Starting phenix.real_space_refine on Fri Feb 23 00:47:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v8z_21112/02_2024/6v8z_21112_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v8z_21112/02_2024/6v8z_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v8z_21112/02_2024/6v8z_21112.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v8z_21112/02_2024/6v8z_21112.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v8z_21112/02_2024/6v8z_21112_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v8z_21112/02_2024/6v8z_21112_neut.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Residue "A TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 503": "NH1" <-> "NH2" Residue "D PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 503": "NH1" <-> "NH2" Residue "J PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 503": "NH1" <-> "NH2" Residue "P PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/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: 19.21, per 1000 atoms: 0.54 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 - 3.50 Amino acid : False - 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: 15.37 Conformation dependent library (CDL) restraints added in 6.7 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: 5.10 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: 17.46 Time building geometry restraints manager: 16.41 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: 96.61 - 107.09: 1635 107.09 - 117.56: 26482 117.56 - 128.03: 21302 128.03 - 138.51: 447 138.51 - 148.98: 6 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 2.440 nonbonded pdb=" O PRO Q 120 " pdb=" OG1 THR Q 132 " model vdw 2.185 2.440 nonbonded pdb=" O PRO K 120 " pdb=" OG1 THR K 132 " model vdw 2.185 2.440 nonbonded pdb=" O TYR L 186 " pdb=" OH TYR L 192 " model vdw 2.207 2.440 nonbonded pdb=" O TYR R 186 " pdb=" OH TYR R 192 " model vdw 2.207 2.440 ... (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 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: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 5.040 Check model and map are aligned: 0.530 Set scattering table: 0.350 Process input model: 100.680 Find NCS groups from input model: 2.610 Set up NCS constraints: 0.810 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:12.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.120 ------------------------------------------------------------------------------- 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 : 0.009 0.077 36672 Z= 0.606 Angle : 1.330 26.272 49872 Z= 0.735 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 : 3.67 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.040 0.005 TRP M 45 HIS 0.016 0.004 HIS M 72 PHE 0.041 0.004 PHE Q 140 TYR 0.043 0.006 TYR L 49 ARG 0.013 0.002 ARG A 500 *********************** 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 fitting. rotamer outliers: 27 poor density : 885 time to evaluate : 4.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 HIS cc_start: 0.8300 (OUTLIER) cc_final: 0.8025 (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: 0.2882 (t) REVERT: E 168 GLN cc_start: 0.4514 (mt0) cc_final: 0.3760 (mp10) REVERT: E 193 SER cc_start: 0.1186 (t) cc_final: 0.0820 (p) REVERT: G 72 HIS cc_start: 0.8192 (OUTLIER) cc_final: 0.7903 (m-70) REVERT: J 45 LEU cc_start: 0.4084 (mm) cc_final: 0.3808 (tp) REVERT: K 168 GLN cc_start: 0.4122 (mt0) cc_final: 0.3734 (mt0) REVERT: M 72 HIS cc_start: 0.8163 (OUTLIER) cc_final: 0.7879 (m-70) REVERT: P 37 ILE cc_start: 0.4843 (OUTLIER) cc_final: 0.4583 (mt) REVERT: Q 168 GLN cc_start: 0.4114 (mt0) cc_final: 0.3217 (mp10) REVERT: Q 193 SER cc_start: 0.1366 (t) cc_final: 0.0584 (p) outliers start: 27 outliers final: 11 residues processed: 909 average time/residue: 1.4512 time to fit residues: 1581.9191 Evaluate side-chains 478 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 463 time to evaluate : 3.892 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain P residue 37 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 364 optimal weight: 1.9990 chunk 327 optimal weight: 2.9990 chunk 181 optimal weight: 4.9990 chunk 111 optimal weight: 9.9990 chunk 220 optimal weight: 0.7980 chunk 174 optimal weight: 0.8980 chunk 338 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 205 optimal weight: 9.9990 chunk 252 optimal weight: 3.9990 chunk 392 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN A 216 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN B 554 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 GLN ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 440 GLN H 562 GLN H 658 GLN ** J 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN K 50 ASN K 89 HIS ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 28 ASN I 101 GLN I 195 ASN ** M 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 552 GLN N 554 ASN N 562 GLN N 563 GLN N 590 GLN N 630 GLN ** P 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 89 HIS ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 35 HIS O 101 GLN R 89 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6201 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 36672 Z= 0.235 Angle : 0.804 13.252 49872 Z= 0.407 Chirality : 0.052 0.543 5946 Planarity : 0.005 0.075 6201 Dihedral : 11.929 102.829 7226 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.25 % Favored : 93.26 % Rotamer: Outliers : 4.45 % Allowed : 11.67 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.97 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.12), residues: 4350 helix: -4.02 (0.14), residues: 417 sheet: -1.11 (0.13), residues: 1521 loop : -2.12 (0.11), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP I 150 HIS 0.010 0.002 HIS J 195 PHE 0.022 0.002 PHE R 116 TYR 0.019 0.002 TYR F 49 ARG 0.007 0.001 ARG G 192 *********************** 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 717 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 546 time to evaluate : 3.826 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 320 MET cc_start: 0.7250 (mtm) cc_final: 0.7035 (mtp) REVERT: B 656 ASN cc_start: 0.5715 (OUTLIER) cc_final: 0.5251 (t0) REVERT: D 30 ASN cc_start: 0.4497 (m-40) cc_final: 0.3806 (m-40) REVERT: D 81 LYS cc_start: 0.3406 (OUTLIER) cc_final: 0.2954 (ptpt) REVERT: E 96 TRP cc_start: 0.3813 (m-10) cc_final: 0.3382 (m-10) REVERT: E 133 LEU cc_start: 0.1131 (tp) cc_final: 0.0853 (mp) REVERT: E 168 GLN cc_start: 0.4688 (mt0) cc_final: 0.4310 (mt0) REVERT: C 69 MET cc_start: 0.7288 (OUTLIER) cc_final: 0.7082 (ptm) REVERT: F 97 PHE cc_start: 0.6834 (m-10) cc_final: 0.6500 (m-80) REVERT: G 335 LYS cc_start: 0.6910 (OUTLIER) cc_final: 0.6700 (ttpp) REVERT: J 96 ARG cc_start: 0.5500 (OUTLIER) cc_final: 0.5043 (pmm-80) REVERT: K 168 GLN cc_start: 0.4267 (mt0) cc_final: 0.3954 (mt0) REVERT: I 75 GLN cc_start: 0.5933 (OUTLIER) cc_final: 0.5654 (mt0) REVERT: I 81 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.7050 (tt0) REVERT: M 440 GLN cc_start: 0.6900 (OUTLIER) cc_final: 0.6253 (tm-30) REVERT: Q 13 VAL cc_start: 0.4744 (OUTLIER) cc_final: 0.4452 (p) REVERT: Q 133 LEU cc_start: 0.1687 (tp) cc_final: 0.1074 (mm) REVERT: Q 168 GLN cc_start: 0.4237 (mt0) cc_final: 0.3491 (mt0) REVERT: O 206 LYS cc_start: 0.5326 (ptmm) cc_final: 0.4601 (ptmm) REVERT: R 27 GLN cc_start: 0.6222 (OUTLIER) cc_final: 0.5777 (pt0) outliers start: 171 outliers final: 44 residues processed: 652 average time/residue: 1.4076 time to fit residues: 1116.9759 Evaluate side-chains 458 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 404 time to evaluate : 4.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain B residue 656 ASN Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 68 ILE 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 335 LYS Chi-restraints excluded: chain H residue 580 VAL Chi-restraints excluded: chain H residue 617 ARG Chi-restraints excluded: chain J residue 96 ARG Chi-restraints excluded: chain K residue 164 THR Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 75 GLN Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 201 THR Chi-restraints excluded: chain L residue 54 ARG Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 244 THR Chi-restraints excluded: chain M residue 254 VAL Chi-restraints excluded: chain M residue 440 GLN Chi-restraints excluded: chain N residue 617 ARG Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain P residue 200 THR Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain Q residue 105 THR Chi-restraints excluded: chain Q residue 164 THR Chi-restraints excluded: chain O residue 61 ARG Chi-restraints excluded: chain O residue 86 ASP Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain O residue 169 SER Chi-restraints excluded: chain O residue 201 THR Chi-restraints excluded: chain R residue 27 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 218 optimal weight: 5.9990 chunk 121 optimal weight: 20.0000 chunk 326 optimal weight: 0.0770 chunk 267 optimal weight: 8.9990 chunk 108 optimal weight: 9.9990 chunk 393 optimal weight: 10.0000 chunk 424 optimal weight: 20.0000 chunk 350 optimal weight: 9.9990 chunk 389 optimal weight: 2.9990 chunk 133 optimal weight: 6.9990 chunk 315 optimal weight: 0.7980 overall best weight: 3.3744 ------------------------------------------------------------------------------- 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 590 GLN E 52 GLN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN C 101 GLN ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 554 ASN ** H 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 630 GLN K 50 ASN K 52 GLN K 198 HIS I 3 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 72 GLN ** I 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 66 HIS ** M 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 543 ASN N 552 GLN N 564 HIS N 630 GLN P 30 ASN Q 50 ASN Q 52 GLN Q 198 HIS ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6330 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 36672 Z= 0.282 Angle : 0.794 9.762 49872 Z= 0.403 Chirality : 0.052 0.506 5946 Planarity : 0.005 0.071 6201 Dihedral : 10.927 106.417 7202 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.47 % Favored : 92.21 % Rotamer: Outliers : 5.73 % Allowed : 13.49 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.97 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.12), residues: 4350 helix: -3.44 (0.18), residues: 411 sheet: -1.02 (0.13), residues: 1539 loop : -1.94 (0.12), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 150 HIS 0.013 0.002 HIS Q 89 PHE 0.026 0.002 PHE R 97 TYR 0.026 0.002 TYR D 140 ARG 0.008 0.001 ARG G 500 *********************** 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 681 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 461 time to evaluate : 3.980 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 83 GLU cc_start: 0.7148 (tt0) cc_final: 0.6893 (tt0) REVERT: A 161 MET cc_start: 0.5298 (mmm) cc_final: 0.4867 (mmm) REVERT: B 581 LEU cc_start: 0.7218 (OUTLIER) cc_final: 0.6878 (tt) REVERT: B 656 ASN cc_start: 0.5636 (OUTLIER) cc_final: 0.5180 (t0) REVERT: D 13 LYS cc_start: 0.6585 (OUTLIER) cc_final: 0.6328 (tppt) REVERT: D 46 GLU cc_start: 0.5191 (mt-10) cc_final: 0.4790 (mt-10) REVERT: E 92 ASP cc_start: 0.5445 (OUTLIER) cc_final: 0.5211 (t0) REVERT: E 96 TRP cc_start: 0.3857 (m-10) cc_final: 0.2912 (m-10) REVERT: E 133 LEU cc_start: 0.1318 (tp) cc_final: 0.0911 (mp) REVERT: E 168 GLN cc_start: 0.4833 (mt0) cc_final: 0.4478 (mt0) REVERT: C 112 SER cc_start: 0.6206 (t) cc_final: 0.5872 (p) REVERT: C 150 TRP cc_start: 0.3313 (t-100) cc_final: 0.2865 (m100) REVERT: J 96 ARG cc_start: 0.5622 (OUTLIER) cc_final: 0.5218 (pmm-80) REVERT: J 111 VAL cc_start: 0.2462 (OUTLIER) cc_final: 0.2203 (m) REVERT: J 154 LEU cc_start: 0.3117 (OUTLIER) cc_final: 0.2407 (tt) REVERT: K 11 LEU cc_start: 0.5333 (OUTLIER) cc_final: 0.4858 (tm) REVERT: K 87 TYR cc_start: 0.5463 (OUTLIER) cc_final: 0.4283 (m-80) REVERT: K 168 GLN cc_start: 0.3929 (mt0) cc_final: 0.3429 (mt0) REVERT: I 75 GLN cc_start: 0.5966 (OUTLIER) cc_final: 0.5590 (mt0) REVERT: I 167 GLN cc_start: 0.6183 (OUTLIER) cc_final: 0.4338 (mm110) REVERT: I 206 LYS cc_start: 0.3661 (OUTLIER) cc_final: 0.3069 (ptmt) REVERT: L 77 LYS cc_start: 0.6728 (OUTLIER) cc_final: 0.6295 (ptmm) REVERT: N 581 LEU cc_start: 0.7199 (OUTLIER) cc_final: 0.6966 (tt) REVERT: N 656 ASN cc_start: 0.5942 (OUTLIER) cc_final: 0.5204 (t0) REVERT: Q 13 VAL cc_start: 0.4509 (OUTLIER) cc_final: 0.4260 (p) REVERT: Q 87 TYR cc_start: 0.5646 (OUTLIER) cc_final: 0.5386 (m-10) REVERT: Q 92 ASP cc_start: 0.5156 (OUTLIER) cc_final: 0.4949 (t0) REVERT: Q 133 LEU cc_start: 0.1631 (tp) cc_final: 0.1362 (mm) REVERT: Q 168 GLN cc_start: 0.4352 (mt0) cc_final: 0.3714 (mt0) REVERT: O 167 GLN cc_start: 0.6270 (OUTLIER) cc_final: 0.4575 (mm110) REVERT: R 27 GLN cc_start: 0.6412 (OUTLIER) cc_final: 0.5928 (pt0) REVERT: R 40 ARG cc_start: 0.6079 (OUTLIER) cc_final: 0.5845 (mtt-85) REVERT: R 77 LYS cc_start: 0.6552 (OUTLIER) cc_final: 0.6194 (ptmm) REVERT: R 142 ARG cc_start: 0.4822 (OUTLIER) cc_final: 0.4453 (ttt180) REVERT: R 187 GLU cc_start: 0.5604 (mt-10) cc_final: 0.5308 (pm20) outliers start: 220 outliers final: 91 residues processed: 602 average time/residue: 1.3349 time to fit residues: 976.7229 Evaluate side-chains 504 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 390 time to evaluate : 3.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR 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 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 656 ASN Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 99 GLN Chi-restraints excluded: chain D residue 100 VAL 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 E residue 92 ASP Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 68 ILE 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 276 ASN Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 424 ILE Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain H residue 553 SER Chi-restraints excluded: chain H residue 569 THR Chi-restraints excluded: chain H residue 580 VAL 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 38 ARG Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 96 ARG Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 50 ASN Chi-restraints excluded: chain K residue 87 TYR 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 86 ASP 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 167 GLN Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 201 THR Chi-restraints excluded: chain I residue 206 LYS Chi-restraints excluded: chain L residue 54 ARG Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 77 LYS Chi-restraints excluded: chain L residue 102 SER Chi-restraints excluded: chain M residue 50 THR 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 306 SER Chi-restraints excluded: chain M residue 308 ARG Chi-restraints excluded: chain M residue 333 VAL Chi-restraints excluded: chain M residue 467 THR Chi-restraints excluded: chain M residue 494 LEU Chi-restraints excluded: chain N residue 543 ASN Chi-restraints excluded: chain N residue 580 VAL Chi-restraints excluded: chain N residue 581 LEU Chi-restraints excluded: chain N residue 639 THR Chi-restraints excluded: chain N residue 656 ASN 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 196 LYS Chi-restraints excluded: chain P residue 200 THR Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 50 ASN Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain Q residue 87 TYR Chi-restraints excluded: chain Q residue 92 ASP 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 86 ASP 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 167 GLN Chi-restraints excluded: chain O residue 169 SER Chi-restraints excluded: chain O residue 201 THR Chi-restraints excluded: chain R residue 10 ILE Chi-restraints excluded: chain R residue 27 GLN Chi-restraints excluded: chain R residue 40 ARG Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 77 LYS Chi-restraints excluded: chain R residue 142 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 388 optimal weight: 20.0000 chunk 295 optimal weight: 8.9990 chunk 203 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 187 optimal weight: 8.9990 chunk 263 optimal weight: 0.0980 chunk 394 optimal weight: 7.9990 chunk 417 optimal weight: 8.9990 chunk 206 optimal weight: 4.9990 chunk 373 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 overall best weight: 3.2188 ------------------------------------------------------------------------------- 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 ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 GLN B 650 GLN D 150 ASN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN G 66 HIS ** G 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 280 ASN ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 554 ASN H 564 HIS H 630 GLN K 52 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 280 ASN ** M 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 562 GLN ** N 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 52 GLN ** O 6 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: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6365 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 36672 Z= 0.260 Angle : 0.760 12.802 49872 Z= 0.385 Chirality : 0.051 0.684 5946 Planarity : 0.005 0.094 6201 Dihedral : 10.319 105.110 7202 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.49 % Favored : 92.18 % Rotamer: Outliers : 5.70 % Allowed : 15.89 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.97 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.12), residues: 4350 helix: -3.13 (0.19), residues: 417 sheet: -0.93 (0.13), residues: 1491 loop : -1.92 (0.12), residues: 2442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP J 47 HIS 0.008 0.001 HIS J 195 PHE 0.030 0.002 PHE L 22 TYR 0.024 0.002 TYR D 140 ARG 0.009 0.001 ARG Q 20 *********************** 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 672 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 453 time to evaluate : 4.298 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: 0.6289 (OUTLIER) cc_final: 0.5896 (pp30) REVERT: A 83 GLU cc_start: 0.7204 (tt0) cc_final: 0.6960 (tt0) REVERT: A 161 MET cc_start: 0.5337 (mmm) cc_final: 0.4867 (mmm) REVERT: B 581 LEU cc_start: 0.7265 (OUTLIER) cc_final: 0.6948 (tt) REVERT: B 656 ASN cc_start: 0.5760 (OUTLIER) cc_final: 0.5224 (t0) REVERT: E 96 TRP cc_start: 0.4371 (OUTLIER) cc_final: 0.2548 (m-10) REVERT: E 133 LEU cc_start: 0.1289 (tp) cc_final: 0.0939 (mp) REVERT: E 168 GLN cc_start: 0.4550 (mt0) cc_final: 0.4078 (mt0) REVERT: C 112 SER cc_start: 0.6139 (t) cc_final: 0.5850 (p) REVERT: C 206 LYS cc_start: 0.4387 (ptmm) cc_final: 0.3851 (ptmm) REVERT: G 95 MET cc_start: 0.7881 (ptm) cc_final: 0.7591 (ttp) REVERT: G 207 LYS cc_start: 0.6264 (OUTLIER) cc_final: 0.5641 (tttm) REVERT: J 96 ARG cc_start: 0.5805 (OUTLIER) cc_final: 0.5276 (pmm-80) REVERT: J 97 ARG cc_start: 0.6267 (mtp-110) cc_final: 0.6057 (ttm110) REVERT: J 154 LEU cc_start: 0.3132 (OUTLIER) cc_final: 0.2374 (tt) REVERT: K 11 LEU cc_start: 0.5127 (OUTLIER) cc_final: 0.4743 (tm) REVERT: K 87 TYR cc_start: 0.5379 (OUTLIER) cc_final: 0.4044 (m-80) REVERT: K 168 GLN cc_start: 0.4181 (mt0) cc_final: 0.3806 (mt0) REVERT: I 75 GLN cc_start: 0.5905 (OUTLIER) cc_final: 0.5546 (mt0) REVERT: I 112 SER cc_start: 0.6519 (t) cc_final: 0.6155 (p) REVERT: I 206 LYS cc_start: 0.3559 (ptmm) cc_final: 0.2985 (ptmt) REVERT: L 77 LYS cc_start: 0.7168 (OUTLIER) cc_final: 0.6728 (ptmm) REVERT: N 581 LEU cc_start: 0.7168 (OUTLIER) cc_final: 0.6925 (tt) REVERT: P 29 MET cc_start: 0.1884 (pp-130) cc_final: 0.1673 (pp-130) REVERT: P 154 LEU cc_start: 0.3214 (OUTLIER) cc_final: 0.2914 (tt) REVERT: Q 13 VAL cc_start: 0.4454 (OUTLIER) cc_final: 0.4205 (p) REVERT: Q 87 TYR cc_start: 0.5613 (OUTLIER) cc_final: 0.5394 (m-10) REVERT: Q 133 LEU cc_start: 0.1611 (tp) cc_final: 0.1397 (mm) REVERT: Q 168 GLN cc_start: 0.4390 (mt0) cc_final: 0.3619 (mt0) REVERT: O 167 GLN cc_start: 0.6401 (OUTLIER) cc_final: 0.4607 (mm110) REVERT: R 142 ARG cc_start: 0.4831 (OUTLIER) cc_final: 0.4284 (ttt180) REVERT: R 187 GLU cc_start: 0.5623 (mt-10) cc_final: 0.5398 (pm20) outliers start: 219 outliers final: 106 residues processed: 610 average time/residue: 1.3598 time to fit residues: 1009.5666 Evaluate side-chains 509 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 386 time to evaluate : 4.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR 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 181 VAL Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 280 ASN 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 544 LEU 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 656 ASN Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 107 THR 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 E residue 96 TRP Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 33 MET Chi-restraints excluded: chain F residue 100 LEU 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 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 605 CYS Chi-restraints excluded: chain H residue 617 ARG Chi-restraints excluded: chain H residue 626 MET Chi-restraints excluded: chain H residue 632 ASP Chi-restraints excluded: chain H residue 639 THR Chi-restraints excluded: chain H residue 642 ILE Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 81 LYS 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 11 LEU Chi-restraints excluded: chain K residue 87 TYR 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 75 GLN Chi-restraints excluded: chain I residue 86 ASP 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 169 SER Chi-restraints excluded: chain I residue 201 THR Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 54 ARG Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 77 LYS Chi-restraints excluded: chain L residue 102 SER Chi-restraints excluded: chain M residue 50 THR 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 306 SER 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 467 THR Chi-restraints excluded: chain M residue 494 LEU Chi-restraints excluded: chain N residue 536 THR Chi-restraints excluded: chain N residue 580 VAL Chi-restraints excluded: chain N residue 581 LEU Chi-restraints excluded: chain N residue 639 THR 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 154 LEU 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 86 ASP 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 167 GLN Chi-restraints excluded: chain O residue 201 THR Chi-restraints excluded: chain O residue 208 GLU Chi-restraints excluded: chain R residue 10 ILE Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 142 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 347 optimal weight: 8.9990 chunk 237 optimal weight: 20.0000 chunk 6 optimal weight: 9.9990 chunk 310 optimal weight: 10.0000 chunk 172 optimal weight: 5.9990 chunk 356 optimal weight: 6.9990 chunk 288 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 213 optimal weight: 0.9980 chunk 374 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 HIS B 552 GLN ** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN B 630 GLN C 3 GLN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 186 ASN ** 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** H 591 GLN J 166 GLN ** J 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 50 ASN K 52 GLN ** K 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 189 HIS I 3 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 188 GLN ** I 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 66 HIS ** M 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 374 HIS N 543 ASN ** N 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 38 HIS Q 50 ASN Q 52 GLN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 76 ASN R 89 GLN R 137 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6480 moved from start: 0.4740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.120 36672 Z= 0.409 Angle : 0.883 12.309 49872 Z= 0.446 Chirality : 0.056 0.827 5946 Planarity : 0.006 0.067 6201 Dihedral : 10.819 106.229 7200 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.34 % Allowed : 10.18 % Favored : 89.47 % Rotamer: Outliers : 6.98 % Allowed : 16.85 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.97 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.12), residues: 4350 helix: -3.29 (0.18), residues: 459 sheet: -1.10 (0.13), residues: 1467 loop : -2.12 (0.12), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP I 150 HIS 0.014 0.002 HIS E 38 PHE 0.028 0.003 PHE L 22 TYR 0.036 0.003 TYR J 140 ARG 0.007 0.001 ARG N 617 *********************** 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 716 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 268 poor density : 448 time to evaluate : 4.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLU cc_start: 0.7299 (tt0) cc_final: 0.7045 (tt0) REVERT: A 161 MET cc_start: 0.5246 (mmm) cc_final: 0.4800 (mmm) REVERT: A 308 ARG cc_start: 0.6833 (OUTLIER) cc_final: 0.6479 (ptm160) REVERT: B 535 MET cc_start: 0.7291 (OUTLIER) cc_final: 0.6567 (mmt) REVERT: B 581 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.7157 (tt) REVERT: B 588 ARG cc_start: 0.7684 (OUTLIER) cc_final: 0.7480 (ttm-80) REVERT: B 656 ASN cc_start: 0.5882 (OUTLIER) cc_final: 0.5222 (t0) REVERT: D 53 ASP cc_start: 0.4224 (t0) cc_final: 0.4015 (m-30) REVERT: D 100 MET cc_start: 0.5583 (mpt) cc_final: 0.5358 (mmm) REVERT: E 96 TRP cc_start: 0.5669 (OUTLIER) cc_final: 0.3982 (m-10) REVERT: E 133 LEU cc_start: 0.1533 (tp) cc_final: 0.1191 (mp) REVERT: C 76 ASP cc_start: 0.6520 (OUTLIER) cc_final: 0.6283 (t0) REVERT: C 144 GLU cc_start: 0.6134 (OUTLIER) cc_final: 0.5330 (mm-30) REVERT: C 167 GLN cc_start: 0.6485 (OUTLIER) cc_final: 0.4409 (mm110) REVERT: F 33 MET cc_start: 0.7750 (OUTLIER) cc_final: 0.7157 (ttp) REVERT: G 207 LYS cc_start: 0.6317 (OUTLIER) cc_final: 0.5755 (tttm) REVERT: G 217 TYR cc_start: 0.7219 (m-80) cc_final: 0.6928 (m-80) REVERT: H 535 MET cc_start: 0.7540 (OUTLIER) cc_final: 0.6675 (mmt) REVERT: J 96 ARG cc_start: 0.5593 (OUTLIER) cc_final: 0.5228 (pmm-80) REVERT: J 100 MET cc_start: 0.5229 (OUTLIER) cc_final: 0.4358 (mmm) REVERT: J 154 LEU cc_start: 0.3433 (OUTLIER) cc_final: 0.2755 (tt) REVERT: K 11 LEU cc_start: 0.5406 (OUTLIER) cc_final: 0.5017 (tm) REVERT: K 87 TYR cc_start: 0.5632 (OUTLIER) cc_final: 0.4490 (m-80) REVERT: K 90 MET cc_start: 0.5754 (OUTLIER) cc_final: 0.4999 (tpp) REVERT: K 92 ASP cc_start: 0.6310 (m-30) cc_final: 0.6093 (m-30) REVERT: I 75 GLN cc_start: 0.5960 (OUTLIER) cc_final: 0.5679 (mt0) REVERT: I 81 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.7200 (tt0) REVERT: I 167 GLN cc_start: 0.6842 (OUTLIER) cc_final: 0.5064 (mm110) REVERT: M 440 GLN cc_start: 0.6968 (OUTLIER) cc_final: 0.6313 (tm-30) REVERT: M 476 ARG cc_start: 0.6780 (OUTLIER) cc_final: 0.5737 (mmt-90) REVERT: N 576 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7522 (tt) REVERT: N 581 LEU cc_start: 0.7233 (OUTLIER) cc_final: 0.7027 (tt) REVERT: P 29 MET cc_start: 0.1779 (pp-130) cc_final: 0.1178 (pp-130) REVERT: Q 13 VAL cc_start: 0.4585 (OUTLIER) cc_final: 0.4228 (p) REVERT: Q 87 TYR cc_start: 0.5832 (OUTLIER) cc_final: 0.3683 (m-80) REVERT: Q 133 LEU cc_start: 0.1539 (tp) cc_final: 0.1289 (mm) REVERT: Q 168 GLN cc_start: 0.4048 (mt0) cc_final: 0.3295 (mt0) REVERT: O 167 GLN cc_start: 0.6462 (OUTLIER) cc_final: 0.4599 (mm110) REVERT: O 173 SER cc_start: 0.5537 (OUTLIER) cc_final: 0.5259 (t) REVERT: R 40 ARG cc_start: 0.6126 (OUTLIER) cc_final: 0.5896 (ttt-90) REVERT: R 142 ARG cc_start: 0.4638 (OUTLIER) cc_final: 0.4295 (ttt180) REVERT: R 187 GLU cc_start: 0.5696 (mt-10) cc_final: 0.5354 (pm20) outliers start: 268 outliers final: 142 residues processed: 641 average time/residue: 1.3947 time to fit residues: 1084.5282 Evaluate side-chains 561 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 388 time to evaluate : 4.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR 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 181 VAL Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 308 ARG 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 A residue 499 THR Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 588 ARG Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 656 ASN Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 150 ASN 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 51 ASN Chi-restraints excluded: chain E residue 96 TRP Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 90 TYR Chi-restraints excluded: chain C residue 93 VAL 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 148 VAL Chi-restraints excluded: chain C residue 167 GLN Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 33 MET Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 100 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 163 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 276 ASN 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 G residue 499 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 604 CYS Chi-restraints excluded: chain H residue 617 ARG Chi-restraints excluded: chain H residue 626 MET 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 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 100 TYR Chi-restraints excluded: chain J residue 100 MET Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 204 LYS Chi-restraints excluded: chain J residue 206 VAL Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 50 ASN Chi-restraints excluded: chain K residue 51 ASN Chi-restraints excluded: chain K residue 87 TYR Chi-restraints excluded: chain K residue 90 MET Chi-restraints excluded: chain K residue 105 THR 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 75 GLN Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 86 ASP 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 167 GLN Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 201 THR Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 54 ARG Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 102 SER Chi-restraints excluded: chain L residue 168 SER Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain M residue 110 SER Chi-restraints excluded: chain M residue 123 THR 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 248 THR Chi-restraints excluded: chain M residue 254 VAL Chi-restraints excluded: chain M residue 268 GLU 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 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 499 THR Chi-restraints excluded: chain M residue 500 ARG Chi-restraints excluded: chain N residue 534 SER Chi-restraints excluded: chain N residue 543 ASN Chi-restraints excluded: chain N residue 576 LEU Chi-restraints excluded: chain N residue 580 VAL Chi-restraints excluded: chain N residue 581 LEU Chi-restraints excluded: chain N residue 639 THR 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 100 TYR 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 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 52 GLN 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 37 VAL Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 69 MET Chi-restraints excluded: chain O residue 86 ASP 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 167 GLN Chi-restraints excluded: chain O residue 169 SER Chi-restraints excluded: chain O residue 173 SER Chi-restraints excluded: chain O residue 201 THR Chi-restraints excluded: chain R residue 10 ILE Chi-restraints excluded: chain R residue 40 ARG Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 100 LEU 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 140 optimal weight: 6.9990 chunk 376 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 245 optimal weight: 0.3980 chunk 103 optimal weight: 0.9980 chunk 417 optimal weight: 8.9990 chunk 346 optimal weight: 6.9990 chunk 193 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 138 optimal weight: 5.9990 chunk 219 optimal weight: 4.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 GLN B 630 GLN D 166 GLN E 189 HIS ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 50 ASN ** K 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 147 GLN ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 166 GLN Q 50 ASN Q 52 GLN Q 189 HIS ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6422 moved from start: 0.4939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 36672 Z= 0.244 Angle : 0.768 10.869 49872 Z= 0.386 Chirality : 0.051 0.625 5946 Planarity : 0.005 0.052 6201 Dihedral : 10.169 103.088 7200 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.21 % Favored : 91.49 % Rotamer: Outliers : 6.04 % Allowed : 19.38 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.97 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.12), residues: 4350 helix: -2.81 (0.21), residues: 423 sheet: -0.95 (0.13), residues: 1446 loop : -2.00 (0.12), residues: 2481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 96 HIS 0.010 0.001 HIS F 189 PHE 0.031 0.002 PHE L 22 TYR 0.025 0.002 TYR J 140 ARG 0.009 0.001 ARG E 20 *********************** 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 649 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 417 time to evaluate : 4.191 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 83 GLU cc_start: 0.7240 (tt0) cc_final: 0.7034 (tt0) REVERT: A 161 MET cc_start: 0.5238 (mmm) cc_final: 0.4798 (mmm) REVERT: A 308 ARG cc_start: 0.6717 (OUTLIER) cc_final: 0.6402 (ptm160) REVERT: B 581 LEU cc_start: 0.7343 (OUTLIER) cc_final: 0.7064 (tt) REVERT: B 617 ARG cc_start: 0.4621 (pmm150) cc_final: 0.4057 (pmm150) REVERT: B 656 ASN cc_start: 0.5633 (OUTLIER) cc_final: 0.4937 (t0) REVERT: E 90 MET cc_start: 0.5593 (OUTLIER) cc_final: 0.5323 (tpt) REVERT: E 96 TRP cc_start: 0.5405 (OUTLIER) cc_final: 0.3802 (m-10) REVERT: E 168 GLN cc_start: 0.3963 (mt0) cc_final: 0.3748 (tt0) REVERT: C 112 SER cc_start: 0.5524 (t) cc_final: 0.5284 (p) REVERT: C 144 GLU cc_start: 0.6189 (OUTLIER) cc_final: 0.5394 (mm-30) REVERT: F 33 MET cc_start: 0.7557 (OUTLIER) cc_final: 0.6919 (ttp) REVERT: G 95 MET cc_start: 0.7952 (ptm) cc_final: 0.7550 (ttp) REVERT: G 207 LYS cc_start: 0.6258 (OUTLIER) cc_final: 0.5642 (tttm) REVERT: G 217 TYR cc_start: 0.7309 (m-80) cc_final: 0.7059 (m-80) REVERT: G 308 ARG cc_start: 0.6934 (OUTLIER) cc_final: 0.6728 (ptm160) REVERT: J 96 ARG cc_start: 0.5770 (OUTLIER) cc_final: 0.5291 (pmm-80) REVERT: J 154 LEU cc_start: 0.3380 (OUTLIER) cc_final: 0.2575 (tt) REVERT: K 11 LEU cc_start: 0.5129 (OUTLIER) cc_final: 0.4823 (tm) REVERT: K 87 TYR cc_start: 0.5393 (OUTLIER) cc_final: 0.4006 (m-80) REVERT: M 125 LEU cc_start: 0.6927 (OUTLIER) cc_final: 0.6592 (tp) REVERT: M 440 GLN cc_start: 0.6939 (OUTLIER) cc_final: 0.6312 (tm-30) REVERT: M 476 ARG cc_start: 0.6652 (OUTLIER) cc_final: 0.5641 (mmt-90) REVERT: N 576 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7359 (tt) REVERT: N 581 LEU cc_start: 0.7199 (OUTLIER) cc_final: 0.6969 (tt) REVERT: P 29 MET cc_start: 0.1821 (pp-130) cc_final: 0.1175 (pp-130) REVERT: Q 87 TYR cc_start: 0.5629 (OUTLIER) cc_final: 0.3535 (m-80) REVERT: Q 133 LEU cc_start: 0.1426 (tp) cc_final: 0.0887 (mm) REVERT: Q 168 GLN cc_start: 0.4055 (mt0) cc_final: 0.3395 (mt0) REVERT: R 53 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.7080 (ttm-80) REVERT: R 142 ARG cc_start: 0.4511 (OUTLIER) cc_final: 0.4059 (ttt180) REVERT: R 187 GLU cc_start: 0.5571 (mt-10) cc_final: 0.5290 (pm20) outliers start: 232 outliers final: 133 residues processed: 587 average time/residue: 1.3709 time to fit residues: 979.3364 Evaluate side-chains 534 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 380 time to evaluate : 3.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR 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 181 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 308 ARG 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 A residue 500 ARG Chi-restraints excluded: chain B residue 544 LEU 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 656 ASN Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 150 ASN 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 62 PHE Chi-restraints excluded: chain E residue 66 ILE Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 96 TRP Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 33 MET Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 100 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 248 THR Chi-restraints excluded: chain G residue 276 ASN Chi-restraints excluded: chain G residue 308 ARG 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 G residue 501 CYS Chi-restraints excluded: chain H residue 568 LEU Chi-restraints excluded: chain H residue 580 VAL Chi-restraints excluded: chain H residue 604 CYS Chi-restraints excluded: chain H residue 617 ARG Chi-restraints excluded: chain H residue 626 MET 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 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 100 TYR 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 204 LYS Chi-restraints excluded: chain J residue 206 VAL Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 49 TYR Chi-restraints excluded: chain K residue 50 ASN Chi-restraints excluded: chain K residue 66 ILE Chi-restraints excluded: chain K residue 87 TYR 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 86 ASP 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 169 SER 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 54 ARG Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 102 SER Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 168 SER Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain M residue 123 THR 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 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 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 499 THR Chi-restraints excluded: chain N residue 534 SER Chi-restraints excluded: chain N residue 576 LEU Chi-restraints excluded: chain N residue 580 VAL Chi-restraints excluded: chain N residue 581 LEU Chi-restraints excluded: chain N residue 639 THR Chi-restraints excluded: chain P residue 12 VAL 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 176 VAL Chi-restraints excluded: chain P residue 200 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 37 VAL Chi-restraints excluded: chain O residue 86 ASP 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 169 SER Chi-restraints excluded: chain O residue 201 THR Chi-restraints excluded: chain O residue 208 GLU Chi-restraints excluded: chain R residue 10 ILE Chi-restraints excluded: chain R residue 13 LEU Chi-restraints excluded: chain R residue 53 ARG Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 100 LEU Chi-restraints excluded: chain R residue 142 ARG Chi-restraints excluded: chain R residue 168 SER Chi-restraints excluded: chain R residue 172 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 402 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 238 optimal weight: 5.9990 chunk 305 optimal weight: 5.9990 chunk 236 optimal weight: 0.8980 chunk 351 optimal weight: 2.9990 chunk 233 optimal weight: 9.9990 chunk 416 optimal weight: 2.9990 chunk 260 optimal weight: 20.0000 chunk 253 optimal weight: 5.9990 chunk 192 optimal weight: 9.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 GLN ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 GLN ** F 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 552 GLN ** J 192 ASN ** 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 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 50 ASN ** O 6 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6450 moved from start: 0.5164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 36672 Z= 0.293 Angle : 0.786 10.518 49872 Z= 0.395 Chirality : 0.052 0.679 5946 Planarity : 0.005 0.055 6201 Dihedral : 9.990 99.321 7200 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.05 % Favored : 89.66 % Rotamer: Outliers : 6.64 % Allowed : 19.69 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.97 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.12), residues: 4350 helix: -2.71 (0.21), residues: 423 sheet: -0.96 (0.14), residues: 1428 loop : -2.08 (0.12), residues: 2499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP I 150 HIS 0.008 0.001 HIS E 38 PHE 0.031 0.002 PHE L 22 TYR 0.027 0.002 TYR J 140 ARG 0.007 0.001 ARG B 617 *********************** 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 683 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 428 time to evaluate : 4.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.6371 (OUTLIER) cc_final: 0.6000 (pp30) REVERT: A 83 GLU cc_start: 0.7285 (tt0) cc_final: 0.7068 (tt0) REVERT: A 161 MET cc_start: 0.5254 (mmm) cc_final: 0.4834 (mmm) REVERT: A 308 ARG cc_start: 0.6729 (OUTLIER) cc_final: 0.6425 (ptm160) REVERT: B 535 MET cc_start: 0.6991 (mpp) cc_final: 0.6641 (mtt) REVERT: B 576 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7498 (tt) REVERT: B 581 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.7114 (tt) REVERT: B 617 ARG cc_start: 0.4495 (pmm150) cc_final: 0.4013 (pmm150) REVERT: B 656 ASN cc_start: 0.5710 (OUTLIER) cc_final: 0.4967 (t0) REVERT: D 100 MET cc_start: 0.5265 (OUTLIER) cc_final: 0.3411 (mmm) REVERT: E 87 TYR cc_start: 0.5205 (OUTLIER) cc_final: 0.4425 (m-80) REVERT: E 90 MET cc_start: 0.5699 (OUTLIER) cc_final: 0.5427 (tpt) REVERT: E 96 TRP cc_start: 0.5403 (OUTLIER) cc_final: 0.3897 (m-10) REVERT: E 168 GLN cc_start: 0.4258 (OUTLIER) cc_final: 0.4037 (tt0) REVERT: C 144 GLU cc_start: 0.5845 (OUTLIER) cc_final: 0.5061 (mm-30) REVERT: F 33 MET cc_start: 0.7554 (OUTLIER) cc_final: 0.6932 (ttp) REVERT: F 49 TYR cc_start: 0.5722 (OUTLIER) cc_final: 0.5056 (t80) REVERT: G 95 MET cc_start: 0.7947 (ptm) cc_final: 0.7633 (ttp) REVERT: G 207 LYS cc_start: 0.6286 (OUTLIER) cc_final: 0.5743 (tttm) REVERT: G 217 TYR cc_start: 0.7344 (m-80) cc_final: 0.7133 (m-80) REVERT: J 96 ARG cc_start: 0.5782 (OUTLIER) cc_final: 0.5314 (pmm-80) REVERT: J 154 LEU cc_start: 0.3228 (OUTLIER) cc_final: 0.2513 (tt) REVERT: K 87 TYR cc_start: 0.5499 (OUTLIER) cc_final: 0.4300 (m-80) REVERT: L 49 TYR cc_start: 0.5566 (OUTLIER) cc_final: 0.4384 (t80) REVERT: L 142 ARG cc_start: 0.5304 (OUTLIER) cc_final: 0.4308 (ttp80) REVERT: M 104 MET cc_start: 0.6296 (ttt) cc_final: 0.6062 (ptm) REVERT: M 440 GLN cc_start: 0.6950 (OUTLIER) cc_final: 0.6309 (tm-30) REVERT: M 476 ARG cc_start: 0.6746 (OUTLIER) cc_final: 0.5723 (mmt-90) REVERT: N 576 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7435 (tt) REVERT: N 581 LEU cc_start: 0.7282 (OUTLIER) cc_final: 0.7049 (tt) REVERT: P 29 MET cc_start: 0.1662 (pp-130) cc_final: 0.1093 (pp-130) REVERT: Q 87 TYR cc_start: 0.5661 (OUTLIER) cc_final: 0.3519 (m-80) REVERT: Q 168 GLN cc_start: 0.4061 (mt0) cc_final: 0.3472 (mt0) REVERT: O 76 ASP cc_start: 0.7409 (t0) cc_final: 0.7192 (t0) REVERT: R 53 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7098 (ttm-80) REVERT: R 142 ARG cc_start: 0.4653 (OUTLIER) cc_final: 0.4243 (ttt180) outliers start: 255 outliers final: 157 residues processed: 615 average time/residue: 1.3858 time to fit residues: 1036.8482 Evaluate side-chains 577 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 394 time to evaluate : 3.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR 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 128 THR Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 308 ARG 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 461 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 576 LEU 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 656 ASN Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 150 ASN 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 62 PHE Chi-restraints excluded: chain E residue 66 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 87 TYR Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 96 TRP Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 168 GLN Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 144 GLU 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 13 LEU Chi-restraints excluded: chain F residue 33 MET Chi-restraints excluded: chain F residue 49 TYR Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 161 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 276 ASN Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 356 ASN Chi-restraints excluded: chain G residue 418 CYS Chi-restraints excluded: chain G residue 422 MET Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain G residue 500 ARG Chi-restraints excluded: chain G residue 501 CYS 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 604 CYS Chi-restraints excluded: chain H residue 617 ARG Chi-restraints excluded: chain H residue 626 MET 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 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 204 LYS Chi-restraints excluded: chain J residue 206 VAL Chi-restraints excluded: chain K residue 49 TYR Chi-restraints excluded: chain K residue 51 ASN Chi-restraints excluded: chain K residue 87 TYR 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 86 ASP 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 169 SER 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 54 ARG Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 102 SER Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 142 ARG Chi-restraints excluded: chain L residue 161 GLU Chi-restraints excluded: chain L residue 168 SER Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain M residue 110 SER Chi-restraints excluded: chain M residue 123 THR Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain M residue 128 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 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 499 THR Chi-restraints excluded: chain N residue 534 SER Chi-restraints excluded: chain N residue 576 LEU Chi-restraints excluded: chain N residue 580 VAL Chi-restraints excluded: chain N residue 581 LEU Chi-restraints excluded: chain N residue 617 ARG Chi-restraints excluded: chain N residue 639 THR Chi-restraints excluded: chain P residue 12 VAL 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 107 THR Chi-restraints excluded: chain P residue 176 VAL Chi-restraints excluded: chain P residue 200 THR Chi-restraints excluded: chain Q residue 50 ASN 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 169 SER 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 68 SER Chi-restraints excluded: chain O residue 86 ASP 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 169 SER Chi-restraints excluded: chain O residue 201 THR Chi-restraints excluded: chain R residue 10 ILE Chi-restraints excluded: chain R residue 13 LEU Chi-restraints excluded: chain R residue 53 ARG Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 100 LEU Chi-restraints excluded: chain R residue 142 ARG Chi-restraints excluded: chain R residue 161 GLU Chi-restraints excluded: chain R residue 168 SER Chi-restraints excluded: chain R residue 172 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 257 optimal weight: 5.9990 chunk 166 optimal weight: 9.9990 chunk 248 optimal weight: 7.9990 chunk 125 optimal weight: 20.0000 chunk 81 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 264 optimal weight: 0.7980 chunk 283 optimal weight: 20.0000 chunk 205 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 327 optimal weight: 10.0000 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 GLN D 3 GLN ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 552 GLN J 3 GLN ** J 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 607 ASN ** Q 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6502 moved from start: 0.5468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 36672 Z= 0.389 Angle : 0.866 10.421 49872 Z= 0.437 Chirality : 0.056 0.810 5946 Planarity : 0.006 0.060 6201 Dihedral : 10.309 96.119 7200 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.90 % Favored : 88.80 % Rotamer: Outliers : 7.11 % Allowed : 20.16 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.97 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.12), residues: 4350 helix: -2.90 (0.20), residues: 441 sheet: -1.13 (0.14), residues: 1434 loop : -2.26 (0.12), residues: 2475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP I 150 HIS 0.012 0.002 HIS Q 38 PHE 0.030 0.003 PHE L 22 TYR 0.035 0.003 TYR Q 49 ARG 0.009 0.001 ARG B 617 *********************** 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 684 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 273 poor density : 411 time to evaluate : 4.046 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: 0.6543 (OUTLIER) cc_final: 0.6162 (pp30) REVERT: A 83 GLU cc_start: 0.7359 (tt0) cc_final: 0.7127 (tt0) REVERT: A 161 MET cc_start: 0.5479 (mmm) cc_final: 0.5039 (mmm) REVERT: A 308 ARG cc_start: 0.6752 (OUTLIER) cc_final: 0.6430 (ptm160) REVERT: B 535 MET cc_start: 0.6840 (OUTLIER) cc_final: 0.6586 (mtt) REVERT: B 576 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7547 (tt) REVERT: B 581 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.7115 (tt) REVERT: B 656 ASN cc_start: 0.5963 (OUTLIER) cc_final: 0.5187 (t0) REVERT: D 37 ILE cc_start: 0.4683 (OUTLIER) cc_final: 0.4350 (mt) REVERT: D 53 ASP cc_start: 0.3123 (m-30) cc_final: 0.2878 (m-30) REVERT: D 100 MET cc_start: 0.5289 (OUTLIER) cc_final: 0.3315 (mmm) REVERT: E 90 MET cc_start: 0.5777 (OUTLIER) cc_final: 0.5468 (tpt) REVERT: E 168 GLN cc_start: 0.4275 (OUTLIER) cc_final: 0.4055 (tt0) REVERT: C 144 GLU cc_start: 0.5883 (OUTLIER) cc_final: 0.5092 (mm-30) REVERT: C 167 GLN cc_start: 0.6537 (OUTLIER) cc_final: 0.4469 (mm110) REVERT: F 49 TYR cc_start: 0.5978 (OUTLIER) cc_final: 0.5186 (t80) REVERT: F 165 GLU cc_start: 0.5278 (OUTLIER) cc_final: 0.4899 (pm20) REVERT: G 95 MET cc_start: 0.8017 (ptm) cc_final: 0.7774 (ttp) REVERT: G 207 LYS cc_start: 0.6268 (OUTLIER) cc_final: 0.5722 (tttm) REVERT: H 576 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7592 (tt) REVERT: J 96 ARG cc_start: 0.5896 (OUTLIER) cc_final: 0.5515 (pmm-80) REVERT: J 154 LEU cc_start: 0.3460 (OUTLIER) cc_final: 0.2855 (tt) REVERT: K 50 ASN cc_start: 0.6044 (t0) cc_final: 0.5732 (t0) REVERT: K 87 TYR cc_start: 0.5680 (OUTLIER) cc_final: 0.4337 (m-80) REVERT: I 167 GLN cc_start: 0.6964 (OUTLIER) cc_final: 0.5141 (mm110) REVERT: L 49 TYR cc_start: 0.5769 (OUTLIER) cc_final: 0.4802 (t80) REVERT: L 142 ARG cc_start: 0.5187 (OUTLIER) cc_final: 0.4196 (ttp80) REVERT: M 440 GLN cc_start: 0.6970 (OUTLIER) cc_final: 0.6310 (tm-30) REVERT: M 476 ARG cc_start: 0.6786 (OUTLIER) cc_final: 0.5785 (mmt-90) REVERT: N 576 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7501 (tt) REVERT: N 581 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.7104 (tt) REVERT: P 29 MET cc_start: 0.1666 (pp-130) cc_final: 0.0997 (pp-130) REVERT: Q 87 TYR cc_start: 0.5716 (OUTLIER) cc_final: 0.3498 (m-80) REVERT: O 61 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7235 (ptm160) REVERT: O 76 ASP cc_start: 0.7489 (t0) cc_final: 0.7245 (t0) REVERT: O 121 VAL cc_start: 0.4711 (p) cc_final: 0.4472 (p) REVERT: O 167 GLN cc_start: 0.6893 (OUTLIER) cc_final: 0.4913 (mm110) REVERT: R 40 ARG cc_start: 0.6077 (OUTLIER) cc_final: 0.5700 (mtt-85) REVERT: R 49 TYR cc_start: 0.5953 (OUTLIER) cc_final: 0.5405 (t80) REVERT: R 53 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7080 (ttm-80) REVERT: R 142 ARG cc_start: 0.4525 (OUTLIER) cc_final: 0.4116 (ttt180) outliers start: 273 outliers final: 172 residues processed: 614 average time/residue: 1.3359 time to fit residues: 1002.1315 Evaluate side-chains 588 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 383 time to evaluate : 3.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR 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 181 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 576 LEU 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 621 GLU Chi-restraints excluded: chain B residue 656 ASN Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 150 ASN 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 13 VAL Chi-restraints excluded: chain E residue 62 PHE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 96 TRP Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 168 GLN Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 167 GLN Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 205 LYS Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 33 MET Chi-restraints excluded: chain F residue 49 TYR Chi-restraints excluded: chain F residue 79 ASP 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 276 ASN 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 418 CYS Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain G residue 500 ARG Chi-restraints excluded: chain H residue 568 LEU Chi-restraints excluded: chain H residue 576 LEU Chi-restraints excluded: chain H residue 580 VAL Chi-restraints excluded: chain H residue 604 CYS Chi-restraints excluded: chain H residue 617 ARG Chi-restraints excluded: chain H residue 626 MET Chi-restraints excluded: chain H residue 639 THR 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 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 183 SER Chi-restraints excluded: chain J residue 204 LYS Chi-restraints excluded: chain J residue 206 VAL Chi-restraints excluded: chain K residue 62 PHE Chi-restraints excluded: chain K residue 87 TYR 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 69 MET Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 100 ASP 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 167 GLN Chi-restraints excluded: chain I residue 169 SER 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 54 ARG Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 102 SER Chi-restraints excluded: chain L residue 109 THR 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 M residue 50 THR 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 163 THR Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 208 LEU 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 415 THR 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 499 THR Chi-restraints excluded: chain M residue 500 ARG Chi-restraints excluded: chain M residue 501 CYS Chi-restraints excluded: chain N residue 534 SER Chi-restraints excluded: chain N residue 576 LEU Chi-restraints excluded: chain N residue 580 VAL Chi-restraints excluded: chain N residue 581 LEU Chi-restraints excluded: chain N residue 617 ARG Chi-restraints excluded: chain N residue 629 LEU Chi-restraints excluded: chain N residue 639 THR Chi-restraints excluded: chain P residue 12 VAL 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 102 VAL Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain P residue 124 LEU 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 51 ASN Chi-restraints excluded: chain Q residue 62 PHE 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 Q residue 169 SER 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 86 ASP Chi-restraints excluded: chain O residue 93 VAL 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 167 GLN Chi-restraints excluded: chain O residue 169 SER Chi-restraints excluded: chain O residue 201 THR Chi-restraints excluded: chain O residue 208 GLU Chi-restraints excluded: chain R residue 10 ILE Chi-restraints excluded: chain R residue 13 LEU Chi-restraints excluded: chain R residue 40 ARG Chi-restraints excluded: chain R residue 49 TYR Chi-restraints excluded: chain R residue 53 ARG Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 142 ARG Chi-restraints excluded: chain R residue 161 GLU Chi-restraints excluded: chain R residue 168 SER Chi-restraints excluded: chain R residue 172 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 378 optimal weight: 10.0000 chunk 398 optimal weight: 4.9990 chunk 363 optimal weight: 20.0000 chunk 388 optimal weight: 8.9990 chunk 233 optimal weight: 0.7980 chunk 169 optimal weight: 3.9990 chunk 304 optimal weight: 5.9990 chunk 119 optimal weight: 10.0000 chunk 350 optimal weight: 8.9990 chunk 366 optimal weight: 6.9990 chunk 386 optimal weight: 9.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 GLN ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN ** J 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 GLN ** I 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 103 GLN ** N 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 50 ASN Q 168 GLN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 160 GLN ** R 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6491 moved from start: 0.5637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 36672 Z= 0.334 Angle : 0.827 9.765 49872 Z= 0.417 Chirality : 0.054 0.727 5946 Planarity : 0.006 0.060 6201 Dihedral : 10.016 91.079 7200 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.21 % Favored : 89.49 % Rotamer: Outliers : 6.35 % Allowed : 21.33 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.97 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.12), residues: 4350 helix: -2.81 (0.21), residues: 441 sheet: -1.18 (0.13), residues: 1422 loop : -2.23 (0.12), residues: 2487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP I 150 HIS 0.008 0.002 HIS E 38 PHE 0.031 0.002 PHE L 22 TYR 0.026 0.003 TYR D 140 ARG 0.008 0.001 ARG M 350 *********************** 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 653 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 409 time to evaluate : 4.103 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: 0.6490 (OUTLIER) cc_final: 0.6125 (pp30) REVERT: A 83 GLU cc_start: 0.7307 (tt0) cc_final: 0.7083 (tt0) REVERT: A 161 MET cc_start: 0.5470 (mmm) cc_final: 0.5116 (mmm) REVERT: A 308 ARG cc_start: 0.6690 (OUTLIER) cc_final: 0.6398 (ptm160) REVERT: B 576 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7530 (tt) REVERT: B 581 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.7128 (tt) REVERT: B 656 ASN cc_start: 0.5858 (OUTLIER) cc_final: 0.5092 (t0) REVERT: D 146 THR cc_start: 0.4895 (OUTLIER) cc_final: 0.4552 (p) REVERT: E 20 ARG cc_start: 0.5520 (mmm160) cc_final: 0.5229 (mmt-90) REVERT: E 87 TYR cc_start: 0.5280 (OUTLIER) cc_final: 0.4650 (m-10) REVERT: E 90 MET cc_start: 0.5688 (OUTLIER) cc_final: 0.5430 (tpt) REVERT: C 167 GLN cc_start: 0.6575 (OUTLIER) cc_final: 0.4544 (mm110) REVERT: F 33 MET cc_start: 0.7641 (OUTLIER) cc_final: 0.7027 (ttp) REVERT: F 49 TYR cc_start: 0.5959 (OUTLIER) cc_final: 0.5256 (t80) REVERT: G 95 MET cc_start: 0.8012 (ptm) cc_final: 0.7761 (ttp) REVERT: G 207 LYS cc_start: 0.6290 (OUTLIER) cc_final: 0.5743 (tttm) REVERT: H 576 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7584 (tt) REVERT: J 96 ARG cc_start: 0.5766 (OUTLIER) cc_final: 0.5300 (pmm-80) REVERT: K 50 ASN cc_start: 0.6396 (t0) cc_final: 0.6138 (t160) REVERT: K 87 TYR cc_start: 0.5620 (OUTLIER) cc_final: 0.4344 (m-80) REVERT: L 49 TYR cc_start: 0.5840 (OUTLIER) cc_final: 0.4865 (t80) REVERT: L 139 PHE cc_start: 0.3326 (p90) cc_final: 0.3091 (p90) REVERT: L 145 LYS cc_start: 0.5371 (pttm) cc_final: 0.5083 (pttm) REVERT: M 161 MET cc_start: 0.5256 (mmm) cc_final: 0.5001 (mtp) REVERT: M 440 GLN cc_start: 0.6915 (OUTLIER) cc_final: 0.6262 (tm-30) REVERT: M 476 ARG cc_start: 0.6810 (OUTLIER) cc_final: 0.5712 (mmt-90) REVERT: N 576 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7489 (tt) REVERT: N 581 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.7067 (tt) REVERT: N 656 ASN cc_start: 0.5998 (OUTLIER) cc_final: 0.5165 (t0) REVERT: P 29 MET cc_start: 0.1670 (pp-130) cc_final: 0.1039 (pp-130) REVERT: Q 42 GLN cc_start: 0.2721 (mp10) cc_final: 0.2436 (mm-40) REVERT: Q 87 TYR cc_start: 0.5669 (OUTLIER) cc_final: 0.3482 (m-80) REVERT: Q 96 TRP cc_start: 0.6264 (OUTLIER) cc_final: 0.4439 (m100) REVERT: O 61 ARG cc_start: 0.7686 (OUTLIER) cc_final: 0.7216 (ptm160) REVERT: O 76 ASP cc_start: 0.7441 (t0) cc_final: 0.7204 (t0) REVERT: O 121 VAL cc_start: 0.4549 (p) cc_final: 0.4336 (p) REVERT: O 167 GLN cc_start: 0.6820 (OUTLIER) cc_final: 0.4918 (mm110) REVERT: R 49 TYR cc_start: 0.5890 (OUTLIER) cc_final: 0.5373 (t80) REVERT: R 53 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7240 (ttm-80) REVERT: R 142 ARG cc_start: 0.4498 (OUTLIER) cc_final: 0.4062 (ttt180) outliers start: 244 outliers final: 171 residues processed: 593 average time/residue: 1.3808 time to fit residues: 993.2076 Evaluate side-chains 584 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 385 time to evaluate : 3.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR 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 128 THR 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 308 ARG 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 461 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 500 ARG Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 576 LEU 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 621 GLU Chi-restraints excluded: chain B residue 656 ASN Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 150 ASN 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 13 VAL Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 62 PHE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 87 TYR Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 96 TRP Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 136 CYS 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 167 GLN Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 205 LYS Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 33 MET Chi-restraints excluded: chain F residue 49 TYR Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 100 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 182 VAL Chi-restraints excluded: chain G residue 207 LYS Chi-restraints excluded: chain G residue 248 THR Chi-restraints excluded: chain G residue 276 ASN 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 418 CYS Chi-restraints excluded: chain G residue 424 ILE Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain G residue 500 ARG Chi-restraints excluded: chain H residue 568 LEU Chi-restraints excluded: chain H residue 576 LEU Chi-restraints excluded: chain H residue 580 VAL 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 626 MET Chi-restraints excluded: chain H residue 639 THR 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 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 102 VAL 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 183 SER Chi-restraints excluded: chain J residue 204 LYS Chi-restraints excluded: chain J residue 206 VAL Chi-restraints excluded: chain K residue 87 TYR 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 69 MET Chi-restraints excluded: chain I residue 86 ASP 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 169 SER Chi-restraints excluded: chain I residue 201 THR Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 100 LEU Chi-restraints excluded: chain L residue 102 SER Chi-restraints excluded: chain L residue 109 THR 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 50 THR 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 163 THR Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 208 LEU 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 376 PHE Chi-restraints excluded: chain M residue 415 THR 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 499 THR Chi-restraints excluded: chain M residue 500 ARG Chi-restraints excluded: chain M residue 501 CYS Chi-restraints excluded: chain N residue 534 SER Chi-restraints excluded: chain N residue 553 SER Chi-restraints excluded: chain N residue 576 LEU Chi-restraints excluded: chain N residue 580 VAL Chi-restraints excluded: chain N residue 581 LEU Chi-restraints excluded: chain N residue 617 ARG Chi-restraints excluded: chain N residue 629 LEU Chi-restraints excluded: chain N residue 639 THR Chi-restraints excluded: chain N residue 656 ASN Chi-restraints excluded: chain P residue 12 VAL 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 107 THR Chi-restraints excluded: chain P residue 124 LEU Chi-restraints excluded: chain P residue 176 VAL Chi-restraints excluded: chain P residue 200 THR Chi-restraints excluded: chain Q residue 50 ASN Chi-restraints excluded: chain Q residue 62 PHE 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 96 TRP 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 86 ASP 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 167 GLN Chi-restraints excluded: chain O residue 169 SER Chi-restraints excluded: chain O residue 201 THR Chi-restraints excluded: chain O residue 208 GLU 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 53 ARG Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 142 ARG Chi-restraints excluded: chain R residue 161 GLU Chi-restraints excluded: chain R residue 168 SER Chi-restraints excluded: chain R residue 172 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 254 optimal weight: 8.9990 chunk 410 optimal weight: 10.0000 chunk 250 optimal weight: 10.0000 chunk 194 optimal weight: 1.9990 chunk 285 optimal weight: 0.9990 chunk 430 optimal weight: 0.3980 chunk 396 optimal weight: 4.9990 chunk 342 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 264 optimal weight: 0.1980 chunk 210 optimal weight: 5.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- 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 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 ASN ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 GLN ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 562 GLN J 3 GLN ** K 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 103 GLN ** N 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 160 GLN ** R 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6375 moved from start: 0.5694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.148 36672 Z= 0.181 Angle : 0.725 9.860 49872 Z= 0.364 Chirality : 0.049 0.457 5946 Planarity : 0.005 0.052 6201 Dihedral : 8.874 75.921 7200 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.26 % Favored : 92.48 % Rotamer: Outliers : 3.10 % Allowed : 24.84 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.97 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.12), residues: 4350 helix: -2.41 (0.22), residues: 441 sheet: -0.76 (0.14), residues: 1416 loop : -1.98 (0.12), residues: 2493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 96 HIS 0.005 0.001 HIS G 72 PHE 0.035 0.001 PHE L 22 TYR 0.036 0.002 TYR K 49 ARG 0.009 0.000 ARG R 54 ********************** 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 536 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 417 time to evaluate : 3.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.6319 (OUTLIER) cc_final: 0.5897 (pp30) REVERT: A 83 GLU cc_start: 0.7077 (tt0) cc_final: 0.6871 (tt0) REVERT: A 161 MET cc_start: 0.5392 (mmm) cc_final: 0.4959 (mmm) REVERT: A 475 MET cc_start: 0.6649 (mmp) cc_final: 0.6433 (mmp) REVERT: B 656 ASN cc_start: 0.5692 (OUTLIER) cc_final: 0.4982 (t0) REVERT: E 96 TRP cc_start: 0.5385 (OUTLIER) cc_final: 0.4244 (m-10) REVERT: F 211 ARG cc_start: 0.4653 (mmm160) cc_final: 0.2928 (mmt-90) REVERT: G 95 MET cc_start: 0.7874 (ptm) cc_final: 0.7668 (ttp) REVERT: J 96 ARG cc_start: 0.5794 (OUTLIER) cc_final: 0.5262 (pmm-80) REVERT: J 204 LYS cc_start: 0.3264 (OUTLIER) cc_final: 0.2357 (mppt) REVERT: K 20 ARG cc_start: 0.5802 (mmm160) cc_final: 0.5467 (mmm-85) REVERT: I 112 SER cc_start: 0.6462 (t) cc_final: 0.6177 (p) REVERT: L 139 PHE cc_start: 0.3311 (p90) cc_final: 0.2994 (p90) REVERT: M 161 MET cc_start: 0.5213 (mmm) cc_final: 0.4711 (mtm) REVERT: N 581 LEU cc_start: 0.7227 (OUTLIER) cc_final: 0.6817 (tt) REVERT: N 617 ARG cc_start: 0.3824 (OUTLIER) cc_final: 0.2426 (ptp90) REVERT: P 29 MET cc_start: 0.1408 (pp-130) cc_final: 0.0910 (pp-130) REVERT: P 37 ILE cc_start: 0.4585 (OUTLIER) cc_final: 0.4256 (mt) REVERT: Q 87 TYR cc_start: 0.5188 (OUTLIER) cc_final: 0.2825 (m-80) REVERT: Q 209 PRO cc_start: 0.1771 (Cg_endo) cc_final: 0.1438 (Cg_exo) REVERT: O 137 LEU cc_start: 0.3435 (OUTLIER) cc_final: 0.3195 (tt) outliers start: 119 outliers final: 66 residues processed: 511 average time/residue: 1.4302 time to fit residues: 888.2186 Evaluate side-chains 450 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 374 time to evaluate : 3.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLN 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 452 LEU Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 500 ARG Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 656 ASN Chi-restraints excluded: chain D residue 24 VAL 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 E residue 13 VAL Chi-restraints excluded: chain E residue 62 PHE Chi-restraints excluded: chain E residue 96 TRP Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 161 GLU 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 276 ASN Chi-restraints excluded: chain G residue 296 CYS Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 418 CYS Chi-restraints excluded: chain G residue 424 ILE Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain H residue 568 LEU Chi-restraints excluded: chain H residue 604 CYS Chi-restraints excluded: chain H residue 619 LEU Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 69 ILE Chi-restraints excluded: chain J residue 96 ARG Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 204 LYS Chi-restraints excluded: chain K residue 105 THR Chi-restraints excluded: chain I residue 37 VAL 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 L residue 13 LEU Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 163 THR Chi-restraints excluded: chain M residue 248 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 494 LEU Chi-restraints excluded: chain N residue 534 SER Chi-restraints excluded: chain N residue 581 LEU Chi-restraints excluded: chain N residue 617 ARG Chi-restraints excluded: chain P residue 37 ILE 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 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 137 LEU Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain R residue 10 ILE Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 161 GLU Chi-restraints excluded: chain R residue 172 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 272 optimal weight: 7.9990 chunk 365 optimal weight: 20.0000 chunk 104 optimal weight: 6.9990 chunk 316 optimal weight: 9.9990 chunk 50 optimal weight: 9.9990 chunk 95 optimal weight: 4.9990 chunk 343 optimal weight: 0.7980 chunk 143 optimal weight: 4.9990 chunk 352 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 GLN D 150 ASN ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN ** F 189 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** J 3 GLN ** K 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 GLN ** L 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 66 HIS N 543 ASN ** N 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 50 ASN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 147 GLN ** R 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 160 GLN ** 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 = 0.4480 r_free = 0.4480 target = 0.192198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.165813 restraints weight = 73620.102| |-----------------------------------------------------------------------------| r_work (start): 0.4164 rms_B_bonded: 3.15 r_work: 0.4002 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3914 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 moved from start: 0.5777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 36672 Z= 0.264 Angle : 0.768 16.221 49872 Z= 0.382 Chirality : 0.051 0.589 5946 Planarity : 0.006 0.088 6201 Dihedral : 8.769 59.736 7200 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.22 % Favored : 90.51 % Rotamer: Outliers : 3.46 % Allowed : 24.77 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.97 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.12), residues: 4350 helix: -2.27 (0.23), residues: 423 sheet: -0.77 (0.14), residues: 1407 loop : -2.03 (0.12), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 96 HIS 0.011 0.001 HIS J 195 PHE 0.031 0.002 PHE L 22 TYR 0.037 0.002 TYR J 140 ARG 0.009 0.001 ARG R 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15619.41 seconds wall clock time: 277 minutes 50.50 seconds (16670.50 seconds total)