Starting phenix.real_space_refine on Sat Mar 7 06:34:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i9c_35266/03_2026/8i9c_35266.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i9c_35266/03_2026/8i9c_35266.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8i9c_35266/03_2026/8i9c_35266.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i9c_35266/03_2026/8i9c_35266.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8i9c_35266/03_2026/8i9c_35266.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i9c_35266/03_2026/8i9c_35266.map" } resolution = 3.85 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= 0.004 sd= 0.057 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 195 5.16 5 C 25198 2.51 5 N 6420 2.21 5 O 7722 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 156 residue(s): 0.04s 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: 39535 Number of models: 1 Model: "" Number of chains: 50 Chain: "A" Number of atoms: 7821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7821 Classifications: {'peptide': 998} Link IDs: {'PTRANS': 54, 'TRANS': 943} Chain breaks: 8 Chain: "B" Number of atoms: 7827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 999, 7827 Classifications: {'peptide': 999} Link IDs: {'PTRANS': 54, 'TRANS': 944} Chain breaks: 9 Chain: "C" Number of atoms: 7821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7821 Classifications: {'peptide': 998} Link IDs: {'PTRANS': 54, 'TRANS': 943} Chain breaks: 9 Chain: "F" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 27, 'TRANS': 569} Chain: "D" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 27, 'TRANS': 569} Chain: "E" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 27, 'TRANS': 569} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 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: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 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: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 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: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 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: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "F" 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: "D" 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: "E" 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: 10.21, per 1000 atoms: 0.26 Number of scatterers: 39535 At special positions: 0 Unit cell: (183.703, 204.356, 247.836, 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 195 16.00 O 7722 8.00 N 6420 7.00 C 25198 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=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.01 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.05 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 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=2.06 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 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=2.35 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.05 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.05 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 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=2.47 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.06 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.05 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS F 133 " - pdb=" SG CYS F 141 " distance=2.04 Simple disulfide: pdb=" SG CYS F 344 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.04 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.04 Simple disulfide: pdb=" SG CYS E 344 " - pdb=" SG CYS E 361 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 165 " " NAG A1404 " - " ASN A 234 " " NAG A1405 " - " ASN A 282 " " NAG A1406 " - " ASN A 603 " " NAG A1407 " - " ASN A 616 " " NAG A1408 " - " ASN A 657 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 122 " " NAG B1403 " - " ASN B 165 " " NAG B1404 " - " ASN B 234 " " NAG B1405 " - " ASN B 282 " " NAG B1406 " - " ASN B 603 " " NAG B1407 " - " ASN B 616 " " NAG B1408 " - " ASN B 657 " " NAG B1409 " - " ASN B 709 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 122 " " NAG C1403 " - " ASN C 165 " " NAG C1404 " - " ASN C 234 " " NAG C1405 " - " ASN C 282 " " NAG C1406 " - " ASN C 603 " " NAG C1407 " - " ASN C 616 " " NAG C1408 " - " ASN C 657 " " NAG D 701 " - " ASN D 322 " " NAG E 701 " - " ASN E 322 " " NAG F 701 " - " ASN F 322 " " NAG G 1 " - " ASN A 331 " " NAG H 1 " - " ASN A 343 " " NAG I 1 " - " ASN A 709 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN A 801 " " NAG L 1 " - " ASN A1074 " " NAG M 1 " - " ASN A1098 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN B 331 " " NAG P 1 " - " ASN B 343 " " NAG Q 1 " - " ASN B 717 " " NAG R 1 " - " ASN B 801 " " NAG S 1 " - " ASN B1074 " " NAG T 1 " - " ASN B1098 " " NAG U 1 " - " ASN B1134 " " NAG V 1 " - " ASN C 331 " " NAG W 1 " - " ASN C 343 " " NAG X 1 " - " ASN C 709 " " NAG Y 1 " - " ASN C 717 " " NAG Z 1 " - " ASN C 801 " " NAG a 1 " - " ASN C1074 " " NAG b 1 " - " ASN C1098 " " NAG c 1 " - " ASN C1134 " " NAG d 1 " - " ASN F 53 " " NAG e 1 " - " ASN F 90 " " NAG f 1 " - " ASN F 103 " " NAG g 1 " - " ASN F 432 " " NAG h 1 " - " ASN F 546 " " NAG i 1 " - " ASN D 53 " " NAG j 1 " - " ASN D 90 " " NAG k 1 " - " ASN D 103 " " NAG l 1 " - " ASN D 432 " " NAG m 1 " - " ASN D 546 " " NAG n 1 " - " ASN E 53 " " NAG o 1 " - " ASN E 90 " " NAG p 1 " - " ASN E 103 " " NAG q 1 " - " ASN E 432 " " NAG r 1 " - " ASN E 546 " Time building additional restraints: 3.95 Conformation dependent library (CDL) restraints added in 1.7 seconds 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9008 Finding SS restraints... Secondary structure from input PDB file: 147 helices and 47 sheets defined 38.5% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 342 removed outlier: 4.380A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.699A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 4.977A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.717A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) 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 758 through 783 removed outlier: 3.560A pdb=" N ILE A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.700A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.590A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.356A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR A 961 " --> pdb=" O GLN A 957 " (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 981 removed outlier: 3.739A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 976 through 981' Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.221A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.552A pdb=" N GLU B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 342 removed outlier: 4.380A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.699A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.976A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.630A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) 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 758 through 783 removed outlier: 3.773A pdb=" N LYS B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN B 774 " --> pdb=" O ILE B 770 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.589A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 815 removed outlier: 3.634A pdb=" N LYS B 814 " --> pdb=" O LYS B 811 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG B 815 " --> pdb=" O PRO B 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 811 through 815' Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.773A pdb=" N LEU B 821 " --> pdb=" O PRO B 817 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.572A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 918 removed outlier: 3.993A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.627A pdb=" N LYS B 933 " --> pdb=" O SER B 929 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 964 removed outlier: 3.879A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 981 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.632A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.646A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 342 removed outlier: 4.339A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.699A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 4.976A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 747 through 754 removed outlier: 3.695A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) 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 758 through 783 removed outlier: 3.964A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 823 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.544A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.603A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.020A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU C 962 " --> pdb=" O ALA C 958 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 983 removed outlier: 4.269A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.244A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER C1021 " --> pdb=" O GLU C1017 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 Processing helix chain 'F' and resid 22 through 53 removed outlier: 3.775A pdb=" N LYS F 26 " --> pdb=" O GLU F 22 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS F 31 " --> pdb=" O THR F 27 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN F 53 " --> pdb=" O ASN F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 80 removed outlier: 3.797A pdb=" N GLN F 60 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA F 65 " --> pdb=" O ASN F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 83 No H-bonds generated for 'chain 'F' and resid 81 through 83' Processing helix chain 'F' and resid 90 through 102 removed outlier: 3.893A pdb=" N GLN F 102 " --> pdb=" O GLN F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 129 Processing helix chain 'F' and resid 147 through 155 removed outlier: 3.944A pdb=" N ALA F 153 " --> pdb=" O ASN F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 172 removed outlier: 3.778A pdb=" N ARG F 169 " --> pdb=" O TRP F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 193 removed outlier: 3.909A pdb=" N GLU F 182 " --> pdb=" O PRO F 178 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL F 185 " --> pdb=" O GLU F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 205 removed outlier: 3.640A pdb=" N TYR F 202 " --> pdb=" O ASP F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 208 No H-bonds generated for 'chain 'F' and resid 206 through 208' Processing helix chain 'F' and resid 220 through 230 removed outlier: 4.122A pdb=" N GLU F 224 " --> pdb=" O GLY F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 249 removed outlier: 3.834A pdb=" N HIS F 239 " --> pdb=" O PRO F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 279 removed outlier: 3.728A pdb=" N TYR F 279 " --> pdb=" O THR F 276 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 300 Processing helix chain 'F' and resid 305 through 318 removed outlier: 3.857A pdb=" N VAL F 318 " --> pdb=" O PHE F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 331 removed outlier: 3.857A pdb=" N ASN F 330 " --> pdb=" O GLY F 326 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER F 331 " --> pdb=" O PHE F 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 326 through 331' Processing helix chain 'F' and resid 366 through 385 removed outlier: 4.070A pdb=" N HIS F 373 " --> pdb=" O PHE F 369 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR F 385 " --> pdb=" O TYR F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 393 removed outlier: 3.692A pdb=" N ARG F 393 " --> pdb=" O PHE F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 412 removed outlier: 3.877A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N SER F 409 " --> pdb=" O GLY F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 422 removed outlier: 3.913A pdb=" N SER F 420 " --> pdb=" O LYS F 416 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE F 421 " --> pdb=" O HIS F 417 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY F 422 " --> pdb=" O LEU F 418 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 447 removed outlier: 3.632A pdb=" N GLU F 435 " --> pdb=" O ASP F 431 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N THR F 445 " --> pdb=" O LYS F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 465 Processing helix chain 'F' and resid 472 through 484 Processing helix chain 'F' and resid 499 through 502 Processing helix chain 'F' and resid 503 through 508 Processing helix chain 'F' and resid 513 through 533 removed outlier: 4.163A pdb=" N THR F 519 " --> pdb=" O TYR F 515 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU F 520 " --> pdb=" O TYR F 516 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE F 523 " --> pdb=" O THR F 519 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN F 531 " --> pdb=" O GLU F 527 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA F 532 " --> pdb=" O ALA F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 542 removed outlier: 3.608A pdb=" N LYS F 541 " --> pdb=" O PRO F 538 " (cutoff:3.500A) Processing helix chain 'F' and resid 547 through 559 removed outlier: 3.897A pdb=" N GLY F 551 " --> pdb=" O SER F 547 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N MET F 557 " --> pdb=" O LYS F 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 570 Processing helix chain 'F' and resid 570 through 575 Processing helix chain 'F' and resid 581 through 599 removed outlier: 3.532A pdb=" N LEU F 585 " --> pdb=" O VAL F 581 " (cutoff:3.500A) Proline residue: F 590 - end of helix Processing helix chain 'D' and resid 22 through 53 removed outlier: 3.776A pdb=" N LYS D 26 " --> pdb=" O GLU D 22 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS D 31 " --> pdb=" O THR D 27 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN D 53 " --> pdb=" O ASN D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 80 removed outlier: 3.796A pdb=" N GLN D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA D 65 " --> pdb=" O ASN D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 83 No H-bonds generated for 'chain 'D' and resid 81 through 83' Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.893A pdb=" N GLN D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 147 through 155 removed outlier: 3.944A pdb=" N ALA D 153 " --> pdb=" O ASN D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 172 removed outlier: 3.779A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 193 removed outlier: 3.909A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.640A pdb=" N TYR D 202 " --> pdb=" O ASP D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 220 through 230 removed outlier: 4.122A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 249 removed outlier: 3.833A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 279 removed outlier: 3.728A pdb=" N TYR D 279 " --> pdb=" O THR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 300 Processing helix chain 'D' and resid 305 through 318 removed outlier: 3.857A pdb=" N VAL D 318 " --> pdb=" O PHE D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 331 removed outlier: 3.856A pdb=" N ASN D 330 " --> pdb=" O GLY D 326 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER D 331 " --> pdb=" O PHE D 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 326 through 331' Processing helix chain 'D' and resid 366 through 385 removed outlier: 4.071A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 removed outlier: 3.692A pdb=" N ARG D 393 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 412 removed outlier: 3.877A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 422 removed outlier: 3.913A pdb=" N SER D 420 " --> pdb=" O LYS D 416 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE D 421 " --> pdb=" O HIS D 417 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY D 422 " --> pdb=" O LEU D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.631A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 465 Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 499 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 533 removed outlier: 4.162A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN D 531 " --> pdb=" O GLU D 527 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA D 532 " --> pdb=" O ALA D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.608A pdb=" N LYS D 541 " --> pdb=" O PRO D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.896A pdb=" N GLY D 551 " --> pdb=" O SER D 547 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 570 Processing helix chain 'D' and resid 570 through 575 Processing helix chain 'D' and resid 581 through 599 removed outlier: 3.532A pdb=" N LEU D 585 " --> pdb=" O VAL D 581 " (cutoff:3.500A) Proline residue: D 590 - end of helix Processing helix chain 'E' and resid 22 through 53 removed outlier: 3.776A pdb=" N LYS E 26 " --> pdb=" O GLU E 22 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS E 31 " --> pdb=" O THR E 27 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN E 53 " --> pdb=" O ASN E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 80 removed outlier: 3.796A pdb=" N GLN E 60 " --> pdb=" O GLU E 56 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA E 65 " --> pdb=" O ASN E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 83 No H-bonds generated for 'chain 'E' and resid 81 through 83' Processing helix chain 'E' and resid 90 through 102 removed outlier: 3.892A pdb=" N GLN E 102 " --> pdb=" O GLN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 129 Processing helix chain 'E' and resid 147 through 155 removed outlier: 3.944A pdb=" N ALA E 153 " --> pdb=" O ASN E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 172 removed outlier: 3.779A pdb=" N ARG E 169 " --> pdb=" O TRP E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 193 removed outlier: 3.908A pdb=" N GLU E 182 " --> pdb=" O PRO E 178 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL E 185 " --> pdb=" O GLU E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 205 removed outlier: 3.640A pdb=" N TYR E 202 " --> pdb=" O ASP E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 208 No H-bonds generated for 'chain 'E' and resid 206 through 208' Processing helix chain 'E' and resid 220 through 230 removed outlier: 4.122A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 249 removed outlier: 3.832A pdb=" N HIS E 239 " --> pdb=" O PRO E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 279 removed outlier: 3.728A pdb=" N TYR E 279 " --> pdb=" O THR E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 300 Processing helix chain 'E' and resid 305 through 318 removed outlier: 3.858A pdb=" N VAL E 318 " --> pdb=" O PHE E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 331 removed outlier: 3.858A pdb=" N ASN E 330 " --> pdb=" O GLY E 326 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER E 331 " --> pdb=" O PHE E 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 326 through 331' Processing helix chain 'E' and resid 366 through 385 removed outlier: 4.070A pdb=" N HIS E 373 " --> pdb=" O PHE E 369 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 393 removed outlier: 3.693A pdb=" N ARG E 393 " --> pdb=" O PHE E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 412 removed outlier: 3.876A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N SER E 409 " --> pdb=" O GLY E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 422 removed outlier: 3.914A pdb=" N SER E 420 " --> pdb=" O LYS E 416 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE E 421 " --> pdb=" O HIS E 417 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY E 422 " --> pdb=" O LEU E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 447 removed outlier: 3.631A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N THR E 445 " --> pdb=" O LYS E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 465 Processing helix chain 'E' and resid 472 through 484 Processing helix chain 'E' and resid 499 through 502 Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 513 through 533 removed outlier: 4.162A pdb=" N THR E 519 " --> pdb=" O TYR E 515 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU E 520 " --> pdb=" O TYR E 516 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN E 531 " --> pdb=" O GLU E 527 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA E 532 " --> pdb=" O ALA E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 removed outlier: 3.608A pdb=" N LYS E 541 " --> pdb=" O PRO E 538 " (cutoff:3.500A) Processing helix chain 'E' and resid 547 through 559 removed outlier: 3.898A pdb=" N GLY E 551 " --> pdb=" O SER E 547 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 570 Processing helix chain 'E' and resid 570 through 575 Processing helix chain 'E' and resid 581 through 599 removed outlier: 3.532A pdb=" N LEU E 585 " --> pdb=" O VAL E 581 " (cutoff:3.500A) Proline residue: E 590 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.062A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 55 removed outlier: 3.857A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 116 through 121 removed outlier: 3.730A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN A 134 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 317 removed outlier: 3.947A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.338A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.656A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASP A 398 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'A' and resid 664 through 667 removed outlier: 6.417A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 702 through 704 removed outlier: 6.911A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.593A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.593A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 735 removed outlier: 4.568A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.808A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.061A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 49 through 55 removed outlier: 3.858A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC1, first strand: chain 'B' and resid 116 through 121 removed outlier: 3.731A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN B 134 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.929A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 327 removed outlier: 5.338A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.655A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASP B 398 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU B 513 " --> pdb=" O CYS B 432 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.631A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 9.026A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.589A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.589A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.504A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.713A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.061A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 49 through 55 removed outlier: 3.857A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD5, first strand: chain 'C' and resid 116 through 121 removed outlier: 3.730A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ILE C 128 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE C 168 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N VAL C 130 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N CYS C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN C 134 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.902A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 325 through 328 removed outlier: 7.146A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.656A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU C 513 " --> pdb=" O CYS C 432 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE1, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.576A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 9.010A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.542A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.542A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.579A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE6, first strand: chain 'F' and resid 262 through 263 removed outlier: 5.920A pdb=" N LEU F 262 " --> pdb=" O VAL F 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'F' and resid 347 through 352 removed outlier: 6.243A pdb=" N ASP F 355 " --> pdb=" O LEU F 351 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.921A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.243A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 262 through 263 removed outlier: 5.921A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'E' and resid 347 through 352 removed outlier: 6.242A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 1561 hydrogen bonds defined for protein. 4398 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: 11.17 Time building geometry restraints manager: 5.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.48: 23459 1.48 - 1.75: 16748 1.75 - 2.02: 285 2.02 - 2.30: 0 2.30 - 2.57: 1 Bond restraints: 40493 Sorted by residual: bond pdb=" C THR A 676 " pdb=" N GLN A 690 " ideal model delta sigma weight residual 1.332 2.573 -1.241 1.40e-02 5.10e+03 7.85e+03 bond pdb=" CA SER B 698 " pdb=" C SER B 698 " ideal model delta sigma weight residual 1.522 1.444 0.078 1.20e-02 6.94e+03 4.27e+01 bond pdb=" C HIS C1088 " pdb=" N PHE C1089 " ideal model delta sigma weight residual 1.331 1.263 0.068 1.59e-02 3.96e+03 1.83e+01 bond pdb=" N PRO B 209 " pdb=" CD PRO B 209 " ideal model delta sigma weight residual 1.473 1.529 -0.056 1.40e-02 5.10e+03 1.62e+01 bond pdb=" N PRO A 209 " pdb=" CD PRO A 209 " ideal model delta sigma weight residual 1.473 1.529 -0.056 1.40e-02 5.10e+03 1.58e+01 ... (remaining 40488 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.92: 55043 10.92 - 21.85: 8 21.85 - 32.77: 1 32.77 - 43.70: 1 43.70 - 54.62: 1 Bond angle restraints: 55054 Sorted by residual: angle pdb=" O THR A 676 " pdb=" C THR A 676 " pdb=" N GLN A 690 " ideal model delta sigma weight residual 122.59 67.97 54.62 1.33e+00 5.65e-01 1.69e+03 angle pdb=" C THR A 676 " pdb=" N GLN A 690 " pdb=" CA GLN A 690 " ideal model delta sigma weight residual 121.54 159.69 -38.15 1.91e+00 2.74e-01 3.99e+02 angle pdb=" CA THR A 676 " pdb=" C THR A 676 " pdb=" N GLN A 690 " ideal model delta sigma weight residual 116.84 92.81 24.03 1.71e+00 3.42e-01 1.98e+02 angle pdb=" N PHE C 157 " pdb=" CA PHE C 157 " pdb=" C PHE C 157 " ideal model delta sigma weight residual 111.74 123.23 -11.49 1.35e+00 5.49e-01 7.24e+01 angle pdb=" N PHE A 157 " pdb=" CA PHE A 157 " pdb=" C PHE A 157 " ideal model delta sigma weight residual 111.74 123.21 -11.47 1.35e+00 5.49e-01 7.22e+01 ... (remaining 55049 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 21853 17.93 - 35.85: 2467 35.85 - 53.78: 783 53.78 - 71.70: 229 71.70 - 89.63: 56 Dihedral angle restraints: 25388 sinusoidal: 11404 harmonic: 13984 Sorted by residual: dihedral pdb=" CA THR A 676 " pdb=" C THR A 676 " pdb=" N GLN A 690 " pdb=" CA GLN A 690 " ideal model delta harmonic sigma weight residual -180.00 -111.11 -68.89 0 5.00e+00 4.00e-02 1.90e+02 dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual 93.00 12.17 80.83 1 1.00e+01 1.00e-02 8.07e+01 dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.05 71.95 1 1.00e+01 1.00e-02 6.63e+01 ... (remaining 25385 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.366: 6341 0.366 - 0.733: 5 0.733 - 1.099: 2 1.099 - 1.466: 0 1.466 - 1.832: 2 Chirality restraints: 6350 Sorted by residual: chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-02 2.50e+03 2.15e+02 chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN A1134 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.57 -1.83 2.00e-01 2.50e+01 8.39e+01 chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN B 801 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.80 -1.60 2.00e-01 2.50e+01 6.37e+01 ... (remaining 6347 not shown) Planarity restraints: 7045 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 676 " -0.183 2.00e-02 2.50e+03 2.67e-01 7.12e+02 pdb=" C THR A 676 " 0.424 2.00e-02 2.50e+03 pdb=" O THR A 676 " -0.266 2.00e-02 2.50e+03 pdb=" N GLN A 690 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " 0.114 2.00e-02 2.50e+03 1.30e-01 2.12e+02 pdb=" CG ASN C 331 " -0.044 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " -0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " -0.211 2.00e-02 2.50e+03 pdb=" C1 NAG V 1 " 0.158 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 801 " 0.097 2.00e-02 2.50e+03 1.29e-01 2.07e+02 pdb=" CG ASN B 801 " -0.043 2.00e-02 2.50e+03 pdb=" OD1 ASN B 801 " 0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN B 801 " -0.222 2.00e-02 2.50e+03 pdb=" C1 NAG R 1 " 0.148 2.00e-02 2.50e+03 ... (remaining 7042 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 219 2.48 - 3.08: 26947 3.08 - 3.69: 54882 3.69 - 4.29: 83558 4.29 - 4.90: 139891 Nonbonded interactions: 305497 Sorted by model distance: nonbonded pdb=" O GLY C 799 " pdb=" O PHE C 800 " model vdw 1.871 3.040 nonbonded pdb=" O ALA A 694 " pdb=" CB TYR A 695 " model vdw 2.095 3.440 nonbonded pdb=" N GLU C 748 " pdb=" OE1 GLU C 748 " model vdw 2.142 3.120 nonbonded pdb=" O GLY B 700 " pdb=" O ALA B 701 " model vdw 2.166 3.040 nonbonded pdb=" O SER B 813 " pdb=" OG SER B 813 " model vdw 2.183 3.040 ... (remaining 305492 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 27 through 939 or resid 944 through 1408)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' } 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 group one per residue 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: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.040 Extract box with map and model: 0.820 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 41.430 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.280 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:1.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5005 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 : 0.011 1.241 40639 Z= 0.599 Angle : 1.075 54.624 55450 Z= 0.584 Chirality : 0.067 1.832 6350 Planarity : 0.007 0.267 6979 Dihedral : 17.289 89.631 16254 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 1.53 % Allowed : 8.14 % Favored : 90.34 % Rotamer: Outliers : 9.03 % Allowed : 16.77 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.62 (0.10), residues: 4720 helix: -1.39 (0.12), residues: 1643 sheet: -2.05 (0.17), residues: 747 loop : -3.35 (0.10), residues: 2330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1039 TYR 0.027 0.002 TYR C1067 PHE 0.025 0.002 PHE B 898 TRP 0.025 0.002 TRP A 104 HIS 0.009 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.01051 (40493) covalent geometry : angle 0.93909 (55054) SS BOND : bond 0.08473 ( 42) SS BOND : angle 8.16085 ( 84) hydrogen bonds : bond 0.18629 ( 1525) hydrogen bonds : angle 7.15785 ( 4398) link_BETA1-4 : bond 0.00647 ( 38) link_BETA1-4 : angle 3.61730 ( 114) link_NAG-ASN : bond 0.00739 ( 66) link_NAG-ASN : angle 6.53138 ( 198) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 910 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 380 poor density : 530 time to evaluate : 1.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 LEU cc_start: 0.2278 (OUTLIER) cc_final: 0.1921 (mp) REVERT: A 324 GLU cc_start: 0.3722 (OUTLIER) cc_final: 0.3161 (tm-30) REVERT: A 395 VAL cc_start: 0.4229 (OUTLIER) cc_final: 0.3603 (p) REVERT: A 480 CYS cc_start: 0.2270 (OUTLIER) cc_final: -0.0646 (m) REVERT: A 929 SER cc_start: 0.7866 (OUTLIER) cc_final: 0.7494 (m) REVERT: B 692 ILE cc_start: 0.7389 (OUTLIER) cc_final: 0.7105 (mm) REVERT: B 722 VAL cc_start: 0.7158 (OUTLIER) cc_final: 0.6873 (m) REVERT: B 973 ILE cc_start: 0.4641 (OUTLIER) cc_final: 0.4419 (pt) REVERT: F 132 VAL cc_start: -0.5874 (OUTLIER) cc_final: -0.6378 (m) REVERT: F 270 MET cc_start: 0.0161 (tpp) cc_final: -0.0090 (mmm) REVERT: E 256 ILE cc_start: -0.2311 (OUTLIER) cc_final: -0.2681 (mt) REVERT: E 401 HIS cc_start: 0.0477 (OUTLIER) cc_final: 0.0086 (p90) outliers start: 380 outliers final: 57 residues processed: 855 average time/residue: 0.2337 time to fit residues: 333.6774 Evaluate side-chains 317 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 249 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 795 LYS Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 795 LYS Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 133 CYS Chi-restraints excluded: chain F residue 247 LYS Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain E residue 133 CYS Chi-restraints excluded: chain E residue 256 ILE Chi-restraints excluded: chain E residue 401 HIS Chi-restraints excluded: chain E residue 530 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 432 optimal weight: 20.0000 chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 6.9990 chunk 455 optimal weight: 6.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 6.9990 chunk 470 optimal weight: 50.0000 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 134 GLN A 137 ASN A 188 ASN A 314 GLN A 317 ASN A 460 ASN A 540 ASN A 542 ASN A 544 ASN A 613 GLN A 644 GLN A 675 GLN A 703 ASN A 751 ASN A 784 GLN A 804 GLN A 901 GLN A 914 ASN A 935 GLN A 954 HIS A1071 GLN A1101 HIS B 134 GLN B 137 ASN B 188 ASN B 354 ASN B 460 ASN B 542 ASN B 613 GLN B 658 ASN B 762 GLN B 784 GLN B 901 GLN B 914 ASN B 919 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN B 992 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS C 134 GLN C 137 ASN C 188 ASN C 239 GLN C 354 ASN C 460 ASN C 542 ASN C 644 GLN C 658 ASN C 675 GLN C 703 ASN C 901 GLN C 914 ASN C 919 ASN C 926 GLN C 992 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN F 58 ASN F 96 GLN F 139 GLN F 221 GLN F 239 HIS F 277 ASN F 378 HIS F 472 GLN F 505 HIS F 522 GLN F 599 ASN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN D 96 GLN D 239 HIS D 378 HIS D 505 HIS D 522 GLN D 599 ASN E 42 GLN E 58 ASN ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 149 ASN E 239 HIS E 378 HIS E 437 ASN E 472 GLN E 493 HIS E 505 HIS E 522 GLN E 599 ASN Total number of N/Q/H flips: 85 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.109888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.077147 restraints weight = 263575.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.078533 restraints weight = 130639.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.078297 restraints weight = 75822.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.078532 restraints weight = 55996.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.078549 restraints weight = 49776.806| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.108 40639 Z= 0.218 Angle : 0.828 19.240 55450 Z= 0.405 Chirality : 0.049 0.641 6350 Planarity : 0.005 0.091 6979 Dihedral : 9.104 72.873 7435 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.16 % Favored : 93.69 % Rotamer: Outliers : 4.92 % Allowed : 20.17 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.11), residues: 4722 helix: -0.05 (0.13), residues: 1680 sheet: -1.42 (0.17), residues: 763 loop : -2.72 (0.11), residues: 2279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 905 TYR 0.028 0.002 TYR B1067 PHE 0.027 0.002 PHE F 504 TRP 0.021 0.001 TRP A 104 HIS 0.010 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00480 (40493) covalent geometry : angle 0.79857 (55054) SS BOND : bond 0.01882 ( 42) SS BOND : angle 2.63226 ( 84) hydrogen bonds : bond 0.04939 ( 1525) hydrogen bonds : angle 5.41959 ( 4398) link_BETA1-4 : bond 0.00860 ( 38) link_BETA1-4 : angle 2.24290 ( 114) link_NAG-ASN : bond 0.00790 ( 66) link_NAG-ASN : angle 2.93986 ( 198) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9444 Ramachandran restraints generated. 4722 Oldfield, 0 Emsley, 4722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9444 Ramachandran restraints generated. 4722 Oldfield, 0 Emsley, 4722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 207 poor density : 264 time to evaluate : 1.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 GLN cc_start: 0.9164 (tt0) cc_final: 0.8936 (tm-30) REVERT: A 278 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8666 (ttmm) REVERT: A 324 GLU cc_start: 0.6701 (OUTLIER) cc_final: 0.6395 (tm-30) REVERT: A 900 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.8360 (mtm) REVERT: B 48 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.7704 (pp) REVERT: B 229 LEU cc_start: 0.8905 (mt) cc_final: 0.8635 (mp) REVERT: B 643 PHE cc_start: 0.7198 (t80) cc_final: 0.6770 (t80) REVERT: B 690 GLN cc_start: 0.7455 (OUTLIER) cc_final: 0.6559 (mt0) REVERT: B 692 ILE cc_start: 0.9047 (mm) cc_final: 0.8714 (mm) REVERT: B 731 MET cc_start: 0.8245 (ppp) cc_final: 0.7773 (ppp) REVERT: B 869 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.8269 (ptp) REVERT: C 55 PHE cc_start: 0.7937 (m-80) cc_final: 0.7433 (m-10) REVERT: C 97 LYS cc_start: 0.3568 (OUTLIER) cc_final: 0.3351 (tppt) REVERT: C 153 MET cc_start: 0.5513 (tpp) cc_final: 0.5142 (tpp) REVERT: C 278 LYS cc_start: 0.8950 (tppt) cc_final: 0.8746 (ptmm) REVERT: C 737 ASP cc_start: 0.7680 (t0) cc_final: 0.7417 (p0) REVERT: C 780 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7569 (mt-10) REVERT: C 900 MET cc_start: 0.9020 (mtp) cc_final: 0.8724 (mtp) REVERT: C 954 HIS cc_start: 0.8861 (m90) cc_final: 0.8598 (m-70) REVERT: C 984 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8479 (mp) REVERT: F 82 MET cc_start: 0.6465 (mtm) cc_final: 0.6089 (mpp) REVERT: F 270 MET cc_start: -0.0556 (tpp) cc_final: -0.1338 (tpp) REVERT: F 579 MET cc_start: 0.7982 (ttp) cc_final: 0.7030 (tpt) REVERT: D 82 MET cc_start: 0.4746 (tmm) cc_final: 0.4459 (ppp) REVERT: E 82 MET cc_start: 0.5858 (mtt) cc_final: 0.5645 (mpp) REVERT: E 249 MET cc_start: 0.6934 (mtt) cc_final: 0.6711 (mpp) REVERT: E 332 MET cc_start: 0.5229 (ppp) cc_final: 0.4619 (ppp) REVERT: E 401 HIS cc_start: 0.1020 (OUTLIER) cc_final: 0.0132 (p-80) outliers start: 207 outliers final: 89 residues processed: 446 average time/residue: 0.2187 time to fit residues: 168.4965 Evaluate side-chains 298 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 200 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1063 LEU Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 690 GLN Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 953 ASN Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1021 SER Chi-restraints excluded: chain B residue 1023 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 313 TYR Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 928 ASN Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1013 ILE Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain F residue 609 ASP Chi-restraints excluded: chain F residue 611 SER Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 401 HIS Chi-restraints excluded: chain E residue 611 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 369 optimal weight: 50.0000 chunk 56 optimal weight: 7.9990 chunk 80 optimal weight: 0.8980 chunk 347 optimal weight: 30.0000 chunk 405 optimal weight: 50.0000 chunk 73 optimal weight: 0.9980 chunk 383 optimal weight: 50.0000 chunk 40 optimal weight: 50.0000 chunk 61 optimal weight: 9.9990 chunk 304 optimal weight: 20.0000 chunk 5 optimal weight: 20.0000 overall best weight: 7.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 ASN A 804 GLN A 992 GLN A1106 GLN B 81 ASN B 121 ASN B 644 GLN B 824 ASN B 955 ASN ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1011 GLN B1058 HIS B1064 HIS B1071 GLN C 317 ASN C 777 ASN C 920 GLN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN C1010 GLN C1011 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN F 117 ASN ** F 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 305 GLN F 437 ASN D 437 ASN E 42 GLN E 89 GLN E 96 GLN E 117 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.104207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.071268 restraints weight = 267956.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.071791 restraints weight = 147043.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.071629 restraints weight = 93755.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.071937 restraints weight = 70116.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.071948 restraints weight = 60388.343| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.4613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.136 40639 Z= 0.295 Angle : 0.867 18.495 55450 Z= 0.423 Chirality : 0.051 0.731 6350 Planarity : 0.005 0.068 6979 Dihedral : 8.065 59.820 7357 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.93 % Favored : 92.95 % Rotamer: Outliers : 5.32 % Allowed : 20.55 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.87 (0.11), residues: 4722 helix: 0.34 (0.13), residues: 1657 sheet: -1.21 (0.18), residues: 755 loop : -2.52 (0.11), residues: 2310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 158 TYR 0.041 0.002 TYR A1067 PHE 0.033 0.003 PHE B 759 TRP 0.024 0.001 TRP A 886 HIS 0.009 0.001 HIS D 265 Details of bonding type rmsd covalent geometry : bond 0.00655 (40493) covalent geometry : angle 0.83899 (55054) SS BOND : bond 0.00883 ( 42) SS BOND : angle 2.18184 ( 84) hydrogen bonds : bond 0.05221 ( 1525) hydrogen bonds : angle 5.48481 ( 4398) link_BETA1-4 : bond 0.00902 ( 38) link_BETA1-4 : angle 2.50845 ( 114) link_NAG-ASN : bond 0.00876 ( 66) link_NAG-ASN : angle 3.05945 ( 198) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9444 Ramachandran restraints generated. 4722 Oldfield, 0 Emsley, 4722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9444 Ramachandran restraints generated. 4722 Oldfield, 0 Emsley, 4722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 224 poor density : 191 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8482 (mt) cc_final: 0.8017 (mt) REVERT: A 81 ASN cc_start: -0.0658 (OUTLIER) cc_final: -0.0988 (t0) REVERT: A 104 TRP cc_start: 0.8809 (m-90) cc_final: 0.8129 (m-90) REVERT: A 218 GLN cc_start: 0.9241 (tt0) cc_final: 0.9031 (tm-30) REVERT: A 324 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.6917 (tm-30) REVERT: A 480 CYS cc_start: 0.6158 (OUTLIER) cc_final: 0.5625 (m) REVERT: A 693 ILE cc_start: 0.9459 (OUTLIER) cc_final: 0.9220 (pp) REVERT: A 705 VAL cc_start: 0.8907 (OUTLIER) cc_final: 0.8565 (p) REVERT: A 731 MET cc_start: 0.8799 (ppp) cc_final: 0.7752 (ppp) REVERT: A 1031 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8464 (tt0) REVERT: B 48 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.7777 (pp) REVERT: B 229 LEU cc_start: 0.8937 (mt) cc_final: 0.8571 (mp) REVERT: B 690 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.6933 (mt0) REVERT: B 731 MET cc_start: 0.8035 (ppp) cc_final: 0.7521 (ppp) REVERT: B 755 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.7529 (tp-100) REVERT: C 46 SER cc_start: 0.9117 (OUTLIER) cc_final: 0.8764 (m) REVERT: C 97 LYS cc_start: 0.3165 (OUTLIER) cc_final: 0.2747 (tppt) REVERT: C 114 THR cc_start: 0.6149 (OUTLIER) cc_final: 0.5771 (p) REVERT: C 133 PHE cc_start: 0.5349 (m-80) cc_final: 0.4934 (m-80) REVERT: C 135 PHE cc_start: 0.7581 (m-10) cc_final: 0.7186 (m-10) REVERT: C 278 LYS cc_start: 0.9090 (tppt) cc_final: 0.8887 (tppt) REVERT: C 780 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7510 (mt-10) REVERT: C 900 MET cc_start: 0.8985 (mtp) cc_final: 0.8661 (mtm) REVERT: C 906 PHE cc_start: 0.8436 (OUTLIER) cc_final: 0.8046 (m-10) REVERT: C 954 HIS cc_start: 0.8850 (m90) cc_final: 0.8637 (m-70) REVERT: C 975 SER cc_start: 0.7658 (OUTLIER) cc_final: 0.7054 (m) REVERT: C 998 THR cc_start: 0.8290 (OUTLIER) cc_final: 0.8050 (p) REVERT: C 1029 MET cc_start: 0.9298 (tpp) cc_final: 0.8961 (tpp) REVERT: F 82 MET cc_start: 0.6697 (mtm) cc_final: 0.6272 (mpp) REVERT: F 270 MET cc_start: -0.1391 (tpp) cc_final: -0.1672 (mmm) REVERT: F 474 MET cc_start: -0.0259 (mmp) cc_final: -0.0534 (mmp) REVERT: F 579 MET cc_start: 0.8142 (ttp) cc_final: 0.7913 (tpp) REVERT: D 152 MET cc_start: 0.1446 (tpt) cc_final: 0.0227 (tpt) REVERT: D 474 MET cc_start: 0.4023 (mmm) cc_final: 0.3389 (mmm) REVERT: E 233 ILE cc_start: -0.3611 (OUTLIER) cc_final: -0.4063 (mt) REVERT: E 332 MET cc_start: 0.5409 (ppp) cc_final: 0.4777 (ppp) REVERT: E 579 MET cc_start: 0.8164 (mtp) cc_final: 0.6860 (mmm) outliers start: 224 outliers final: 129 residues processed: 404 average time/residue: 0.2037 time to fit residues: 145.5752 Evaluate side-chains 312 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 167 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1063 LEU Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 690 GLN Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 953 ASN Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1021 SER Chi-restraints excluded: chain B residue 1023 ASN Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 313 TYR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 928 ASN Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1013 ILE Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1111 GLU Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1142 GLN Chi-restraints excluded: chain F residue 408 MET Chi-restraints excluded: chain F residue 531 GLN Chi-restraints excluded: chain F residue 604 VAL Chi-restraints excluded: chain F residue 609 ASP Chi-restraints excluded: chain F residue 611 SER Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 474 MET Chi-restraints excluded: chain E residue 530 CYS Chi-restraints excluded: chain E residue 611 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 161 optimal weight: 6.9990 chunk 26 optimal weight: 40.0000 chunk 461 optimal weight: 50.0000 chunk 297 optimal weight: 30.0000 chunk 240 optimal weight: 9.9990 chunk 431 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 chunk 41 optimal weight: 40.0000 chunk 125 optimal weight: 50.0000 chunk 350 optimal weight: 0.1980 chunk 183 optimal weight: 7.9990 overall best weight: 5.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN B 388 ASN B 394 ASN ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN C 388 ASN C 751 ASN C 777 ASN C 935 GLN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN F 51 ASN ** F 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 ASN E 401 HIS E 493 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.104326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.071248 restraints weight = 264555.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.070627 restraints weight = 144100.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.071395 restraints weight = 113024.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.071245 restraints weight = 68780.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.071243 restraints weight = 65666.821| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.5125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 40639 Z= 0.208 Angle : 0.743 18.303 55450 Z= 0.357 Chirality : 0.048 0.829 6350 Planarity : 0.004 0.057 6979 Dihedral : 7.494 59.546 7349 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.99 % Favored : 93.90 % Rotamer: Outliers : 4.54 % Allowed : 22.02 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.52 (0.11), residues: 4722 helix: 0.68 (0.13), residues: 1660 sheet: -1.11 (0.18), residues: 724 loop : -2.31 (0.11), residues: 2338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 452 TYR 0.031 0.002 TYR A1067 PHE 0.024 0.002 PHE B 342 TRP 0.015 0.001 TRP E 271 HIS 0.006 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00466 (40493) covalent geometry : angle 0.71232 (55054) SS BOND : bond 0.00462 ( 42) SS BOND : angle 2.41141 ( 84) hydrogen bonds : bond 0.04412 ( 1525) hydrogen bonds : angle 5.21868 ( 4398) link_BETA1-4 : bond 0.00502 ( 38) link_BETA1-4 : angle 2.20463 ( 114) link_NAG-ASN : bond 0.00618 ( 66) link_NAG-ASN : angle 2.90517 ( 198) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9444 Ramachandran restraints generated. 4722 Oldfield, 0 Emsley, 4722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9444 Ramachandran restraints generated. 4722 Oldfield, 0 Emsley, 4722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 175 time to evaluate : 1.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8547 (mt) cc_final: 0.7995 (mt) REVERT: A 324 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.6906 (tm-30) REVERT: A 350 VAL cc_start: 0.3543 (OUTLIER) cc_final: 0.3039 (t) REVERT: A 693 ILE cc_start: 0.9458 (OUTLIER) cc_final: 0.9237 (pp) REVERT: A 725 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7291 (mm-30) REVERT: A 731 MET cc_start: 0.8846 (ppp) cc_final: 0.7879 (ppp) REVERT: A 921 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7734 (pttp) REVERT: B 48 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.7993 (pp) REVERT: B 117 LEU cc_start: 0.9641 (OUTLIER) cc_final: 0.9309 (tt) REVERT: B 388 ASN cc_start: 0.7754 (OUTLIER) cc_final: 0.7369 (m-40) REVERT: B 736 VAL cc_start: 0.9400 (OUTLIER) cc_final: 0.9194 (p) REVERT: B 755 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.7697 (tp-100) REVERT: B 786 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8454 (pttp) REVERT: B 869 MET cc_start: 0.8546 (mtt) cc_final: 0.8232 (ptp) REVERT: B 959 LEU cc_start: 0.9551 (OUTLIER) cc_final: 0.8949 (tt) REVERT: B 1029 MET cc_start: 0.7854 (tmm) cc_final: 0.7450 (tmm) REVERT: C 97 LYS cc_start: 0.3603 (OUTLIER) cc_final: 0.3333 (tppt) REVERT: C 114 THR cc_start: 0.6376 (OUTLIER) cc_final: 0.5991 (p) REVERT: C 133 PHE cc_start: 0.5270 (m-80) cc_final: 0.4930 (m-80) REVERT: C 135 PHE cc_start: 0.7643 (m-10) cc_final: 0.7178 (m-10) REVERT: C 278 LYS cc_start: 0.9107 (tppt) cc_final: 0.8907 (tppt) REVERT: C 705 VAL cc_start: 0.8697 (OUTLIER) cc_final: 0.8379 (m) REVERT: C 900 MET cc_start: 0.9032 (mtp) cc_final: 0.8699 (mtm) REVERT: C 906 PHE cc_start: 0.8478 (OUTLIER) cc_final: 0.8080 (m-10) REVERT: C 954 HIS cc_start: 0.8960 (m90) cc_final: 0.8665 (m-70) REVERT: C 975 SER cc_start: 0.7771 (OUTLIER) cc_final: 0.7197 (m) REVERT: C 1106 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.8190 (mm110) REVERT: F 82 MET cc_start: 0.6846 (mtm) cc_final: 0.6570 (mpp) REVERT: F 152 MET cc_start: -0.3730 (tpp) cc_final: -0.4406 (mtt) REVERT: F 474 MET cc_start: 0.0438 (mmp) cc_final: 0.0149 (mmp) REVERT: D 152 MET cc_start: 0.1415 (tpt) cc_final: 0.0517 (tpt) REVERT: D 249 MET cc_start: 0.5104 (mmm) cc_final: 0.4287 (ptt) REVERT: D 318 VAL cc_start: -0.1026 (OUTLIER) cc_final: -0.1320 (m) REVERT: E 140 GLU cc_start: -0.1749 (OUTLIER) cc_final: -0.2030 (tt0) REVERT: E 233 ILE cc_start: -0.3746 (OUTLIER) cc_final: -0.4167 (mt) REVERT: E 332 MET cc_start: 0.5691 (ppp) cc_final: 0.5123 (ppp) REVERT: E 579 MET cc_start: 0.8220 (mtp) cc_final: 0.7961 (mtp) outliers start: 191 outliers final: 113 residues processed: 356 average time/residue: 0.2090 time to fit residues: 130.6880 Evaluate side-chains 291 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 158 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 953 ASN Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1021 SER Chi-restraints excluded: chain B residue 1023 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 313 TYR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 928 ASN Chi-restraints excluded: chain C residue 960 ASN Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1013 ILE Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1142 GLN Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 408 MET Chi-restraints excluded: chain F residue 531 GLN Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 581 VAL Chi-restraints excluded: chain F residue 609 ASP Chi-restraints excluded: chain F residue 611 SER Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 530 CYS Chi-restraints excluded: chain E residue 611 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 198 optimal weight: 20.0000 chunk 359 optimal weight: 20.0000 chunk 316 optimal weight: 9.9990 chunk 472 optimal weight: 7.9990 chunk 266 optimal weight: 0.7980 chunk 228 optimal weight: 0.1980 chunk 286 optimal weight: 0.9990 chunk 348 optimal weight: 6.9990 chunk 329 optimal weight: 4.9990 chunk 139 optimal weight: 9.9990 chunk 251 optimal weight: 0.1980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 115 GLN A 872 GLN B 121 ASN B 314 GLN B 613 GLN B 965 GLN B1064 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN ** F 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 ASN E 493 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.105884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.072200 restraints weight = 263302.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.073121 restraints weight = 134650.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.073211 restraints weight = 80295.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.073220 restraints weight = 56557.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.073389 restraints weight = 52661.756| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.5251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 40639 Z= 0.118 Angle : 0.675 18.597 55450 Z= 0.318 Chirality : 0.046 0.708 6350 Planarity : 0.004 0.049 6979 Dihedral : 7.041 59.799 7346 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.36 % Favored : 94.54 % Rotamer: Outliers : 3.71 % Allowed : 22.57 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.15 (0.12), residues: 4722 helix: 1.03 (0.13), residues: 1660 sheet: -0.91 (0.18), residues: 729 loop : -2.13 (0.11), residues: 2333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C1107 TYR 0.021 0.001 TYR C 313 PHE 0.019 0.001 PHE C 342 TRP 0.017 0.001 TRP E 271 HIS 0.003 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00255 (40493) covalent geometry : angle 0.64694 (55054) SS BOND : bond 0.00498 ( 42) SS BOND : angle 1.63338 ( 84) hydrogen bonds : bond 0.03817 ( 1525) hydrogen bonds : angle 4.89592 ( 4398) link_BETA1-4 : bond 0.00495 ( 38) link_BETA1-4 : angle 2.14825 ( 114) link_NAG-ASN : bond 0.00525 ( 66) link_NAG-ASN : angle 2.75269 ( 198) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9444 Ramachandran restraints generated. 4722 Oldfield, 0 Emsley, 4722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9444 Ramachandran restraints generated. 4722 Oldfield, 0 Emsley, 4722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 176 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8432 (mt) cc_final: 0.7860 (mt) REVERT: A 81 ASN cc_start: -0.1865 (OUTLIER) cc_final: -0.2363 (m-40) REVERT: A 191 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7756 (tt0) REVERT: A 324 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6748 (tm-30) REVERT: A 731 MET cc_start: 0.8806 (ppp) cc_final: 0.7811 (ppp) REVERT: A 900 MET cc_start: 0.8505 (mtp) cc_final: 0.8246 (mtm) REVERT: A 1029 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.7943 (tpp) REVERT: B 48 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.7967 (pp) REVERT: B 117 LEU cc_start: 0.9584 (OUTLIER) cc_final: 0.9094 (tt) REVERT: B 122 ASN cc_start: 0.8536 (OUTLIER) cc_final: 0.8184 (p0) REVERT: B 690 GLN cc_start: 0.7902 (OUTLIER) cc_final: 0.7070 (mt0) REVERT: B 753 LEU cc_start: 0.8335 (tt) cc_final: 0.8080 (pp) REVERT: B 786 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8200 (ptpt) REVERT: B 869 MET cc_start: 0.8400 (mtt) cc_final: 0.8184 (ptp) REVERT: B 1029 MET cc_start: 0.7903 (tmm) cc_final: 0.7446 (tmm) REVERT: C 55 PHE cc_start: 0.8636 (m-10) cc_final: 0.8253 (m-10) REVERT: C 97 LYS cc_start: 0.3331 (OUTLIER) cc_final: 0.2763 (tppt) REVERT: C 114 THR cc_start: 0.6206 (OUTLIER) cc_final: 0.5830 (p) REVERT: C 135 PHE cc_start: 0.7632 (m-10) cc_final: 0.7149 (m-10) REVERT: C 278 LYS cc_start: 0.9176 (tppt) cc_final: 0.8955 (tppt) REVERT: C 319 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.7606 (tmm-80) REVERT: C 900 MET cc_start: 0.8998 (mtp) cc_final: 0.8648 (mtp) REVERT: C 954 HIS cc_start: 0.8963 (m90) cc_final: 0.8629 (m-70) REVERT: F 474 MET cc_start: 0.0671 (mmp) cc_final: 0.0381 (mmp) REVERT: F 579 MET cc_start: 0.7637 (tpp) cc_final: 0.6498 (tpp) REVERT: D 82 MET cc_start: 0.3661 (ppp) cc_final: 0.3291 (ppp) REVERT: D 152 MET cc_start: 0.1879 (tpt) cc_final: 0.1035 (tpt) REVERT: D 249 MET cc_start: 0.5008 (mmm) cc_final: 0.4338 (ptt) REVERT: D 318 VAL cc_start: -0.0586 (OUTLIER) cc_final: -0.0885 (m) REVERT: D 323 MET cc_start: 0.1925 (mmt) cc_final: 0.1074 (mmt) REVERT: D 557 MET cc_start: 0.2472 (ppp) cc_final: 0.2070 (ppp) REVERT: E 140 GLU cc_start: -0.1717 (OUTLIER) cc_final: -0.1982 (tt0) REVERT: E 233 ILE cc_start: -0.3662 (OUTLIER) cc_final: -0.4085 (mt) REVERT: E 332 MET cc_start: 0.5718 (ppp) cc_final: 0.5168 (ppp) REVERT: E 579 MET cc_start: 0.8466 (mtp) cc_final: 0.8229 (mtp) outliers start: 156 outliers final: 95 residues processed: 320 average time/residue: 0.2014 time to fit residues: 113.7106 Evaluate side-chains 272 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 163 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 690 GLN Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 953 ASN Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1021 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 313 TYR Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 928 ASN Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1142 GLN Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 409 SER Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 581 VAL Chi-restraints excluded: chain F residue 609 ASP Chi-restraints excluded: chain F residue 611 SER Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 474 MET Chi-restraints excluded: chain E residue 530 CYS Chi-restraints excluded: chain E residue 611 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 242 optimal weight: 9.9990 chunk 161 optimal weight: 5.9990 chunk 127 optimal weight: 8.9990 chunk 205 optimal weight: 9.9990 chunk 398 optimal weight: 50.0000 chunk 334 optimal weight: 40.0000 chunk 393 optimal weight: 40.0000 chunk 446 optimal weight: 9.9990 chunk 345 optimal weight: 8.9990 chunk 343 optimal weight: 5.9990 chunk 71 optimal weight: 9.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 658 ASN ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 613 GLN B 751 ASN B 762 GLN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN B1135 ASN C 115 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN C 777 ASN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 522 GLN E 63 ASN E 96 GLN E 277 ASN E 493 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.101469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.068509 restraints weight = 250568.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.066216 restraints weight = 146964.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.065829 restraints weight = 114572.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.065850 restraints weight = 95389.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.065789 restraints weight = 81679.057| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.5996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.134 40639 Z= 0.277 Angle : 0.801 19.227 55450 Z= 0.385 Chirality : 0.049 0.908 6350 Planarity : 0.005 0.058 6979 Dihedral : 7.256 59.357 7341 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.84 % Favored : 93.05 % Rotamer: Outliers : 4.73 % Allowed : 22.09 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.12), residues: 4722 helix: 0.85 (0.13), residues: 1636 sheet: -0.99 (0.18), residues: 697 loop : -2.06 (0.11), residues: 2389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 357 TYR 0.040 0.002 TYR A1067 PHE 0.027 0.002 PHE B 759 TRP 0.018 0.001 TRP A 886 HIS 0.011 0.001 HIS F 228 Details of bonding type rmsd covalent geometry : bond 0.00620 (40493) covalent geometry : angle 0.77252 (55054) SS BOND : bond 0.00600 ( 42) SS BOND : angle 1.84286 ( 84) hydrogen bonds : bond 0.04574 ( 1525) hydrogen bonds : angle 5.33939 ( 4398) link_BETA1-4 : bond 0.00538 ( 38) link_BETA1-4 : angle 2.20199 ( 114) link_NAG-ASN : bond 0.00806 ( 66) link_NAG-ASN : angle 3.05661 ( 198) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9444 Ramachandran restraints generated. 4722 Oldfield, 0 Emsley, 4722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9444 Ramachandran restraints generated. 4722 Oldfield, 0 Emsley, 4722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 161 time to evaluate : 1.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8690 (mt) cc_final: 0.8186 (mt) REVERT: A 191 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8052 (mt-10) REVERT: A 238 PHE cc_start: 0.8332 (p90) cc_final: 0.8076 (p90) REVERT: A 324 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.6971 (pp20) REVERT: A 705 VAL cc_start: 0.8552 (OUTLIER) cc_final: 0.8059 (p) REVERT: A 731 MET cc_start: 0.8725 (ppp) cc_final: 0.7850 (ppp) REVERT: A 921 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.7839 (pttp) REVERT: A 1029 MET cc_start: 0.8881 (OUTLIER) cc_final: 0.8119 (tpp) REVERT: B 48 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8058 (pp) REVERT: B 332 ILE cc_start: 0.1581 (OUTLIER) cc_final: 0.1172 (tp) REVERT: B 654 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7167 (mp0) REVERT: B 690 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7181 (mt0) REVERT: B 755 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.7906 (tp-100) REVERT: B 786 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8322 (pttp) REVERT: B 869 MET cc_start: 0.8574 (mtt) cc_final: 0.7782 (mmp) REVERT: B 959 LEU cc_start: 0.9594 (OUTLIER) cc_final: 0.9062 (tt) REVERT: B 992 GLN cc_start: 0.8655 (mm-40) cc_final: 0.8416 (mm-40) REVERT: B 1029 MET cc_start: 0.8286 (tmm) cc_final: 0.7744 (tmm) REVERT: C 104 TRP cc_start: 0.6838 (m-90) cc_final: 0.6426 (m-90) REVERT: C 114 THR cc_start: 0.6141 (OUTLIER) cc_final: 0.5759 (p) REVERT: C 135 PHE cc_start: 0.7811 (m-10) cc_final: 0.7567 (m-10) REVERT: C 270 LEU cc_start: 0.8900 (mp) cc_final: 0.8460 (mt) REVERT: C 387 LEU cc_start: 0.9609 (tp) cc_final: 0.9356 (mt) REVERT: C 906 PHE cc_start: 0.8648 (OUTLIER) cc_final: 0.8239 (m-10) REVERT: C 954 HIS cc_start: 0.8933 (m90) cc_final: 0.8600 (m-70) REVERT: C 975 SER cc_start: 0.7778 (OUTLIER) cc_final: 0.7323 (m) REVERT: F 474 MET cc_start: 0.1167 (mmp) cc_final: 0.0914 (mmp) REVERT: F 579 MET cc_start: 0.7877 (tpp) cc_final: 0.6723 (tpp) REVERT: D 82 MET cc_start: 0.4072 (ppp) cc_final: 0.3728 (ppp) REVERT: D 152 MET cc_start: 0.2239 (tpt) cc_final: 0.1123 (tpt) REVERT: D 249 MET cc_start: 0.4882 (mmm) cc_final: 0.4410 (ptt) REVERT: D 318 VAL cc_start: -0.0466 (OUTLIER) cc_final: -0.0797 (m) REVERT: E 82 MET cc_start: 0.6749 (mpp) cc_final: 0.6518 (pmm) REVERT: E 140 GLU cc_start: -0.1760 (OUTLIER) cc_final: -0.2031 (tt0) REVERT: E 233 ILE cc_start: -0.3132 (OUTLIER) cc_final: -0.3552 (mt) REVERT: E 332 MET cc_start: 0.6505 (ppp) cc_final: 0.6015 (ppp) outliers start: 199 outliers final: 130 residues processed: 350 average time/residue: 0.2105 time to fit residues: 129.7609 Evaluate side-chains 303 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 156 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1023 ASN Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 690 GLN Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 953 ASN Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1021 SER Chi-restraints excluded: chain B residue 1023 ASN Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 313 TYR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 928 ASN Chi-restraints excluded: chain C residue 960 ASN Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1024 LEU Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1142 GLN Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 581 VAL Chi-restraints excluded: chain F residue 609 ASP Chi-restraints excluded: chain F residue 611 SER Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 530 CYS Chi-restraints excluded: chain E residue 611 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 102 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 315 optimal weight: 50.0000 chunk 115 optimal weight: 6.9990 chunk 250 optimal weight: 6.9990 chunk 322 optimal weight: 40.0000 chunk 439 optimal weight: 40.0000 chunk 316 optimal weight: 50.0000 chunk 426 optimal weight: 50.0000 chunk 348 optimal weight: 20.0000 chunk 184 optimal weight: 3.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN F 139 GLN D 89 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.102184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.067821 restraints weight = 266845.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.068454 restraints weight = 141688.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.067822 restraints weight = 95521.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.068387 restraints weight = 78097.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.068225 restraints weight = 64551.069| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.6506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 40639 Z= 0.230 Angle : 0.758 18.808 55450 Z= 0.362 Chirality : 0.048 0.756 6350 Planarity : 0.004 0.056 6979 Dihedral : 7.237 59.730 7339 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.42 % Favored : 93.48 % Rotamer: Outliers : 4.54 % Allowed : 22.54 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.12), residues: 4722 helix: 0.89 (0.13), residues: 1638 sheet: -1.04 (0.19), residues: 657 loop : -2.01 (0.11), residues: 2427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 319 TYR 0.037 0.002 TYR A1067 PHE 0.028 0.002 PHE A 168 TRP 0.013 0.001 TRP C 886 HIS 0.006 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00513 (40493) covalent geometry : angle 0.73070 (55054) SS BOND : bond 0.00643 ( 42) SS BOND : angle 1.73874 ( 84) hydrogen bonds : bond 0.04278 ( 1525) hydrogen bonds : angle 5.26880 ( 4398) link_BETA1-4 : bond 0.00525 ( 38) link_BETA1-4 : angle 2.15998 ( 114) link_NAG-ASN : bond 0.00611 ( 66) link_NAG-ASN : angle 2.90282 ( 198) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9444 Ramachandran restraints generated. 4722 Oldfield, 0 Emsley, 4722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9444 Ramachandran restraints generated. 4722 Oldfield, 0 Emsley, 4722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 167 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8797 (mt) cc_final: 0.8318 (mt) REVERT: A 191 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8124 (tt0) REVERT: A 238 PHE cc_start: 0.8453 (p90) cc_final: 0.8199 (p90) REVERT: A 324 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.6796 (pp20) REVERT: A 731 MET cc_start: 0.8657 (ppp) cc_final: 0.7863 (ppp) REVERT: A 921 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.7857 (pttp) REVERT: A 1029 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8152 (tpp) REVERT: B 48 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8291 (pp) REVERT: B 332 ILE cc_start: 0.1979 (OUTLIER) cc_final: 0.1561 (tp) REVERT: B 654 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7194 (mp0) REVERT: B 690 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7325 (mt0) REVERT: B 753 LEU cc_start: 0.8976 (tt) cc_final: 0.8637 (pp) REVERT: B 755 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.8239 (tp-100) REVERT: B 786 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8263 (pttp) REVERT: B 869 MET cc_start: 0.8433 (mtt) cc_final: 0.7670 (mmp) REVERT: B 959 LEU cc_start: 0.9533 (OUTLIER) cc_final: 0.8964 (tt) REVERT: B 992 GLN cc_start: 0.8793 (mm-40) cc_final: 0.8554 (mm-40) REVERT: C 104 TRP cc_start: 0.6868 (m-90) cc_final: 0.6632 (m-90) REVERT: C 114 THR cc_start: 0.6078 (OUTLIER) cc_final: 0.5729 (p) REVERT: C 135 PHE cc_start: 0.7878 (m-10) cc_final: 0.7612 (m-10) REVERT: C 223 LEU cc_start: 0.8731 (mp) cc_final: 0.7506 (mp) REVERT: C 270 LEU cc_start: 0.8941 (mp) cc_final: 0.8469 (mt) REVERT: C 906 PHE cc_start: 0.8677 (OUTLIER) cc_final: 0.8359 (m-10) REVERT: C 954 HIS cc_start: 0.8873 (m90) cc_final: 0.8571 (m-70) REVERT: C 975 SER cc_start: 0.8032 (OUTLIER) cc_final: 0.7587 (m) REVERT: F 408 MET cc_start: 0.7545 (pmm) cc_final: 0.7124 (pmm) REVERT: F 579 MET cc_start: 0.7774 (tpp) cc_final: 0.7414 (tpp) REVERT: D 82 MET cc_start: 0.4284 (ppp) cc_final: 0.3834 (ppp) REVERT: D 152 MET cc_start: 0.2477 (tpt) cc_final: 0.1452 (tpt) REVERT: D 249 MET cc_start: 0.4637 (mmm) cc_final: 0.4146 (ptt) REVERT: D 318 VAL cc_start: -0.0151 (OUTLIER) cc_final: -0.0493 (p) REVERT: D 557 MET cc_start: 0.2969 (ppp) cc_final: 0.2586 (ppp) REVERT: D 579 MET cc_start: 0.5724 (mtt) cc_final: 0.2331 (mmm) REVERT: E 140 GLU cc_start: -0.1692 (OUTLIER) cc_final: -0.1945 (tt0) REVERT: E 233 ILE cc_start: -0.2860 (OUTLIER) cc_final: -0.3300 (mt) REVERT: E 332 MET cc_start: 0.6566 (ppp) cc_final: 0.6090 (ppp) REVERT: E 579 MET cc_start: 0.8493 (mtp) cc_final: 0.8224 (mmt) outliers start: 191 outliers final: 133 residues processed: 348 average time/residue: 0.2128 time to fit residues: 129.1403 Evaluate side-chains 308 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 159 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 690 GLN Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 953 ASN Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1021 SER Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 313 TYR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 928 ASN Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1013 ILE Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1024 LEU Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 581 VAL Chi-restraints excluded: chain F residue 609 ASP Chi-restraints excluded: chain F residue 611 SER Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 409 SER Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 530 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 44 optimal weight: 20.0000 chunk 210 optimal weight: 6.9990 chunk 233 optimal weight: 9.9990 chunk 15 optimal weight: 0.8980 chunk 73 optimal weight: 8.9990 chunk 236 optimal weight: 0.2980 chunk 1 optimal weight: 4.9990 chunk 449 optimal weight: 40.0000 chunk 373 optimal weight: 50.0000 chunk 50 optimal weight: 0.8980 chunk 266 optimal weight: 0.7980 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 872 GLN B 121 ASN B 613 GLN B 787 GLN B 907 ASN C 422 ASN C 777 ASN C 901 GLN C1048 HIS F 139 GLN D 51 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.104127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.071230 restraints weight = 266090.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.071210 restraints weight = 144439.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.070990 restraints weight = 111996.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.071347 restraints weight = 76459.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.071364 restraints weight = 64806.095| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.6526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 40639 Z= 0.118 Angle : 0.682 18.690 55450 Z= 0.320 Chirality : 0.046 0.630 6350 Planarity : 0.004 0.049 6979 Dihedral : 6.833 59.889 7339 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.61 % Favored : 94.30 % Rotamer: Outliers : 3.21 % Allowed : 23.85 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.12), residues: 4722 helix: 1.17 (0.13), residues: 1663 sheet: -0.79 (0.18), residues: 672 loop : -1.85 (0.12), residues: 2387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 466 TYR 0.021 0.001 TYR C 313 PHE 0.027 0.001 PHE C 133 TRP 0.015 0.001 TRP E 203 HIS 0.009 0.001 HIS F 228 Details of bonding type rmsd covalent geometry : bond 0.00258 (40493) covalent geometry : angle 0.65584 (55054) SS BOND : bond 0.00396 ( 42) SS BOND : angle 1.47626 ( 84) hydrogen bonds : bond 0.03700 ( 1525) hydrogen bonds : angle 4.97286 ( 4398) link_BETA1-4 : bond 0.00520 ( 38) link_BETA1-4 : angle 2.13649 ( 114) link_NAG-ASN : bond 0.00502 ( 66) link_NAG-ASN : angle 2.68873 ( 198) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9444 Ramachandran restraints generated. 4722 Oldfield, 0 Emsley, 4722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9444 Ramachandran restraints generated. 4722 Oldfield, 0 Emsley, 4722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 174 time to evaluate : 1.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8629 (mt) cc_final: 0.8111 (mt) REVERT: A 191 GLU cc_start: 0.8357 (mt-10) cc_final: 0.8003 (tt0) REVERT: A 238 PHE cc_start: 0.8512 (p90) cc_final: 0.8184 (p90) REVERT: A 324 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.7088 (pp20) REVERT: A 731 MET cc_start: 0.8607 (ppp) cc_final: 0.7788 (ppp) REVERT: A 921 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.7923 (pttp) REVERT: A 1029 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.7841 (tpp) REVERT: B 48 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8253 (pp) REVERT: B 332 ILE cc_start: 0.2218 (OUTLIER) cc_final: 0.1797 (tp) REVERT: B 611 LEU cc_start: 0.9409 (tp) cc_final: 0.9082 (pp) REVERT: B 654 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7169 (mp0) REVERT: B 690 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7319 (mt0) REVERT: B 753 LEU cc_start: 0.8935 (tt) cc_final: 0.8588 (pp) REVERT: B 755 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.8262 (tp-100) REVERT: B 786 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8132 (pttp) REVERT: B 869 MET cc_start: 0.8406 (mtt) cc_final: 0.8142 (ptp) REVERT: B 992 GLN cc_start: 0.8685 (mm-40) cc_final: 0.8450 (mm-40) REVERT: B 1029 MET cc_start: 0.8277 (tmm) cc_final: 0.7751 (tmm) REVERT: C 104 TRP cc_start: 0.7094 (m-90) cc_final: 0.6860 (m-90) REVERT: C 114 THR cc_start: 0.5836 (OUTLIER) cc_final: 0.5470 (p) REVERT: C 223 LEU cc_start: 0.8551 (mp) cc_final: 0.7221 (mp) REVERT: C 270 LEU cc_start: 0.8946 (mp) cc_final: 0.8491 (mt) REVERT: C 906 PHE cc_start: 0.8472 (OUTLIER) cc_final: 0.8110 (m-10) REVERT: C 954 HIS cc_start: 0.8905 (m90) cc_final: 0.8524 (m-70) REVERT: F 376 MET cc_start: 0.7067 (tmm) cc_final: 0.6843 (ppp) REVERT: F 408 MET cc_start: 0.7279 (pmm) cc_final: 0.6905 (pmm) REVERT: F 579 MET cc_start: 0.7590 (tpp) cc_final: 0.6440 (tpp) REVERT: D 82 MET cc_start: 0.4002 (ppp) cc_final: 0.3491 (ppp) REVERT: D 152 MET cc_start: 0.1456 (tpt) cc_final: 0.0536 (tpt) REVERT: D 249 MET cc_start: 0.4417 (mmm) cc_final: 0.3852 (ptt) REVERT: D 579 MET cc_start: 0.4390 (mtt) cc_final: 0.0849 (mmm) REVERT: E 140 GLU cc_start: -0.1728 (OUTLIER) cc_final: -0.1980 (tt0) REVERT: E 233 ILE cc_start: -0.3161 (OUTLIER) cc_final: -0.3583 (mt) REVERT: E 332 MET cc_start: 0.6102 (ppp) cc_final: 0.5569 (ppp) REVERT: E 579 MET cc_start: 0.8363 (mtp) cc_final: 0.7450 (mmt) outliers start: 135 outliers final: 95 residues processed: 301 average time/residue: 0.2133 time to fit residues: 112.8893 Evaluate side-chains 269 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 161 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 690 GLN Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 953 ASN Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 313 TYR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 928 ASN Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1142 GLN Chi-restraints excluded: chain F residue 139 GLN Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 481 LYS Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 581 VAL Chi-restraints excluded: chain F residue 609 ASP Chi-restraints excluded: chain F residue 611 SER Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 530 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 379 optimal weight: 0.8980 chunk 253 optimal weight: 9.9990 chunk 226 optimal weight: 0.9990 chunk 442 optimal weight: 20.0000 chunk 283 optimal weight: 0.7980 chunk 415 optimal weight: 40.0000 chunk 141 optimal weight: 6.9990 chunk 207 optimal weight: 7.9990 chunk 50 optimal weight: 10.0000 chunk 126 optimal weight: 8.9990 chunk 16 optimal weight: 20.0000 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 334 ASN B 907 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C1036 GLN F 139 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.103270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.070259 restraints weight = 266901.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.069593 restraints weight = 145564.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.070189 restraints weight = 103685.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.069918 restraints weight = 66132.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.070039 restraints weight = 67621.890| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.6677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 40639 Z= 0.149 Angle : 0.695 18.903 55450 Z= 0.327 Chirality : 0.046 0.666 6350 Planarity : 0.004 0.051 6979 Dihedral : 6.751 59.788 7337 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.76 % Favored : 94.16 % Rotamer: Outliers : 3.21 % Allowed : 23.78 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.12), residues: 4722 helix: 1.25 (0.13), residues: 1648 sheet: -0.74 (0.19), residues: 667 loop : -1.80 (0.12), residues: 2407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 158 TYR 0.023 0.001 TYR C 313 PHE 0.027 0.001 PHE C 133 TRP 0.008 0.001 TRP B1102 HIS 0.005 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00335 (40493) covalent geometry : angle 0.66892 (55054) SS BOND : bond 0.00429 ( 42) SS BOND : angle 1.57490 ( 84) hydrogen bonds : bond 0.03745 ( 1525) hydrogen bonds : angle 4.98194 ( 4398) link_BETA1-4 : bond 0.00461 ( 38) link_BETA1-4 : angle 2.12022 ( 114) link_NAG-ASN : bond 0.00514 ( 66) link_NAG-ASN : angle 2.70034 ( 198) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9444 Ramachandran restraints generated. 4722 Oldfield, 0 Emsley, 4722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9444 Ramachandran restraints generated. 4722 Oldfield, 0 Emsley, 4722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 161 time to evaluate : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8713 (mt) cc_final: 0.8225 (mt) REVERT: A 191 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8100 (tt0) REVERT: A 238 PHE cc_start: 0.8609 (p90) cc_final: 0.8301 (p90) REVERT: A 324 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.7036 (pp20) REVERT: A 731 MET cc_start: 0.8653 (ppp) cc_final: 0.7813 (ppp) REVERT: A 753 LEU cc_start: 0.8217 (tt) cc_final: 0.7921 (mt) REVERT: A 921 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.7881 (pttp) REVERT: A 1029 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.7930 (tpp) REVERT: B 48 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8267 (pp) REVERT: B 332 ILE cc_start: 0.2245 (OUTLIER) cc_final: 0.1809 (tp) REVERT: B 495 TYR cc_start: 0.7428 (m-10) cc_final: 0.6892 (m-80) REVERT: B 611 LEU cc_start: 0.9395 (tp) cc_final: 0.9084 (pp) REVERT: B 654 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7191 (mp0) REVERT: B 690 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7375 (mt0) REVERT: B 753 LEU cc_start: 0.9005 (tt) cc_final: 0.8668 (pp) REVERT: B 755 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.8150 (tp-100) REVERT: B 786 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8130 (pttp) REVERT: B 869 MET cc_start: 0.8408 (mtt) cc_final: 0.8129 (ptp) REVERT: B 959 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.8920 (tt) REVERT: B 992 GLN cc_start: 0.8693 (mm-40) cc_final: 0.8444 (mm-40) REVERT: B 1029 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.7784 (tmm) REVERT: C 104 TRP cc_start: 0.7034 (m-90) cc_final: 0.6833 (m-90) REVERT: C 114 THR cc_start: 0.5957 (OUTLIER) cc_final: 0.5633 (p) REVERT: C 122 ASN cc_start: 0.6334 (OUTLIER) cc_final: 0.5894 (p0) REVERT: C 223 LEU cc_start: 0.8543 (mp) cc_final: 0.7197 (mp) REVERT: C 270 LEU cc_start: 0.9008 (mp) cc_final: 0.8527 (mt) REVERT: C 906 PHE cc_start: 0.8504 (OUTLIER) cc_final: 0.8205 (m-10) REVERT: F 203 TRP cc_start: 0.6274 (OUTLIER) cc_final: 0.6028 (m-10) REVERT: F 270 MET cc_start: -0.2250 (tpp) cc_final: -0.2778 (mmp) REVERT: F 376 MET cc_start: 0.6967 (tmm) cc_final: 0.6765 (ppp) REVERT: F 408 MET cc_start: 0.7373 (pmm) cc_final: 0.6896 (pmm) REVERT: F 579 MET cc_start: 0.7608 (OUTLIER) cc_final: 0.6905 (tpp) REVERT: D 82 MET cc_start: 0.4059 (ppp) cc_final: 0.3655 (ppp) REVERT: D 152 MET cc_start: 0.1725 (tpt) cc_final: 0.0214 (tpt) REVERT: D 249 MET cc_start: 0.4534 (mmm) cc_final: 0.4013 (ptt) REVERT: D 557 MET cc_start: 0.2713 (ppp) cc_final: 0.2384 (ppp) REVERT: D 579 MET cc_start: 0.4766 (mtt) cc_final: 0.1249 (mmm) REVERT: E 140 GLU cc_start: -0.1550 (OUTLIER) cc_final: -0.1795 (tt0) REVERT: E 233 ILE cc_start: -0.3073 (OUTLIER) cc_final: -0.3491 (mt) REVERT: E 332 MET cc_start: 0.6222 (ppp) cc_final: 0.5711 (ppp) REVERT: E 579 MET cc_start: 0.8489 (mtp) cc_final: 0.7724 (mmt) outliers start: 135 outliers final: 97 residues processed: 286 average time/residue: 0.2039 time to fit residues: 103.2994 Evaluate side-chains 273 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 158 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 690 GLN Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 953 ASN Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 313 TYR Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 928 ASN Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1142 GLN Chi-restraints excluded: chain F residue 139 GLN Chi-restraints excluded: chain F residue 203 TRP Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 481 LYS Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 579 MET Chi-restraints excluded: chain F residue 609 ASP Chi-restraints excluded: chain F residue 611 SER Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 530 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 176 optimal weight: 1.9990 chunk 179 optimal weight: 0.1980 chunk 108 optimal weight: 0.0670 chunk 11 optimal weight: 40.0000 chunk 420 optimal weight: 6.9990 chunk 271 optimal weight: 0.5980 chunk 219 optimal weight: 8.9990 chunk 44 optimal weight: 5.9990 chunk 193 optimal weight: 0.8980 chunk 209 optimal weight: 10.0000 chunk 406 optimal weight: 50.0000 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN B 926 GLN C 239 GLN F 139 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.104577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.071631 restraints weight = 266818.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.072170 restraints weight = 140718.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.071752 restraints weight = 101756.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.072185 restraints weight = 73834.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.072103 restraints weight = 61731.559| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.6682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 40639 Z= 0.111 Angle : 0.679 18.707 55450 Z= 0.317 Chirality : 0.046 0.581 6350 Planarity : 0.004 0.058 6979 Dihedral : 6.536 59.923 7337 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.06 % Favored : 94.85 % Rotamer: Outliers : 2.49 % Allowed : 24.39 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.12), residues: 4722 helix: 1.34 (0.13), residues: 1645 sheet: -0.55 (0.18), residues: 682 loop : -1.70 (0.12), residues: 2395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 319 TYR 0.017 0.001 TYR C 313 PHE 0.027 0.001 PHE C 133 TRP 0.014 0.001 TRP A 104 HIS 0.003 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00240 (40493) covalent geometry : angle 0.65405 (55054) SS BOND : bond 0.00342 ( 42) SS BOND : angle 1.41478 ( 84) hydrogen bonds : bond 0.03473 ( 1525) hydrogen bonds : angle 4.86515 ( 4398) link_BETA1-4 : bond 0.00502 ( 38) link_BETA1-4 : angle 2.10021 ( 114) link_NAG-ASN : bond 0.00504 ( 66) link_NAG-ASN : angle 2.60053 ( 198) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9444 Ramachandran restraints generated. 4722 Oldfield, 0 Emsley, 4722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9444 Ramachandran restraints generated. 4722 Oldfield, 0 Emsley, 4722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 166 time to evaluate : 1.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8648 (mt) cc_final: 0.8144 (mt) REVERT: A 191 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7945 (tt0) REVERT: A 238 PHE cc_start: 0.8545 (p90) cc_final: 0.8229 (p90) REVERT: A 324 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.7054 (pp20) REVERT: A 731 MET cc_start: 0.8570 (ppp) cc_final: 0.7767 (ppp) REVERT: A 753 LEU cc_start: 0.8142 (tt) cc_final: 0.7852 (mt) REVERT: A 1029 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.7811 (tpp) REVERT: B 48 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8266 (pp) REVERT: B 332 ILE cc_start: 0.2410 (OUTLIER) cc_final: 0.1982 (tp) REVERT: B 495 TYR cc_start: 0.7475 (m-10) cc_final: 0.7003 (m-80) REVERT: B 611 LEU cc_start: 0.9380 (tp) cc_final: 0.9066 (pp) REVERT: B 654 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7180 (mp0) REVERT: B 690 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.7276 (mt0) REVERT: B 753 LEU cc_start: 0.8944 (tt) cc_final: 0.8599 (pp) REVERT: B 786 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8120 (pttp) REVERT: B 869 MET cc_start: 0.8427 (mtt) cc_final: 0.8191 (ptp) REVERT: B 992 GLN cc_start: 0.8665 (mm-40) cc_final: 0.8433 (mm-40) REVERT: B 1029 MET cc_start: 0.8290 (tmm) cc_final: 0.7762 (tmm) REVERT: C 114 THR cc_start: 0.5776 (OUTLIER) cc_final: 0.5456 (p) REVERT: C 122 ASN cc_start: 0.6259 (OUTLIER) cc_final: 0.5922 (p0) REVERT: C 223 LEU cc_start: 0.8308 (mp) cc_final: 0.6935 (mp) REVERT: C 270 LEU cc_start: 0.8990 (mp) cc_final: 0.8515 (mt) REVERT: C 906 PHE cc_start: 0.8468 (OUTLIER) cc_final: 0.8120 (m-10) REVERT: F 203 TRP cc_start: 0.6252 (OUTLIER) cc_final: 0.6033 (m-10) REVERT: F 270 MET cc_start: -0.3419 (tpp) cc_final: -0.4119 (mmp) REVERT: F 376 MET cc_start: 0.6817 (tmm) cc_final: 0.6606 (ppp) REVERT: F 408 MET cc_start: 0.7202 (pmm) cc_final: 0.6738 (pmm) REVERT: F 474 MET cc_start: -0.0133 (mmp) cc_final: -0.0348 (mmp) REVERT: F 579 MET cc_start: 0.7533 (OUTLIER) cc_final: 0.6835 (tpp) REVERT: D 82 MET cc_start: 0.4193 (ppp) cc_final: 0.3794 (ppp) REVERT: D 152 MET cc_start: 0.1555 (tpt) cc_final: 0.1027 (tpt) REVERT: D 249 MET cc_start: 0.4884 (mmm) cc_final: 0.4319 (ptt) REVERT: D 474 MET cc_start: 0.4155 (mmm) cc_final: 0.3506 (mmm) REVERT: D 557 MET cc_start: 0.2412 (ppp) cc_final: 0.2066 (ppp) REVERT: E 140 GLU cc_start: -0.1554 (OUTLIER) cc_final: -0.1800 (tt0) REVERT: E 233 ILE cc_start: -0.3156 (OUTLIER) cc_final: -0.3564 (mt) REVERT: E 332 MET cc_start: 0.6202 (ppp) cc_final: 0.5403 (ppp) REVERT: E 579 MET cc_start: 0.8405 (mtp) cc_final: 0.7613 (mmt) outliers start: 105 outliers final: 81 residues processed: 262 average time/residue: 0.2115 time to fit residues: 98.0729 Evaluate side-chains 256 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 161 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1023 ASN Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 690 GLN Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 953 ASN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain F residue 139 GLN Chi-restraints excluded: chain F residue 203 TRP Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 481 LYS Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 579 MET Chi-restraints excluded: chain F residue 609 ASP Chi-restraints excluded: chain F residue 611 SER Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 530 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 218 optimal weight: 5.9990 chunk 384 optimal weight: 4.9990 chunk 28 optimal weight: 30.0000 chunk 210 optimal weight: 20.0000 chunk 184 optimal weight: 8.9990 chunk 266 optimal weight: 1.9990 chunk 293 optimal weight: 9.9990 chunk 133 optimal weight: 50.0000 chunk 453 optimal weight: 50.0000 chunk 363 optimal weight: 40.0000 chunk 50 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 856 ASN B 613 GLN B 919 ASN B 926 GLN C 901 GLN F 139 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.101903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.067586 restraints weight = 269224.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.067470 restraints weight = 141154.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.067186 restraints weight = 94755.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.067736 restraints weight = 68492.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.067710 restraints weight = 52782.671| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.7056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 40639 Z= 0.229 Angle : 0.753 19.169 55450 Z= 0.359 Chirality : 0.048 0.751 6350 Planarity : 0.004 0.069 6979 Dihedral : 6.809 59.812 7335 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.59 % Favored : 93.33 % Rotamer: Outliers : 3.14 % Allowed : 23.68 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.12), residues: 4722 helix: 1.18 (0.13), residues: 1635 sheet: -0.67 (0.19), residues: 673 loop : -1.76 (0.12), residues: 2414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 158 TYR 0.035 0.002 TYR C 313 PHE 0.038 0.002 PHE C 133 TRP 0.013 0.001 TRP A 886 HIS 0.008 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00515 (40493) covalent geometry : angle 0.72668 (55054) SS BOND : bond 0.00487 ( 42) SS BOND : angle 1.77453 ( 84) hydrogen bonds : bond 0.04117 ( 1525) hydrogen bonds : angle 5.16451 ( 4398) link_BETA1-4 : bond 0.00450 ( 38) link_BETA1-4 : angle 2.15876 ( 114) link_NAG-ASN : bond 0.00657 ( 66) link_NAG-ASN : angle 2.79920 ( 198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11250.26 seconds wall clock time: 193 minutes 26.33 seconds (11606.33 seconds total)