_final: 0.4985 (m-80) REVERT: A 99 ASN cc_start: 0.7422 (t0) cc_final: 0.7011 (t0) REVERT: A 196 ASN cc_start: 0.6073 (OUTLIER) cc_final: 0.5682 (m-40) REVERT: A 233 ILE cc_start: 0.1921 (OUTLIER) cc_final: 0.1315 (mt) REVERT: A 360 ASN cc_start: 0.7940 (t0) cc_final: 0.7646 (t0) REVERT: A 512 VAL cc_start: 0.8145 (OUTLIER) cc_final: 0.7914 (m) REVERT: A 532 ASN cc_start: 0.7986 (t0) cc_final: 0.7733 (t0) REVERT: A 571 ASP cc_start: 0.8483 (t0) cc_final: 0.8140 (t0) REVERT: A 988 GLU cc_start: 0.8244 (mp0) cc_final: 0.7811 (mp0) REVERT: B 571 ASP cc_start: 0.8416 (t0) cc_final: 0.8102 (t0) REVERT: B 581 THR cc_start: 0.8463 (OUTLIER) cc_final: 0.8210 (p) REVERT: B 936 ASP cc_start: 0.8407 (t0) cc_final: 0.8132 (t0) REVERT: B 988 GLU cc_start: 0.8181 (mp0) cc_final: 0.7597 (mp0) REVERT: C 99 ASN cc_start: 0.7650 (t0) cc_final: 0.7218 (t0) REVERT: C 306 PHE cc_start: 0.8472 (m-80) cc_final: 0.8147 (m-10) REVERT: C 571 ASP cc_start: 0.8330 (t0) cc_final: 0.7883 (t0) REVERT: C 574 ASP cc_start: 0.7904 (t0) cc_final: 0.7547 (t0) REVERT: C 578 ASP cc_start: 0.8101 (t0) cc_final: 0.7851 (t0) REVERT: C 988 GLU cc_start: 0.7677 (mp0) cc_final: 0.7429 (mp0) REVERT: C 995 ARG cc_start: 0.8184 (mtt-85) cc_final: 0.7960 (mtt180) REVERT: I 50 ASP cc_start: 0.7829 (p0) cc_final: 0.7249 (t0) REVERT: I 100 ASP cc_start: 0.6653 (p0) cc_final: 0.6130 (t0) REVERT: I 108 ASP cc_start: 0.7405 (m-30) cc_final: 0.6733 (p0) REVERT: I 109 TYR cc_start: 0.6636 (m-80) cc_final: 0.5978 (m-80) REVERT: J 108 ASP cc_start: 0.7218 (m-30) cc_final: 0.6287 (p0) REVERT: J 109 TYR cc_start: 0.6626 (m-80) cc_final: 0.5945 (m-80) REVERT: M 3 VAL cc_start: 0.8586 (t) cc_final: 0.8349 (p) REVERT: M 90 GLN cc_start: 0.7838 (pp30) cc_final: 0.7459 (pp30) REVERT: N 37 GLN cc_start: 0.6564 (pm20) cc_final: 0.5948 (pm20) REVERT: N 90 GLN cc_start: 0.7862 (pp30) cc_final: 0.7507 (pp30) outliers start: 37 outliers final: 21 residues processed: 245 average time/residue: 0.3996 time to fit residues: 126.4026 Evaluate side-chains 231 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 204 time to evaluate : 0.907 ------------------------------------------------------------------------------- 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 226 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 562 PHE 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 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: 0.8980 chunk 136 optimal weight: 20.0000 chunk 276 optimal weight: 2.9990 chunk 249 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 321 optimal weight: 9.9990 chunk 320 optimal weight: 9.9990 chunk 346 optimal weight: 40.0000 chunk 93 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A1119 ASN B 196 ASN B 394 ASN B 957 GLN B1002 GLN B1119 ASN L 27 GLN ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.205181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.139221 restraints weight = 38425.236| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 2.78 r_work: 0.3709 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 30561 Z= 0.147 Angle : 0.641 12.413 41778 Z= 0.306 Chirality : 0.046 0.377 5022 Planarity : 0.005 0.058 5157 Dihedral : 8.086 62.665 6149 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.01 % Allowed : 14.07 % Favored : 84.91 % 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: -0.26 (0.14), residues: 3561 helix: 1.93 (0.21), residues: 654 sheet: -0.02 (0.16), residues: 1002 loop : -1.02 (0.14), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 357 TYR 0.026 0.001 TYR B 453 PHE 0.042 0.001 PHE J 64 TRP 0.035 0.002 TRP H 99 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00350 (30408) covalent geometry : angle 0.60404 (41361) SS BOND : bond 0.00298 ( 42) SS BOND : angle 1.33027 ( 84) hydrogen bonds : bond 0.04338 ( 1063) hydrogen bonds : angle 5.27991 ( 2943) link_ALPHA1-6 : bond 0.00543 ( 3) link_ALPHA1-6 : angle 1.43767 ( 9) link_BETA1-4 : bond 0.00761 ( 57) link_BETA1-4 : angle 2.44807 ( 171) link_BETA1-6 : bond 0.00282 ( 6) link_BETA1-6 : angle 1.55828 ( 18) link_NAG-ASN : bond 0.00403 ( 45) link_NAG-ASN : angle 2.46055 ( 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 239 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 207 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7682 (OUTLIER) cc_final: 0.7428 (mmtt) REVERT: A 58 PHE cc_start: 0.6616 (OUTLIER) cc_final: 0.5085 (m-80) REVERT: A 99 ASN cc_start: 0.7446 (t0) cc_final: 0.6995 (t0) REVERT: A 196 ASN cc_start: 0.6239 (OUTLIER) cc_final: 0.5815 (m-40) REVERT: A 233 ILE cc_start: 0.2197 (OUTLIER) cc_final: 0.1513 (mt) REVERT: A 360 ASN cc_start: 0.7931 (t0) cc_final: 0.7622 (t0) REVERT: A 512 VAL cc_start: 0.8457 (OUTLIER) cc_final: 0.8216 (m) REVERT: A 532 ASN cc_start: 0.8027 (t0) cc_final: 0.7791 (t0) REVERT: A 571 ASP cc_start: 0.8531 (t0) cc_final: 0.8191 (t0) REVERT: A 651 ILE cc_start: 0.8793 (OUTLIER) cc_final: 0.8529 (mt) REVERT: A 988 GLU cc_start: 0.8395 (mp0) cc_final: 0.7937 (mp0) REVERT: B 571 ASP cc_start: 0.8476 (t0) cc_final: 0.8185 (t0) REVERT: B 581 THR cc_start: 0.8475 (OUTLIER) cc_final: 0.8217 (p) REVERT: B 988 GLU cc_start: 0.8336 (mp0) cc_final: 0.7724 (mp0) REVERT: C 99 ASN cc_start: 0.7675 (t0) cc_final: 0.7222 (t0) REVERT: C 306 PHE cc_start: 0.8537 (m-80) cc_final: 0.8189 (m-10) REVERT: C 571 ASP cc_start: 0.8370 (t0) cc_final: 0.7969 (t0) REVERT: C 574 ASP cc_start: 0.8020 (t0) cc_final: 0.7679 (t0) REVERT: C 578 ASP cc_start: 0.8207 (t0) cc_final: 0.7946 (t0) REVERT: C 988 GLU cc_start: 0.7874 (mp0) cc_final: 0.7646 (mp0) REVERT: C 995 ARG cc_start: 0.8300 (mtt-85) cc_final: 0.8084 (mtt180) REVERT: I 50 ASP cc_start: 0.7821 (p0) cc_final: 0.7194 (t0) REVERT: I 100 ASP cc_start: 0.6668 (p0) cc_final: 0.6118 (t0) REVERT: I 108 ASP cc_start: 0.7394 (m-30) cc_final: 0.6698 (p0) REVERT: I 109 TYR cc_start: 0.6690 (m-80) cc_final: 0.6010 (m-80) REVERT: J 50 ASP cc_start: 0.7983 (p0) cc_final: 0.7051 (OUTLIER) REVERT: J 108 ASP cc_start: 0.7278 (m-30) cc_final: 0.6302 (p0) REVERT: J 109 TYR cc_start: 0.6667 (m-80) cc_final: 0.5963 (m-80) REVERT: M 3 VAL cc_start: 0.8717 (t) cc_final: 0.8471 (p) REVERT: M 90 GLN cc_start: 0.7962 (pp30) cc_final: 0.7602 (pp30) REVERT: N 37 GLN cc_start: 0.6554 (pm20) cc_final: 0.5959 (pm20) REVERT: N 90 GLN cc_start: 0.7988 (pp30) cc_final: 0.7646 (pp30) outliers start: 32 outliers final: 20 residues processed: 232 average time/residue: 0.4014 time to fit residues: 120.1316 Evaluate side-chains 225 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 199 time to evaluate : 1.017 ------------------------------------------------------------------------------- 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 226 LEU 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 512 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 515 PHE 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 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: 7.9990 chunk 255 optimal weight: 2.9990 chunk 205 optimal weight: 9.9990 chunk 105 optimal weight: 7.9990 chunk 138 optimal weight: 0.7980 chunk 41 optimal weight: 0.0030 chunk 157 optimal weight: 0.7980 chunk 217 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 overall best weight: 0.8592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 957 GLN B 196 ASN B 394 ASN B 935 GLN B 957 GLN B1002 GLN C 935 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4597 r_free = 0.4597 target = 0.206163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.140198 restraints weight = 38390.114| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 2.83 r_work: 0.3711 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30561 Z= 0.124 Angle : 0.633 16.146 41778 Z= 0.301 Chirality : 0.045 0.374 5022 Planarity : 0.005 0.060 5157 Dihedral : 7.864 61.055 6149 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.79 % Allowed : 14.48 % Favored : 84.72 % 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: -0.19 (0.14), residues: 3561 helix: 2.01 (0.21), residues: 654 sheet: 0.01 (0.16), residues: 1005 loop : -0.97 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 357 TYR 0.058 0.001 TYR B 453 PHE 0.048 0.001 PHE J 64 TRP 0.030 0.002 TRP H 99 HIS 0.004 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00284 (30408) covalent geometry : angle 0.59787 (41361) SS BOND : bond 0.00293 ( 42) SS BOND : angle 1.16739 ( 84) hydrogen bonds : bond 0.04115 ( 1063) hydrogen bonds : angle 5.23072 ( 2943) link_ALPHA1-6 : bond 0.00540 ( 3) link_ALPHA1-6 : angle 1.43401 ( 9) link_BETA1-4 : bond 0.00761 ( 57) link_BETA1-4 : angle 2.42712 ( 171) link_BETA1-6 : bond 0.00349 ( 6) link_BETA1-6 : angle 1.54588 ( 18) link_NAG-ASN : bond 0.00410 ( 45) link_NAG-ASN : angle 2.41699 ( 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 232 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 207 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.7431 (t0) cc_final: 0.6963 (t0) REVERT: A 196 ASN cc_start: 0.6164 (OUTLIER) cc_final: 0.5828 (m-40) REVERT: A 233 ILE cc_start: 0.2072 (OUTLIER) cc_final: 0.1424 (mt) REVERT: A 360 ASN cc_start: 0.7956 (t0) cc_final: 0.7658 (t0) REVERT: A 512 VAL cc_start: 0.8447 (OUTLIER) cc_final: 0.8215 (m) REVERT: A 532 ASN cc_start: 0.8038 (t0) cc_final: 0.7781 (t0) REVERT: A 571 ASP cc_start: 0.8542 (t0) cc_final: 0.8233 (t0) REVERT: A 988 GLU cc_start: 0.8432 (mp0) cc_final: 0.7941 (mp0) REVERT: B 99 ASN cc_start: 0.7626 (t0) cc_final: 0.7380 (t0) REVERT: B 277 LEU cc_start: 0.8069 (mp) cc_final: 0.7846 (mp) REVERT: B 571 ASP cc_start: 0.8475 (t0) cc_final: 0.8188 (t0) REVERT: B 581 THR cc_start: 0.8469 (OUTLIER) cc_final: 0.8214 (p) REVERT: B 988 GLU cc_start: 0.8358 (mp0) cc_final: 0.7724 (mp0) REVERT: C 99 ASN cc_start: 0.7657 (t0) cc_final: 0.7191 (t0) REVERT: C 306 PHE cc_start: 0.8522 (m-80) cc_final: 0.8167 (m-10) REVERT: C 571 ASP cc_start: 0.8359 (t0) cc_final: 0.7959 (t0) REVERT: C 578 ASP cc_start: 0.8188 (t0) cc_final: 0.7920 (t0) REVERT: C 995 ARG cc_start: 0.8271 (mtt-85) cc_final: 0.8053 (mtt180) REVERT: I 50 ASP cc_start: 0.7813 (p0) cc_final: 0.7157 (t0) REVERT: I 100 ASP cc_start: 0.6682 (p0) cc_final: 0.6167 (t70) REVERT: I 108 ASP cc_start: 0.7418 (m-30) cc_final: 0.6736 (p0) REVERT: I 109 TYR cc_start: 0.6643 (m-80) cc_final: 0.6011 (m-80) REVERT: J 50 ASP cc_start: 0.7990 (p0) cc_final: 0.6979 (t0) REVERT: J 81 MET cc_start: 0.5252 (tmm) cc_final: 0.4842 (tmm) REVERT: J 108 ASP cc_start: 0.7251 (m-30) cc_final: 0.6300 (p0) REVERT: J 109 TYR cc_start: 0.6642 (m-80) cc_final: 0.5949 (m-80) REVERT: M 3 VAL cc_start: 0.8666 (t) cc_final: 0.8422 (p) REVERT: M 90 GLN cc_start: 0.7893 (pp30) cc_final: 0.7519 (pp30) REVERT: N 37 GLN cc_start: 0.6548 (pm20) cc_final: 0.5964 (pm20) REVERT: N 90 GLN cc_start: 0.7954 (pp30) cc_final: 0.7594 (pp30) outliers start: 25 outliers final: 18 residues processed: 227 average time/residue: 0.4015 time to fit residues: 117.7372 Evaluate side-chains 222 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 200 time to evaluate : 1.075 ------------------------------------------------------------------------------- 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 226 LEU 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 512 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 350 VAL 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 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: 0.9980 chunk 243 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 chunk 224 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 chunk 291 optimal weight: 0.8980 chunk 123 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 213 optimal weight: 9.9990 chunk 271 optimal weight: 0.6980 chunk 164 optimal weight: 0.1980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 ASN B 394 ASN B1002 GLN B1119 ASN L 27 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.205653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.141279 restraints weight = 38568.558| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 3.53 r_work: 0.3652 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30561 Z= 0.137 Angle : 0.637 15.734 41778 Z= 0.304 Chirality : 0.046 0.370 5022 Planarity : 0.005 0.060 5157 Dihedral : 7.673 59.981 6149 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.85 % Allowed : 14.55 % Favored : 84.60 % 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: 1.98 (0.21), residues: 654 sheet: 0.03 (0.16), residues: 996 loop : -0.99 (0.14), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 357 TYR 0.025 0.001 TYR C 453 PHE 0.054 0.001 PHE J 64 TRP 0.043 0.002 TRP H 99 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00322 (30408) covalent geometry : angle 0.60241 (41361) SS BOND : bond 0.00311 ( 42) SS BOND : angle 1.18557 ( 84) hydrogen bonds : bond 0.04203 ( 1063) hydrogen bonds : angle 5.20573 ( 2943) link_ALPHA1-6 : bond 0.00522 ( 3) link_ALPHA1-6 : angle 1.43524 ( 9) link_BETA1-4 : bond 0.00760 ( 57) link_BETA1-4 : angle 2.41373 ( 171) link_BETA1-6 : bond 0.00301 ( 6) link_BETA1-6 : angle 1.54361 ( 18) link_NAG-ASN : bond 0.00404 ( 45) link_NAG-ASN : angle 2.41403 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9905.34 seconds wall clock time: 169 minutes 35.03 seconds (10175.03 seconds total)