Starting phenix.real_space_refine on Fri Mar 6 23:30:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6v8z_21112/03_2026/6v8z_21112_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v8z_21112/03_2026/6v8z_21112.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6v8z_21112/03_2026/6v8z_21112_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v8z_21112/03_2026/6v8z_21112_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6v8z_21112/03_2026/6v8z_21112.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v8z_21112/03_2026/6v8z_21112.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.169 sd= 1.863 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 189 5.16 5 C 22539 2.51 5 N 5988 2.21 5 O 7161 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35877 Number of models: 1 Model: "" Number of chains: 60 Chain: "A" Number of atoms: 3534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3534 Classifications: {'peptide': 449} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 425} Chain breaks: 3 Chain: "B" Number of atoms: 1171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1171 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 2, 'TRANS': 144} Chain: "D" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1753 Classifications: {'peptide': 230} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 215} Chain breaks: 1 Chain: "E" Number of atoms: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1607 Classifications: {'peptide': 211} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 193} Chain: "C" Number of atoms: 1739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1739 Classifications: {'peptide': 227} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 14, 'TRANS': 208} Chain breaks: 1 Chain: "F" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1622 Classifications: {'peptide': 208} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 198} Chain: "G" Number of atoms: 3534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3534 Classifications: {'peptide': 449} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 425} Chain breaks: 3 Chain: "H" Number of atoms: 1171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1171 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 2, 'TRANS': 144} Chain: "J" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1753 Classifications: {'peptide': 230} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 215} Chain breaks: 1 Chain: "K" Number of atoms: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1607 Classifications: {'peptide': 211} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 193} Chain: "I" Number of atoms: 1739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1739 Classifications: {'peptide': 227} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 14, 'TRANS': 208} Chain breaks: 1 Chain: "L" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1622 Classifications: {'peptide': 208} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 198} Chain: "M" Number of atoms: 3534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3534 Classifications: {'peptide': 449} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 425} Chain breaks: 3 Chain: "N" Number of atoms: 1171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1171 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 2, 'TRANS': 144} Chain: "P" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1753 Classifications: {'peptide': 230} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 215} Chain breaks: 1 Chain: "Q" Number of atoms: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1607 Classifications: {'peptide': 211} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 193} Chain: "O" Number of atoms: 1739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1739 Classifications: {'peptide': 227} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 14, 'TRANS': 208} Chain breaks: 1 Chain: "R" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1622 Classifications: {'peptide': 208} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 198} 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} 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: "a" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "g" Number of atoms: 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: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} 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: "m" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} 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: "y" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: "0" 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: "1" 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "H" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "N" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 8.45, per 1000 atoms: 0.24 Number of scatterers: 35877 At special positions: 0 Unit cell: (207.959, 198.211, 177.632, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 189 16.00 O 7161 8.00 N 5988 7.00 C 22539 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=63, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=1.84 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=1.73 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.13 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.32 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=1.67 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.12 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.27 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.25 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.32 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.00 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.07 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.34 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 191 " distance=2.07 Simple disulfide: pdb=" SG CYS D 211 " - pdb=" SG CYS E 212 " distance=2.27 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=1.99 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 194 " distance=2.47 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.08 Simple disulfide: pdb=" SG CYS C 98 " - pdb=" SG CYS C 100A" distance=1.99 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 192 " distance=2.20 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.30 Simple disulfide: pdb=" SG CYS F 134 " - pdb=" SG CYS F 194 " distance=1.99 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=1.84 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=1.73 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.13 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.32 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=1.67 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.12 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.27 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.25 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.32 Simple disulfide: pdb=" SG CYS G 501 " - pdb=" SG CYS H 605 " distance=2.00 Simple disulfide: pdb=" SG CYS H 598 " - pdb=" SG CYS H 604 " distance=2.07 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.34 Simple disulfide: pdb=" SG CYS J 135 " - pdb=" SG CYS J 191 " distance=2.07 Simple disulfide: pdb=" SG CYS J 211 " - pdb=" SG CYS K 212 " distance=2.27 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=1.99 Simple disulfide: pdb=" SG CYS K 135 " - pdb=" SG CYS K 194 " distance=2.47 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.08 Simple disulfide: pdb=" SG CYS I 98 " - pdb=" SG CYS I 100A" distance=1.99 Simple disulfide: pdb=" SG CYS I 136 " - pdb=" SG CYS I 192 " distance=2.20 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.30 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=1.99 Simple disulfide: pdb=" SG CYS M 54 " - pdb=" SG CYS M 74 " distance=1.84 Simple disulfide: pdb=" SG CYS M 119 " - pdb=" SG CYS M 205 " distance=1.73 Simple disulfide: pdb=" SG CYS M 126 " - pdb=" SG CYS M 196 " distance=2.13 Simple disulfide: pdb=" SG CYS M 131 " - pdb=" SG CYS M 157 " distance=2.32 Simple disulfide: pdb=" SG CYS M 218 " - pdb=" SG CYS M 247 " distance=1.67 Simple disulfide: pdb=" SG CYS M 228 " - pdb=" SG CYS M 239 " distance=2.12 Simple disulfide: pdb=" SG CYS M 296 " - pdb=" SG CYS M 331 " distance=2.27 Simple disulfide: pdb=" SG CYS M 378 " - pdb=" SG CYS M 445 " distance=2.25 Simple disulfide: pdb=" SG CYS M 385 " - pdb=" SG CYS M 418 " distance=2.32 Simple disulfide: pdb=" SG CYS M 501 " - pdb=" SG CYS N 605 " distance=2.00 Simple disulfide: pdb=" SG CYS N 598 " - pdb=" SG CYS N 604 " distance=2.07 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " distance=2.34 Simple disulfide: pdb=" SG CYS P 135 " - pdb=" SG CYS P 191 " distance=2.07 Simple disulfide: pdb=" SG CYS P 211 " - pdb=" SG CYS Q 212 " distance=2.27 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=1.99 Simple disulfide: pdb=" SG CYS Q 135 " - pdb=" SG CYS Q 194 " distance=2.47 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.08 Simple disulfide: pdb=" SG CYS O 98 " - pdb=" SG CYS O 100A" distance=1.99 Simple disulfide: pdb=" SG CYS O 136 " - pdb=" SG CYS O 192 " distance=2.20 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.30 Simple disulfide: pdb=" SG CYS R 134 " - pdb=" SG CYS R 194 " distance=1.99 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN Z 4 " - " MAN Z 5 " " MAN Z 5 " - " MAN Z 6 " " MAN l 4 " - " MAN l 5 " " MAN l 5 " - " MAN l 6 " " MAN x 4 " - " MAN x 5 " " MAN x 5 " - " MAN x 6 " ALPHA1-3 " BMA Z 3 " - " MAN Z 4 " " BMA a 3 " - " MAN a 4 " " BMA l 3 " - " MAN l 4 " " BMA m 3 " - " MAN m 4 " " BMA x 3 " - " MAN x 4 " " BMA y 3 " - " MAN y 4 " ALPHA1-6 " BMA Z 3 " - " MAN Z 7 " " MAN Z 7 " - " MAN Z 8 " " BMA l 3 " - " MAN l 7 " " MAN l 7 " - " MAN l 8 " " BMA x 3 " - " MAN x 7 " " MAN x 7 " - " MAN x 8 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " 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 l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " NAG-ASN " NAG 0 1 " - " ASN M 156 " " NAG 1 1 " - " ASN M 133 " " NAG A 603 " - " ASN A 276 " " NAG A 607 " - " ASN A 355 " " NAG A 608 " - " ASN A 339 " " NAG A 609 " - " ASN A 392 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 611 " " NAG B 703 " - " ASN B 618 " " NAG G 603 " - " ASN G 276 " " NAG G 607 " - " ASN G 355 " " NAG G 608 " - " ASN G 339 " " NAG G 609 " - " ASN G 392 " " NAG H 701 " - " ASN H 637 " " NAG H 702 " - " ASN H 611 " " NAG H 703 " - " ASN H 618 " " NAG M 603 " - " ASN M 276 " " NAG M 607 " - " ASN M 355 " " NAG M 608 " - " ASN M 339 " " NAG M 609 " - " ASN M 392 " " NAG N 701 " - " ASN N 637 " " NAG N 702 " - " ASN N 611 " " NAG N 703 " - " ASN N 618 " " NAG S 1 " - " ASN A 88 " " NAG T 1 " - " ASN A 234 " " NAG U 1 " - " ASN A 363 " " NAG V 1 " - " ASN A 386 " " NAG W 1 " - " ASN A 448 " " NAG X 1 " - " ASN A 295 " " NAG Y 1 " - " ASN A 301 " " NAG Z 1 " - " ASN A 332 " " NAG a 1 " - " ASN A 262 " " NAG b 1 " - " ASN A 197 " " NAG c 1 " - " ASN A 156 " " NAG d 1 " - " ASN A 133 " " NAG e 1 " - " ASN G 88 " " NAG f 1 " - " ASN G 234 " " NAG g 1 " - " ASN G 363 " " NAG h 1 " - " ASN G 386 " " NAG i 1 " - " ASN G 448 " " NAG j 1 " - " ASN G 295 " " NAG k 1 " - " ASN G 301 " " NAG l 1 " - " ASN G 332 " " NAG m 1 " - " ASN G 262 " " NAG n 1 " - " ASN G 197 " " NAG o 1 " - " ASN G 156 " " NAG p 1 " - " ASN G 133 " " NAG q 1 " - " ASN M 88 " " NAG r 1 " - " ASN M 234 " " NAG s 1 " - " ASN M 363 " " NAG t 1 " - " ASN M 386 " " NAG u 1 " - " ASN M 448 " " NAG v 1 " - " ASN M 295 " " NAG w 1 " - " ASN M 301 " " NAG x 1 " - " ASN M 332 " " NAG y 1 " - " ASN M 262 " " NAG z 1 " - " ASN M 197 " Time building additional restraints: 3.47 Conformation dependent library (CDL) restraints added in 1.4 seconds 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8202 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 105 sheets defined 13.0% alpha, 37.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.91 Creating SS restraints... Processing helix chain 'A' and resid 99 through 116 removed outlier: 3.860A pdb=" N THR A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE A 109 " --> pdb=" O HIS A 105 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.587A pdb=" N GLY A 343 " --> pdb=" O ASN A 339 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS A 344 " --> pdb=" O GLU A 340 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL A 345 " --> pdb=" O THR A 341 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS A 347 " --> pdb=" O GLY A 343 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.824A pdb=" N THR A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 480 removed outlier: 3.596A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 527 removed outlier: 4.535A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 546 removed outlier: 3.894A pdb=" N LEU B 544 " --> pdb=" O GLN B 540 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 555 removed outlier: 3.652A pdb=" N GLN B 550 " --> pdb=" O GLY B 547 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN B 552 " --> pdb=" O VAL B 549 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N SER B 553 " --> pdb=" O GLN B 550 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU B 555 " --> pdb=" O GLN B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 585 removed outlier: 3.672A pdb=" N GLY B 572 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE B 573 " --> pdb=" O THR B 569 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ALA B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG B 579 " --> pdb=" O GLN B 575 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA B 582 " --> pdb=" O ALA B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 596 removed outlier: 3.662A pdb=" N LEU B 592 " --> pdb=" O ARG B 588 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU B 593 " --> pdb=" O ASP B 589 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY B 594 " --> pdb=" O GLN B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.630A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 647 removed outlier: 3.604A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B 645 " --> pdb=" O ILE B 641 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU B 646 " --> pdb=" O ILE B 642 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 655 Processing helix chain 'B' and resid 656 through 664 removed outlier: 3.954A pdb=" N LEU B 663 " --> pdb=" O ASP B 659 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.550A pdb=" N TYR D 32 " --> pdb=" O MET D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.510A pdb=" N THR D 87 " --> pdb=" O PRO D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 185 removed outlier: 3.674A pdb=" N GLY D 185 " --> pdb=" O SER D 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 removed outlier: 4.098A pdb=" N GLU E 83 " --> pdb=" O ALA E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 187 removed outlier: 3.870A pdb=" N LYS E 187 " --> pdb=" O PRO E 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'C' and resid 183 through 187 removed outlier: 3.582A pdb=" N GLY C 186 " --> pdb=" O SER C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 200 Processing helix chain 'F' and resid 121 through 126 Processing helix chain 'F' and resid 183 through 187 removed outlier: 3.971A pdb=" N GLU F 187 " --> pdb=" O LYS F 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 183 through 187' Processing helix chain 'G' and resid 99 through 116 removed outlier: 3.859A pdb=" N THR G 106 " --> pdb=" O GLU G 102 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE G 109 " --> pdb=" O HIS G 105 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER G 115 " --> pdb=" O LEU G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 354 removed outlier: 3.586A pdb=" N GLY G 343 " --> pdb=" O ASN G 339 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS G 344 " --> pdb=" O GLU G 340 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL G 345 " --> pdb=" O THR G 341 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS G 347 " --> pdb=" O GLY G 343 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LYS G 351 " --> pdb=" O LYS G 347 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N HIS G 352 " --> pdb=" O GLN G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.825A pdb=" N THR G 373 " --> pdb=" O LEU G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 480 removed outlier: 3.597A pdb=" N TRP G 479 " --> pdb=" O MET G 475 " (cutoff:3.500A) Processing helix chain 'H' and resid 523 through 527 removed outlier: 4.535A pdb=" N GLY H 527 " --> pdb=" O GLY H 524 " (cutoff:3.500A) Processing helix chain 'H' and resid 538 through 546 removed outlier: 3.894A pdb=" N LEU H 544 " --> pdb=" O GLN H 540 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU H 545 " --> pdb=" O ALA H 541 " (cutoff:3.500A) Processing helix chain 'H' and resid 547 through 555 removed outlier: 3.652A pdb=" N GLN H 550 " --> pdb=" O GLY H 547 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN H 552 " --> pdb=" O VAL H 549 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N SER H 553 " --> pdb=" O GLN H 550 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU H 555 " --> pdb=" O GLN H 552 " (cutoff:3.500A) Processing helix chain 'H' and resid 566 through 585 removed outlier: 3.671A pdb=" N GLY H 572 " --> pdb=" O LEU H 568 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE H 573 " --> pdb=" O THR H 569 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LYS H 574 " --> pdb=" O VAL H 570 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN H 575 " --> pdb=" O TRP H 571 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ALA H 578 " --> pdb=" O LYS H 574 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG H 579 " --> pdb=" O GLN H 575 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA H 582 " --> pdb=" O ALA H 578 " (cutoff:3.500A) Processing helix chain 'H' and resid 586 through 596 removed outlier: 3.662A pdb=" N LEU H 592 " --> pdb=" O ARG H 588 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU H 593 " --> pdb=" O ASP H 589 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY H 594 " --> pdb=" O GLN H 590 " (cutoff:3.500A) Processing helix chain 'H' and resid 627 through 636 removed outlier: 3.630A pdb=" N GLU H 634 " --> pdb=" O GLN H 630 " (cutoff:3.500A) Processing helix chain 'H' and resid 638 through 647 removed outlier: 3.603A pdb=" N GLY H 644 " --> pdb=" O GLN H 640 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU H 645 " --> pdb=" O ILE H 641 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU H 646 " --> pdb=" O ILE H 642 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU H 647 " --> pdb=" O TYR H 643 " (cutoff:3.500A) Processing helix chain 'H' and resid 650 through 655 Processing helix chain 'H' and resid 656 through 664 removed outlier: 3.954A pdb=" N LEU H 663 " --> pdb=" O ASP H 659 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.550A pdb=" N TYR J 32 " --> pdb=" O MET J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 87 removed outlier: 3.510A pdb=" N THR J 87 " --> pdb=" O PRO J 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 180 through 185 removed outlier: 3.674A pdb=" N GLY J 185 " --> pdb=" O SER J 181 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 removed outlier: 4.098A pdb=" N GLU K 83 " --> pdb=" O ALA K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 182 through 187 removed outlier: 3.870A pdb=" N LYS K 187 " --> pdb=" O PRO K 183 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'I' and resid 183 through 187 removed outlier: 3.583A pdb=" N GLY I 186 " --> pdb=" O SER I 183 " (cutoff:3.500A) Processing helix chain 'I' and resid 197 through 200 Processing helix chain 'L' and resid 121 through 126 Processing helix chain 'L' and resid 183 through 187 removed outlier: 3.971A pdb=" N GLU L 187 " --> pdb=" O LYS L 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 183 through 187' Processing helix chain 'M' and resid 99 through 116 removed outlier: 3.859A pdb=" N THR M 106 " --> pdb=" O GLU M 102 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE M 109 " --> pdb=" O HIS M 105 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER M 115 " --> pdb=" O LEU M 111 " (cutoff:3.500A) Processing helix chain 'M' and resid 335 through 354 removed outlier: 3.587A pdb=" N GLY M 343 " --> pdb=" O ASN M 339 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS M 344 " --> pdb=" O GLU M 340 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL M 345 " --> pdb=" O THR M 341 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS M 347 " --> pdb=" O GLY M 343 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LYS M 351 " --> pdb=" O LYS M 347 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N HIS M 352 " --> pdb=" O GLN M 348 " (cutoff:3.500A) Processing helix chain 'M' and resid 368 through 373 removed outlier: 3.825A pdb=" N THR M 373 " --> pdb=" O LEU M 369 " (cutoff:3.500A) Processing helix chain 'M' and resid 475 through 480 removed outlier: 3.596A pdb=" N TRP M 479 " --> pdb=" O MET M 475 " (cutoff:3.500A) Processing helix chain 'N' and resid 523 through 527 removed outlier: 4.536A pdb=" N GLY N 527 " --> pdb=" O GLY N 524 " (cutoff:3.500A) Processing helix chain 'N' and resid 538 through 546 removed outlier: 3.894A pdb=" N LEU N 544 " --> pdb=" O GLN N 540 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU N 545 " --> pdb=" O ALA N 541 " (cutoff:3.500A) Processing helix chain 'N' and resid 547 through 555 removed outlier: 3.652A pdb=" N GLN N 550 " --> pdb=" O GLY N 547 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN N 552 " --> pdb=" O VAL N 549 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N SER N 553 " --> pdb=" O GLN N 550 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU N 555 " --> pdb=" O GLN N 552 " (cutoff:3.500A) Processing helix chain 'N' and resid 566 through 585 removed outlier: 3.671A pdb=" N GLY N 572 " --> pdb=" O LEU N 568 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE N 573 " --> pdb=" O THR N 569 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS N 574 " --> pdb=" O VAL N 570 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN N 575 " --> pdb=" O TRP N 571 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ALA N 578 " --> pdb=" O LYS N 574 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG N 579 " --> pdb=" O GLN N 575 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA N 582 " --> pdb=" O ALA N 578 " (cutoff:3.500A) Processing helix chain 'N' and resid 586 through 596 removed outlier: 3.662A pdb=" N LEU N 592 " --> pdb=" O ARG N 588 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU N 593 " --> pdb=" O ASP N 589 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY N 594 " --> pdb=" O GLN N 590 " (cutoff:3.500A) Processing helix chain 'N' and resid 627 through 636 removed outlier: 3.630A pdb=" N GLU N 634 " --> pdb=" O GLN N 630 " (cutoff:3.500A) Processing helix chain 'N' and resid 638 through 647 removed outlier: 3.603A pdb=" N GLY N 644 " --> pdb=" O GLN N 640 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU N 645 " --> pdb=" O ILE N 641 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU N 646 " --> pdb=" O ILE N 642 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU N 647 " --> pdb=" O TYR N 643 " (cutoff:3.500A) Processing helix chain 'N' and resid 650 through 655 Processing helix chain 'N' and resid 656 through 664 removed outlier: 3.954A pdb=" N LEU N 663 " --> pdb=" O ASP N 659 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 32 removed outlier: 3.551A pdb=" N TYR P 32 " --> pdb=" O MET P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 83 through 87 removed outlier: 3.510A pdb=" N THR P 87 " --> pdb=" O PRO P 84 " (cutoff:3.500A) Processing helix chain 'P' and resid 180 through 185 removed outlier: 3.675A pdb=" N GLY P 185 " --> pdb=" O SER P 181 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 83 removed outlier: 4.097A pdb=" N GLU Q 83 " --> pdb=" O ALA Q 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 182 through 187 removed outlier: 3.870A pdb=" N LYS Q 187 " --> pdb=" O PRO Q 183 " (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'O' and resid 183 through 187 removed outlier: 3.582A pdb=" N GLY O 186 " --> pdb=" O SER O 183 " (cutoff:3.500A) Processing helix chain 'O' and resid 197 through 200 Processing helix chain 'R' and resid 121 through 126 Processing helix chain 'R' and resid 183 through 187 removed outlier: 3.972A pdb=" N GLU R 187 " --> pdb=" O LYS R 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 183 through 187' Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 6.676A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.773A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.560A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 129 through 130 Processing sheet with id=AA5, first strand: chain 'A' and resid 132 through 133 removed outlier: 3.883A pdb=" N SER A 174 " --> pdb=" O CYS A 157 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 200 through 201 removed outlier: 4.103A pdb=" N ALA A 433 " --> pdb=" O ALA A 200 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 4.937A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 273 removed outlier: 3.690A pdb=" N SER A 393 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 302 through 304 removed outlier: 6.969A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY A 321 " --> pdb=" O THR A 303 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 307 through 312 removed outlier: 5.064A pdb=" N ARG A 308 " --> pdb=" O PHE A 317 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N PHE A 317 " --> pdb=" O ARG A 308 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AB3, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.560A pdb=" N VAL D 109 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA D 88 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N TRP D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TYR D 50 " --> pdb=" O TRP D 34 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.560A pdb=" N VAL D 109 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA D 88 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N CYS D 92 " --> pdb=" O TRP D 103 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N TRP D 103 " --> pdb=" O CYS D 92 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N THR D 94 " --> pdb=" O ASP D 101 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP D 101 " --> pdb=" O THR D 94 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER D 100O" --> pdb=" O ARG D 96 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 120 through 124 removed outlier: 3.760A pdb=" N GLY D 134 " --> pdb=" O LEU D 124 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL D 179 " --> pdb=" O ALA D 131 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N CYS D 135 " --> pdb=" O SER D 175 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP D 139 " --> pdb=" O TYR D 171 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N TYR D 171 " --> pdb=" O ASP D 139 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 120 through 124 removed outlier: 3.760A pdb=" N GLY D 134 " --> pdb=" O LEU D 124 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL D 179 " --> pdb=" O ALA D 131 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N CYS D 135 " --> pdb=" O SER D 175 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP D 139 " --> pdb=" O TYR D 171 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N TYR D 171 " --> pdb=" O ASP D 139 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 146 through 149 removed outlier: 4.050A pdb=" N THR D 146 " --> pdb=" O ASN D 194 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS D 204 " --> pdb=" O CYS D 191 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL D 202 " --> pdb=" O VAL D 193 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 6 through 14 removed outlier: 7.061A pdb=" N ARG E 6 " --> pdb=" O ARG E 103 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N THR E 105 " --> pdb=" O ARG E 6 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N LEU E 11 " --> pdb=" O THR E 105 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N LEU E 106A" --> pdb=" O LEU E 11 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL E 13 " --> pdb=" O LEU E 106A" (cutoff:3.500A) removed outlier: 4.297A pdb=" N THR E 102 " --> pdb=" O TYR E 86 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 19 through 22 removed outlier: 3.525A pdb=" N SER E 63 " --> pdb=" O THR E 74 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 44 through 48 removed outlier: 6.556A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TRP E 91 " --> pdb=" O ALA E 32 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 115 through 119 removed outlier: 4.046A pdb=" N SER E 115 " --> pdb=" O SER E 138 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N SER E 138 " --> pdb=" O SER E 115 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU E 136 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL E 134 " --> pdb=" O PHE E 119 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N CYS E 135 " --> pdb=" O SER E 177 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER E 177 " --> pdb=" O CYS E 135 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 115 through 119 removed outlier: 4.046A pdb=" N SER E 115 " --> pdb=" O SER E 138 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N SER E 138 " --> pdb=" O SER E 115 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU E 136 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL E 134 " --> pdb=" O PHE E 119 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N CYS E 135 " --> pdb=" O SER E 177 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER E 177 " --> pdb=" O CYS E 135 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER E 166 " --> pdb=" O ALA E 174 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 146 through 150 removed outlier: 3.634A pdb=" N THR E 146 " --> pdb=" O THR E 197 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS E 150 " --> pdb=" O SER E 193 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR E 192 " --> pdb=" O VAL E 207 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.690A pdb=" N VAL C 18 " --> pdb=" O PHE C 82 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.690A pdb=" N VAL C 18 " --> pdb=" O PHE C 82 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.618A pdb=" N ALA C 88 " --> pdb=" O VAL C 109 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU C 89 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ILE C 40 " --> pdb=" O PHE C 45 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N PHE C 45 " --> pdb=" O ILE C 40 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.618A pdb=" N ALA C 88 " --> pdb=" O VAL C 109 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 122 through 124 removed outlier: 5.990A pdb=" N TYR C 172 " --> pdb=" O ASP C 140 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 122 through 124 removed outlier: 5.990A pdb=" N TYR C 172 " --> pdb=" O ASP C 140 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N LEU C 171 " --> pdb=" O GLN C 167 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLN C 167 " --> pdb=" O LEU C 171 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 149 through 150 removed outlier: 3.819A pdb=" N LYS C 205 " --> pdb=" O CYS C 192 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL C 203 " --> pdb=" O VAL C 194 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 5 through 7 removed outlier: 3.521A pdb=" N SER F 7 " --> pdb=" O PHE F 22 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER F 65 " --> pdb=" O PHE F 72 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR F 74 " --> pdb=" O VAL F 63 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.594A pdb=" N GLU F 105 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU F 13 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.594A pdb=" N GLU F 105 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU F 13 " --> pdb=" O GLU F 105 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 116 through 118 removed outlier: 4.051A pdb=" N LEU F 135 " --> pdb=" O PHE F 116 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL F 133 " --> pdb=" O PHE F 118 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N LEU F 135 " --> pdb=" O SER F 177 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N SER F 177 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N ASN F 137 " --> pdb=" O LEU F 175 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N LEU F 175 " --> pdb=" O ASN F 137 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 129 through 130 removed outlier: 3.984A pdb=" N ALA F 130 " --> pdb=" O LEU F 181 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU F 181 " --> pdb=" O ALA F 130 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'F' and resid 147 through 150 Processing sheet with id=AD9, first strand: chain 'G' and resid 494 through 499 removed outlier: 6.676A pdb=" N VAL G 36 " --> pdb=" O THR H 606 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.774A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 91 through 94 removed outlier: 3.560A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 129 through 130 Processing sheet with id=AE4, first strand: chain 'G' and resid 132 through 133 removed outlier: 3.882A pdb=" N SER G 174 " --> pdb=" O CYS G 157 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 200 through 201 removed outlier: 4.103A pdb=" N ALA G 433 " --> pdb=" O ALA G 200 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'G' and resid 259 through 261 removed outlier: 4.937A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE G 443 " --> pdb=" O ARG G 298 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 271 through 273 removed outlier: 3.690A pdb=" N SER G 393 " --> pdb=" O PHE G 361 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 302 through 304 removed outlier: 6.969A pdb=" N THR G 303 " --> pdb=" O GLY G 321 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY G 321 " --> pdb=" O THR G 303 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'G' and resid 307 through 312 removed outlier: 5.063A pdb=" N ARG G 308 " --> pdb=" O PHE G 317 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N PHE G 317 " --> pdb=" O ARG G 308 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 4 through 6 Processing sheet with id=AF2, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.561A pdb=" N VAL J 109 " --> pdb=" O ALA J 88 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA J 88 " --> pdb=" O VAL J 109 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N TRP J 34 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TYR J 50 " --> pdb=" O TRP J 34 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.561A pdb=" N VAL J 109 " --> pdb=" O ALA J 88 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA J 88 " --> pdb=" O VAL J 109 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N CYS J 92 " --> pdb=" O TRP J 103 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N TRP J 103 " --> pdb=" O CYS J 92 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N THR J 94 " --> pdb=" O ASP J 101 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP J 101 " --> pdb=" O THR J 94 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER J 100O" --> pdb=" O ARG J 96 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 120 through 124 removed outlier: 3.761A pdb=" N GLY J 134 " --> pdb=" O LEU J 124 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL J 179 " --> pdb=" O ALA J 131 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N CYS J 135 " --> pdb=" O SER J 175 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP J 139 " --> pdb=" O TYR J 171 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N TYR J 171 " --> pdb=" O ASP J 139 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 120 through 124 removed outlier: 3.761A pdb=" N GLY J 134 " --> pdb=" O LEU J 124 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL J 179 " --> pdb=" O ALA J 131 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N CYS J 135 " --> pdb=" O SER J 175 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP J 139 " --> pdb=" O TYR J 171 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N TYR J 171 " --> pdb=" O ASP J 139 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 146 through 149 removed outlier: 4.050A pdb=" N THR J 146 " --> pdb=" O ASN J 194 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS J 204 " --> pdb=" O CYS J 191 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL J 202 " --> pdb=" O VAL J 193 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 6 through 14 removed outlier: 7.061A pdb=" N ARG K 6 " --> pdb=" O ARG K 103 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N THR K 105 " --> pdb=" O ARG K 6 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N LEU K 11 " --> pdb=" O THR K 105 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N LEU K 106A" --> pdb=" O LEU K 11 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL K 13 " --> pdb=" O LEU K 106A" (cutoff:3.500A) removed outlier: 4.296A pdb=" N THR K 102 " --> pdb=" O TYR K 86 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 19 through 22 removed outlier: 3.526A pdb=" N SER K 63 " --> pdb=" O THR K 74 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K' and resid 44 through 48 removed outlier: 6.556A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N TRP K 91 " --> pdb=" O ALA K 32 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 115 through 119 removed outlier: 4.045A pdb=" N SER K 115 " --> pdb=" O SER K 138 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N SER K 138 " --> pdb=" O SER K 115 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU K 136 " --> pdb=" O THR K 117 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL K 134 " --> pdb=" O PHE K 119 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N CYS K 135 " --> pdb=" O SER K 177 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER K 177 " --> pdb=" O CYS K 135 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 115 through 119 removed outlier: 4.045A pdb=" N SER K 115 " --> pdb=" O SER K 138 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N SER K 138 " --> pdb=" O SER K 115 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU K 136 " --> pdb=" O THR K 117 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL K 134 " --> pdb=" O PHE K 119 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N CYS K 135 " --> pdb=" O SER K 177 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER K 177 " --> pdb=" O CYS K 135 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER K 166 " --> pdb=" O ALA K 174 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'K' and resid 146 through 150 removed outlier: 3.634A pdb=" N THR K 146 " --> pdb=" O THR K 197 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS K 150 " --> pdb=" O SER K 193 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR K 192 " --> pdb=" O VAL K 207 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.689A pdb=" N VAL I 18 " --> pdb=" O PHE I 82 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.689A pdb=" N VAL I 18 " --> pdb=" O PHE I 82 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.618A pdb=" N ALA I 88 " --> pdb=" O VAL I 109 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU I 89 " --> pdb=" O LEU I 39 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ILE I 40 " --> pdb=" O PHE I 45 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N PHE I 45 " --> pdb=" O ILE I 40 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.618A pdb=" N ALA I 88 " --> pdb=" O VAL I 109 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'I' and resid 122 through 124 removed outlier: 5.990A pdb=" N TYR I 172 " --> pdb=" O ASP I 140 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'I' and resid 122 through 124 removed outlier: 5.990A pdb=" N TYR I 172 " --> pdb=" O ASP I 140 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N LEU I 171 " --> pdb=" O GLN I 167 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLN I 167 " --> pdb=" O LEU I 171 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'I' and resid 149 through 150 removed outlier: 3.819A pdb=" N LYS I 205 " --> pdb=" O CYS I 192 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL I 203 " --> pdb=" O VAL I 194 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.521A pdb=" N SER L 7 " --> pdb=" O PHE L 22 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER L 65 " --> pdb=" O PHE L 72 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR L 74 " --> pdb=" O VAL L 63 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.594A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU L 13 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.594A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU L 13 " --> pdb=" O GLU L 105 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'L' and resid 116 through 118 removed outlier: 4.051A pdb=" N LEU L 135 " --> pdb=" O PHE L 116 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LEU L 135 " --> pdb=" O SER L 177 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N SER L 177 " --> pdb=" O LEU L 135 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N ASN L 137 " --> pdb=" O LEU L 175 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LEU L 175 " --> pdb=" O ASN L 137 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'L' and resid 129 through 130 removed outlier: 3.983A pdb=" N ALA L 130 " --> pdb=" O LEU L 181 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU L 181 " --> pdb=" O ALA L 130 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH6 Processing sheet with id=AH7, first strand: chain 'L' and resid 147 through 150 Processing sheet with id=AH8, first strand: chain 'M' and resid 494 through 499 removed outlier: 6.676A pdb=" N VAL M 36 " --> pdb=" O THR N 606 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'M' and resid 45 through 47 removed outlier: 3.773A pdb=" N ILE M 225 " --> pdb=" O VAL M 245 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'M' and resid 91 through 94 removed outlier: 3.561A pdb=" N GLU M 91 " --> pdb=" O CYS M 239 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'M' and resid 129 through 130 Processing sheet with id=AI3, first strand: chain 'M' and resid 132 through 133 removed outlier: 3.883A pdb=" N SER M 174 " --> pdb=" O CYS M 157 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'M' and resid 200 through 201 removed outlier: 4.103A pdb=" N ALA M 433 " --> pdb=" O ALA M 200 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI4 Processing sheet with id=AI5, first strand: chain 'M' and resid 259 through 261 removed outlier: 4.937A pdb=" N LEU M 260 " --> pdb=" O THR M 450 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE M 443 " --> pdb=" O ARG M 298 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N GLN M 293 " --> pdb=" O SER M 334 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N SER M 334 " --> pdb=" O GLN M 293 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'M' and resid 271 through 273 removed outlier: 3.691A pdb=" N SER M 393 " --> pdb=" O PHE M 361 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'M' and resid 302 through 304 removed outlier: 6.969A pdb=" N THR M 303 " --> pdb=" O GLY M 321 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY M 321 " --> pdb=" O THR M 303 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI7 Processing sheet with id=AI8, first strand: chain 'M' and resid 307 through 312 removed outlier: 5.064A pdb=" N ARG M 308 " --> pdb=" O PHE M 317 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N PHE M 317 " --> pdb=" O ARG M 308 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'P' and resid 4 through 6 Processing sheet with id=AJ1, first strand: chain 'P' and resid 11 through 12 removed outlier: 3.560A pdb=" N VAL P 109 " --> pdb=" O ALA P 88 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA P 88 " --> pdb=" O VAL P 109 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N TRP P 34 " --> pdb=" O TYR P 50 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TYR P 50 " --> pdb=" O TRP P 34 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TRP P 36 " --> pdb=" O ILE P 48 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'P' and resid 11 through 12 removed outlier: 3.560A pdb=" N VAL P 109 " --> pdb=" O ALA P 88 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA P 88 " --> pdb=" O VAL P 109 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N CYS P 92 " --> pdb=" O TRP P 103 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N TRP P 103 " --> pdb=" O CYS P 92 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N THR P 94 " --> pdb=" O ASP P 101 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP P 101 " --> pdb=" O THR P 94 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER P 100O" --> pdb=" O ARG P 96 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'P' and resid 120 through 124 removed outlier: 3.760A pdb=" N GLY P 134 " --> pdb=" O LEU P 124 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL P 179 " --> pdb=" O ALA P 131 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N CYS P 135 " --> pdb=" O SER P 175 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP P 139 " --> pdb=" O TYR P 171 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N TYR P 171 " --> pdb=" O ASP P 139 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'P' and resid 120 through 124 removed outlier: 3.760A pdb=" N GLY P 134 " --> pdb=" O LEU P 124 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL P 179 " --> pdb=" O ALA P 131 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N CYS P 135 " --> pdb=" O SER P 175 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP P 139 " --> pdb=" O TYR P 171 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N TYR P 171 " --> pdb=" O ASP P 139 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'P' and resid 146 through 149 removed outlier: 4.050A pdb=" N THR P 146 " --> pdb=" O ASN P 194 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS P 204 " --> pdb=" O CYS P 191 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL P 202 " --> pdb=" O VAL P 193 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'Q' and resid 6 through 14 removed outlier: 7.061A pdb=" N ARG Q 6 " --> pdb=" O ARG Q 103 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N THR Q 105 " --> pdb=" O ARG Q 6 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N LEU Q 11 " --> pdb=" O THR Q 105 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N LEU Q 106A" --> pdb=" O LEU Q 11 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL Q 13 " --> pdb=" O LEU Q 106A" (cutoff:3.500A) removed outlier: 4.297A pdb=" N THR Q 102 " --> pdb=" O TYR Q 86 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'Q' and resid 19 through 22 removed outlier: 3.525A pdb=" N SER Q 63 " --> pdb=" O THR Q 74 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'Q' and resid 44 through 48 removed outlier: 6.556A pdb=" N TRP Q 35 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TRP Q 91 " --> pdb=" O ALA Q 32 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'Q' and resid 115 through 119 removed outlier: 4.045A pdb=" N SER Q 115 " --> pdb=" O SER Q 138 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N SER Q 138 " --> pdb=" O SER Q 115 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU Q 136 " --> pdb=" O THR Q 117 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL Q 134 " --> pdb=" O PHE Q 119 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N CYS Q 135 " --> pdb=" O SER Q 177 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER Q 177 " --> pdb=" O CYS Q 135 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'Q' and resid 115 through 119 removed outlier: 4.045A pdb=" N SER Q 115 " --> pdb=" O SER Q 138 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N SER Q 138 " --> pdb=" O SER Q 115 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU Q 136 " --> pdb=" O THR Q 117 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL Q 134 " --> pdb=" O PHE Q 119 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N CYS Q 135 " --> pdb=" O SER Q 177 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER Q 177 " --> pdb=" O CYS Q 135 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER Q 166 " --> pdb=" O ALA Q 174 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'Q' and resid 146 through 150 removed outlier: 3.634A pdb=" N THR Q 146 " --> pdb=" O THR Q 197 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS Q 150 " --> pdb=" O SER Q 193 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR Q 192 " --> pdb=" O VAL Q 207 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'O' and resid 3 through 7 removed outlier: 3.689A pdb=" N VAL O 18 " --> pdb=" O PHE O 82 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'O' and resid 3 through 7 removed outlier: 3.689A pdb=" N VAL O 18 " --> pdb=" O PHE O 82 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'O' and resid 10 through 12 removed outlier: 3.617A pdb=" N ALA O 88 " --> pdb=" O VAL O 109 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU O 89 " --> pdb=" O LEU O 39 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ARG O 38 " --> pdb=" O TRP O 47 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N TRP O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ILE O 40 " --> pdb=" O PHE O 45 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N PHE O 45 " --> pdb=" O ILE O 40 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'O' and resid 10 through 12 removed outlier: 3.617A pdb=" N ALA O 88 " --> pdb=" O VAL O 109 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'O' and resid 122 through 124 removed outlier: 5.990A pdb=" N TYR O 172 " --> pdb=" O ASP O 140 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'O' and resid 122 through 124 removed outlier: 5.990A pdb=" N TYR O 172 " --> pdb=" O ASP O 140 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N LEU O 171 " --> pdb=" O GLN O 167 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLN O 167 " --> pdb=" O LEU O 171 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'O' and resid 149 through 150 removed outlier: 3.819A pdb=" N LYS O 205 " --> pdb=" O CYS O 192 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL O 203 " --> pdb=" O VAL O 194 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'R' and resid 5 through 7 removed outlier: 3.521A pdb=" N SER R 7 " --> pdb=" O PHE R 22 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER R 65 " --> pdb=" O PHE R 72 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR R 74 " --> pdb=" O VAL R 63 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'R' and resid 10 through 13 removed outlier: 3.593A pdb=" N GLU R 105 " --> pdb=" O LEU R 11 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU R 13 " --> pdb=" O GLU R 105 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'R' and resid 10 through 13 removed outlier: 3.593A pdb=" N GLU R 105 " --> pdb=" O LEU R 11 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU R 13 " --> pdb=" O GLU R 105 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'R' and resid 116 through 118 removed outlier: 4.051A pdb=" N LEU R 135 " --> pdb=" O PHE R 116 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL R 133 " --> pdb=" O PHE R 118 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N LEU R 135 " --> pdb=" O SER R 177 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N SER R 177 " --> pdb=" O LEU R 135 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N ASN R 137 " --> pdb=" O LEU R 175 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N LEU R 175 " --> pdb=" O ASN R 137 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'R' and resid 129 through 130 removed outlier: 3.984A pdb=" N ALA R 130 " --> pdb=" O LEU R 181 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU R 181 " --> pdb=" O ALA R 130 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL5 Processing sheet with id=AL6, first strand: chain 'R' and resid 147 through 150 1128 hydrogen bonds defined for protein. 2817 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: 11.31 Time building geometry restraints manager: 4.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5790 1.32 - 1.45: 10665 1.45 - 1.58: 19968 1.58 - 1.71: 0 1.71 - 1.84: 249 Bond restraints: 36672 Sorted by residual: bond pdb=" C VAL G 204 " pdb=" O VAL G 204 " ideal model delta sigma weight residual 1.238 1.185 0.052 1.06e-02 8.90e+03 2.42e+01 bond pdb=" C VAL A 204 " pdb=" O VAL A 204 " ideal model delta sigma weight residual 1.238 1.185 0.052 1.06e-02 8.90e+03 2.42e+01 bond pdb=" C VAL M 204 " pdb=" O VAL M 204 " ideal model delta sigma weight residual 1.238 1.185 0.052 1.06e-02 8.90e+03 2.42e+01 bond pdb=" CA TRP H 596 " pdb=" C TRP H 596 " ideal model delta sigma weight residual 1.522 1.455 0.067 1.37e-02 5.33e+03 2.42e+01 bond pdb=" CA TRP B 596 " pdb=" C TRP B 596 " ideal model delta sigma weight residual 1.522 1.455 0.067 1.37e-02 5.33e+03 2.40e+01 ... (remaining 36667 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.25: 49517 5.25 - 10.51: 328 10.51 - 15.76: 21 15.76 - 21.02: 3 21.02 - 26.27: 3 Bond angle restraints: 49872 Sorted by residual: angle pdb=" C THR P 160 " pdb=" N PHE P 161 " pdb=" CA PHE P 161 " ideal model delta sigma weight residual 122.71 148.98 -26.27 3.03e+00 1.09e-01 7.52e+01 angle pdb=" C THR D 160 " pdb=" N PHE D 161 " pdb=" CA PHE D 161 " ideal model delta sigma weight residual 122.71 148.98 -26.27 3.03e+00 1.09e-01 7.51e+01 angle pdb=" C THR J 160 " pdb=" N PHE J 161 " pdb=" CA PHE J 161 " ideal model delta sigma weight residual 122.71 148.96 -26.25 3.03e+00 1.09e-01 7.51e+01 angle pdb=" C ILE G 251 " pdb=" N LYS G 252 " pdb=" CA LYS G 252 " ideal model delta sigma weight residual 121.80 142.23 -20.43 2.44e+00 1.68e-01 7.01e+01 angle pdb=" C ILE A 251 " pdb=" N LYS A 252 " pdb=" CA LYS A 252 " ideal model delta sigma weight residual 121.80 142.22 -20.42 2.44e+00 1.68e-01 7.00e+01 ... (remaining 49867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.02: 22692 24.02 - 48.05: 612 48.05 - 72.07: 129 72.07 - 96.10: 66 96.10 - 120.12: 36 Dihedral angle restraints: 23535 sinusoidal: 10788 harmonic: 12747 Sorted by residual: dihedral pdb=" CB CYS N 598 " pdb=" SG CYS N 598 " pdb=" SG CYS N 604 " pdb=" CB CYS N 604 " ideal model delta sinusoidal sigma weight residual -86.00 1.33 -87.33 1 1.00e+01 1.00e-02 9.15e+01 dihedral pdb=" CB CYS H 598 " pdb=" SG CYS H 598 " pdb=" SG CYS H 604 " pdb=" CB CYS H 604 " ideal model delta sinusoidal sigma weight residual -86.00 1.32 -87.32 1 1.00e+01 1.00e-02 9.15e+01 dihedral pdb=" CB CYS B 598 " pdb=" SG CYS B 598 " pdb=" SG CYS B 604 " pdb=" CB CYS B 604 " ideal model delta sinusoidal sigma weight residual -86.00 1.31 -87.31 1 1.00e+01 1.00e-02 9.15e+01 ... (remaining 23532 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 4918 0.093 - 0.186: 893 0.186 - 0.280: 108 0.280 - 0.373: 12 0.373 - 0.466: 15 Chirality restraints: 5946 Sorted by residual: chirality pdb=" CA PHE A 53 " pdb=" N PHE A 53 " pdb=" C PHE A 53 " pdb=" CB PHE A 53 " both_signs ideal model delta sigma weight residual False 2.51 2.98 -0.47 2.00e-01 2.50e+01 5.43e+00 chirality pdb=" CA PHE M 53 " pdb=" N PHE M 53 " pdb=" C PHE M 53 " pdb=" CB PHE M 53 " both_signs ideal model delta sigma weight residual False 2.51 2.98 -0.47 2.00e-01 2.50e+01 5.42e+00 chirality pdb=" CA PHE G 53 " pdb=" N PHE G 53 " pdb=" C PHE G 53 " pdb=" CB PHE G 53 " both_signs ideal model delta sigma weight residual False 2.51 2.98 -0.47 2.00e-01 2.50e+01 5.41e+00 ... (remaining 5943 not shown) Planarity restraints: 6258 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS M 205 " -0.021 2.00e-02 2.50e+03 4.21e-02 1.77e+01 pdb=" C CYS M 205 " 0.073 2.00e-02 2.50e+03 pdb=" O CYS M 205 " -0.027 2.00e-02 2.50e+03 pdb=" N PRO M 206 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 205 " -0.021 2.00e-02 2.50e+03 4.19e-02 1.76e+01 pdb=" C CYS A 205 " 0.072 2.00e-02 2.50e+03 pdb=" O CYS A 205 " -0.027 2.00e-02 2.50e+03 pdb=" N PRO A 206 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS G 205 " -0.021 2.00e-02 2.50e+03 4.19e-02 1.75e+01 pdb=" C CYS G 205 " 0.072 2.00e-02 2.50e+03 pdb=" O CYS G 205 " -0.027 2.00e-02 2.50e+03 pdb=" N PRO G 206 " -0.025 2.00e-02 2.50e+03 ... (remaining 6255 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 2938 2.73 - 3.27: 30999 3.27 - 3.81: 53420 3.81 - 4.36: 64959 4.36 - 4.90: 112129 Nonbonded interactions: 264445 Sorted by model distance: nonbonded pdb=" O PRO E 120 " pdb=" OG1 THR E 132 " model vdw 2.185 3.040 nonbonded pdb=" O PRO Q 120 " pdb=" OG1 THR Q 132 " model vdw 2.185 3.040 nonbonded pdb=" O PRO K 120 " pdb=" OG1 THR K 132 " model vdw 2.185 3.040 nonbonded pdb=" O TYR L 186 " pdb=" OH TYR L 192 " model vdw 2.207 3.040 nonbonded pdb=" O TYR R 186 " pdb=" OH TYR R 192 " model vdw 2.207 3.040 ... (remaining 264440 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.08 Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'z' } ncs_group { reference = chain 'A' selection = chain 'G' selection = chain 'M' } ncs_group { reference = chain 'B' selection = chain 'H' selection = chain 'N' } ncs_group { reference = chain 'C' selection = chain 'I' selection = chain 'O' } ncs_group { reference = chain 'D' selection = chain 'J' selection = chain 'P' } ncs_group { reference = chain 'E' selection = chain 'K' selection = chain 'Q' } ncs_group { reference = chain 'F' selection = chain 'L' selection = chain 'R' } ncs_group { reference = chain 'T' selection = chain 'f' selection = chain 'r' } ncs_group { reference = chain 'Z' selection = chain 'l' selection = chain 'x' } ncs_group { reference = chain 'a' selection = chain 'm' selection = chain 'y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.690 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 37.640 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6065 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 : 0.013 0.441 36855 Z= 0.636 Angle : 1.515 46.201 50358 Z= 0.801 Chirality : 0.073 0.466 5946 Planarity : 0.007 0.055 6201 Dihedral : 13.181 120.125 15144 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.62 % Allowed : 7.49 % Favored : 91.89 % Rotamer: Outliers : 0.70 % Allowed : 2.19 % Favored : 97.11 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 8.97 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -3.63 (0.11), residues: 4350 helix: -4.86 (0.08), residues: 456 sheet: -1.58 (0.13), residues: 1440 loop : -2.48 (0.10), residues: 2454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG A 500 TYR 0.043 0.006 TYR L 49 PHE 0.041 0.004 PHE Q 140 TRP 0.040 0.005 TRP M 45 HIS 0.016 0.004 HIS M 72 Details of bonding type rmsd covalent geometry : bond 0.00929 (36672) covalent geometry : angle 1.32990 (49872) SS BOND : bond 0.21800 ( 63) SS BOND : angle 12.64910 ( 126) hydrogen bonds : bond 0.28555 ( 969) hydrogen bonds : angle 10.35480 ( 2817) link_ALPHA1-2 : bond 0.00755 ( 6) link_ALPHA1-2 : angle 2.96201 ( 18) link_ALPHA1-3 : bond 0.00440 ( 6) link_ALPHA1-3 : angle 1.85182 ( 18) link_ALPHA1-6 : bond 0.00514 ( 6) link_ALPHA1-6 : angle 2.14261 ( 18) link_BETA1-4 : bond 0.01105 ( 45) link_BETA1-4 : angle 4.71980 ( 135) link_NAG-ASN : bond 0.01016 ( 57) link_NAG-ASN : angle 4.77657 ( 171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 912 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 885 time to evaluate : 1.487 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: A 72 HIS cc_start: 0.8300 (OUTLIER) cc_final: 0.8023 (m-70) REVERT: B 643 TYR cc_start: 0.7854 (m-10) cc_final: 0.7647 (m-10) REVERT: D 24 VAL cc_start: 0.3102 (t) cc_final: 0.2885 (t) REVERT: D 47 TRP cc_start: 0.2995 (m-10) cc_final: 0.2749 (m-10) REVERT: E 168 GLN cc_start: 0.4514 (mt0) cc_final: 0.3758 (mp10) REVERT: E 193 SER cc_start: 0.1186 (t) cc_final: 0.0821 (p) REVERT: G 72 HIS cc_start: 0.8192 (OUTLIER) cc_final: 0.7900 (m-70) REVERT: K 168 GLN cc_start: 0.4122 (mt0) cc_final: 0.3733 (mt0) REVERT: M 72 HIS cc_start: 0.8163 (OUTLIER) cc_final: 0.7878 (m-70) REVERT: Q 168 GLN cc_start: 0.4114 (mt0) cc_final: 0.3216 (mp10) REVERT: Q 193 SER cc_start: 0.1366 (t) cc_final: 0.0582 (p) outliers start: 27 outliers final: 11 residues processed: 909 average time/residue: 0.7252 time to fit residues: 785.4292 Evaluate side-chains 477 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 463 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain G residue 53 PHE Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain G residue 72 HIS Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain M residue 53 PHE Chi-restraints excluded: chain M residue 54 CYS Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 72 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 9.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 8.9990 chunk 401 optimal weight: 0.7980 chunk 424 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN B 562 GLN B 563 GLN B 564 HIS ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 GLN E 89 HIS E 198 HIS C 6 GLN ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 440 GLN H 552 GLN H 564 HIS H 658 GLN K 37 GLN K 89 HIS K 198 HIS I 6 GLN I 28 ASN I 101 GLN I 195 ASN ** I 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 552 GLN N 563 GLN N 564 HIS N 590 GLN ** N 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 52 GLN Q 89 HIS Q 198 HIS O 6 GLN O 35 HIS O 101 GLN R 89 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.195893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.167769 restraints weight = 74313.983| |-----------------------------------------------------------------------------| r_work (start): 0.4187 rms_B_bonded: 3.61 r_work: 0.4009 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.4009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6660 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 36855 Z= 0.224 Angle : 0.938 16.878 50358 Z= 0.461 Chirality : 0.055 0.538 5946 Planarity : 0.006 0.077 6201 Dihedral : 11.997 104.694 7224 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.31 % Favored : 92.32 % Rotamer: Outliers : 5.00 % Allowed : 11.33 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.97 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -3.15 (0.11), residues: 4350 helix: -4.18 (0.12), residues: 429 sheet: -1.32 (0.13), residues: 1512 loop : -2.22 (0.11), residues: 2409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 94 TYR 0.020 0.003 TYR E 36 PHE 0.030 0.003 PHE R 116 TRP 0.023 0.002 TRP I 150 HIS 0.010 0.002 HIS J 195 Details of bonding type rmsd covalent geometry : bond 0.00526 (36672) covalent geometry : angle 0.88980 (49872) SS BOND : bond 0.00525 ( 63) SS BOND : angle 1.26161 ( 126) hydrogen bonds : bond 0.05013 ( 969) hydrogen bonds : angle 7.43462 ( 2817) link_ALPHA1-2 : bond 0.00433 ( 6) link_ALPHA1-2 : angle 2.19523 ( 18) link_ALPHA1-3 : bond 0.00988 ( 6) link_ALPHA1-3 : angle 3.00059 ( 18) link_ALPHA1-6 : bond 0.00599 ( 6) link_ALPHA1-6 : angle 2.11821 ( 18) link_BETA1-4 : bond 0.00848 ( 45) link_BETA1-4 : angle 2.98697 ( 135) link_NAG-ASN : bond 0.00526 ( 57) link_NAG-ASN : angle 4.25519 ( 171) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 749 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 557 time to evaluate : 1.247 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 83 GLU cc_start: 0.7420 (tt0) cc_final: 0.7182 (tt0) REVERT: A 163 THR cc_start: 0.7629 (OUTLIER) cc_final: 0.7419 (t) REVERT: B 581 LEU cc_start: 0.7228 (tm) cc_final: 0.6863 (tt) REVERT: B 654 GLU cc_start: 0.6332 (tp30) cc_final: 0.5852 (mt-10) REVERT: D 13 LYS cc_start: 0.6826 (mttt) cc_final: 0.6333 (mptt) REVERT: D 43 LYS cc_start: 0.4857 (mmtt) cc_final: 0.4445 (ptpt) REVERT: D 81 LYS cc_start: 0.3356 (OUTLIER) cc_final: 0.3138 (ptpt) REVERT: D 209 LYS cc_start: 0.2541 (tptt) cc_final: 0.2075 (mttp) REVERT: E 26 GLN cc_start: 0.6251 (mm110) cc_final: 0.5987 (mp-120) REVERT: E 83 GLU cc_start: 0.4823 (mt-10) cc_final: 0.4581 (pt0) REVERT: E 96 TRP cc_start: 0.3944 (m-10) cc_final: 0.3634 (m-10) REVERT: E 133 LEU cc_start: -0.0236 (tp) cc_final: -0.0647 (mp) REVERT: E 168 GLN cc_start: 0.2962 (mt0) cc_final: 0.2682 (mt0) REVERT: E 181 LEU cc_start: 0.2416 (mt) cc_final: 0.1668 (pt) REVERT: C 61 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.7278 (ptm160) REVERT: C 79 TYR cc_start: 0.7107 (m-80) cc_final: 0.6784 (m-80) REVERT: C 144 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.6463 (pm20) REVERT: C 150 TRP cc_start: 0.2601 (t-100) cc_final: 0.2360 (m100) REVERT: F 77 LYS cc_start: 0.6947 (OUTLIER) cc_final: 0.6726 (ptmm) REVERT: F 97 PHE cc_start: 0.7356 (m-10) cc_final: 0.7084 (m-10) REVERT: F 145 LYS cc_start: 0.5753 (OUTLIER) cc_final: 0.5124 (pttm) REVERT: F 211 ARG cc_start: 0.3964 (mmm160) cc_final: 0.3751 (mmm160) REVERT: G 83 GLU cc_start: 0.7232 (tt0) cc_final: 0.7028 (tt0) REVERT: H 588 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.7498 (ttm110) REVERT: H 601 LYS cc_start: 0.7768 (OUTLIER) cc_final: 0.7440 (mtpp) REVERT: J 96 ARG cc_start: 0.5563 (OUTLIER) cc_final: 0.5236 (pmm-80) REVERT: J 129 LYS cc_start: 0.1185 (tttt) cc_final: 0.0985 (ptmm) REVERT: J 154 LEU cc_start: 0.2662 (OUTLIER) cc_final: 0.2386 (tt) REVERT: K 83 GLU cc_start: 0.4914 (mt-10) cc_final: 0.4257 (pt0) REVERT: K 86 TYR cc_start: 0.3893 (m-10) cc_final: 0.3602 (m-80) REVERT: K 87 TYR cc_start: 0.5449 (OUTLIER) cc_final: 0.4174 (m-80) REVERT: K 96 TRP cc_start: 0.5212 (OUTLIER) cc_final: 0.4830 (m100) REVERT: K 168 GLN cc_start: 0.2827 (mt0) cc_final: 0.2602 (mt0) REVERT: K 181 LEU cc_start: 0.2039 (mt) cc_final: 0.1477 (pt) REVERT: I 75 GLN cc_start: 0.6618 (OUTLIER) cc_final: 0.6259 (mt0) REVERT: L 54 ARG cc_start: 0.7383 (OUTLIER) cc_final: 0.7118 (mtt90) REVERT: L 142 ARG cc_start: 0.4883 (OUTLIER) cc_final: 0.4465 (ttm170) REVERT: L 145 LYS cc_start: 0.6017 (OUTLIER) cc_final: 0.5398 (pttm) REVERT: L 147 GLN cc_start: 0.3744 (mm-40) cc_final: 0.3024 (mp10) REVERT: L 187 GLU cc_start: 0.5533 (mt-10) cc_final: 0.5254 (mp0) REVERT: M 83 GLU cc_start: 0.7344 (tt0) cc_final: 0.7018 (tt0) REVERT: M 161 MET cc_start: 0.5598 (mmp) cc_final: 0.5311 (mmp) REVERT: N 581 LEU cc_start: 0.7288 (tm) cc_final: 0.7059 (tt) REVERT: P 13 LYS cc_start: 0.6734 (mttt) cc_final: 0.6138 (mmtp) REVERT: P 43 LYS cc_start: 0.4456 (ttpt) cc_final: 0.4116 (ptmm) REVERT: Q 13 VAL cc_start: 0.4753 (OUTLIER) cc_final: 0.4255 (p) REVERT: Q 76 SER cc_start: 0.5928 (p) cc_final: 0.5663 (t) REVERT: Q 87 TYR cc_start: 0.5671 (OUTLIER) cc_final: 0.3670 (m-80) REVERT: Q 133 LEU cc_start: 0.0353 (tp) cc_final: 0.0004 (mm) REVERT: Q 168 GLN cc_start: 0.3122 (mt0) cc_final: 0.2673 (mt0) REVERT: Q 181 LEU cc_start: 0.2594 (mt) cc_final: 0.1972 (pt) REVERT: O 206 LYS cc_start: 0.5363 (OUTLIER) cc_final: 0.4892 (ptmt) REVERT: O 208 GLU cc_start: 0.4128 (pt0) cc_final: 0.2885 (pm20) REVERT: R 27 GLN cc_start: 0.6765 (OUTLIER) cc_final: 0.6309 (pt0) REVERT: R 142 ARG cc_start: 0.4988 (OUTLIER) cc_final: 0.4640 (ttt180) outliers start: 192 outliers final: 57 residues processed: 685 average time/residue: 0.6976 time to fit residues: 573.8312 Evaluate side-chains 506 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 428 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain E residue 87 TYR Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 61 ARG Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 145 LYS Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain H residue 580 VAL Chi-restraints excluded: chain H residue 588 ARG Chi-restraints excluded: chain H residue 601 LYS Chi-restraints excluded: chain H residue 617 ARG Chi-restraints excluded: chain H residue 632 ASP Chi-restraints excluded: chain J residue 96 ARG Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 87 TYR Chi-restraints excluded: chain K residue 96 TRP Chi-restraints excluded: chain K residue 164 THR Chi-restraints excluded: chain I residue 13 THR Chi-restraints excluded: chain I residue 75 GLN Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 201 THR Chi-restraints excluded: chain L residue 54 ARG Chi-restraints excluded: chain L residue 142 ARG Chi-restraints excluded: chain L residue 145 LYS Chi-restraints excluded: chain M residue 110 SER Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 244 THR Chi-restraints excluded: chain M residue 254 VAL Chi-restraints excluded: chain M residue 494 LEU Chi-restraints excluded: chain N residue 580 VAL Chi-restraints excluded: chain N residue 617 ARG Chi-restraints excluded: chain P residue 176 VAL Chi-restraints excluded: chain P residue 196 LYS Chi-restraints excluded: chain P residue 200 THR Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain Q residue 87 TYR Chi-restraints excluded: chain Q residue 105 THR Chi-restraints excluded: chain Q residue 164 THR Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 61 ARG Chi-restraints excluded: chain O residue 137 LEU Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain O residue 201 THR Chi-restraints excluded: chain O residue 206 LYS Chi-restraints excluded: chain R residue 27 GLN Chi-restraints excluded: chain R residue 142 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 48 optimal weight: 9.9990 chunk 428 optimal weight: 8.9990 chunk 427 optimal weight: 9.9990 chunk 257 optimal weight: 0.9980 chunk 337 optimal weight: 0.9980 chunk 303 optimal weight: 7.9990 chunk 202 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 chunk 70 optimal weight: 0.6980 chunk 376 optimal weight: 8.9990 chunk 17 optimal weight: 0.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 GLN F 76 ASN G 66 HIS G 280 ASN ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 440 GLN H 630 GLN J 166 GLN ** K 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 GLN ** I 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 107 HIS ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 66 HIS ** M 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 543 ASN ** N 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 30 ASN ** Q 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 76 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.195936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.168301 restraints weight = 74108.327| |-----------------------------------------------------------------------------| r_work (start): 0.4192 rms_B_bonded: 3.45 r_work: 0.4012 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6672 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 36855 Z= 0.155 Angle : 0.809 11.988 50358 Z= 0.397 Chirality : 0.051 0.461 5946 Planarity : 0.005 0.071 6201 Dihedral : 10.731 106.013 7202 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.87 % Favored : 92.92 % Rotamer: Outliers : 5.08 % Allowed : 14.79 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.97 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -2.69 (0.12), residues: 4350 helix: -3.57 (0.16), residues: 435 sheet: -1.02 (0.13), residues: 1485 loop : -1.95 (0.12), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 500 TYR 0.039 0.002 TYR P 59 PHE 0.016 0.002 PHE L 118 TRP 0.033 0.002 TRP A 35 HIS 0.010 0.001 HIS Q 89 Details of bonding type rmsd covalent geometry : bond 0.00350 (36672) covalent geometry : angle 0.76703 (49872) SS BOND : bond 0.00479 ( 63) SS BOND : angle 1.83909 ( 126) hydrogen bonds : bond 0.04557 ( 969) hydrogen bonds : angle 6.66663 ( 2817) link_ALPHA1-2 : bond 0.00272 ( 6) link_ALPHA1-2 : angle 1.98285 ( 18) link_ALPHA1-3 : bond 0.01127 ( 6) link_ALPHA1-3 : angle 1.90358 ( 18) link_ALPHA1-6 : bond 0.00798 ( 6) link_ALPHA1-6 : angle 1.50474 ( 18) link_BETA1-4 : bond 0.00680 ( 45) link_BETA1-4 : angle 2.88164 ( 135) link_NAG-ASN : bond 0.00520 ( 57) link_NAG-ASN : angle 3.35956 ( 171) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 467 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLU cc_start: 0.7488 (tt0) cc_final: 0.7231 (tt0) REVERT: A 163 THR cc_start: 0.7529 (p) cc_final: 0.7318 (t) REVERT: B 581 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.7127 (tt) REVERT: D 13 LYS cc_start: 0.6875 (mttt) cc_final: 0.6324 (mptt) REVERT: D 43 LYS cc_start: 0.4322 (mmtt) cc_final: 0.4041 (ptpt) REVERT: D 154 LEU cc_start: 0.2423 (OUTLIER) cc_final: 0.2212 (mt) REVERT: D 209 LYS cc_start: 0.2344 (tptt) cc_final: 0.2059 (tptt) REVERT: E 26 GLN cc_start: 0.6108 (mm110) cc_final: 0.5906 (mp-120) REVERT: E 51 ASN cc_start: 0.4716 (m-40) cc_final: 0.4247 (t0) REVERT: E 83 GLU cc_start: 0.5033 (mt-10) cc_final: 0.4750 (pt0) REVERT: E 96 TRP cc_start: 0.3909 (m-10) cc_final: 0.2804 (m-10) REVERT: E 169 SER cc_start: 0.4577 (p) cc_final: 0.4311 (t) REVERT: C 112 SER cc_start: 0.6323 (t) cc_final: 0.5923 (p) REVERT: C 206 LYS cc_start: 0.4660 (ptmm) cc_final: 0.4332 (ptmm) REVERT: F 145 LYS cc_start: 0.5828 (OUTLIER) cc_final: 0.5170 (pttm) REVERT: G 207 LYS cc_start: 0.6640 (OUTLIER) cc_final: 0.6093 (tttm) REVERT: J 96 ARG cc_start: 0.5711 (OUTLIER) cc_final: 0.5288 (pmm-80) REVERT: J 154 LEU cc_start: 0.2544 (OUTLIER) cc_final: 0.2282 (tt) REVERT: K 20 ARG cc_start: 0.5474 (mpt-90) cc_final: 0.5026 (mmm-85) REVERT: K 83 GLU cc_start: 0.4821 (mt-10) cc_final: 0.4161 (pt0) REVERT: K 86 TYR cc_start: 0.3567 (m-10) cc_final: 0.3314 (m-80) REVERT: K 96 TRP cc_start: 0.4989 (OUTLIER) cc_final: 0.4692 (m100) REVERT: K 168 GLN cc_start: 0.2617 (mt0) cc_final: 0.2326 (mt0) REVERT: K 169 SER cc_start: 0.4261 (p) cc_final: 0.3933 (t) REVERT: I 75 GLN cc_start: 0.6638 (OUTLIER) cc_final: 0.6348 (mt0) REVERT: I 112 SER cc_start: 0.6959 (t) cc_final: 0.6400 (p) REVERT: L 2 ILE cc_start: 0.6842 (OUTLIER) cc_final: 0.6599 (pp) REVERT: L 145 LYS cc_start: 0.6024 (ptmm) cc_final: 0.5418 (pttm) REVERT: L 160 GLN cc_start: 0.4749 (tp-100) cc_final: 0.4286 (pp30) REVERT: L 187 GLU cc_start: 0.5272 (mt-10) cc_final: 0.4689 (pm20) REVERT: M 161 MET cc_start: 0.5361 (mmp) cc_final: 0.5056 (mmp) REVERT: M 440 GLN cc_start: 0.7439 (OUTLIER) cc_final: 0.6767 (tm-30) REVERT: N 581 LEU cc_start: 0.7384 (OUTLIER) cc_final: 0.7073 (tt) REVERT: P 13 LYS cc_start: 0.6777 (mttt) cc_final: 0.6259 (mmtp) REVERT: P 43 LYS cc_start: 0.4272 (OUTLIER) cc_final: 0.3944 (ptmm) REVERT: Q 13 VAL cc_start: 0.4599 (OUTLIER) cc_final: 0.4219 (p) REVERT: Q 87 TYR cc_start: 0.5633 (OUTLIER) cc_final: 0.3608 (m-80) REVERT: Q 168 GLN cc_start: 0.3101 (mt0) cc_final: 0.2679 (mt0) REVERT: O 137 LEU cc_start: 0.3670 (OUTLIER) cc_final: 0.3198 (tt) REVERT: O 144 GLU cc_start: 0.6614 (OUTLIER) cc_final: 0.6083 (pm20) REVERT: O 206 LYS cc_start: 0.5273 (OUTLIER) cc_final: 0.4791 (ptmt) REVERT: O 208 GLU cc_start: 0.3979 (pt0) cc_final: 0.2790 (pm20) REVERT: R 187 GLU cc_start: 0.5282 (mt-10) cc_final: 0.4667 (pm20) outliers start: 195 outliers final: 79 residues processed: 602 average time/residue: 0.6547 time to fit residues: 475.2447 Evaluate side-chains 499 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 403 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 99 GLN Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain E residue 87 TYR Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 145 LYS Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 207 LYS Chi-restraints excluded: chain G residue 276 ASN Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 335 LYS Chi-restraints excluded: chain G residue 422 MET Chi-restraints excluded: chain G residue 424 ILE Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain H residue 568 LEU Chi-restraints excluded: chain H residue 580 VAL Chi-restraints excluded: chain H residue 581 LEU Chi-restraints excluded: chain H residue 604 CYS Chi-restraints excluded: chain H residue 617 ARG Chi-restraints excluded: chain H residue 639 THR Chi-restraints excluded: chain H residue 642 ILE Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 96 ARG Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain K residue 22 SER Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 96 TRP Chi-restraints excluded: chain K residue 105 THR Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 75 GLN Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain M residue 110 SER Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 208 LEU Chi-restraints excluded: chain M residue 244 THR Chi-restraints excluded: chain M residue 254 VAL Chi-restraints excluded: chain M residue 333 VAL Chi-restraints excluded: chain M residue 440 GLN Chi-restraints excluded: chain M residue 467 THR Chi-restraints excluded: chain N residue 580 VAL Chi-restraints excluded: chain N residue 581 LEU Chi-restraints excluded: chain N residue 588 ARG Chi-restraints excluded: chain N residue 639 THR Chi-restraints excluded: chain P residue 43 LYS Chi-restraints excluded: chain P residue 67 VAL Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain Q residue 87 TYR Chi-restraints excluded: chain Q residue 105 THR Chi-restraints excluded: chain O residue 61 ARG Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 137 LEU Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain O residue 139 LYS Chi-restraints excluded: chain O residue 144 GLU Chi-restraints excluded: chain O residue 148 VAL Chi-restraints excluded: chain O residue 206 LYS Chi-restraints excluded: chain R residue 10 ILE Chi-restraints excluded: chain R residue 88 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 32 optimal weight: 9.9990 chunk 159 optimal weight: 6.9990 chunk 340 optimal weight: 9.9990 chunk 315 optimal weight: 8.9990 chunk 318 optimal weight: 0.9990 chunk 198 optimal weight: 4.9990 chunk 335 optimal weight: 9.9990 chunk 170 optimal weight: 10.0000 chunk 81 optimal weight: 20.0000 chunk 68 optimal weight: 2.9990 chunk 84 optimal weight: 0.0270 overall best weight: 3.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 GLN B 650 GLN E 168 GLN C 72 GLN C 101 GLN ** F 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 52 GLN I 72 GLN ** I 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 76 ASN L 160 GLN ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 543 ASN N 552 GLN ** N 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 630 GLN Q 52 GLN ** O 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 137 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.193734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.165603 restraints weight = 73530.926| |-----------------------------------------------------------------------------| r_work (start): 0.4153 rms_B_bonded: 3.64 r_work: 0.3976 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6711 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 36855 Z= 0.175 Angle : 0.814 12.069 50358 Z= 0.400 Chirality : 0.052 0.651 5946 Planarity : 0.005 0.053 6201 Dihedral : 10.197 104.539 7200 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.44 % Favored : 91.33 % Rotamer: Outliers : 5.78 % Allowed : 15.83 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.97 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -2.64 (0.12), residues: 4350 helix: -3.25 (0.18), residues: 444 sheet: -0.96 (0.13), residues: 1467 loop : -1.99 (0.12), residues: 2439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG Q 20 TYR 0.026 0.002 TYR J 140 PHE 0.030 0.002 PHE L 22 TRP 0.027 0.002 TRP J 47 HIS 0.008 0.002 HIS E 38 Details of bonding type rmsd covalent geometry : bond 0.00410 (36672) covalent geometry : angle 0.77403 (49872) SS BOND : bond 0.00427 ( 63) SS BOND : angle 1.68130 ( 126) hydrogen bonds : bond 0.04298 ( 969) hydrogen bonds : angle 6.48097 ( 2817) link_ALPHA1-2 : bond 0.00207 ( 6) link_ALPHA1-2 : angle 1.84123 ( 18) link_ALPHA1-3 : bond 0.01034 ( 6) link_ALPHA1-3 : angle 2.28009 ( 18) link_ALPHA1-6 : bond 0.00697 ( 6) link_ALPHA1-6 : angle 1.51579 ( 18) link_BETA1-4 : bond 0.00761 ( 45) link_BETA1-4 : angle 2.74677 ( 135) link_NAG-ASN : bond 0.00454 ( 57) link_NAG-ASN : angle 3.32185 ( 171) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 222 poor density : 460 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.6596 (OUTLIER) cc_final: 0.5975 (pp30) REVERT: A 83 GLU cc_start: 0.7609 (tt0) cc_final: 0.7366 (tt0) REVERT: A 161 MET cc_start: 0.5687 (mmm) cc_final: 0.4851 (mmm) REVERT: A 163 THR cc_start: 0.7380 (OUTLIER) cc_final: 0.7176 (t) REVERT: B 581 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.7214 (tt) REVERT: B 632 ASP cc_start: 0.7555 (OUTLIER) cc_final: 0.7244 (t0) REVERT: D 13 LYS cc_start: 0.6878 (mttt) cc_final: 0.6377 (mptt) REVERT: D 53 ASP cc_start: 0.2999 (m-30) cc_final: 0.2744 (m-30) REVERT: D 97 ARG cc_start: 0.6498 (mtp-110) cc_final: 0.6290 (ttm170) REVERT: D 100 MET cc_start: 0.5500 (mpt) cc_final: 0.5298 (mmm) REVERT: D 113 SER cc_start: 0.3957 (p) cc_final: 0.3379 (m) REVERT: D 154 LEU cc_start: 0.2523 (OUTLIER) cc_final: 0.2243 (mt) REVERT: E 83 GLU cc_start: 0.5211 (mt-10) cc_final: 0.4668 (pt0) REVERT: E 96 TRP cc_start: 0.4700 (OUTLIER) cc_final: 0.2993 (m-10) REVERT: E 181 LEU cc_start: 0.2613 (mt) cc_final: 0.1895 (pt) REVERT: E 186 TRP cc_start: 0.1455 (OUTLIER) cc_final: 0.1239 (t60) REVERT: C 61 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.6934 (ptm160) REVERT: C 79 TYR cc_start: 0.7337 (m-80) cc_final: 0.7114 (m-80) REVERT: C 112 SER cc_start: 0.6155 (t) cc_final: 0.5819 (p) REVERT: C 206 LYS cc_start: 0.4296 (ptmm) cc_final: 0.3953 (ptmm) REVERT: G 207 LYS cc_start: 0.6605 (OUTLIER) cc_final: 0.6030 (tttm) REVERT: G 217 TYR cc_start: 0.7342 (m-80) cc_final: 0.6915 (m-80) REVERT: G 335 LYS cc_start: 0.7286 (OUTLIER) cc_final: 0.7058 (ttpp) REVERT: J 96 ARG cc_start: 0.5695 (OUTLIER) cc_final: 0.5236 (pmm-80) REVERT: J 97 ARG cc_start: 0.6439 (mtp-110) cc_final: 0.6157 (ttm110) REVERT: J 154 LEU cc_start: 0.2559 (OUTLIER) cc_final: 0.2288 (tt) REVERT: J 171 TYR cc_start: 0.2414 (m-80) cc_final: 0.1654 (m-80) REVERT: K 83 GLU cc_start: 0.5238 (mt-10) cc_final: 0.4258 (tm-30) REVERT: K 86 TYR cc_start: 0.3646 (m-10) cc_final: 0.3328 (m-80) REVERT: K 96 TRP cc_start: 0.5496 (OUTLIER) cc_final: 0.4914 (m100) REVERT: K 168 GLN cc_start: 0.2418 (mt0) cc_final: 0.2082 (mt0) REVERT: I 61 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7499 (ptm160) REVERT: I 75 GLN cc_start: 0.6642 (OUTLIER) cc_final: 0.6345 (mt0) REVERT: I 208 GLU cc_start: 0.3913 (pt0) cc_final: 0.3648 (pm20) REVERT: L 142 ARG cc_start: 0.4834 (OUTLIER) cc_final: 0.4391 (ttm170) REVERT: L 145 LYS cc_start: 0.6074 (OUTLIER) cc_final: 0.5296 (pttm) REVERT: L 160 GLN cc_start: 0.4778 (tp40) cc_final: 0.4362 (pp30) REVERT: L 175 LEU cc_start: 0.4605 (OUTLIER) cc_final: 0.4232 (mp) REVERT: L 187 GLU cc_start: 0.5072 (mt-10) cc_final: 0.4531 (pm20) REVERT: M 161 MET cc_start: 0.5401 (mmp) cc_final: 0.5129 (mmp) REVERT: M 308 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.7070 (ptm160) REVERT: M 440 GLN cc_start: 0.7328 (OUTLIER) cc_final: 0.6686 (tm-30) REVERT: M 476 ARG cc_start: 0.7057 (OUTLIER) cc_final: 0.5994 (mmt-90) REVERT: N 581 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.7052 (tt) REVERT: N 601 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7597 (mtpp) REVERT: N 625 ASN cc_start: 0.7118 (p0) cc_final: 0.6903 (p0) REVERT: P 13 LYS cc_start: 0.6868 (mttt) cc_final: 0.6277 (mmtp) REVERT: P 43 LYS cc_start: 0.4456 (OUTLIER) cc_final: 0.4074 (ptmm) REVERT: Q 13 VAL cc_start: 0.4513 (OUTLIER) cc_final: 0.4150 (p) REVERT: Q 87 TYR cc_start: 0.5593 (OUTLIER) cc_final: 0.3495 (m-80) REVERT: Q 168 GLN cc_start: 0.2750 (mt0) cc_final: 0.2225 (mt0) REVERT: O 206 LYS cc_start: 0.5184 (OUTLIER) cc_final: 0.4623 (tmtm) REVERT: O 208 GLU cc_start: 0.3934 (pt0) cc_final: 0.3179 (pm20) REVERT: R 142 ARG cc_start: 0.4519 (OUTLIER) cc_final: 0.4146 (ttt180) REVERT: R 187 GLU cc_start: 0.5281 (mt-10) cc_final: 0.4602 (pm20) outliers start: 222 outliers final: 102 residues processed: 610 average time/residue: 0.6606 time to fit residues: 485.9259 Evaluate side-chains 534 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 404 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 99 GLN Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 87 TYR Chi-restraints excluded: chain E residue 96 TRP Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 186 TRP Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 61 ARG Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 161 GLU Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 207 LYS Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 335 LYS Chi-restraints excluded: chain G residue 418 CYS Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain H residue 568 LEU Chi-restraints excluded: chain H residue 580 VAL Chi-restraints excluded: chain H residue 581 LEU Chi-restraints excluded: chain H residue 604 CYS Chi-restraints excluded: chain H residue 617 ARG Chi-restraints excluded: chain H residue 632 ASP Chi-restraints excluded: chain H residue 642 ILE Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 69 ILE Chi-restraints excluded: chain J residue 81 LYS Chi-restraints excluded: chain J residue 96 ARG Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 96 TRP Chi-restraints excluded: chain K residue 164 THR Chi-restraints excluded: chain I residue 13 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 61 ARG Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 75 GLN Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 201 THR Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 33 MET Chi-restraints excluded: chain L residue 142 ARG Chi-restraints excluded: chain L residue 145 LYS Chi-restraints excluded: chain L residue 168 SER Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain M residue 102 GLU Chi-restraints excluded: chain M residue 110 SER Chi-restraints excluded: chain M residue 123 THR Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 244 THR Chi-restraints excluded: chain M residue 254 VAL Chi-restraints excluded: chain M residue 308 ARG Chi-restraints excluded: chain M residue 333 VAL Chi-restraints excluded: chain M residue 418 CYS Chi-restraints excluded: chain M residue 422 MET Chi-restraints excluded: chain M residue 440 GLN Chi-restraints excluded: chain M residue 467 THR Chi-restraints excluded: chain M residue 476 ARG Chi-restraints excluded: chain M residue 494 LEU Chi-restraints excluded: chain N residue 580 VAL Chi-restraints excluded: chain N residue 581 LEU Chi-restraints excluded: chain N residue 601 LYS Chi-restraints excluded: chain N residue 639 THR Chi-restraints excluded: chain P residue 43 LYS Chi-restraints excluded: chain P residue 67 VAL Chi-restraints excluded: chain P residue 81 LYS Chi-restraints excluded: chain P residue 100 VAL Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain P residue 146 THR Chi-restraints excluded: chain P residue 176 VAL Chi-restraints excluded: chain P residue 200 THR Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain Q residue 87 TYR Chi-restraints excluded: chain Q residue 105 THR Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 61 ARG Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 69 MET Chi-restraints excluded: chain O residue 137 LEU Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain O residue 148 VAL Chi-restraints excluded: chain O residue 201 THR Chi-restraints excluded: chain O residue 206 LYS Chi-restraints excluded: chain R residue 10 ILE Chi-restraints excluded: chain R residue 142 ARG Chi-restraints excluded: chain R residue 168 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 240 optimal weight: 0.1980 chunk 135 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 242 optimal weight: 8.9990 chunk 81 optimal weight: 30.0000 chunk 371 optimal weight: 1.9990 chunk 224 optimal weight: 3.9990 chunk 42 optimal weight: 8.9990 chunk 420 optimal weight: 4.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 GLN B 591 GLN D 166 GLN ** E 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN C 72 GLN C 101 GLN ** F 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 552 GLN ** H 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 52 GLN K 89 HIS ** K 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 GLN ** I 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 374 HIS N 543 ASN ** N 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 30 ASN Q 52 GLN ** O 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 89 GLN ** R 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.194643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.166476 restraints weight = 73581.008| |-----------------------------------------------------------------------------| r_work (start): 0.4165 rms_B_bonded: 3.51 r_work: 0.3991 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6691 moved from start: 0.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 36855 Z= 0.138 Angle : 0.761 11.223 50358 Z= 0.371 Chirality : 0.049 0.412 5946 Planarity : 0.005 0.051 6201 Dihedral : 9.594 102.569 7200 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.26 % Favored : 92.53 % Rotamer: Outliers : 5.18 % Allowed : 17.37 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.97 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.41 (0.12), residues: 4350 helix: -2.89 (0.20), residues: 441 sheet: -0.77 (0.14), residues: 1434 loop : -1.89 (0.12), residues: 2475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 20 TYR 0.021 0.002 TYR J 140 PHE 0.031 0.002 PHE L 22 TRP 0.030 0.001 TRP J 47 HIS 0.005 0.001 HIS G 72 Details of bonding type rmsd covalent geometry : bond 0.00315 (36672) covalent geometry : angle 0.72173 (49872) SS BOND : bond 0.00361 ( 63) SS BOND : angle 1.81785 ( 126) hydrogen bonds : bond 0.03863 ( 969) hydrogen bonds : angle 6.15202 ( 2817) link_ALPHA1-2 : bond 0.00332 ( 6) link_ALPHA1-2 : angle 1.70815 ( 18) link_ALPHA1-3 : bond 0.01063 ( 6) link_ALPHA1-3 : angle 2.13062 ( 18) link_ALPHA1-6 : bond 0.00821 ( 6) link_ALPHA1-6 : angle 1.57209 ( 18) link_BETA1-4 : bond 0.00740 ( 45) link_BETA1-4 : angle 2.63990 ( 135) link_NAG-ASN : bond 0.00445 ( 57) link_NAG-ASN : angle 3.12440 ( 171) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 444 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.6598 (OUTLIER) cc_final: 0.5839 (pp30) REVERT: A 83 GLU cc_start: 0.7552 (tt0) cc_final: 0.7284 (tt0) REVERT: A 125 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.7080 (tp) REVERT: A 161 MET cc_start: 0.5599 (mmm) cc_final: 0.4923 (mmm) REVERT: A 163 THR cc_start: 0.7307 (p) cc_final: 0.7026 (t) REVERT: B 535 MET cc_start: 0.7827 (OUTLIER) cc_final: 0.7268 (mmt) REVERT: B 550 GLN cc_start: 0.7616 (OUTLIER) cc_final: 0.7392 (tp-100) REVERT: B 581 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.7295 (tt) REVERT: D 13 LYS cc_start: 0.6927 (mttt) cc_final: 0.6363 (mptt) REVERT: D 53 ASP cc_start: 0.3032 (m-30) cc_final: 0.2736 (m-30) REVERT: D 100 MET cc_start: 0.5337 (mpt) cc_final: 0.4947 (mmm) REVERT: D 154 LEU cc_start: 0.2529 (OUTLIER) cc_final: 0.2271 (mt) REVERT: E 83 GLU cc_start: 0.5167 (mt-10) cc_final: 0.4639 (pt0) REVERT: E 96 TRP cc_start: 0.4704 (OUTLIER) cc_final: 0.3351 (m-10) REVERT: E 181 LEU cc_start: 0.2607 (mt) cc_final: 0.1915 (pt) REVERT: C 61 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.6914 (ptm160) REVERT: C 112 SER cc_start: 0.6096 (t) cc_final: 0.5824 (p) REVERT: F 49 TYR cc_start: 0.6493 (OUTLIER) cc_final: 0.5799 (t80) REVERT: F 160 GLN cc_start: 0.3703 (mt0) cc_final: 0.3448 (tp-100) REVERT: F 187 GLU cc_start: 0.4951 (mt-10) cc_final: 0.4449 (pm20) REVERT: G 125 LEU cc_start: 0.6746 (mp) cc_final: 0.6426 (tt) REVERT: G 207 LYS cc_start: 0.6662 (OUTLIER) cc_final: 0.6086 (tttm) REVERT: G 217 TYR cc_start: 0.7370 (m-80) cc_final: 0.6915 (m-80) REVERT: H 535 MET cc_start: 0.8068 (OUTLIER) cc_final: 0.7503 (mmt) REVERT: H 601 LYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7372 (mtpp) REVERT: J 96 ARG cc_start: 0.5794 (OUTLIER) cc_final: 0.5378 (pmm-80) REVERT: J 97 ARG cc_start: 0.6331 (mtp-110) cc_final: 0.6110 (ttm170) REVERT: J 154 LEU cc_start: 0.2540 (OUTLIER) cc_final: 0.2269 (tt) REVERT: J 171 TYR cc_start: 0.2481 (m-80) cc_final: 0.1707 (m-80) REVERT: K 62 PHE cc_start: 0.5048 (m-10) cc_final: 0.4765 (m-80) REVERT: K 83 GLU cc_start: 0.5217 (mt-10) cc_final: 0.4376 (tm-30) REVERT: K 168 GLN cc_start: 0.2393 (mt0) cc_final: 0.2047 (mt0) REVERT: I 61 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.7458 (ptm160) REVERT: I 75 GLN cc_start: 0.6613 (OUTLIER) cc_final: 0.6291 (mt0) REVERT: I 112 SER cc_start: 0.6887 (t) cc_final: 0.6468 (p) REVERT: L 49 TYR cc_start: 0.6317 (OUTLIER) cc_final: 0.4949 (t80) REVERT: L 145 LYS cc_start: 0.5991 (OUTLIER) cc_final: 0.5391 (pttm) REVERT: L 160 GLN cc_start: 0.4831 (tp40) cc_final: 0.4415 (pp30) REVERT: L 175 LEU cc_start: 0.4642 (OUTLIER) cc_final: 0.4358 (mp) REVERT: L 187 GLU cc_start: 0.5147 (mt-10) cc_final: 0.4659 (pm20) REVERT: M 161 MET cc_start: 0.5459 (mmp) cc_final: 0.5144 (mmp) REVERT: M 440 GLN cc_start: 0.7275 (OUTLIER) cc_final: 0.6622 (tm-30) REVERT: M 476 ARG cc_start: 0.7102 (OUTLIER) cc_final: 0.6256 (mmt-90) REVERT: N 581 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.7077 (tt) REVERT: N 625 ASN cc_start: 0.7038 (p0) cc_final: 0.6796 (p0) REVERT: P 13 LYS cc_start: 0.6960 (mttt) cc_final: 0.6369 (mmtp) REVERT: P 43 LYS cc_start: 0.4367 (OUTLIER) cc_final: 0.4011 (ptmm) REVERT: Q 13 VAL cc_start: 0.4338 (OUTLIER) cc_final: 0.4124 (p) REVERT: Q 87 TYR cc_start: 0.5494 (OUTLIER) cc_final: 0.3452 (m-80) REVERT: Q 168 GLN cc_start: 0.2755 (mt0) cc_final: 0.2187 (mt0) REVERT: O 6 GLN cc_start: 0.6780 (pt0) cc_final: 0.6400 (pt0) REVERT: O 81 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7687 (tt0) REVERT: O 206 LYS cc_start: 0.5247 (OUTLIER) cc_final: 0.4675 (tmtm) REVERT: O 208 GLU cc_start: 0.3876 (pt0) cc_final: 0.3203 (pm20) REVERT: R 142 ARG cc_start: 0.4485 (OUTLIER) cc_final: 0.4055 (ttt180) outliers start: 199 outliers final: 107 residues processed: 585 average time/residue: 0.6986 time to fit residues: 490.1800 Evaluate side-chains 538 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 403 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 550 GLN Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 99 GLN Chi-restraints excluded: chain D residue 100 PHE Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 87 TYR Chi-restraints excluded: chain E residue 96 TRP Chi-restraints excluded: chain E residue 186 TRP Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 61 ARG Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 101 GLN Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 49 TYR Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 161 GLU Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 207 LYS Chi-restraints excluded: chain G residue 268 GLU Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 418 CYS Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain H residue 535 MET Chi-restraints excluded: chain H residue 544 LEU Chi-restraints excluded: chain H residue 568 LEU Chi-restraints excluded: chain H residue 580 VAL Chi-restraints excluded: chain H residue 581 LEU Chi-restraints excluded: chain H residue 601 LYS Chi-restraints excluded: chain H residue 604 CYS Chi-restraints excluded: chain H residue 617 ARG Chi-restraints excluded: chain H residue 632 ASP Chi-restraints excluded: chain H residue 642 ILE Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 69 ILE Chi-restraints excluded: chain J residue 81 LYS Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 96 ARG Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 206 VAL Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 52 GLN Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 105 THR Chi-restraints excluded: chain I residue 13 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 61 ARG Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 75 GLN Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 201 THR Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 33 MET Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 145 LYS Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain M residue 102 GLU Chi-restraints excluded: chain M residue 110 SER Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 162 THR Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 244 THR Chi-restraints excluded: chain M residue 254 VAL Chi-restraints excluded: chain M residue 333 VAL Chi-restraints excluded: chain M residue 418 CYS Chi-restraints excluded: chain M residue 422 MET Chi-restraints excluded: chain M residue 440 GLN Chi-restraints excluded: chain M residue 467 THR Chi-restraints excluded: chain M residue 476 ARG Chi-restraints excluded: chain M residue 494 LEU Chi-restraints excluded: chain N residue 580 VAL Chi-restraints excluded: chain N residue 581 LEU Chi-restraints excluded: chain P residue 43 LYS Chi-restraints excluded: chain P residue 67 VAL Chi-restraints excluded: chain P residue 100 VAL Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain P residue 176 VAL Chi-restraints excluded: chain P residue 200 THR Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain Q residue 87 TYR Chi-restraints excluded: chain Q residue 105 THR Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 61 ARG Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 81 GLU Chi-restraints excluded: chain O residue 137 LEU Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain O residue 139 LYS Chi-restraints excluded: chain O residue 148 VAL Chi-restraints excluded: chain O residue 201 THR Chi-restraints excluded: chain O residue 206 LYS Chi-restraints excluded: chain R residue 10 ILE Chi-restraints excluded: chain R residue 142 ARG Chi-restraints excluded: chain R residue 168 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 84 optimal weight: 4.9990 chunk 417 optimal weight: 20.0000 chunk 183 optimal weight: 10.0000 chunk 213 optimal weight: 4.9990 chunk 344 optimal weight: 2.9990 chunk 314 optimal weight: 10.0000 chunk 155 optimal weight: 5.9990 chunk 214 optimal weight: 7.9990 chunk 161 optimal weight: 5.9990 chunk 136 optimal weight: 10.0000 chunk 117 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 GLN E 37 GLN ** E 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 591 GLN H 630 GLN ** K 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 HIS K 52 GLN ** K 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 189 HIS ** I 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 66 HIS M 280 ASN N 543 ASN ** N 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 38 HIS Q 50 ASN ** Q 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.191478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.163735 restraints weight = 73488.900| |-----------------------------------------------------------------------------| r_work (start): 0.4133 rms_B_bonded: 3.50 r_work: 0.3963 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3877 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 0.4899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 36855 Z= 0.233 Angle : 0.888 15.090 50358 Z= 0.434 Chirality : 0.055 0.779 5946 Planarity : 0.006 0.085 6201 Dihedral : 10.109 101.795 7200 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.07 % Favored : 89.70 % Rotamer: Outliers : 5.99 % Allowed : 18.05 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.97 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -2.66 (0.12), residues: 4350 helix: -2.92 (0.20), residues: 444 sheet: -0.96 (0.13), residues: 1455 loop : -2.09 (0.12), residues: 2451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 500 TYR 0.031 0.003 TYR J 140 PHE 0.031 0.002 PHE L 22 TRP 0.023 0.003 TRP C 150 HIS 0.011 0.002 HIS E 38 Details of bonding type rmsd covalent geometry : bond 0.00557 (36672) covalent geometry : angle 0.84427 (49872) SS BOND : bond 0.00417 ( 63) SS BOND : angle 2.45338 ( 126) hydrogen bonds : bond 0.04629 ( 969) hydrogen bonds : angle 6.56211 ( 2817) link_ALPHA1-2 : bond 0.00300 ( 6) link_ALPHA1-2 : angle 1.96730 ( 18) link_ALPHA1-3 : bond 0.01031 ( 6) link_ALPHA1-3 : angle 2.36325 ( 18) link_ALPHA1-6 : bond 0.00898 ( 6) link_ALPHA1-6 : angle 1.55316 ( 18) link_BETA1-4 : bond 0.00836 ( 45) link_BETA1-4 : angle 2.86220 ( 135) link_NAG-ASN : bond 0.00514 ( 57) link_NAG-ASN : angle 3.48717 ( 171) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 230 poor density : 450 time to evaluate : 1.230 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 82 GLN cc_start: 0.6969 (OUTLIER) cc_final: 0.6170 (pp30) REVERT: A 83 GLU cc_start: 0.7982 (tt0) cc_final: 0.7768 (tt0) REVERT: A 161 MET cc_start: 0.5911 (mmm) cc_final: 0.5087 (mmm) REVERT: B 535 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.7671 (mmt) REVERT: B 581 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7212 (tt) REVERT: D 53 ASP cc_start: 0.3308 (m-30) cc_final: 0.2957 (m-30) REVERT: D 100 MET cc_start: 0.5404 (mpt) cc_final: 0.4891 (mmm) REVERT: E 62 PHE cc_start: 0.5180 (m-10) cc_final: 0.4771 (m-80) REVERT: E 83 GLU cc_start: 0.5176 (mt-10) cc_final: 0.4533 (tm-30) REVERT: E 96 TRP cc_start: 0.5658 (OUTLIER) cc_final: 0.4206 (m-10) REVERT: E 181 LEU cc_start: 0.2648 (mt) cc_final: 0.1817 (pt) REVERT: C 61 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.6940 (ptm160) REVERT: F 49 TYR cc_start: 0.7166 (OUTLIER) cc_final: 0.6335 (t80) REVERT: F 147 GLN cc_start: 0.3582 (mm-40) cc_final: 0.3252 (mp10) REVERT: F 165 GLU cc_start: 0.5618 (OUTLIER) cc_final: 0.5206 (pm20) REVERT: F 187 GLU cc_start: 0.4698 (mt-10) cc_final: 0.4373 (pm20) REVERT: F 190 LYS cc_start: 0.5095 (tttt) cc_final: 0.4855 (tptp) REVERT: G 207 LYS cc_start: 0.6703 (OUTLIER) cc_final: 0.6218 (tttm) REVERT: H 535 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.7739 (mmt) REVERT: J 96 ARG cc_start: 0.5759 (OUTLIER) cc_final: 0.5487 (pmm-80) REVERT: J 154 LEU cc_start: 0.2656 (OUTLIER) cc_final: 0.2346 (tt) REVERT: J 171 TYR cc_start: 0.2605 (m-80) cc_final: 0.1896 (m-80) REVERT: K 11 LEU cc_start: 0.4977 (OUTLIER) cc_final: 0.4681 (tm) REVERT: K 52 GLN cc_start: 0.6120 (mt0) cc_final: 0.5839 (mt0) REVERT: K 83 GLU cc_start: 0.5471 (mt-10) cc_final: 0.4335 (tm-30) REVERT: K 96 TRP cc_start: 0.6084 (OUTLIER) cc_final: 0.5487 (m100) REVERT: K 168 GLN cc_start: 0.2382 (mt0) cc_final: 0.2018 (mt0) REVERT: I 61 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7467 (ptm160) REVERT: I 75 GLN cc_start: 0.6779 (OUTLIER) cc_final: 0.6560 (mt0) REVERT: I 208 GLU cc_start: 0.3997 (pt0) cc_final: 0.3606 (pm20) REVERT: L 24 LYS cc_start: 0.7766 (tmmt) cc_final: 0.7519 (tttp) REVERT: L 49 TYR cc_start: 0.6901 (OUTLIER) cc_final: 0.6075 (t80) REVERT: L 139 PHE cc_start: 0.3603 (p90) cc_final: 0.3294 (p90) REVERT: L 142 ARG cc_start: 0.4694 (OUTLIER) cc_final: 0.4167 (ttm170) REVERT: L 145 LYS cc_start: 0.5945 (OUTLIER) cc_final: 0.5278 (pttm) REVERT: L 175 LEU cc_start: 0.4981 (OUTLIER) cc_final: 0.4717 (mp) REVERT: L 187 GLU cc_start: 0.4978 (mt-10) cc_final: 0.4399 (pm20) REVERT: L 190 LYS cc_start: 0.4650 (tttt) cc_final: 0.4231 (tptp) REVERT: M 440 GLN cc_start: 0.7289 (OUTLIER) cc_final: 0.6672 (tm-30) REVERT: M 476 ARG cc_start: 0.6993 (OUTLIER) cc_final: 0.5961 (mmt-90) REVERT: N 581 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.7082 (tt) REVERT: N 625 ASN cc_start: 0.7383 (p0) cc_final: 0.7025 (p0) REVERT: P 13 LYS cc_start: 0.6896 (mttt) cc_final: 0.6321 (mmtp) REVERT: P 43 LYS cc_start: 0.4374 (OUTLIER) cc_final: 0.4016 (ptmm) REVERT: Q 13 VAL cc_start: 0.4618 (OUTLIER) cc_final: 0.4241 (p) REVERT: Q 87 TYR cc_start: 0.5771 (OUTLIER) cc_final: 0.3712 (m-80) REVERT: Q 168 GLN cc_start: 0.2601 (mt0) cc_final: 0.2063 (mt0) REVERT: O 6 GLN cc_start: 0.7032 (pt0) cc_final: 0.6565 (pt0) REVERT: O 81 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7995 (tt0) REVERT: O 206 LYS cc_start: 0.5069 (OUTLIER) cc_final: 0.4484 (tmtm) REVERT: O 208 GLU cc_start: 0.4111 (pt0) cc_final: 0.3589 (pm20) REVERT: R 24 LYS cc_start: 0.7491 (tptp) cc_final: 0.7111 (tppp) REVERT: R 49 TYR cc_start: 0.7063 (OUTLIER) cc_final: 0.6403 (t80) REVERT: R 142 ARG cc_start: 0.4492 (OUTLIER) cc_final: 0.4127 (ttt180) REVERT: R 175 LEU cc_start: 0.4374 (OUTLIER) cc_final: 0.3882 (mt) REVERT: R 187 GLU cc_start: 0.4997 (mt-10) cc_final: 0.4462 (pm20) REVERT: R 190 LYS cc_start: 0.4611 (tttt) cc_final: 0.4357 (tptt) outliers start: 230 outliers final: 131 residues processed: 622 average time/residue: 0.6876 time to fit residues: 514.9955 Evaluate side-chains 552 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 391 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 99 GLN Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 87 TYR Chi-restraints excluded: chain E residue 96 TRP Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 186 TRP Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 61 ARG Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 205 LYS Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 49 TYR Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 161 GLU Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 207 LYS Chi-restraints excluded: chain G residue 248 THR Chi-restraints excluded: chain G residue 296 CYS Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 335 LYS Chi-restraints excluded: chain G residue 364 SER Chi-restraints excluded: chain G residue 418 CYS Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain H residue 535 MET Chi-restraints excluded: chain H residue 568 LEU Chi-restraints excluded: chain H residue 580 VAL Chi-restraints excluded: chain H residue 581 LEU Chi-restraints excluded: chain H residue 604 CYS Chi-restraints excluded: chain H residue 617 ARG Chi-restraints excluded: chain H residue 619 LEU Chi-restraints excluded: chain H residue 632 ASP Chi-restraints excluded: chain H residue 642 ILE Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 69 ILE Chi-restraints excluded: chain J residue 81 LYS Chi-restraints excluded: chain J residue 96 ARG Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 206 VAL Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 49 TYR Chi-restraints excluded: chain K residue 66 ILE Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 96 TRP Chi-restraints excluded: chain K residue 169 SER Chi-restraints excluded: chain I residue 13 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 61 ARG Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 75 GLN Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 201 THR Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 33 MET Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 142 ARG Chi-restraints excluded: chain L residue 145 LYS Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain M residue 110 SER Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 162 THR Chi-restraints excluded: chain M residue 163 THR Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 208 LEU Chi-restraints excluded: chain M residue 244 THR Chi-restraints excluded: chain M residue 248 THR Chi-restraints excluded: chain M residue 254 VAL Chi-restraints excluded: chain M residue 306 SER Chi-restraints excluded: chain M residue 308 ARG Chi-restraints excluded: chain M residue 333 VAL Chi-restraints excluded: chain M residue 364 SER Chi-restraints excluded: chain M residue 418 CYS Chi-restraints excluded: chain M residue 440 GLN Chi-restraints excluded: chain M residue 467 THR Chi-restraints excluded: chain M residue 476 ARG Chi-restraints excluded: chain M residue 494 LEU Chi-restraints excluded: chain M residue 500 ARG Chi-restraints excluded: chain N residue 580 VAL Chi-restraints excluded: chain N residue 581 LEU Chi-restraints excluded: chain N residue 588 ARG Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 43 LYS Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 67 VAL Chi-restraints excluded: chain P residue 81 LYS Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 100 VAL Chi-restraints excluded: chain P residue 100 TYR Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain P residue 176 VAL Chi-restraints excluded: chain P residue 200 THR Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain Q residue 87 TYR Chi-restraints excluded: chain Q residue 105 THR Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 81 GLU Chi-restraints excluded: chain O residue 137 LEU Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain O residue 139 LYS Chi-restraints excluded: chain O residue 148 VAL Chi-restraints excluded: chain O residue 201 THR Chi-restraints excluded: chain O residue 206 LYS Chi-restraints excluded: chain R residue 10 ILE Chi-restraints excluded: chain R residue 13 LEU Chi-restraints excluded: chain R residue 49 TYR Chi-restraints excluded: chain R residue 142 ARG Chi-restraints excluded: chain R residue 168 SER Chi-restraints excluded: chain R residue 175 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 184 optimal weight: 3.9990 chunk 375 optimal weight: 6.9990 chunk 113 optimal weight: 0.8980 chunk 285 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 413 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 430 optimal weight: 20.0000 chunk 104 optimal weight: 7.9990 chunk 337 optimal weight: 5.9990 chunk 128 optimal weight: 0.8980 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN C 72 GLN F 160 GLN ** F 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 GLN ** I 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 543 ASN ** N 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 607 ASN N 630 GLN P 166 GLN ** Q 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.192203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.165539 restraints weight = 73676.523| |-----------------------------------------------------------------------------| r_work (start): 0.4161 rms_B_bonded: 3.27 r_work: 0.3975 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3890 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 moved from start: 0.5126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 36855 Z= 0.177 Angle : 0.817 15.750 50358 Z= 0.399 Chirality : 0.052 0.769 5946 Planarity : 0.006 0.059 6201 Dihedral : 9.692 97.880 7200 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.07 % Favored : 91.72 % Rotamer: Outliers : 5.83 % Allowed : 19.22 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.97 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -2.59 (0.12), residues: 4350 helix: -2.75 (0.21), residues: 441 sheet: -0.86 (0.14), residues: 1362 loop : -2.07 (0.12), residues: 2547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG N 617 TYR 0.023 0.002 TYR D 140 PHE 0.031 0.002 PHE L 22 TRP 0.018 0.002 TRP C 150 HIS 0.007 0.001 HIS Q 38 Details of bonding type rmsd covalent geometry : bond 0.00418 (36672) covalent geometry : angle 0.77752 (49872) SS BOND : bond 0.00364 ( 63) SS BOND : angle 1.78794 ( 126) hydrogen bonds : bond 0.04129 ( 969) hydrogen bonds : angle 6.29051 ( 2817) link_ALPHA1-2 : bond 0.00433 ( 6) link_ALPHA1-2 : angle 1.67934 ( 18) link_ALPHA1-3 : bond 0.01058 ( 6) link_ALPHA1-3 : angle 2.20143 ( 18) link_ALPHA1-6 : bond 0.00967 ( 6) link_ALPHA1-6 : angle 1.60342 ( 18) link_BETA1-4 : bond 0.00736 ( 45) link_BETA1-4 : angle 2.68259 ( 135) link_NAG-ASN : bond 0.00482 ( 57) link_NAG-ASN : angle 3.37317 ( 171) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 224 poor density : 430 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.6916 (OUTLIER) cc_final: 0.6126 (pp30) REVERT: A 83 GLU cc_start: 0.7967 (tt0) cc_final: 0.7742 (tt0) REVERT: A 161 MET cc_start: 0.5924 (mmm) cc_final: 0.5091 (mmm) REVERT: B 581 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7185 (tt) REVERT: B 624 ASP cc_start: 0.6743 (m-30) cc_final: 0.6527 (m-30) REVERT: D 53 ASP cc_start: 0.3474 (m-30) cc_final: 0.3207 (m-30) REVERT: D 100 MET cc_start: 0.5351 (mpt) cc_final: 0.4968 (mmm) REVERT: E 83 GLU cc_start: 0.4905 (mt-10) cc_final: 0.4297 (tm-30) REVERT: E 96 TRP cc_start: 0.5276 (OUTLIER) cc_final: 0.3875 (m-10) REVERT: E 97 SER cc_start: 0.7306 (t) cc_final: 0.7096 (p) REVERT: E 181 LEU cc_start: 0.2908 (mt) cc_final: 0.2099 (pt) REVERT: C 61 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.6876 (ptm160) REVERT: F 33 MET cc_start: 0.7952 (ttm) cc_final: 0.7734 (mtp) REVERT: F 49 TYR cc_start: 0.7138 (OUTLIER) cc_final: 0.6385 (t80) REVERT: F 165 GLU cc_start: 0.5768 (OUTLIER) cc_final: 0.5374 (pm20) REVERT: F 175 LEU cc_start: 0.3999 (OUTLIER) cc_final: 0.3659 (mt) REVERT: F 187 GLU cc_start: 0.4625 (mt-10) cc_final: 0.4348 (pm20) REVERT: G 207 LYS cc_start: 0.6618 (OUTLIER) cc_final: 0.6136 (tttm) REVERT: G 217 TYR cc_start: 0.7650 (m-80) cc_final: 0.7214 (m-80) REVERT: J 96 ARG cc_start: 0.5943 (OUTLIER) cc_final: 0.5553 (pmm-80) REVERT: J 154 LEU cc_start: 0.2540 (OUTLIER) cc_final: 0.2211 (tt) REVERT: J 171 TYR cc_start: 0.2851 (m-80) cc_final: 0.2100 (m-80) REVERT: K 20 ARG cc_start: 0.6012 (mmm160) cc_final: 0.5595 (mpt180) REVERT: K 35 TRP cc_start: 0.6833 (m100) cc_final: 0.6390 (m100) REVERT: K 83 GLU cc_start: 0.5391 (mt-10) cc_final: 0.4308 (tm-30) REVERT: K 168 GLN cc_start: 0.2250 (mt0) cc_final: 0.1891 (mt0) REVERT: I 61 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7298 (ptm160) REVERT: I 76 ASP cc_start: 0.7686 (t0) cc_final: 0.7419 (t0) REVERT: L 24 LYS cc_start: 0.7773 (tmmt) cc_final: 0.7486 (tttp) REVERT: L 49 TYR cc_start: 0.7013 (OUTLIER) cc_final: 0.6161 (t80) REVERT: L 139 PHE cc_start: 0.3408 (p90) cc_final: 0.3183 (p90) REVERT: L 142 ARG cc_start: 0.4873 (OUTLIER) cc_final: 0.4337 (ttm170) REVERT: L 145 LYS cc_start: 0.5725 (ptmm) cc_final: 0.5151 (pttm) REVERT: L 175 LEU cc_start: 0.5240 (OUTLIER) cc_final: 0.4960 (mp) REVERT: L 188 LYS cc_start: 0.5306 (ttpp) cc_final: 0.5094 (ptpp) REVERT: M 82 GLN cc_start: 0.7026 (OUTLIER) cc_final: 0.5913 (pp30) REVERT: M 161 MET cc_start: 0.5608 (mmp) cc_final: 0.5385 (mmp) REVERT: M 308 ARG cc_start: 0.7580 (OUTLIER) cc_final: 0.7275 (ptm160) REVERT: M 440 GLN cc_start: 0.7283 (OUTLIER) cc_final: 0.6666 (tm-30) REVERT: M 476 ARG cc_start: 0.7062 (OUTLIER) cc_final: 0.6017 (mmt-90) REVERT: N 581 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.7149 (tt) REVERT: P 13 LYS cc_start: 0.6992 (mttt) cc_final: 0.6421 (mmtp) REVERT: P 43 LYS cc_start: 0.4476 (OUTLIER) cc_final: 0.4065 (ptmm) REVERT: Q 87 TYR cc_start: 0.5692 (OUTLIER) cc_final: 0.3632 (m-80) REVERT: Q 168 GLN cc_start: 0.2863 (mt0) cc_final: 0.2213 (mt0) REVERT: O 61 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7485 (ptm160) REVERT: O 81 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.8001 (tt0) REVERT: O 206 LYS cc_start: 0.5002 (OUTLIER) cc_final: 0.4423 (ptmm) REVERT: O 208 GLU cc_start: 0.4120 (pt0) cc_final: 0.3752 (pm20) REVERT: R 49 TYR cc_start: 0.7106 (OUTLIER) cc_final: 0.6531 (t80) REVERT: R 142 ARG cc_start: 0.4343 (OUTLIER) cc_final: 0.3974 (ttt180) REVERT: R 147 GLN cc_start: 0.3650 (mm-40) cc_final: 0.3250 (tp-100) REVERT: R 187 GLU cc_start: 0.4574 (mt-10) cc_final: 0.4193 (pm20) REVERT: R 190 LYS cc_start: 0.4487 (tttt) cc_final: 0.4251 (tptt) outliers start: 224 outliers final: 137 residues processed: 598 average time/residue: 0.6760 time to fit residues: 486.2139 Evaluate side-chains 559 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 396 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 99 GLN Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 87 TYR Chi-restraints excluded: chain E residue 96 TRP Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 186 TRP Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 61 ARG Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 49 TYR Chi-restraints excluded: chain F residue 161 GLU Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 207 LYS Chi-restraints excluded: chain G residue 248 THR Chi-restraints excluded: chain G residue 296 CYS Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 364 SER Chi-restraints excluded: chain G residue 418 CYS Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain H residue 544 LEU Chi-restraints excluded: chain H residue 568 LEU Chi-restraints excluded: chain H residue 580 VAL Chi-restraints excluded: chain H residue 581 LEU Chi-restraints excluded: chain H residue 604 CYS Chi-restraints excluded: chain H residue 617 ARG Chi-restraints excluded: chain H residue 619 LEU Chi-restraints excluded: chain H residue 639 THR Chi-restraints excluded: chain H residue 642 ILE Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 69 ILE Chi-restraints excluded: chain J residue 81 LYS Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 96 ARG Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 101 ASP Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 206 VAL Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 49 TYR Chi-restraints excluded: chain K residue 66 ILE Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 105 THR Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 169 SER Chi-restraints excluded: chain I residue 13 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 61 ARG Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 69 MET Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 201 THR Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 33 MET Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 142 ARG Chi-restraints excluded: chain L residue 168 SER Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain M residue 82 GLN Chi-restraints excluded: chain M residue 110 SER Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 162 THR Chi-restraints excluded: chain M residue 163 THR Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 208 LEU Chi-restraints excluded: chain M residue 244 THR Chi-restraints excluded: chain M residue 248 THR Chi-restraints excluded: chain M residue 254 VAL Chi-restraints excluded: chain M residue 306 SER Chi-restraints excluded: chain M residue 308 ARG Chi-restraints excluded: chain M residue 333 VAL Chi-restraints excluded: chain M residue 364 SER Chi-restraints excluded: chain M residue 418 CYS Chi-restraints excluded: chain M residue 440 GLN Chi-restraints excluded: chain M residue 467 THR Chi-restraints excluded: chain M residue 476 ARG Chi-restraints excluded: chain N residue 580 VAL Chi-restraints excluded: chain N residue 581 LEU Chi-restraints excluded: chain N residue 629 LEU Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 43 LYS Chi-restraints excluded: chain P residue 67 VAL Chi-restraints excluded: chain P residue 81 LYS Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain P residue 176 VAL Chi-restraints excluded: chain P residue 200 THR Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 69 THR Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain Q residue 87 TYR Chi-restraints excluded: chain Q residue 105 THR Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 61 ARG Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 81 GLU Chi-restraints excluded: chain O residue 137 LEU Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain O residue 139 LYS Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 148 VAL Chi-restraints excluded: chain O residue 201 THR Chi-restraints excluded: chain O residue 206 LYS Chi-restraints excluded: chain R residue 10 ILE Chi-restraints excluded: chain R residue 13 LEU Chi-restraints excluded: chain R residue 49 TYR Chi-restraints excluded: chain R residue 142 ARG Chi-restraints excluded: chain R residue 168 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 34 optimal weight: 0.0970 chunk 132 optimal weight: 10.0000 chunk 309 optimal weight: 5.9990 chunk 354 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 258 optimal weight: 4.9990 chunk 67 optimal weight: 20.0000 chunk 263 optimal weight: 7.9990 chunk 274 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 GLN ** E 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN F 160 GLN ** F 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 GLN ** I 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 543 ASN ** N 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.192983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.165835 restraints weight = 73547.816| |-----------------------------------------------------------------------------| r_work (start): 0.4161 rms_B_bonded: 3.17 r_work: 0.3989 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3903 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.5295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 36855 Z= 0.164 Angle : 0.811 17.277 50358 Z= 0.394 Chirality : 0.051 0.814 5946 Planarity : 0.005 0.080 6201 Dihedral : 9.386 90.118 7200 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.13 % Favored : 90.67 % Rotamer: Outliers : 5.83 % Allowed : 19.71 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.97 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -2.51 (0.12), residues: 4350 helix: -2.70 (0.20), residues: 459 sheet: -0.71 (0.14), residues: 1389 loop : -2.08 (0.12), residues: 2502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 617 TYR 0.026 0.002 TYR J 140 PHE 0.032 0.002 PHE L 22 TRP 0.018 0.002 TRP E 96 HIS 0.008 0.001 HIS E 38 Details of bonding type rmsd covalent geometry : bond 0.00384 (36672) covalent geometry : angle 0.77148 (49872) SS BOND : bond 0.00315 ( 63) SS BOND : angle 1.81640 ( 126) hydrogen bonds : bond 0.03969 ( 969) hydrogen bonds : angle 6.11118 ( 2817) link_ALPHA1-2 : bond 0.00464 ( 6) link_ALPHA1-2 : angle 1.68964 ( 18) link_ALPHA1-3 : bond 0.01068 ( 6) link_ALPHA1-3 : angle 2.31257 ( 18) link_ALPHA1-6 : bond 0.00999 ( 6) link_ALPHA1-6 : angle 1.68472 ( 18) link_BETA1-4 : bond 0.00758 ( 45) link_BETA1-4 : angle 2.64264 ( 135) link_NAG-ASN : bond 0.00408 ( 57) link_NAG-ASN : angle 3.34609 ( 171) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 224 poor density : 420 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.6773 (OUTLIER) cc_final: 0.6058 (pp30) REVERT: A 161 MET cc_start: 0.5833 (mmm) cc_final: 0.5052 (mmm) REVERT: B 535 MET cc_start: 0.7707 (mpp) cc_final: 0.7422 (mtt) REVERT: B 581 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7266 (tt) REVERT: B 624 ASP cc_start: 0.6752 (m-30) cc_final: 0.6531 (m-30) REVERT: D 13 LYS cc_start: 0.6884 (mttt) cc_final: 0.6289 (tppt) REVERT: D 53 ASP cc_start: 0.3840 (m-30) cc_final: 0.3579 (m-30) REVERT: D 100 MET cc_start: 0.5349 (mpt) cc_final: 0.4972 (mmm) REVERT: E 83 GLU cc_start: 0.5092 (mt-10) cc_final: 0.4376 (tm-30) REVERT: E 96 TRP cc_start: 0.5331 (OUTLIER) cc_final: 0.4010 (m-10) REVERT: E 97 SER cc_start: 0.7311 (t) cc_final: 0.7095 (p) REVERT: E 181 LEU cc_start: 0.2686 (mt) cc_final: 0.1911 (pt) REVERT: C 61 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.6889 (ptm160) REVERT: F 49 TYR cc_start: 0.6998 (OUTLIER) cc_final: 0.6257 (t80) REVERT: F 187 GLU cc_start: 0.4635 (mt-10) cc_final: 0.4334 (pm20) REVERT: F 188 LYS cc_start: 0.5547 (ttmm) cc_final: 0.5205 (tmtt) REVERT: G 207 LYS cc_start: 0.6539 (OUTLIER) cc_final: 0.5993 (tttm) REVERT: G 217 TYR cc_start: 0.7574 (m-80) cc_final: 0.7151 (m-80) REVERT: J 96 ARG cc_start: 0.5931 (OUTLIER) cc_final: 0.5584 (pmm-80) REVERT: J 154 LEU cc_start: 0.2534 (OUTLIER) cc_final: 0.2215 (tt) REVERT: J 171 TYR cc_start: 0.2806 (m-80) cc_final: 0.2127 (m-80) REVERT: K 35 TRP cc_start: 0.6820 (m100) cc_final: 0.6399 (m100) REVERT: K 83 GLU cc_start: 0.5388 (mt-10) cc_final: 0.4277 (tm-30) REVERT: I 61 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7286 (ptm160) REVERT: I 208 GLU cc_start: 0.3959 (pt0) cc_final: 0.3662 (pm20) REVERT: L 49 TYR cc_start: 0.6889 (OUTLIER) cc_final: 0.6022 (t80) REVERT: L 139 PHE cc_start: 0.3505 (p90) cc_final: 0.3170 (p90) REVERT: L 142 ARG cc_start: 0.4837 (OUTLIER) cc_final: 0.4298 (ttm170) REVERT: L 175 LEU cc_start: 0.5270 (OUTLIER) cc_final: 0.4993 (mp) REVERT: L 187 GLU cc_start: 0.4979 (mt-10) cc_final: 0.4129 (pp20) REVERT: L 188 LYS cc_start: 0.5375 (ttpp) cc_final: 0.5005 (ptpp) REVERT: M 82 GLN cc_start: 0.6967 (OUTLIER) cc_final: 0.6195 (pp30) REVERT: M 161 MET cc_start: 0.5595 (mmp) cc_final: 0.5350 (mmp) REVERT: M 308 ARG cc_start: 0.7532 (OUTLIER) cc_final: 0.7211 (ptm160) REVERT: M 440 GLN cc_start: 0.7421 (OUTLIER) cc_final: 0.6815 (tm-30) REVERT: M 476 ARG cc_start: 0.7109 (OUTLIER) cc_final: 0.6083 (mmt-90) REVERT: N 581 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.7034 (tt) REVERT: P 43 LYS cc_start: 0.4423 (OUTLIER) cc_final: 0.4023 (ptmm) REVERT: P 45 LEU cc_start: 0.4697 (OUTLIER) cc_final: 0.4392 (mp) REVERT: Q 87 TYR cc_start: 0.5599 (OUTLIER) cc_final: 0.3595 (m-80) REVERT: Q 168 GLN cc_start: 0.2748 (mt0) cc_final: 0.2104 (mt0) REVERT: O 61 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7529 (ptm160) REVERT: O 69 MET cc_start: 0.7311 (OUTLIER) cc_final: 0.7080 (mtm) REVERT: O 76 ASP cc_start: 0.7745 (t0) cc_final: 0.7478 (t0) REVERT: O 80 MET cc_start: 0.8117 (tmm) cc_final: 0.7753 (ttp) REVERT: O 81 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.8007 (tt0) REVERT: O 206 LYS cc_start: 0.5025 (OUTLIER) cc_final: 0.4430 (ptmm) REVERT: O 208 GLU cc_start: 0.4098 (pt0) cc_final: 0.3721 (pm20) REVERT: R 49 TYR cc_start: 0.6971 (OUTLIER) cc_final: 0.6423 (t80) REVERT: R 142 ARG cc_start: 0.4301 (OUTLIER) cc_final: 0.3965 (ttt180) REVERT: R 147 GLN cc_start: 0.3581 (mm-40) cc_final: 0.3191 (tp-100) REVERT: R 175 LEU cc_start: 0.4802 (OUTLIER) cc_final: 0.4276 (mt) REVERT: R 187 GLU cc_start: 0.4846 (mt-10) cc_final: 0.4370 (pm20) outliers start: 224 outliers final: 145 residues processed: 598 average time/residue: 0.6736 time to fit residues: 486.3622 Evaluate side-chains 567 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 395 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 99 GLN Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain E residue 87 TYR Chi-restraints excluded: chain E residue 96 TRP Chi-restraints excluded: chain E residue 186 TRP Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 61 ARG Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 49 TYR Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 207 LYS Chi-restraints excluded: chain G residue 248 THR Chi-restraints excluded: chain G residue 296 CYS Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 356 ASN Chi-restraints excluded: chain G residue 364 SER Chi-restraints excluded: chain G residue 418 CYS Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain H residue 544 LEU Chi-restraints excluded: chain H residue 568 LEU Chi-restraints excluded: chain H residue 580 VAL Chi-restraints excluded: chain H residue 581 LEU Chi-restraints excluded: chain H residue 604 CYS Chi-restraints excluded: chain H residue 617 ARG Chi-restraints excluded: chain H residue 619 LEU Chi-restraints excluded: chain H residue 639 THR Chi-restraints excluded: chain H residue 642 ILE Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 69 ILE Chi-restraints excluded: chain J residue 81 LYS Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 96 ARG Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 101 ASP Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 206 VAL Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 66 ILE Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 105 THR Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 169 SER Chi-restraints excluded: chain I residue 13 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 61 ARG Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 201 THR Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 142 ARG Chi-restraints excluded: chain L residue 168 SER Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain M residue 82 GLN Chi-restraints excluded: chain M residue 110 SER Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 162 THR Chi-restraints excluded: chain M residue 163 THR Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 208 LEU Chi-restraints excluded: chain M residue 244 THR Chi-restraints excluded: chain M residue 248 THR Chi-restraints excluded: chain M residue 254 VAL Chi-restraints excluded: chain M residue 308 ARG Chi-restraints excluded: chain M residue 333 VAL Chi-restraints excluded: chain M residue 364 SER Chi-restraints excluded: chain M residue 415 THR Chi-restraints excluded: chain M residue 418 CYS Chi-restraints excluded: chain M residue 422 MET Chi-restraints excluded: chain M residue 440 GLN Chi-restraints excluded: chain M residue 467 THR Chi-restraints excluded: chain M residue 476 ARG Chi-restraints excluded: chain M residue 494 LEU Chi-restraints excluded: chain N residue 580 VAL Chi-restraints excluded: chain N residue 581 LEU Chi-restraints excluded: chain N residue 588 ARG Chi-restraints excluded: chain N residue 629 LEU Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 43 LYS Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 67 VAL Chi-restraints excluded: chain P residue 69 ILE Chi-restraints excluded: chain P residue 81 LYS Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 100 VAL Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain P residue 176 VAL Chi-restraints excluded: chain P residue 200 THR Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 69 THR Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain Q residue 87 TYR Chi-restraints excluded: chain Q residue 105 THR Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 61 ARG Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 69 MET Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 81 GLU Chi-restraints excluded: chain O residue 137 LEU Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain O residue 139 LYS Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 148 VAL Chi-restraints excluded: chain O residue 189 THR Chi-restraints excluded: chain O residue 201 THR Chi-restraints excluded: chain O residue 206 LYS Chi-restraints excluded: chain R residue 10 ILE Chi-restraints excluded: chain R residue 13 LEU Chi-restraints excluded: chain R residue 49 TYR Chi-restraints excluded: chain R residue 142 ARG Chi-restraints excluded: chain R residue 168 SER Chi-restraints excluded: chain R residue 175 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 261 optimal weight: 9.9990 chunk 341 optimal weight: 8.9990 chunk 66 optimal weight: 0.9980 chunk 210 optimal weight: 0.3980 chunk 171 optimal weight: 0.0470 chunk 108 optimal weight: 0.8980 chunk 305 optimal weight: 0.4980 chunk 79 optimal weight: 2.9990 chunk 278 optimal weight: 30.0000 chunk 430 optimal weight: 9.9990 chunk 194 optimal weight: 3.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN ** F 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 GLN G 249 HIS ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 42 GLN K 52 GLN K 108 GLN ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 103 GLN N 543 ASN ** N 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 50 ASN ** R 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.195488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.168295 restraints weight = 73841.770| |-----------------------------------------------------------------------------| r_work (start): 0.4188 rms_B_bonded: 3.40 r_work: 0.4012 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6662 moved from start: 0.5397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 36855 Z= 0.123 Angle : 0.746 15.342 50358 Z= 0.361 Chirality : 0.049 0.726 5946 Planarity : 0.005 0.067 6201 Dihedral : 8.541 74.121 7200 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.03 % Favored : 92.76 % Rotamer: Outliers : 3.88 % Allowed : 21.95 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.97 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.23 (0.12), residues: 4350 helix: -2.39 (0.21), residues: 462 sheet: -0.48 (0.14), residues: 1353 loop : -1.92 (0.12), residues: 2535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 40 TYR 0.021 0.001 TYR G 173 PHE 0.034 0.001 PHE L 22 TRP 0.020 0.001 TRP E 96 HIS 0.012 0.001 HIS R 189 Details of bonding type rmsd covalent geometry : bond 0.00275 (36672) covalent geometry : angle 0.70880 (49872) SS BOND : bond 0.00461 ( 63) SS BOND : angle 1.55957 ( 126) hydrogen bonds : bond 0.03397 ( 969) hydrogen bonds : angle 5.71792 ( 2817) link_ALPHA1-2 : bond 0.00569 ( 6) link_ALPHA1-2 : angle 1.51433 ( 18) link_ALPHA1-3 : bond 0.01224 ( 6) link_ALPHA1-3 : angle 2.20013 ( 18) link_ALPHA1-6 : bond 0.01091 ( 6) link_ALPHA1-6 : angle 2.07425 ( 18) link_BETA1-4 : bond 0.00793 ( 45) link_BETA1-4 : angle 2.49341 ( 135) link_NAG-ASN : bond 0.00408 ( 57) link_NAG-ASN : angle 3.05914 ( 171) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 467 time to evaluate : 1.314 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 82 GLN cc_start: 0.6528 (OUTLIER) cc_final: 0.5678 (pp30) REVERT: A 125 LEU cc_start: 0.7310 (OUTLIER) cc_final: 0.6986 (tp) REVERT: A 161 MET cc_start: 0.5630 (mmm) cc_final: 0.4879 (mmm) REVERT: B 581 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.7303 (tt) REVERT: D 13 LYS cc_start: 0.6784 (mttt) cc_final: 0.6190 (tppt) REVERT: D 43 LYS cc_start: 0.4031 (ptmm) cc_final: 0.3722 (ptmm) REVERT: D 45 LEU cc_start: 0.4357 (mp) cc_final: 0.3784 (mm) REVERT: D 53 ASP cc_start: 0.4024 (m-30) cc_final: 0.3759 (m-30) REVERT: D 100 MET cc_start: 0.5182 (mpt) cc_final: 0.4767 (mmm) REVERT: E 83 GLU cc_start: 0.5203 (mt-10) cc_final: 0.4515 (tm-30) REVERT: E 96 TRP cc_start: 0.5170 (OUTLIER) cc_final: 0.3782 (m-10) REVERT: E 97 SER cc_start: 0.7241 (t) cc_final: 0.6970 (p) REVERT: E 181 LEU cc_start: 0.2649 (mt) cc_final: 0.1902 (pt) REVERT: C 61 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.6800 (ptm160) REVERT: C 79 TYR cc_start: 0.7695 (m-80) cc_final: 0.7490 (m-80) REVERT: C 112 SER cc_start: 0.6041 (t) cc_final: 0.5796 (p) REVERT: F 49 TYR cc_start: 0.6514 (OUTLIER) cc_final: 0.5892 (t80) REVERT: F 187 GLU cc_start: 0.4682 (mt-10) cc_final: 0.4370 (pm20) REVERT: G 47 ASP cc_start: 0.7660 (m-30) cc_final: 0.7306 (t0) REVERT: G 217 TYR cc_start: 0.7491 (m-80) cc_final: 0.7071 (m-80) REVERT: J 124 LEU cc_start: 0.0463 (OUTLIER) cc_final: 0.0166 (tp) REVERT: K 35 TRP cc_start: 0.6742 (m100) cc_final: 0.6365 (m100) REVERT: K 83 GLU cc_start: 0.5307 (mt-10) cc_final: 0.4243 (tm-30) REVERT: I 61 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.7085 (ptm160) REVERT: I 112 SER cc_start: 0.6803 (t) cc_final: 0.6384 (p) REVERT: I 208 GLU cc_start: 0.3951 (pt0) cc_final: 0.3736 (pm20) REVERT: L 22 PHE cc_start: 0.4264 (t80) cc_final: 0.3937 (t80) REVERT: L 49 TYR cc_start: 0.6460 (OUTLIER) cc_final: 0.5354 (t80) REVERT: L 145 LYS cc_start: 0.5835 (ptmm) cc_final: 0.5354 (pmtt) REVERT: L 187 GLU cc_start: 0.4863 (mt-10) cc_final: 0.4042 (pp20) REVERT: L 188 LYS cc_start: 0.5411 (ttpp) cc_final: 0.5033 (ptpp) REVERT: M 82 GLN cc_start: 0.6482 (OUTLIER) cc_final: 0.5713 (pp30) REVERT: M 161 MET cc_start: 0.5332 (mmp) cc_final: 0.5081 (mmp) REVERT: N 581 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.7032 (tt) REVERT: P 43 LYS cc_start: 0.3808 (OUTLIER) cc_final: 0.3481 (ptmm) REVERT: P 100 MET cc_start: 0.4920 (mmm) cc_final: 0.4632 (mmt) REVERT: Q 82 ASP cc_start: 0.4379 (m-30) cc_final: 0.4123 (m-30) REVERT: Q 168 GLN cc_start: 0.2702 (mt0) cc_final: 0.2011 (mt0) REVERT: O 61 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7195 (ptm160) REVERT: O 80 MET cc_start: 0.7965 (tmm) cc_final: 0.7654 (ttp) REVERT: O 81 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7656 (tt0) REVERT: O 137 LEU cc_start: 0.3332 (OUTLIER) cc_final: 0.3046 (tt) REVERT: O 206 LYS cc_start: 0.5036 (OUTLIER) cc_final: 0.4468 (ptmm) REVERT: O 208 GLU cc_start: 0.4015 (pt0) cc_final: 0.3772 (pm20) REVERT: R 49 TYR cc_start: 0.6471 (OUTLIER) cc_final: 0.6053 (t80) REVERT: R 142 ARG cc_start: 0.4175 (OUTLIER) cc_final: 0.3734 (ttt180) REVERT: R 175 LEU cc_start: 0.4570 (OUTLIER) cc_final: 0.4124 (mt) REVERT: R 187 GLU cc_start: 0.4631 (mt-10) cc_final: 0.4119 (pm20) outliers start: 149 outliers final: 94 residues processed: 583 average time/residue: 0.6848 time to fit residues: 481.9769 Evaluate side-chains 530 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 417 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 99 GLN Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 96 TRP Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 186 TRP Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 61 ARG Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 49 TYR Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 248 THR Chi-restraints excluded: chain G residue 296 CYS Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 415 THR Chi-restraints excluded: chain G residue 418 CYS Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain H residue 544 LEU Chi-restraints excluded: chain H residue 604 CYS Chi-restraints excluded: chain H residue 619 LEU Chi-restraints excluded: chain H residue 642 ILE Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 69 ILE Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 206 VAL Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 52 GLN Chi-restraints excluded: chain K residue 66 ILE Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 105 THR Chi-restraints excluded: chain I residue 13 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 61 ARG Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 168 SER Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain M residue 82 GLN Chi-restraints excluded: chain M residue 110 SER Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 162 THR Chi-restraints excluded: chain M residue 163 THR Chi-restraints excluded: chain M residue 244 THR Chi-restraints excluded: chain M residue 254 VAL Chi-restraints excluded: chain M residue 306 SER Chi-restraints excluded: chain M residue 333 VAL Chi-restraints excluded: chain M residue 376 PHE Chi-restraints excluded: chain M residue 415 THR Chi-restraints excluded: chain M residue 418 CYS Chi-restraints excluded: chain M residue 467 THR Chi-restraints excluded: chain N residue 534 SER Chi-restraints excluded: chain N residue 581 LEU Chi-restraints excluded: chain P residue 43 LYS Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 100 VAL Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain P residue 176 VAL Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 69 THR Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain Q residue 105 THR Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 61 ARG Chi-restraints excluded: chain O residue 81 GLU Chi-restraints excluded: chain O residue 137 LEU Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain O residue 139 LYS Chi-restraints excluded: chain O residue 189 THR Chi-restraints excluded: chain O residue 206 LYS Chi-restraints excluded: chain R residue 10 ILE Chi-restraints excluded: chain R residue 49 TYR Chi-restraints excluded: chain R residue 142 ARG Chi-restraints excluded: chain R residue 168 SER Chi-restraints excluded: chain R residue 175 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 236 optimal weight: 0.2980 chunk 95 optimal weight: 8.9990 chunk 148 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 405 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 354 optimal weight: 0.0010 chunk 321 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 122 optimal weight: 10.0000 overall best weight: 1.2592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 GLN D 150 ASN E 34 GLN E 42 GLN ** E 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN C 6 GLN C 72 GLN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 GLN G 374 HIS ** K 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 42 GLN I 3 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 103 GLN N 543 ASN ** N 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 50 ASN O 6 GLN R 198 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.195223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.168562 restraints weight = 73980.290| |-----------------------------------------------------------------------------| r_work (start): 0.4195 rms_B_bonded: 3.07 r_work: 0.4022 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3938 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6743 moved from start: 0.5527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 36855 Z= 0.130 Angle : 0.766 17.986 50358 Z= 0.368 Chirality : 0.050 0.967 5946 Planarity : 0.005 0.061 6201 Dihedral : 8.160 58.128 7200 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.56 % Favored : 92.23 % Rotamer: Outliers : 3.57 % Allowed : 22.81 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.97 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.06 (0.12), residues: 4350 helix: -2.15 (0.22), residues: 444 sheet: -0.39 (0.14), residues: 1353 loop : -1.83 (0.12), residues: 2553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 40 TYR 0.030 0.002 TYR P 140 PHE 0.032 0.001 PHE L 22 TRP 0.019 0.001 TRP E 96 HIS 0.005 0.001 HIS J 195 Details of bonding type rmsd covalent geometry : bond 0.00298 (36672) covalent geometry : angle 0.72934 (49872) SS BOND : bond 0.00347 ( 63) SS BOND : angle 1.74669 ( 126) hydrogen bonds : bond 0.03429 ( 969) hydrogen bonds : angle 5.65067 ( 2817) link_ALPHA1-2 : bond 0.00547 ( 6) link_ALPHA1-2 : angle 1.62802 ( 18) link_ALPHA1-3 : bond 0.01353 ( 6) link_ALPHA1-3 : angle 1.64344 ( 18) link_ALPHA1-6 : bond 0.01083 ( 6) link_ALPHA1-6 : angle 2.15983 ( 18) link_BETA1-4 : bond 0.00770 ( 45) link_BETA1-4 : angle 2.52323 ( 135) link_NAG-ASN : bond 0.00363 ( 57) link_NAG-ASN : angle 3.08788 ( 171) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 433 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.7904 (m-30) cc_final: 0.7692 (m-30) REVERT: A 82 GLN cc_start: 0.6807 (OUTLIER) cc_final: 0.5837 (pp30) REVERT: A 125 LEU cc_start: 0.7229 (OUTLIER) cc_final: 0.6942 (tp) REVERT: A 161 MET cc_start: 0.5873 (mmm) cc_final: 0.5091 (mmm) REVERT: B 581 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7174 (tt) REVERT: D 13 LYS cc_start: 0.6865 (mttt) cc_final: 0.6230 (tppt) REVERT: D 45 LEU cc_start: 0.4346 (mp) cc_final: 0.3762 (mm) REVERT: D 53 ASP cc_start: 0.4097 (m-30) cc_final: 0.3786 (m-30) REVERT: D 97 ARG cc_start: 0.6201 (ttm170) cc_final: 0.5780 (mtm110) REVERT: D 100 MET cc_start: 0.5217 (mpt) cc_final: 0.4829 (mmm) REVERT: E 83 GLU cc_start: 0.4944 (mt-10) cc_final: 0.4422 (tm-30) REVERT: E 96 TRP cc_start: 0.5349 (OUTLIER) cc_final: 0.3794 (m-10) REVERT: E 97 SER cc_start: 0.7459 (t) cc_final: 0.7179 (p) REVERT: E 181 LEU cc_start: 0.2552 (mt) cc_final: 0.1792 (pt) REVERT: C 61 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.6948 (ptm160) REVERT: C 112 SER cc_start: 0.6039 (t) cc_final: 0.5703 (p) REVERT: F 24 LYS cc_start: 0.7686 (tmmt) cc_final: 0.7260 (tptp) REVERT: F 49 TYR cc_start: 0.6771 (OUTLIER) cc_final: 0.6078 (t80) REVERT: F 147 GLN cc_start: 0.3530 (mm-40) cc_final: 0.3254 (mp10) REVERT: F 187 GLU cc_start: 0.4938 (mt-10) cc_final: 0.4501 (pm20) REVERT: G 47 ASP cc_start: 0.7878 (m-30) cc_final: 0.7467 (t0) REVERT: G 217 TYR cc_start: 0.7629 (m-80) cc_final: 0.7181 (m-80) REVERT: G 267 GLU cc_start: 0.6745 (pm20) cc_final: 0.6395 (mp0) REVERT: J 78 LEU cc_start: 0.2417 (OUTLIER) cc_final: 0.2186 (tm) REVERT: J 124 LEU cc_start: 0.0528 (OUTLIER) cc_final: 0.0203 (tp) REVERT: K 83 GLU cc_start: 0.5429 (mt-10) cc_final: 0.4364 (tm-30) REVERT: I 61 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7207 (ptm160) REVERT: I 112 SER cc_start: 0.6767 (t) cc_final: 0.6347 (p) REVERT: L 22 PHE cc_start: 0.4276 (t80) cc_final: 0.3917 (t80) REVERT: L 49 TYR cc_start: 0.6718 (OUTLIER) cc_final: 0.5617 (t80) REVERT: L 145 LYS cc_start: 0.5957 (ptmm) cc_final: 0.5461 (pmtt) REVERT: L 187 GLU cc_start: 0.4861 (mt-10) cc_final: 0.4053 (pp20) REVERT: L 188 LYS cc_start: 0.5534 (ttpp) cc_final: 0.5121 (ptpp) REVERT: M 82 GLN cc_start: 0.6579 (OUTLIER) cc_final: 0.5835 (pp30) REVERT: M 161 MET cc_start: 0.5633 (mmp) cc_final: 0.5421 (mmp) REVERT: N 581 LEU cc_start: 0.7281 (OUTLIER) cc_final: 0.6972 (tt) REVERT: P 43 LYS cc_start: 0.3864 (OUTLIER) cc_final: 0.3559 (ptmm) REVERT: P 100 MET cc_start: 0.5038 (mmm) cc_final: 0.4698 (mmt) REVERT: P 124 LEU cc_start: 0.0665 (mm) cc_final: 0.0371 (tp) REVERT: Q 50 ASN cc_start: 0.6342 (OUTLIER) cc_final: 0.6132 (t0) REVERT: Q 82 ASP cc_start: 0.4439 (m-30) cc_final: 0.4192 (m-30) REVERT: Q 168 GLN cc_start: 0.2749 (mt0) cc_final: 0.2053 (mt0) REVERT: O 61 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7535 (ptm160) REVERT: O 80 MET cc_start: 0.8075 (tmm) cc_final: 0.7727 (ttp) REVERT: O 81 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.8028 (tt0) REVERT: O 137 LEU cc_start: 0.3434 (OUTLIER) cc_final: 0.3136 (tt) REVERT: O 206 LYS cc_start: 0.4979 (ptmm) cc_final: 0.4391 (ptmm) REVERT: R 49 TYR cc_start: 0.6669 (OUTLIER) cc_final: 0.6310 (t80) REVERT: R 145 LYS cc_start: 0.5362 (pttt) cc_final: 0.4556 (pptt) REVERT: R 147 GLN cc_start: 0.3677 (mm-40) cc_final: 0.3413 (tp-100) REVERT: R 175 LEU cc_start: 0.4786 (OUTLIER) cc_final: 0.4309 (mt) REVERT: R 187 GLU cc_start: 0.4702 (mt-10) cc_final: 0.4195 (pm20) outliers start: 137 outliers final: 90 residues processed: 540 average time/residue: 0.6645 time to fit residues: 433.3526 Evaluate side-chains 516 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 407 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 99 GLN Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain E residue 96 TRP Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 186 TRP Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 61 ARG Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 49 TYR Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 248 THR Chi-restraints excluded: chain G residue 296 CYS Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 356 ASN Chi-restraints excluded: chain G residue 415 THR Chi-restraints excluded: chain G residue 418 CYS Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain H residue 544 LEU Chi-restraints excluded: chain H residue 604 CYS Chi-restraints excluded: chain H residue 619 LEU Chi-restraints excluded: chain H residue 632 ASP Chi-restraints excluded: chain H residue 642 ILE Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 69 ILE Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 206 VAL Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 88 CYS Chi-restraints excluded: chain K residue 105 THR Chi-restraints excluded: chain I residue 13 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 61 ARG Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 168 SER Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain M residue 82 GLN Chi-restraints excluded: chain M residue 95 MET Chi-restraints excluded: chain M residue 110 SER Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 162 THR Chi-restraints excluded: chain M residue 163 THR Chi-restraints excluded: chain M residue 244 THR Chi-restraints excluded: chain M residue 254 VAL Chi-restraints excluded: chain M residue 306 SER Chi-restraints excluded: chain M residue 333 VAL Chi-restraints excluded: chain M residue 376 PHE Chi-restraints excluded: chain M residue 415 THR Chi-restraints excluded: chain M residue 418 CYS Chi-restraints excluded: chain M residue 467 THR Chi-restraints excluded: chain M residue 494 LEU Chi-restraints excluded: chain N residue 534 SER Chi-restraints excluded: chain N residue 581 LEU Chi-restraints excluded: chain P residue 43 LYS Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 100 VAL Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain P residue 176 VAL Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 50 ASN Chi-restraints excluded: chain Q residue 69 THR Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain Q residue 105 THR Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 61 ARG Chi-restraints excluded: chain O residue 81 GLU Chi-restraints excluded: chain O residue 137 LEU Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain O residue 139 LYS Chi-restraints excluded: chain O residue 189 THR Chi-restraints excluded: chain R residue 10 ILE Chi-restraints excluded: chain R residue 49 TYR Chi-restraints excluded: chain R residue 168 SER Chi-restraints excluded: chain R residue 175 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 93 optimal weight: 0.8980 chunk 136 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 chunk 380 optimal weight: 5.9990 chunk 303 optimal weight: 20.0000 chunk 423 optimal weight: 0.0470 chunk 115 optimal weight: 4.9990 chunk 60 optimal weight: 20.0000 chunk 35 optimal weight: 3.9990 chunk 193 optimal weight: 2.9990 chunk 121 optimal weight: 7.9990 overall best weight: 2.5884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 653 GLN E 42 GLN ** E 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 42 GLN I 3 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 103 GLN N 543 ASN ** N 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 160 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.194111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.167244 restraints weight = 73665.430| |-----------------------------------------------------------------------------| r_work (start): 0.4178 rms_B_bonded: 3.16 r_work: 0.4006 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3919 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6783 moved from start: 0.5605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 36855 Z= 0.157 Angle : 0.789 20.474 50358 Z= 0.381 Chirality : 0.052 1.214 5946 Planarity : 0.005 0.060 6201 Dihedral : 8.250 59.539 7200 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.14 % Favored : 91.63 % Rotamer: Outliers : 3.75 % Allowed : 22.79 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.97 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.08 (0.13), residues: 4350 helix: -2.11 (0.22), residues: 441 sheet: -0.43 (0.14), residues: 1371 loop : -1.84 (0.12), residues: 2538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 40 TYR 0.030 0.002 TYR P 140 PHE 0.030 0.002 PHE L 22 TRP 0.019 0.002 TRP E 96 HIS 0.006 0.001 HIS P 195 Details of bonding type rmsd covalent geometry : bond 0.00368 (36672) covalent geometry : angle 0.74885 (49872) SS BOND : bond 0.00387 ( 63) SS BOND : angle 2.02356 ( 126) hydrogen bonds : bond 0.03658 ( 969) hydrogen bonds : angle 5.74119 ( 2817) link_ALPHA1-2 : bond 0.00332 ( 6) link_ALPHA1-2 : angle 1.68142 ( 18) link_ALPHA1-3 : bond 0.01280 ( 6) link_ALPHA1-3 : angle 1.21388 ( 18) link_ALPHA1-6 : bond 0.01091 ( 6) link_ALPHA1-6 : angle 2.03461 ( 18) link_BETA1-4 : bond 0.00830 ( 45) link_BETA1-4 : angle 2.58175 ( 135) link_NAG-ASN : bond 0.00391 ( 57) link_NAG-ASN : angle 3.24581 ( 171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16253.72 seconds wall clock time: 276 minutes 32.52 seconds (16592.52 seconds total)