Starting phenix.real_space_refine on Thu Jul 25 18:34:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jn4_36432/07_2024/8jn4_36432.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jn4_36432/07_2024/8jn4_36432.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jn4_36432/07_2024/8jn4_36432.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jn4_36432/07_2024/8jn4_36432.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jn4_36432/07_2024/8jn4_36432.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jn4_36432/07_2024/8jn4_36432.cif" } resolution = 3.5 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= 0.000 sd= 1.000 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 202 5.16 5 C 19184 2.51 5 N 5062 2.21 5 O 5778 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 2": "NH1" <-> "NH2" Residue "A ARG 9": "NH1" <-> "NH2" Residue "A PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 57": "NH1" <-> "NH2" Residue "A ARG 73": "NH1" <-> "NH2" Residue "A ARG 99": "NH1" <-> "NH2" Residue "A GLU 123": "OE1" <-> "OE2" Residue "A GLU 126": "OE1" <-> "OE2" Residue "A GLU 161": "OE1" <-> "OE2" Residue "A ARG 186": "NH1" <-> "NH2" Residue "A ASP 190": "OD1" <-> "OD2" Residue "A PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 208": "NH1" <-> "NH2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 247": "OE1" <-> "OE2" Residue "A PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 284": "NH1" <-> "NH2" Residue "A ARG 348": "NH1" <-> "NH2" Residue "A ARG 405": "NH1" <-> "NH2" Residue "A ARG 409": "NH1" <-> "NH2" Residue "A PHE 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B GLU 23": "OE1" <-> "OE2" Residue "B ARG 38": "NH1" <-> "NH2" Residue "B PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 2": "NH1" <-> "NH2" Residue "C ARG 9": "NH1" <-> "NH2" Residue "C ARG 57": "NH1" <-> "NH2" Residue "C ARG 73": "NH1" <-> "NH2" Residue "C GLU 84": "OE1" <-> "OE2" Residue "C TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 99": "NH1" <-> "NH2" Residue "C TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 133": "OE1" <-> "OE2" Residue "C GLU 154": "OE1" <-> "OE2" Residue "C ARG 186": "NH1" <-> "NH2" Residue "C ARG 208": "NH1" <-> "NH2" Residue "C GLU 233": "OE1" <-> "OE2" Residue "C GLU 338": "OE1" <-> "OE2" Residue "C GLU 368": "OE1" <-> "OE2" Residue "C GLU 401": "OE1" <-> "OE2" Residue "C ARG 405": "NH1" <-> "NH2" Residue "C ARG 409": "NH1" <-> "NH2" Residue "C ASP 419": "OD1" <-> "OD2" Residue "C TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 38": "NH1" <-> "NH2" Residue "D TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 2": "NH1" <-> "NH2" Residue "E ARG 9": "NH1" <-> "NH2" Residue "E PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 57": "NH1" <-> "NH2" Residue "E ARG 73": "NH1" <-> "NH2" Residue "E GLU 79": "OE1" <-> "OE2" Residue "E ARG 99": "NH1" <-> "NH2" Residue "E GLU 182": "OE1" <-> "OE2" Residue "E ARG 186": "NH1" <-> "NH2" Residue "E ARG 208": "NH1" <-> "NH2" Residue "E ARG 284": "NH1" <-> "NH2" Residue "E PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 348": "NH1" <-> "NH2" Residue "E GLU 361": "OE1" <-> "OE2" Residue "E GLU 401": "OE1" <-> "OE2" Residue "E ARG 405": "NH1" <-> "NH2" Residue "E ARG 409": "NH1" <-> "NH2" Residue "F GLU 33": "OE1" <-> "OE2" Residue "F ARG 38": "NH1" <-> "NH2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 98": "NH1" <-> "NH2" Residue "H GLU 99": "OE1" <-> "OE2" Residue "L TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 66": "OD1" <-> "OD2" Residue "L PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 2": "NH1" <-> "NH2" Residue "O ARG 9": "NH1" <-> "NH2" Residue "O PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 57": "NH1" <-> "NH2" Residue "O ARG 73": "NH1" <-> "NH2" Residue "O ARG 99": "NH1" <-> "NH2" Residue "O GLU 123": "OE1" <-> "OE2" Residue "O GLU 126": "OE1" <-> "OE2" Residue "O GLU 161": "OE1" <-> "OE2" Residue "O ARG 186": "NH1" <-> "NH2" Residue "O ASP 190": "OD1" <-> "OD2" Residue "O PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 208": "NH1" <-> "NH2" Residue "O PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 247": "OE1" <-> "OE2" Residue "O PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 284": "NH1" <-> "NH2" Residue "O ARG 348": "NH1" <-> "NH2" Residue "O ARG 405": "NH1" <-> "NH2" Residue "O ARG 409": "NH1" <-> "NH2" Residue "O PHE 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 15": "NH1" <-> "NH2" Residue "P GLU 23": "OE1" <-> "OE2" Residue "P ARG 38": "NH1" <-> "NH2" Residue "P PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 2": "NH1" <-> "NH2" Residue "Q ARG 9": "NH1" <-> "NH2" Residue "Q ARG 57": "NH1" <-> "NH2" Residue "Q ARG 73": "NH1" <-> "NH2" Residue "Q GLU 84": "OE1" <-> "OE2" Residue "Q TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 99": "NH1" <-> "NH2" Residue "Q TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 133": "OE1" <-> "OE2" Residue "Q GLU 154": "OE1" <-> "OE2" Residue "Q ARG 186": "NH1" <-> "NH2" Residue "Q ARG 208": "NH1" <-> "NH2" Residue "Q GLU 233": "OE1" <-> "OE2" Residue "Q GLU 338": "OE1" <-> "OE2" Residue "Q GLU 368": "OE1" <-> "OE2" Residue "Q GLU 401": "OE1" <-> "OE2" Residue "Q ARG 405": "NH1" <-> "NH2" Residue "Q ARG 409": "NH1" <-> "NH2" Residue "Q ASP 419": "OD1" <-> "OD2" Residue "Q TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 38": "NH1" <-> "NH2" Residue "R TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 2": "NH1" <-> "NH2" Residue "S ARG 9": "NH1" <-> "NH2" Residue "S PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 57": "NH1" <-> "NH2" Residue "S ARG 73": "NH1" <-> "NH2" Residue "S GLU 79": "OE1" <-> "OE2" Residue "S ARG 99": "NH1" <-> "NH2" Residue "S GLU 182": "OE1" <-> "OE2" Residue "S ARG 186": "NH1" <-> "NH2" Residue "S ARG 208": "NH1" <-> "NH2" Residue "S ARG 284": "NH1" <-> "NH2" Residue "S PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 348": "NH1" <-> "NH2" Residue "S GLU 361": "OE1" <-> "OE2" Residue "S GLU 401": "OE1" <-> "OE2" Residue "S ARG 405": "NH1" <-> "NH2" Residue "S ARG 409": "NH1" <-> "NH2" Residue "T GLU 33": "OE1" <-> "OE2" Residue "T ARG 38": "NH1" <-> "NH2" Residue "U PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 98": "NH1" <-> "NH2" Residue "U GLU 99": "OE1" <-> "OE2" Residue "V TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 66": "OD1" <-> "OD2" Residue "V PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 30226 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 3757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3757 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 16, 'TRANS': 476} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 585 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 3757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3757 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 16, 'TRANS': 476} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 585 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "E" Number of atoms: 3757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3757 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 16, 'TRANS': 476} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "F" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 585 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 950 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "L" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 870 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 2, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" 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: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 2, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 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: "O" Number of atoms: 3757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3757 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 16, 'TRANS': 476} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "P" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 585 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "Q" Number of atoms: 3757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3757 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 16, 'TRANS': 476} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "R" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 585 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "S" Number of atoms: 3757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3757 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 16, 'TRANS': 476} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "T" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 585 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "U" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 950 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "V" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 870 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "W" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 2, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 2, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Z" 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: "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: 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 Time building chain proxies: 15.38, per 1000 atoms: 0.51 Number of scatterers: 30226 At special positions: 0 Unit cell: (165.87, 237.69, 117.99, 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 202 16.00 O 5778 8.00 N 5062 7.00 C 19184 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 30 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 121 " distance=2.02 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 116 " distance=2.03 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 283 " distance=2.03 Simple disulfide: pdb=" SG CYS C 3 " - pdb=" SG CYS C 30 " distance=2.03 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 121 " distance=2.03 Simple disulfide: pdb=" SG CYS C 74 " - pdb=" SG CYS C 105 " distance=2.03 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 116 " distance=2.03 Simple disulfide: pdb=" SG CYS C 300 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 3 " - pdb=" SG CYS E 30 " distance=2.02 Simple disulfide: pdb=" SG CYS E 60 " - pdb=" SG CYS E 121 " distance=2.03 Simple disulfide: pdb=" SG CYS E 92 " - pdb=" SG CYS E 116 " distance=2.03 Simple disulfide: pdb=" SG CYS E 300 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " distance=2.03 Simple disulfide: pdb=" SG CYS O 3 " - pdb=" SG CYS O 30 " distance=2.03 Simple disulfide: pdb=" SG CYS O 60 " - pdb=" SG CYS O 121 " distance=2.02 Simple disulfide: pdb=" SG CYS O 92 " - pdb=" SG CYS O 116 " distance=2.03 Simple disulfide: pdb=" SG CYS O 183 " - pdb=" SG CYS O 283 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 3 " - pdb=" SG CYS Q 30 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 60 " - pdb=" SG CYS Q 121 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 74 " - pdb=" SG CYS Q 105 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 92 " - pdb=" SG CYS Q 116 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 300 " - pdb=" SG CYS Q 331 " distance=2.03 Simple disulfide: pdb=" SG CYS S 3 " - pdb=" SG CYS S 30 " distance=2.02 Simple disulfide: pdb=" SG CYS S 60 " - pdb=" SG CYS S 121 " distance=2.03 Simple disulfide: pdb=" SG CYS S 92 " - pdb=" SG CYS S 116 " distance=2.03 Simple disulfide: pdb=" SG CYS S 300 " - pdb=" SG CYS S 331 " distance=2.03 Simple disulfide: pdb=" SG CYS U 22 " - pdb=" SG CYS U 96 " distance=2.03 Simple disulfide: pdb=" SG CYS V 23 " - pdb=" SG CYS V 94 " distance=2.03 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 ALPHA1-3 " BMA G 3 " - " MAN G 4 " " BMA J 3 " - " MAN J 4 " " BMA W 3 " - " MAN W 4 " " BMA Y 3 " - " MAN Y 4 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG 1 2 " - " BMA 1 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " BETA1-6 " BMA G 3 " - " BMA G 5 " " BMA J 3 " - " BMA J 5 " " BMA W 3 " - " BMA W 5 " " BMA Y 3 " - " BMA Y 5 " NAG-ASN " NAG 0 1 " - " ASN S 67 " " NAG 1 1 " - " ASN S 153 " " NAG G 1 " - " ASN A 67 " " NAG I 1 " - " ASN A 153 " " NAG J 1 " - " ASN C 67 " " NAG K 1 " - " ASN C 153 " " NAG M 1 " - " ASN E 67 " " NAG N 1 " - " ASN E 153 " " NAG W 1 " - " ASN O 67 " " NAG X 1 " - " ASN O 153 " " NAG Y 1 " - " ASN Q 67 " " NAG Z 1 " - " ASN Q 153 " Time building additional restraints: 12.66 Conformation dependent library (CDL) restraints added in 6.2 seconds 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6984 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 68 sheets defined 26.0% alpha, 26.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.55 Creating SS restraints... Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 208 through 213 Processing helix chain 'A' and resid 231 through 235 removed outlier: 3.776A pdb=" N LEU A 234 " --> pdb=" O ARG A 231 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 235 " --> pdb=" O LYS A 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 231 through 235' Processing helix chain 'A' and resid 254 through 262 Processing helix chain 'A' and resid 394 through 414 Processing helix chain 'A' and resid 415 through 420 removed outlier: 3.820A pdb=" N PHE A 420 " --> pdb=" O ALA A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 447 Processing helix chain 'A' and resid 450 through 467 Processing helix chain 'A' and resid 470 through 489 removed outlier: 4.010A pdb=" N SER A 476 " --> pdb=" O SER A 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 39 removed outlier: 4.530A pdb=" N VAL B 32 " --> pdb=" O GLN B 28 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU B 33 " --> pdb=" O VAL B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 54 removed outlier: 4.008A pdb=" N ILE B 44 " --> pdb=" O PRO B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 75 Proline residue: B 72 - end of helix Processing helix chain 'C' and resid 82 through 86 removed outlier: 3.799A pdb=" N GLN C 86 " --> pdb=" O PRO C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 104 Processing helix chain 'C' and resid 131 through 135 removed outlier: 3.990A pdb=" N LEU C 135 " --> pdb=" O TYR C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 214 Processing helix chain 'C' and resid 231 through 235 removed outlier: 3.683A pdb=" N LEU C 234 " --> pdb=" O ARG C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 261 Processing helix chain 'C' and resid 394 through 411 Processing helix chain 'C' and resid 415 through 420 Processing helix chain 'C' and resid 425 through 447 removed outlier: 3.553A pdb=" N LEU C 430 " --> pdb=" O VAL C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 468 Processing helix chain 'C' and resid 470 through 491 removed outlier: 3.656A pdb=" N VAL C 490 " --> pdb=" O TYR C 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 39 Processing helix chain 'D' and resid 40 through 54 removed outlier: 3.790A pdb=" N ILE D 44 " --> pdb=" O PRO D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 75 removed outlier: 3.551A pdb=" N THR D 71 " --> pdb=" O LEU D 67 " (cutoff:3.500A) Proline residue: D 72 - end of helix Processing helix chain 'E' and resid 16 through 18 No H-bonds generated for 'chain 'E' and resid 16 through 18' Processing helix chain 'E' and resid 82 through 87 removed outlier: 3.531A pdb=" N GLN E 86 " --> pdb=" O PRO E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 194 removed outlier: 3.890A pdb=" N MET E 194 " --> pdb=" O PHE E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 213 Processing helix chain 'E' and resid 231 through 234 removed outlier: 4.244A pdb=" N LEU E 234 " --> pdb=" O ARG E 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 231 through 234' Processing helix chain 'E' and resid 254 through 262 Processing helix chain 'E' and resid 394 through 413 Processing helix chain 'E' and resid 415 through 419 Processing helix chain 'E' and resid 426 through 446 Processing helix chain 'E' and resid 450 through 468 removed outlier: 4.145A pdb=" N ILE E 455 " --> pdb=" O TRP E 451 " (cutoff:3.500A) Processing helix chain 'E' and resid 471 through 489 removed outlier: 4.380A pdb=" N PHE E 475 " --> pdb=" O THR E 471 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE E 478 " --> pdb=" O SER E 474 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE E 482 " --> pdb=" O ILE E 478 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ILE E 483 " --> pdb=" O ALA E 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 39 Processing helix chain 'F' and resid 40 through 52 removed outlier: 3.893A pdb=" N ILE F 44 " --> pdb=" O PRO F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 75 removed outlier: 3.662A pdb=" N PHE F 64 " --> pdb=" O LYS F 60 " (cutoff:3.500A) Proline residue: F 72 - end of helix Processing helix chain 'O' and resid 100 through 104 Processing helix chain 'O' and resid 131 through 133 No H-bonds generated for 'chain 'O' and resid 131 through 133' Processing helix chain 'O' and resid 208 through 213 Processing helix chain 'O' and resid 231 through 235 removed outlier: 3.776A pdb=" N LEU O 234 " --> pdb=" O ARG O 231 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU O 235 " --> pdb=" O LYS O 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 231 through 235' Processing helix chain 'O' and resid 254 through 262 Processing helix chain 'O' and resid 394 through 414 Processing helix chain 'O' and resid 415 through 420 removed outlier: 3.820A pdb=" N PHE O 420 " --> pdb=" O ALA O 417 " (cutoff:3.500A) Processing helix chain 'O' and resid 426 through 447 Processing helix chain 'O' and resid 450 through 467 Processing helix chain 'O' and resid 470 through 489 removed outlier: 4.010A pdb=" N SER O 476 " --> pdb=" O SER O 472 " (cutoff:3.500A) Processing helix chain 'P' and resid 20 through 39 removed outlier: 4.530A pdb=" N VAL P 32 " --> pdb=" O GLN P 28 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU P 33 " --> pdb=" O VAL P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 54 removed outlier: 4.008A pdb=" N ILE P 44 " --> pdb=" O PRO P 40 " (cutoff:3.500A) Processing helix chain 'P' and resid 56 through 75 Proline residue: P 72 - end of helix Processing helix chain 'Q' and resid 82 through 86 removed outlier: 3.799A pdb=" N GLN Q 86 " --> pdb=" O PRO Q 83 " (cutoff:3.500A) Processing helix chain 'Q' and resid 100 through 104 Processing helix chain 'Q' and resid 131 through 135 removed outlier: 3.990A pdb=" N LEU Q 135 " --> pdb=" O TYR Q 132 " (cutoff:3.500A) Processing helix chain 'Q' and resid 208 through 214 Processing helix chain 'Q' and resid 231 through 235 removed outlier: 3.683A pdb=" N LEU Q 234 " --> pdb=" O ARG Q 231 " (cutoff:3.500A) Processing helix chain 'Q' and resid 254 through 261 Processing helix chain 'Q' and resid 394 through 411 Processing helix chain 'Q' and resid 415 through 420 Processing helix chain 'Q' and resid 425 through 447 removed outlier: 3.553A pdb=" N LEU Q 430 " --> pdb=" O VAL Q 426 " (cutoff:3.500A) Processing helix chain 'Q' and resid 450 through 468 Processing helix chain 'Q' and resid 470 through 491 removed outlier: 3.656A pdb=" N VAL Q 490 " --> pdb=" O TYR Q 486 " (cutoff:3.500A) Processing helix chain 'R' and resid 26 through 39 Processing helix chain 'R' and resid 40 through 54 removed outlier: 3.790A pdb=" N ILE R 44 " --> pdb=" O PRO R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 75 removed outlier: 3.551A pdb=" N THR R 71 " --> pdb=" O LEU R 67 " (cutoff:3.500A) Proline residue: R 72 - end of helix Processing helix chain 'S' and resid 16 through 18 No H-bonds generated for 'chain 'S' and resid 16 through 18' Processing helix chain 'S' and resid 82 through 87 removed outlier: 3.531A pdb=" N GLN S 86 " --> pdb=" O PRO S 83 " (cutoff:3.500A) Processing helix chain 'S' and resid 190 through 194 removed outlier: 3.890A pdb=" N MET S 194 " --> pdb=" O PHE S 191 " (cutoff:3.500A) Processing helix chain 'S' and resid 207 through 213 Processing helix chain 'S' and resid 231 through 234 removed outlier: 4.244A pdb=" N LEU S 234 " --> pdb=" O ARG S 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 231 through 234' Processing helix chain 'S' and resid 254 through 262 Processing helix chain 'S' and resid 394 through 413 Processing helix chain 'S' and resid 415 through 419 Processing helix chain 'S' and resid 426 through 446 Processing helix chain 'S' and resid 450 through 468 removed outlier: 4.145A pdb=" N ILE S 455 " --> pdb=" O TRP S 451 " (cutoff:3.500A) Processing helix chain 'S' and resid 471 through 489 removed outlier: 4.380A pdb=" N PHE S 475 " --> pdb=" O THR S 471 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE S 478 " --> pdb=" O SER S 474 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE S 482 " --> pdb=" O ILE S 478 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ILE S 483 " --> pdb=" O ALA S 479 " (cutoff:3.500A) Processing helix chain 'T' and resid 26 through 39 Processing helix chain 'T' and resid 40 through 52 removed outlier: 3.893A pdb=" N ILE T 44 " --> pdb=" O PRO T 40 " (cutoff:3.500A) Processing helix chain 'T' and resid 58 through 75 removed outlier: 3.662A pdb=" N PHE T 64 " --> pdb=" O LYS T 60 " (cutoff:3.500A) Proline residue: T 72 - end of helix Processing sheet with id=1, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.823A pdb=" N ASP A 10 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N THR A 138 " --> pdb=" O GLN A 46 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N THR A 48 " --> pdb=" O LYS A 136 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LYS A 136 " --> pdb=" O THR A 48 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.823A pdb=" N ASP A 10 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR A 48 " --> pdb=" O ILE A 276 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA A 50 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR A 274 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 20 through 26 removed outlier: 4.044A pdb=" N GLY A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=5, first strand: chain 'A' and resid 58 through 59 Processing sheet with id=6, first strand: chain 'A' and resid 64 through 73 removed outlier: 5.409A pdb=" N ILE A 65 " --> pdb=" O GLN A 120 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N GLN A 120 " --> pdb=" O ILE A 65 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASN A 67 " --> pdb=" O LYS A 118 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL A 114 " --> pdb=" O ASP A 71 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'A' and resid 194 through 195 Processing sheet with id=8, first strand: chain 'A' and resid 198 through 199 removed outlier: 3.829A pdb=" N ALA A 203 " --> pdb=" O ILE A 268 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'A' and resid 237 through 240 Processing sheet with id=10, first strand: chain 'A' and resid 305 through 313 removed outlier: 7.151A pdb=" N LYS A 307 " --> pdb=" O GLU A 323 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N GLU A 323 " --> pdb=" O LYS A 307 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLU A 309 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N LYS A 321 " --> pdb=" O GLU A 309 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 311 " --> pdb=" O LEU A 319 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR A 317 " --> pdb=" O THR A 313 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'A' and resid 336 through 339 removed outlier: 3.673A pdb=" N SER A 374 " --> pdb=" O TRP A 389 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A 387 " --> pdb=" O ILE A 376 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.564A pdb=" N THR C 32 " --> pdb=" O ASP C 10 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR C 138 " --> pdb=" O GLN C 46 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'C' and resid 20 through 26 removed outlier: 3.598A pdb=" N GLY C 177 " --> pdb=" O LEU C 173 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA C 171 " --> pdb=" O LEU C 179 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'C' and resid 54 through 59 removed outlier: 5.584A pdb=" N THR C 55 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL C 129 " --> pdb=" O THR C 55 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG C 57 " --> pdb=" O GLY C 127 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ALA C 203 " --> pdb=" O ILE C 268 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE C 268 " --> pdb=" O ALA C 203 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'C' and resid 62 through 72 removed outlier: 4.420A pdb=" N ILE C 68 " --> pdb=" O CYS C 116 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N CYS C 116 " --> pdb=" O ILE C 68 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N THR C 70 " --> pdb=" O VAL C 114 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL C 114 " --> pdb=" O THR C 70 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N SER C 72 " --> pdb=" O SER C 112 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N SER C 112 " --> pdb=" O SER C 72 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY C 109 " --> pdb=" O ARG C 99 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'C' and resid 237 through 238 Processing sheet with id=17, first strand: chain 'C' and resid 304 through 312 removed outlier: 7.415A pdb=" N LYS C 321 " --> pdb=" O LYS C 307 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N GLU C 309 " --> pdb=" O LEU C 319 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N LEU C 319 " --> pdb=" O GLU C 309 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'C' and resid 373 through 377 removed outlier: 3.666A pdb=" N SER C 374 " --> pdb=" O TRP C 389 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'E' and resid 10 through 12 removed outlier: 7.201A pdb=" N THR E 138 " --> pdb=" O GLN E 46 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N THR E 48 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LYS E 136 " --> pdb=" O THR E 48 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.804A pdb=" N ALA E 50 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR E 274 " --> pdb=" O ALA E 50 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'E' and resid 20 through 25 removed outlier: 4.808A pdb=" N LYS E 282 " --> pdb=" O SER E 184 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER E 184 " --> pdb=" O LYS E 282 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'E' and resid 54 through 72 removed outlier: 5.619A pdb=" N THR E 55 " --> pdb=" O VAL E 129 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL E 129 " --> pdb=" O THR E 55 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE E 61 " --> pdb=" O GLU E 123 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N GLU E 123 " --> pdb=" O ILE E 61 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLY E 63 " --> pdb=" O CYS E 121 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N CYS E 121 " --> pdb=" O GLY E 63 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ILE E 65 " --> pdb=" O PHE E 119 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N PHE E 119 " --> pdb=" O ILE E 65 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ASN E 67 " --> pdb=" O ALA E 117 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ALA E 117 " --> pdb=" O ASN E 67 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N THR E 69 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N THR E 115 " --> pdb=" O THR E 69 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ASP E 71 " --> pdb=" O LEU E 113 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU E 113 " --> pdb=" O ASP E 71 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'E' and resid 54 through 72 removed outlier: 5.619A pdb=" N THR E 55 " --> pdb=" O VAL E 129 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL E 129 " --> pdb=" O THR E 55 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE E 61 " --> pdb=" O GLU E 123 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N GLU E 123 " --> pdb=" O ILE E 61 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLY E 63 " --> pdb=" O CYS E 121 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N CYS E 121 " --> pdb=" O GLY E 63 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ILE E 65 " --> pdb=" O PHE E 119 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N PHE E 119 " --> pdb=" O ILE E 65 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ASN E 67 " --> pdb=" O ALA E 117 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ALA E 117 " --> pdb=" O ASN E 67 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N THR E 69 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N THR E 115 " --> pdb=" O THR E 69 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ASP E 71 " --> pdb=" O LEU E 113 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU E 113 " --> pdb=" O ASP E 71 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU E 126 " --> pdb=" O THR E 198 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N TRP E 204 " --> pdb=" O LEU E 197 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA E 203 " --> pdb=" O ILE E 268 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE E 268 " --> pdb=" O ALA E 203 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'E' and resid 218 through 219 Processing sheet with id=25, first strand: chain 'E' and resid 236 through 239 removed outlier: 3.669A pdb=" N VAL E 249 " --> pdb=" O THR E 237 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'E' and resid 304 through 308 removed outlier: 7.963A pdb=" N LYS E 321 " --> pdb=" O LYS E 307 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'E' and resid 331 through 332 Processing sheet with id=28, first strand: chain 'E' and resid 336 through 338 Processing sheet with id=29, first strand: chain 'E' and resid 348 through 349 Processing sheet with id=30, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=31, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.919A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.611A pdb=" N PHE L 77 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'L' and resid 11 through 13 removed outlier: 3.915A pdb=" N THR L 108 " --> pdb=" O TYR L 92 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY L 90 " --> pdb=" O LEU L 110 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'L' and resid 50 through 54 removed outlier: 6.882A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.823A pdb=" N ASP O 10 " --> pdb=" O THR O 32 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N THR O 138 " --> pdb=" O GLN O 46 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N THR O 48 " --> pdb=" O LYS O 136 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LYS O 136 " --> pdb=" O THR O 48 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.823A pdb=" N ASP O 10 " --> pdb=" O THR O 32 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR O 48 " --> pdb=" O ILE O 276 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA O 50 " --> pdb=" O THR O 274 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR O 274 " --> pdb=" O ALA O 50 " (cutoff:3.500A) Processing sheet with id=37, first strand: chain 'O' and resid 20 through 26 removed outlier: 4.044A pdb=" N GLY O 177 " --> pdb=" O LEU O 173 " (cutoff:3.500A) Processing sheet with id=38, first strand: chain 'O' and resid 54 through 55 Processing sheet with id=39, first strand: chain 'O' and resid 58 through 59 Processing sheet with id=40, first strand: chain 'O' and resid 64 through 73 removed outlier: 5.409A pdb=" N ILE O 65 " --> pdb=" O GLN O 120 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N GLN O 120 " --> pdb=" O ILE O 65 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASN O 67 " --> pdb=" O LYS O 118 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL O 114 " --> pdb=" O ASP O 71 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'O' and resid 194 through 195 Processing sheet with id=42, first strand: chain 'O' and resid 198 through 199 removed outlier: 3.829A pdb=" N ALA O 203 " --> pdb=" O ILE O 268 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain 'O' and resid 237 through 240 Processing sheet with id=44, first strand: chain 'O' and resid 305 through 313 removed outlier: 7.151A pdb=" N LYS O 307 " --> pdb=" O GLU O 323 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N GLU O 323 " --> pdb=" O LYS O 307 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLU O 309 " --> pdb=" O LYS O 321 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N LYS O 321 " --> pdb=" O GLU O 309 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER O 311 " --> pdb=" O LEU O 319 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR O 317 " --> pdb=" O THR O 313 " (cutoff:3.500A) Processing sheet with id=45, first strand: chain 'O' and resid 336 through 339 removed outlier: 3.673A pdb=" N SER O 374 " --> pdb=" O TRP O 389 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE O 387 " --> pdb=" O ILE O 376 " (cutoff:3.500A) Processing sheet with id=46, first strand: chain 'Q' and resid 10 through 12 removed outlier: 3.564A pdb=" N THR Q 32 " --> pdb=" O ASP Q 10 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR Q 138 " --> pdb=" O GLN Q 46 " (cutoff:3.500A) Processing sheet with id=47, first strand: chain 'Q' and resid 20 through 26 removed outlier: 3.598A pdb=" N GLY Q 177 " --> pdb=" O LEU Q 173 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA Q 171 " --> pdb=" O LEU Q 179 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'Q' and resid 54 through 59 removed outlier: 5.584A pdb=" N THR Q 55 " --> pdb=" O VAL Q 129 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL Q 129 " --> pdb=" O THR Q 55 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG Q 57 " --> pdb=" O GLY Q 127 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ALA Q 203 " --> pdb=" O ILE Q 268 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE Q 268 " --> pdb=" O ALA Q 203 " (cutoff:3.500A) Processing sheet with id=49, first strand: chain 'Q' and resid 62 through 72 removed outlier: 4.420A pdb=" N ILE Q 68 " --> pdb=" O CYS Q 116 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N CYS Q 116 " --> pdb=" O ILE Q 68 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N THR Q 70 " --> pdb=" O VAL Q 114 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL Q 114 " --> pdb=" O THR Q 70 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N SER Q 72 " --> pdb=" O SER Q 112 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N SER Q 112 " --> pdb=" O SER Q 72 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY Q 109 " --> pdb=" O ARG Q 99 " (cutoff:3.500A) Processing sheet with id=50, first strand: chain 'Q' and resid 237 through 238 Processing sheet with id=51, first strand: chain 'Q' and resid 304 through 312 removed outlier: 7.415A pdb=" N LYS Q 321 " --> pdb=" O LYS Q 307 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N GLU Q 309 " --> pdb=" O LEU Q 319 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N LEU Q 319 " --> pdb=" O GLU Q 309 " (cutoff:3.500A) Processing sheet with id=52, first strand: chain 'Q' and resid 373 through 377 removed outlier: 3.666A pdb=" N SER Q 374 " --> pdb=" O TRP Q 389 " (cutoff:3.500A) Processing sheet with id=53, first strand: chain 'S' and resid 10 through 12 removed outlier: 7.201A pdb=" N THR S 138 " --> pdb=" O GLN S 46 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N THR S 48 " --> pdb=" O LYS S 136 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LYS S 136 " --> pdb=" O THR S 48 " (cutoff:3.500A) Processing sheet with id=54, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.804A pdb=" N ALA S 50 " --> pdb=" O THR S 274 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR S 274 " --> pdb=" O ALA S 50 " (cutoff:3.500A) Processing sheet with id=55, first strand: chain 'S' and resid 20 through 25 removed outlier: 4.808A pdb=" N LYS S 282 " --> pdb=" O SER S 184 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER S 184 " --> pdb=" O LYS S 282 " (cutoff:3.500A) Processing sheet with id=56, first strand: chain 'S' and resid 54 through 72 removed outlier: 5.619A pdb=" N THR S 55 " --> pdb=" O VAL S 129 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL S 129 " --> pdb=" O THR S 55 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE S 61 " --> pdb=" O GLU S 123 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N GLU S 123 " --> pdb=" O ILE S 61 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLY S 63 " --> pdb=" O CYS S 121 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N CYS S 121 " --> pdb=" O GLY S 63 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ILE S 65 " --> pdb=" O PHE S 119 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N PHE S 119 " --> pdb=" O ILE S 65 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ASN S 67 " --> pdb=" O ALA S 117 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ALA S 117 " --> pdb=" O ASN S 67 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N THR S 69 " --> pdb=" O THR S 115 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N THR S 115 " --> pdb=" O THR S 69 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ASP S 71 " --> pdb=" O LEU S 113 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU S 113 " --> pdb=" O ASP S 71 " (cutoff:3.500A) Processing sheet with id=57, first strand: chain 'S' and resid 54 through 72 removed outlier: 5.619A pdb=" N THR S 55 " --> pdb=" O VAL S 129 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL S 129 " --> pdb=" O THR S 55 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE S 61 " --> pdb=" O GLU S 123 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N GLU S 123 " --> pdb=" O ILE S 61 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLY S 63 " --> pdb=" O CYS S 121 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N CYS S 121 " --> pdb=" O GLY S 63 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ILE S 65 " --> pdb=" O PHE S 119 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N PHE S 119 " --> pdb=" O ILE S 65 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ASN S 67 " --> pdb=" O ALA S 117 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ALA S 117 " --> pdb=" O ASN S 67 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N THR S 69 " --> pdb=" O THR S 115 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N THR S 115 " --> pdb=" O THR S 69 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ASP S 71 " --> pdb=" O LEU S 113 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU S 113 " --> pdb=" O ASP S 71 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU S 126 " --> pdb=" O THR S 198 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N TRP S 204 " --> pdb=" O LEU S 197 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA S 203 " --> pdb=" O ILE S 268 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE S 268 " --> pdb=" O ALA S 203 " (cutoff:3.500A) Processing sheet with id=58, first strand: chain 'S' and resid 218 through 219 Processing sheet with id=59, first strand: chain 'S' and resid 236 through 239 removed outlier: 3.669A pdb=" N VAL S 249 " --> pdb=" O THR S 237 " (cutoff:3.500A) Processing sheet with id=60, first strand: chain 'S' and resid 304 through 308 removed outlier: 7.963A pdb=" N LYS S 321 " --> pdb=" O LYS S 307 " (cutoff:3.500A) Processing sheet with id=61, first strand: chain 'S' and resid 331 through 332 Processing sheet with id=62, first strand: chain 'S' and resid 336 through 338 Processing sheet with id=63, first strand: chain 'S' and resid 348 through 349 Processing sheet with id=64, first strand: chain 'U' and resid 3 through 7 Processing sheet with id=65, first strand: chain 'U' and resid 11 through 12 removed outlier: 6.919A pdb=" N MET U 34 " --> pdb=" O VAL U 50 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N VAL U 50 " --> pdb=" O MET U 34 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TRP U 36 " --> pdb=" O VAL U 48 " (cutoff:3.500A) Processing sheet with id=66, first strand: chain 'V' and resid 4 through 6 removed outlier: 3.611A pdb=" N PHE V 77 " --> pdb=" O CYS V 23 " (cutoff:3.500A) Processing sheet with id=67, first strand: chain 'V' and resid 11 through 13 removed outlier: 3.915A pdb=" N THR V 108 " --> pdb=" O TYR V 92 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY V 90 " --> pdb=" O LEU V 110 " (cutoff:3.500A) Processing sheet with id=68, first strand: chain 'V' and resid 50 through 54 removed outlier: 6.882A pdb=" N TRP V 41 " --> pdb=" O LEU V 53 " (cutoff:3.500A) 1204 hydrogen bonds defined for protein. 3216 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.67 Time building geometry restraints manager: 13.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9516 1.34 - 1.46: 5050 1.46 - 1.58: 15952 1.58 - 1.69: 0 1.69 - 1.81: 318 Bond restraints: 30836 Sorted by residual: bond pdb=" C1 BMA G 5 " pdb=" C2 BMA G 5 " ideal model delta sigma weight residual 1.519 1.558 -0.039 2.00e-02 2.50e+03 3.72e+00 bond pdb=" C1 BMA W 5 " pdb=" C2 BMA W 5 " ideal model delta sigma weight residual 1.519 1.558 -0.039 2.00e-02 2.50e+03 3.72e+00 bond pdb=" C1 BMA J 5 " pdb=" C2 BMA J 5 " ideal model delta sigma weight residual 1.519 1.556 -0.037 2.00e-02 2.50e+03 3.46e+00 bond pdb=" C1 BMA Y 5 " pdb=" C2 BMA Y 5 " ideal model delta sigma weight residual 1.519 1.556 -0.037 2.00e-02 2.50e+03 3.46e+00 bond pdb=" C1 BMA K 3 " pdb=" C2 BMA K 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.40e+00 ... (remaining 30831 not shown) Histogram of bond angle deviations from ideal: 99.71 - 106.59: 838 106.59 - 113.47: 17784 113.47 - 120.35: 10398 120.35 - 127.23: 12394 127.23 - 134.11: 392 Bond angle restraints: 41806 Sorted by residual: angle pdb=" C ALA E 479 " pdb=" N ILE E 480 " pdb=" CA ILE E 480 " ideal model delta sigma weight residual 123.16 117.65 5.51 1.06e+00 8.90e-01 2.70e+01 angle pdb=" C ALA S 479 " pdb=" N ILE S 480 " pdb=" CA ILE S 480 " ideal model delta sigma weight residual 123.16 117.65 5.51 1.06e+00 8.90e-01 2.70e+01 angle pdb=" N ILE B 53 " pdb=" CA ILE B 53 " pdb=" C ILE B 53 " ideal model delta sigma weight residual 112.96 109.47 3.49 1.00e+00 1.00e+00 1.22e+01 angle pdb=" N ILE P 53 " pdb=" CA ILE P 53 " pdb=" C ILE P 53 " ideal model delta sigma weight residual 112.96 109.47 3.49 1.00e+00 1.00e+00 1.22e+01 angle pdb=" N VAL C 491 " pdb=" CA VAL C 491 " pdb=" C VAL C 491 " ideal model delta sigma weight residual 110.62 114.13 -3.51 1.02e+00 9.61e-01 1.19e+01 ... (remaining 41801 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.24: 17658 22.24 - 44.48: 882 44.48 - 66.72: 112 66.72 - 88.96: 108 88.96 - 111.20: 56 Dihedral angle restraints: 18816 sinusoidal: 7878 harmonic: 10938 Sorted by residual: dihedral pdb=" CB CYS S 300 " pdb=" SG CYS S 300 " pdb=" SG CYS S 331 " pdb=" CB CYS S 331 " ideal model delta sinusoidal sigma weight residual -86.00 -158.81 72.81 1 1.00e+01 1.00e-02 6.76e+01 dihedral pdb=" CB CYS E 300 " pdb=" SG CYS E 300 " pdb=" SG CYS E 331 " pdb=" CB CYS E 331 " ideal model delta sinusoidal sigma weight residual -86.00 -158.81 72.81 1 1.00e+01 1.00e-02 6.76e+01 dihedral pdb=" CB CYS Q 74 " pdb=" SG CYS Q 74 " pdb=" SG CYS Q 105 " pdb=" CB CYS Q 105 " ideal model delta sinusoidal sigma weight residual 93.00 146.27 -53.27 1 1.00e+01 1.00e-02 3.86e+01 ... (remaining 18813 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 4014 0.055 - 0.110: 760 0.110 - 0.165: 142 0.165 - 0.221: 6 0.221 - 0.276: 16 Chirality restraints: 4938 Sorted by residual: chirality pdb=" C5 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C6 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" C5 BMA X 3 " pdb=" C4 BMA X 3 " pdb=" C6 BMA X 3 " pdb=" O5 BMA X 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" C5 BMA N 3 " pdb=" C4 BMA N 3 " pdb=" C6 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.89e+00 ... (remaining 4935 not shown) Planarity restraints: 5204 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR E 163 " -0.026 5.00e-02 4.00e+02 3.97e-02 2.52e+00 pdb=" N PRO E 164 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO E 164 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO E 164 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR S 163 " 0.026 5.00e-02 4.00e+02 3.97e-02 2.52e+00 pdb=" N PRO S 164 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO S 164 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO S 164 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 163 " 0.026 5.00e-02 4.00e+02 3.92e-02 2.46e+00 pdb=" N PRO A 164 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 164 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 164 " 0.022 5.00e-02 4.00e+02 ... (remaining 5201 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 556 2.67 - 3.23: 28619 3.23 - 3.79: 44817 3.79 - 4.34: 60117 4.34 - 4.90: 101578 Nonbonded interactions: 235687 Sorted by model distance: nonbonded pdb=" OG SER U 52 " pdb=" OD1 ASP U 54 " model vdw 2.113 2.440 nonbonded pdb=" OG SER H 52 " pdb=" OD1 ASP H 54 " model vdw 2.113 2.440 nonbonded pdb=" O ALA Q 50 " pdb=" OG1 THR Q 274 " model vdw 2.174 2.440 nonbonded pdb=" O ALA C 50 " pdb=" OG1 THR C 274 " model vdw 2.174 2.440 nonbonded pdb=" OD1 ASN H 105 " pdb=" OH TYR L 40 " model vdw 2.174 2.440 ... (remaining 235682 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 'M' } ncs_group { reference = chain '1' selection = chain 'I' selection = chain 'K' selection = chain 'N' selection = chain 'X' selection = chain 'Z' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'O' selection = chain 'Q' selection = chain 'S' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'P' selection = chain 'R' selection = chain 'T' } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'W' selection = chain 'Y' } ncs_group { reference = chain 'H' selection = chain 'U' } ncs_group { reference = chain 'L' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.310 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: 0.020 Extract box with map and model: 1.220 Check model and map are aligned: 0.230 Set scattering table: 0.300 Process input model: 81.650 Find NCS groups from input model: 1.280 Set up NCS constraints: 0.230 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 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 : 0.004 0.058 30836 Z= 0.268 Angle : 0.736 8.359 41806 Z= 0.415 Chirality : 0.047 0.276 4938 Planarity : 0.004 0.040 5192 Dihedral : 15.960 111.197 11742 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.28 (0.13), residues: 3846 helix: 1.15 (0.18), residues: 866 sheet: -1.18 (0.17), residues: 980 loop : -1.60 (0.12), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP P 26 HIS 0.006 0.001 HIS O 345 PHE 0.021 0.002 PHE P 42 TYR 0.014 0.001 TYR Q 486 ARG 0.004 0.001 ARG A 9 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 856 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 856 time to evaluate : 3.494 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: A 36 LYS cc_start: 0.8095 (tptp) cc_final: 0.7707 (tptp) REVERT: A 37 ASN cc_start: 0.7772 (m110) cc_final: 0.7444 (m110) REVERT: A 176 TYR cc_start: 0.8629 (m-80) cc_final: 0.8139 (m-80) REVERT: A 453 MET cc_start: 0.7673 (mmm) cc_final: 0.7258 (mmm) REVERT: A 457 ILE cc_start: 0.8567 (mt) cc_final: 0.8357 (mp) REVERT: B 57 LEU cc_start: 0.7905 (tp) cc_final: 0.7556 (tt) REVERT: B 70 VAL cc_start: 0.9030 (t) cc_final: 0.8582 (p) REVERT: B 73 SER cc_start: 0.8148 (m) cc_final: 0.7819 (p) REVERT: C 182 GLU cc_start: 0.6853 (tt0) cc_final: 0.6344 (tt0) REVERT: C 438 PHE cc_start: 0.7956 (m-10) cc_final: 0.7680 (m-10) REVERT: C 486 TYR cc_start: 0.7730 (t80) cc_final: 0.7256 (t80) REVERT: D 74 MET cc_start: 0.8247 (tpp) cc_final: 0.7587 (mmm) REVERT: E 460 LEU cc_start: 0.9366 (tt) cc_final: 0.9158 (tt) REVERT: E 485 LEU cc_start: 0.8627 (mp) cc_final: 0.8232 (mp) REVERT: H 34 MET cc_start: 0.8244 (mmm) cc_final: 0.8019 (mmm) REVERT: H 83 MET cc_start: 0.7236 (mtp) cc_final: 0.7015 (mtp) REVERT: H 111 TYR cc_start: 0.8043 (m-80) cc_final: 0.7798 (m-10) REVERT: L 55 TYR cc_start: 0.8253 (p90) cc_final: 0.7990 (p90) REVERT: O 36 LYS cc_start: 0.8092 (tptp) cc_final: 0.7710 (tptp) REVERT: O 37 ASN cc_start: 0.7772 (m110) cc_final: 0.7446 (m110) REVERT: O 176 TYR cc_start: 0.8628 (m-80) cc_final: 0.8140 (m-80) REVERT: O 453 MET cc_start: 0.7680 (mmm) cc_final: 0.7228 (mmm) REVERT: O 457 ILE cc_start: 0.8549 (mt) cc_final: 0.8344 (mp) REVERT: P 57 LEU cc_start: 0.7905 (tp) cc_final: 0.7558 (tt) REVERT: P 70 VAL cc_start: 0.9016 (t) cc_final: 0.8575 (p) REVERT: P 73 SER cc_start: 0.8148 (m) cc_final: 0.7835 (p) REVERT: Q 182 GLU cc_start: 0.6837 (tt0) cc_final: 0.6336 (tt0) REVERT: Q 438 PHE cc_start: 0.7954 (m-10) cc_final: 0.7677 (m-10) REVERT: Q 486 TYR cc_start: 0.7731 (t80) cc_final: 0.7263 (t80) REVERT: R 74 MET cc_start: 0.8258 (tpp) cc_final: 0.7576 (mmm) REVERT: S 460 LEU cc_start: 0.9365 (tt) cc_final: 0.9159 (tt) REVERT: S 485 LEU cc_start: 0.8624 (mp) cc_final: 0.8241 (mp) REVERT: U 34 MET cc_start: 0.8249 (mmm) cc_final: 0.8024 (mmm) REVERT: U 83 MET cc_start: 0.7231 (mtp) cc_final: 0.7005 (mtp) REVERT: U 111 TYR cc_start: 0.8039 (m-80) cc_final: 0.7797 (m-10) REVERT: V 55 TYR cc_start: 0.8256 (p90) cc_final: 0.7995 (p90) outliers start: 0 outliers final: 0 residues processed: 856 average time/residue: 0.4435 time to fit residues: 583.8614 Evaluate side-chains 539 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 539 time to evaluate : 3.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 322 optimal weight: 10.0000 chunk 289 optimal weight: 30.0000 chunk 160 optimal weight: 5.9990 chunk 98 optimal weight: 20.0000 chunk 195 optimal weight: 5.9990 chunk 154 optimal weight: 20.0000 chunk 299 optimal weight: 9.9990 chunk 115 optimal weight: 6.9990 chunk 182 optimal weight: 3.9990 chunk 222 optimal weight: 6.9990 chunk 346 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 230 ASN ** B 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 201 ASN E 314 GLN ** H 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 1 HIS O 103 ASN ** O 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 230 ASN ** P 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 201 ASN S 314 GLN ** U 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 1 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 30836 Z= 0.313 Angle : 0.694 9.298 41806 Z= 0.354 Chirality : 0.047 0.188 4938 Planarity : 0.004 0.040 5192 Dihedral : 12.124 79.531 4914 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 3.13 % Allowed : 12.20 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.23 (0.13), residues: 3846 helix: 1.23 (0.18), residues: 874 sheet: -1.11 (0.16), residues: 1020 loop : -1.62 (0.13), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 20 HIS 0.005 0.001 HIS F 7 PHE 0.024 0.002 PHE E 475 TYR 0.018 0.002 TYR Q 486 ARG 0.005 0.001 ARG E 348 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 547 time to evaluate : 3.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.7404 (tm-30) cc_final: 0.6963 (tm-30) REVERT: A 36 LYS cc_start: 0.8185 (tptp) cc_final: 0.7956 (tptp) REVERT: A 56 LEU cc_start: 0.9166 (tp) cc_final: 0.8941 (tt) REVERT: A 176 TYR cc_start: 0.8648 (m-80) cc_final: 0.8164 (m-80) REVERT: A 199 MET cc_start: 0.8460 (ptp) cc_final: 0.8251 (ptm) REVERT: B 70 VAL cc_start: 0.9094 (t) cc_final: 0.8664 (p) REVERT: B 73 SER cc_start: 0.8012 (m) cc_final: 0.7621 (p) REVERT: C 438 PHE cc_start: 0.8134 (m-10) cc_final: 0.7697 (m-80) REVERT: C 473 MET cc_start: 0.7301 (mmp) cc_final: 0.7066 (mtt) REVERT: C 486 TYR cc_start: 0.7886 (t80) cc_final: 0.7222 (t80) REVERT: D 27 ARG cc_start: 0.7828 (ttp80) cc_final: 0.7599 (ttp-110) REVERT: D 59 GLN cc_start: 0.7545 (mt0) cc_final: 0.7007 (mt0) REVERT: D 74 MET cc_start: 0.8349 (tpp) cc_final: 0.7571 (mmm) REVERT: F 64 PHE cc_start: 0.9161 (t80) cc_final: 0.8928 (t80) REVERT: H 34 MET cc_start: 0.8247 (mmm) cc_final: 0.8039 (mmm) REVERT: H 62 ASP cc_start: 0.7986 (OUTLIER) cc_final: 0.7630 (t0) REVERT: H 109 PHE cc_start: 0.8244 (m-10) cc_final: 0.7845 (m-10) REVERT: H 111 TYR cc_start: 0.7933 (m-80) cc_final: 0.7707 (m-10) REVERT: L 24 LYS cc_start: 0.8819 (tptp) cc_final: 0.8551 (mtpp) REVERT: L 31 TRP cc_start: 0.7214 (t60) cc_final: 0.7006 (t60) REVERT: L 55 TYR cc_start: 0.8183 (p90) cc_final: 0.7971 (p90) REVERT: L 85 GLN cc_start: 0.7955 (mp10) cc_final: 0.7557 (mp10) REVERT: O 13 GLU cc_start: 0.7410 (tm-30) cc_final: 0.6960 (tm-30) REVERT: O 36 LYS cc_start: 0.8184 (tptp) cc_final: 0.7959 (tptp) REVERT: O 56 LEU cc_start: 0.9174 (tp) cc_final: 0.8947 (tt) REVERT: O 176 TYR cc_start: 0.8647 (m-80) cc_final: 0.8166 (m-80) REVERT: O 199 MET cc_start: 0.8462 (ptp) cc_final: 0.8233 (ptm) REVERT: P 70 VAL cc_start: 0.9087 (t) cc_final: 0.8651 (p) REVERT: P 73 SER cc_start: 0.8028 (m) cc_final: 0.7644 (p) REVERT: Q 295 MET cc_start: 0.7735 (pmm) cc_final: 0.7463 (ppp) REVERT: Q 438 PHE cc_start: 0.8127 (m-10) cc_final: 0.7688 (m-80) REVERT: Q 473 MET cc_start: 0.7301 (mmp) cc_final: 0.7070 (mtt) REVERT: Q 486 TYR cc_start: 0.7894 (t80) cc_final: 0.7232 (t80) REVERT: R 27 ARG cc_start: 0.7824 (ttp80) cc_final: 0.7587 (ttp-110) REVERT: R 59 GLN cc_start: 0.7542 (mt0) cc_final: 0.6998 (mt0) REVERT: R 74 MET cc_start: 0.8332 (tpp) cc_final: 0.7554 (mmm) REVERT: T 64 PHE cc_start: 0.9162 (t80) cc_final: 0.8919 (t80) REVERT: U 34 MET cc_start: 0.8257 (mmm) cc_final: 0.8046 (mmm) REVERT: U 62 ASP cc_start: 0.7983 (OUTLIER) cc_final: 0.7628 (t0) REVERT: U 109 PHE cc_start: 0.8256 (m-10) cc_final: 0.7847 (m-10) REVERT: U 111 TYR cc_start: 0.7935 (m-80) cc_final: 0.7703 (m-10) REVERT: V 24 LYS cc_start: 0.8811 (tptp) cc_final: 0.8561 (mtpp) REVERT: V 85 GLN cc_start: 0.7947 (mp10) cc_final: 0.7552 (mp10) outliers start: 101 outliers final: 61 residues processed: 603 average time/residue: 0.3975 time to fit residues: 385.3258 Evaluate side-chains 558 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 495 time to evaluate : 3.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 457 ILE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain O residue 233 GLU Chi-restraints excluded: chain O residue 314 GLN Chi-restraints excluded: chain O residue 392 LYS Chi-restraints excluded: chain O residue 466 LEU Chi-restraints excluded: chain O residue 476 SER Chi-restraints excluded: chain P residue 17 GLN Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain Q residue 10 ASP Chi-restraints excluded: chain Q residue 363 VAL Chi-restraints excluded: chain Q residue 371 PHE Chi-restraints excluded: chain Q residue 461 LEU Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 107 LEU Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 237 THR Chi-restraints excluded: chain S residue 301 THR Chi-restraints excluded: chain S residue 359 LYS Chi-restraints excluded: chain S residue 426 VAL Chi-restraints excluded: chain S residue 457 ILE Chi-restraints excluded: chain T residue 47 LEU Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 58 THR Chi-restraints excluded: chain T residue 61 VAL Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 56 ASN Chi-restraints excluded: chain U residue 62 ASP Chi-restraints excluded: chain U residue 102 VAL Chi-restraints excluded: chain V residue 14 THR Chi-restraints excluded: chain V residue 62 SER Chi-restraints excluded: chain V residue 103 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 192 optimal weight: 7.9990 chunk 107 optimal weight: 10.0000 chunk 288 optimal weight: 10.0000 chunk 236 optimal weight: 3.9990 chunk 95 optimal weight: 20.0000 chunk 347 optimal weight: 9.9990 chunk 375 optimal weight: 8.9990 chunk 309 optimal weight: 9.9990 chunk 344 optimal weight: 9.9990 chunk 118 optimal weight: 9.9990 chunk 278 optimal weight: 20.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 1 HIS ** O 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 375 ASN O 388 ASN ** P 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 201 ASN ** R 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 302 ASN ** U 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 1 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.117 30836 Z= 0.399 Angle : 0.705 9.053 41806 Z= 0.360 Chirality : 0.048 0.187 4938 Planarity : 0.004 0.043 5192 Dihedral : 9.922 63.738 4914 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.35 % Allowed : 16.05 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.23 (0.13), residues: 3846 helix: 1.27 (0.18), residues: 874 sheet: -1.03 (0.17), residues: 950 loop : -1.68 (0.12), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP V 31 HIS 0.007 0.001 HIS O 207 PHE 0.028 0.002 PHE E 475 TYR 0.028 0.002 TYR V 55 ARG 0.005 0.001 ARG E 231 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 510 time to evaluate : 3.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.7448 (tm-30) cc_final: 0.6811 (tm-30) REVERT: A 445 LEU cc_start: 0.9004 (tt) cc_final: 0.8797 (tt) REVERT: B 70 VAL cc_start: 0.9145 (t) cc_final: 0.8788 (p) REVERT: B 73 SER cc_start: 0.8067 (m) cc_final: 0.7633 (p) REVERT: C 295 MET cc_start: 0.6825 (ppp) cc_final: 0.6289 (ppp) REVERT: C 438 PHE cc_start: 0.7966 (m-10) cc_final: 0.7748 (m-10) REVERT: C 473 MET cc_start: 0.7322 (mmp) cc_final: 0.7009 (mtt) REVERT: C 482 ILE cc_start: 0.9055 (mm) cc_final: 0.8743 (mt) REVERT: C 486 TYR cc_start: 0.8304 (t80) cc_final: 0.7934 (t80) REVERT: D 27 ARG cc_start: 0.8216 (ttp80) cc_final: 0.7776 (ttp-110) REVERT: D 64 PHE cc_start: 0.8955 (t80) cc_final: 0.8709 (t80) REVERT: E 373 GLU cc_start: 0.6946 (OUTLIER) cc_final: 0.6491 (tp30) REVERT: E 410 MET cc_start: 0.8198 (ttm) cc_final: 0.7924 (ttm) REVERT: F 10 MET cc_start: 0.8714 (ppp) cc_final: 0.8501 (ppp) REVERT: H 62 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.7990 (t0) REVERT: H 80 TYR cc_start: 0.7456 (m-10) cc_final: 0.7210 (m-80) REVERT: L 4 MET cc_start: 0.8357 (mmm) cc_final: 0.8026 (mtp) REVERT: L 24 LYS cc_start: 0.8610 (tptp) cc_final: 0.8382 (mtpp) REVERT: L 80 LYS cc_start: 0.8257 (mppt) cc_final: 0.8000 (mptt) REVERT: O 13 GLU cc_start: 0.7454 (tm-30) cc_final: 0.6811 (tm-30) REVERT: O 445 LEU cc_start: 0.8992 (tt) cc_final: 0.8777 (tt) REVERT: P 70 VAL cc_start: 0.9138 (t) cc_final: 0.8778 (p) REVERT: P 73 SER cc_start: 0.8077 (m) cc_final: 0.7658 (p) REVERT: Q 438 PHE cc_start: 0.7961 (m-10) cc_final: 0.7745 (m-10) REVERT: Q 473 MET cc_start: 0.7314 (mmp) cc_final: 0.7015 (mtt) REVERT: Q 482 ILE cc_start: 0.9053 (mm) cc_final: 0.8738 (mt) REVERT: Q 486 TYR cc_start: 0.8312 (t80) cc_final: 0.7938 (t80) REVERT: R 27 ARG cc_start: 0.8208 (ttp80) cc_final: 0.7766 (ttp-110) REVERT: R 64 PHE cc_start: 0.8944 (t80) cc_final: 0.8700 (t80) REVERT: S 373 GLU cc_start: 0.6867 (OUTLIER) cc_final: 0.6387 (tp30) REVERT: S 410 MET cc_start: 0.8205 (ttm) cc_final: 0.7927 (ttm) REVERT: T 10 MET cc_start: 0.8714 (ppp) cc_final: 0.8503 (ppp) REVERT: U 3 GLU cc_start: 0.7012 (mm-30) cc_final: 0.6778 (mm-30) REVERT: U 62 ASP cc_start: 0.8225 (OUTLIER) cc_final: 0.7984 (t0) REVERT: U 80 TYR cc_start: 0.7446 (m-10) cc_final: 0.7202 (m-80) REVERT: V 4 MET cc_start: 0.8297 (mmm) cc_final: 0.8079 (mtp) REVERT: V 24 LYS cc_start: 0.8603 (tptp) cc_final: 0.8397 (mtpp) REVERT: V 80 LYS cc_start: 0.8263 (mppt) cc_final: 0.8001 (mptt) outliers start: 140 outliers final: 93 residues processed: 594 average time/residue: 0.3750 time to fit residues: 363.0193 Evaluate side-chains 568 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 471 time to evaluate : 3.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 373 GLU Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 457 ILE Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 95 MET Chi-restraints excluded: chain O residue 60 CYS Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 233 GLU Chi-restraints excluded: chain O residue 314 GLN Chi-restraints excluded: chain O residue 466 LEU Chi-restraints excluded: chain O residue 473 MET Chi-restraints excluded: chain O residue 476 SER Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 49 LEU Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 65 ILE Chi-restraints excluded: chain P residue 67 LEU Chi-restraints excluded: chain Q residue 10 ASP Chi-restraints excluded: chain Q residue 266 THR Chi-restraints excluded: chain Q residue 271 SER Chi-restraints excluded: chain Q residue 363 VAL Chi-restraints excluded: chain Q residue 371 PHE Chi-restraints excluded: chain Q residue 430 LEU Chi-restraints excluded: chain Q residue 455 ILE Chi-restraints excluded: chain Q residue 461 LEU Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain S residue 49 GLU Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 205 MET Chi-restraints excluded: chain S residue 223 THR Chi-restraints excluded: chain S residue 236 VAL Chi-restraints excluded: chain S residue 237 THR Chi-restraints excluded: chain S residue 263 THR Chi-restraints excluded: chain S residue 301 THR Chi-restraints excluded: chain S residue 373 GLU Chi-restraints excluded: chain S residue 426 VAL Chi-restraints excluded: chain S residue 457 ILE Chi-restraints excluded: chain T residue 14 THR Chi-restraints excluded: chain T residue 47 LEU Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 55 THR Chi-restraints excluded: chain T residue 58 THR Chi-restraints excluded: chain T residue 61 VAL Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 43 LYS Chi-restraints excluded: chain U residue 56 ASN Chi-restraints excluded: chain U residue 62 ASP Chi-restraints excluded: chain U residue 69 THR Chi-restraints excluded: chain U residue 86 LEU Chi-restraints excluded: chain U residue 102 VAL Chi-restraints excluded: chain V residue 62 SER Chi-restraints excluded: chain V residue 95 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 343 optimal weight: 8.9990 chunk 261 optimal weight: 8.9990 chunk 180 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 165 optimal weight: 9.9990 chunk 233 optimal weight: 10.0000 chunk 348 optimal weight: 9.9990 chunk 369 optimal weight: 7.9990 chunk 182 optimal weight: 9.9990 chunk 330 optimal weight: 20.0000 chunk 99 optimal weight: 5.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 HIS C 201 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 8 ASN O 103 ASN ** O 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 27 HIS Q 201 ASN ** R 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 314 GLN ** U 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 30836 Z= 0.352 Angle : 0.667 8.594 41806 Z= 0.339 Chirality : 0.047 0.197 4938 Planarity : 0.004 0.041 5192 Dihedral : 8.767 61.376 4914 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.97 % Allowed : 18.06 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.27 (0.13), residues: 3846 helix: 1.36 (0.18), residues: 874 sheet: -1.20 (0.16), residues: 1024 loop : -1.68 (0.13), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP S 451 HIS 0.006 0.001 HIS O 207 PHE 0.021 0.002 PHE P 48 TYR 0.026 0.002 TYR L 55 ARG 0.004 0.001 ARG P 15 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 495 time to evaluate : 3.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.7519 (tm-30) cc_final: 0.6809 (tm-30) REVERT: B 30 GLU cc_start: 0.7083 (pt0) cc_final: 0.6850 (pt0) REVERT: B 70 VAL cc_start: 0.9179 (t) cc_final: 0.8800 (p) REVERT: B 73 SER cc_start: 0.7916 (m) cc_final: 0.7598 (p) REVERT: C 295 MET cc_start: 0.6768 (ppp) cc_final: 0.6360 (ppp) REVERT: C 473 MET cc_start: 0.7376 (mmp) cc_final: 0.7045 (mtt) REVERT: C 478 ILE cc_start: 0.9304 (mt) cc_final: 0.9039 (mm) REVERT: C 486 TYR cc_start: 0.8294 (t80) cc_final: 0.7830 (t80) REVERT: D 49 LEU cc_start: 0.8800 (mt) cc_final: 0.8427 (mt) REVERT: E 234 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.7890 (pp) REVERT: H 6 GLU cc_start: 0.7217 (mm-30) cc_final: 0.6486 (mp0) REVERT: H 62 ASP cc_start: 0.8172 (OUTLIER) cc_final: 0.7948 (t0) REVERT: H 107 TRP cc_start: 0.8494 (OUTLIER) cc_final: 0.7576 (p90) REVERT: L 24 LYS cc_start: 0.8592 (tptp) cc_final: 0.8343 (mtpp) REVERT: L 80 LYS cc_start: 0.8250 (mppt) cc_final: 0.8024 (mptt) REVERT: L 85 GLN cc_start: 0.8430 (mp10) cc_final: 0.8226 (mp10) REVERT: O 13 GLU cc_start: 0.7519 (tm-30) cc_final: 0.6810 (tm-30) REVERT: P 30 GLU cc_start: 0.7117 (pt0) cc_final: 0.6870 (pt0) REVERT: P 70 VAL cc_start: 0.9169 (t) cc_final: 0.8784 (p) REVERT: P 73 SER cc_start: 0.7929 (m) cc_final: 0.7618 (p) REVERT: Q 473 MET cc_start: 0.7370 (mmp) cc_final: 0.7050 (mtt) REVERT: Q 478 ILE cc_start: 0.9302 (mt) cc_final: 0.9036 (mm) REVERT: Q 486 TYR cc_start: 0.8294 (t80) cc_final: 0.7974 (t80) REVERT: S 234 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.7900 (pp) REVERT: S 286 LYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7589 (mtmt) REVERT: S 410 MET cc_start: 0.8053 (ttm) cc_final: 0.7842 (ttm) REVERT: U 6 GLU cc_start: 0.7215 (mm-30) cc_final: 0.6479 (mp0) REVERT: U 62 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7953 (t0) REVERT: U 107 TRP cc_start: 0.8495 (OUTLIER) cc_final: 0.7570 (p90) REVERT: V 24 LYS cc_start: 0.8587 (tptp) cc_final: 0.8368 (mtpp) REVERT: V 80 LYS cc_start: 0.8252 (mppt) cc_final: 0.8028 (mptt) REVERT: V 85 GLN cc_start: 0.8440 (mp10) cc_final: 0.8233 (mp10) outliers start: 160 outliers final: 114 residues processed: 609 average time/residue: 0.3788 time to fit residues: 377.8589 Evaluate side-chains 593 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 472 time to evaluate : 3.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 374 SER Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 482 ILE Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 107 TRP Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 60 CYS Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 233 GLU Chi-restraints excluded: chain O residue 314 GLN Chi-restraints excluded: chain O residue 337 THR Chi-restraints excluded: chain O residue 364 ASN Chi-restraints excluded: chain O residue 365 ILE Chi-restraints excluded: chain O residue 466 LEU Chi-restraints excluded: chain O residue 473 MET Chi-restraints excluded: chain O residue 476 SER Chi-restraints excluded: chain P residue 17 GLN Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 49 LEU Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 65 ILE Chi-restraints excluded: chain Q residue 10 ASP Chi-restraints excluded: chain Q residue 271 SER Chi-restraints excluded: chain Q residue 363 VAL Chi-restraints excluded: chain Q residue 371 PHE Chi-restraints excluded: chain Q residue 388 ASN Chi-restraints excluded: chain Q residue 400 PHE Chi-restraints excluded: chain Q residue 423 VAL Chi-restraints excluded: chain Q residue 430 LEU Chi-restraints excluded: chain Q residue 455 ILE Chi-restraints excluded: chain Q residue 461 LEU Chi-restraints excluded: chain Q residue 464 ILE Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain S residue 49 GLU Chi-restraints excluded: chain S residue 62 GLU Chi-restraints excluded: chain S residue 91 VAL Chi-restraints excluded: chain S residue 107 LEU Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 205 MET Chi-restraints excluded: chain S residue 234 LEU Chi-restraints excluded: chain S residue 236 VAL Chi-restraints excluded: chain S residue 237 THR Chi-restraints excluded: chain S residue 266 THR Chi-restraints excluded: chain S residue 286 LYS Chi-restraints excluded: chain S residue 301 THR Chi-restraints excluded: chain S residue 374 SER Chi-restraints excluded: chain S residue 382 ASP Chi-restraints excluded: chain S residue 426 VAL Chi-restraints excluded: chain S residue 482 ILE Chi-restraints excluded: chain T residue 14 THR Chi-restraints excluded: chain T residue 47 LEU Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 58 THR Chi-restraints excluded: chain T residue 61 VAL Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 43 LYS Chi-restraints excluded: chain U residue 56 ASN Chi-restraints excluded: chain U residue 62 ASP Chi-restraints excluded: chain U residue 102 VAL Chi-restraints excluded: chain U residue 107 TRP Chi-restraints excluded: chain V residue 14 THR Chi-restraints excluded: chain V residue 53 LEU Chi-restraints excluded: chain V residue 62 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 307 optimal weight: 8.9990 chunk 209 optimal weight: 0.4980 chunk 5 optimal weight: 7.9990 chunk 274 optimal weight: 10.0000 chunk 152 optimal weight: 9.9990 chunk 315 optimal weight: 8.9990 chunk 255 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 188 optimal weight: 20.0000 chunk 331 optimal weight: 9.9990 chunk 93 optimal weight: 4.9990 overall best weight: 6.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 HIS E 314 GLN ** H 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 1 HIS ** O 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 201 ASN ** R 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 280 HIS ** U 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 1 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 30836 Z= 0.307 Angle : 0.639 9.277 41806 Z= 0.325 Chirality : 0.046 0.195 4938 Planarity : 0.004 0.055 5192 Dihedral : 8.061 60.854 4914 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 5.87 % Allowed : 18.96 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.16 (0.13), residues: 3846 helix: 1.51 (0.18), residues: 866 sheet: -1.13 (0.16), residues: 1024 loop : -1.63 (0.13), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 204 HIS 0.006 0.001 HIS F 7 PHE 0.023 0.002 PHE E 475 TYR 0.029 0.002 TYR L 55 ARG 0.004 0.001 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 499 time to evaluate : 3.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.7541 (tm-30) cc_final: 0.6729 (tm-30) REVERT: A 236 VAL cc_start: 0.9328 (OUTLIER) cc_final: 0.9089 (p) REVERT: A 365 ILE cc_start: 0.9362 (OUTLIER) cc_final: 0.9152 (mm) REVERT: B 30 GLU cc_start: 0.7071 (pt0) cc_final: 0.6806 (pt0) REVERT: B 70 VAL cc_start: 0.9135 (t) cc_final: 0.8736 (p) REVERT: B 73 SER cc_start: 0.7892 (m) cc_final: 0.7586 (p) REVERT: C 473 MET cc_start: 0.7511 (mmp) cc_final: 0.7240 (mtt) REVERT: C 482 ILE cc_start: 0.9069 (mm) cc_final: 0.8757 (mt) REVERT: C 486 TYR cc_start: 0.8254 (t80) cc_final: 0.7965 (t80) REVERT: D 64 PHE cc_start: 0.8995 (t80) cc_final: 0.8780 (t80) REVERT: E 10 ASP cc_start: 0.8905 (OUTLIER) cc_final: 0.8686 (p0) REVERT: E 234 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.7788 (pp) REVERT: H 6 GLU cc_start: 0.7263 (mm-30) cc_final: 0.6636 (mp0) REVERT: H 62 ASP cc_start: 0.8211 (OUTLIER) cc_final: 0.7992 (t0) REVERT: H 73 ASP cc_start: 0.7355 (t0) cc_final: 0.7005 (t0) REVERT: H 107 TRP cc_start: 0.8535 (OUTLIER) cc_final: 0.7530 (p90) REVERT: O 13 GLU cc_start: 0.7547 (tm-30) cc_final: 0.6729 (tm-30) REVERT: O 236 VAL cc_start: 0.9337 (OUTLIER) cc_final: 0.9122 (p) REVERT: O 365 ILE cc_start: 0.9361 (OUTLIER) cc_final: 0.9159 (mm) REVERT: P 30 GLU cc_start: 0.7112 (pt0) cc_final: 0.6833 (pt0) REVERT: P 70 VAL cc_start: 0.9120 (t) cc_final: 0.8724 (p) REVERT: P 73 SER cc_start: 0.7906 (m) cc_final: 0.7617 (p) REVERT: Q 473 MET cc_start: 0.7511 (mmp) cc_final: 0.7245 (mtt) REVERT: Q 482 ILE cc_start: 0.9064 (mm) cc_final: 0.8752 (mt) REVERT: Q 486 TYR cc_start: 0.8257 (t80) cc_final: 0.7968 (t80) REVERT: R 64 PHE cc_start: 0.8998 (t80) cc_final: 0.8784 (t80) REVERT: S 10 ASP cc_start: 0.8924 (OUTLIER) cc_final: 0.8695 (p0) REVERT: S 234 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.7790 (pp) REVERT: S 410 MET cc_start: 0.8056 (ttm) cc_final: 0.7810 (ttm) REVERT: U 6 GLU cc_start: 0.7263 (mm-30) cc_final: 0.6632 (mp0) REVERT: U 62 ASP cc_start: 0.8217 (OUTLIER) cc_final: 0.7988 (t0) REVERT: U 73 ASP cc_start: 0.7342 (t0) cc_final: 0.6974 (t0) REVERT: U 107 TRP cc_start: 0.8536 (OUTLIER) cc_final: 0.7520 (p90) outliers start: 189 outliers final: 127 residues processed: 636 average time/residue: 0.3695 time to fit residues: 387.2659 Evaluate side-chains 618 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 479 time to evaluate : 3.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 374 SER Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 460 LEU Chi-restraints excluded: chain E residue 471 THR Chi-restraints excluded: chain F residue 1 SER Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 107 TRP Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 60 CYS Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 233 GLU Chi-restraints excluded: chain O residue 236 VAL Chi-restraints excluded: chain O residue 314 GLN Chi-restraints excluded: chain O residue 337 THR Chi-restraints excluded: chain O residue 364 ASN Chi-restraints excluded: chain O residue 365 ILE Chi-restraints excluded: chain O residue 399 MET Chi-restraints excluded: chain O residue 466 LEU Chi-restraints excluded: chain O residue 473 MET Chi-restraints excluded: chain O residue 476 SER Chi-restraints excluded: chain P residue 17 GLN Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 49 LEU Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 67 LEU Chi-restraints excluded: chain Q residue 10 ASP Chi-restraints excluded: chain Q residue 266 THR Chi-restraints excluded: chain Q residue 271 SER Chi-restraints excluded: chain Q residue 363 VAL Chi-restraints excluded: chain Q residue 371 PHE Chi-restraints excluded: chain Q residue 388 ASN Chi-restraints excluded: chain Q residue 423 VAL Chi-restraints excluded: chain Q residue 426 VAL Chi-restraints excluded: chain Q residue 430 LEU Chi-restraints excluded: chain Q residue 452 VAL Chi-restraints excluded: chain Q residue 455 ILE Chi-restraints excluded: chain Q residue 461 LEU Chi-restraints excluded: chain Q residue 464 ILE Chi-restraints excluded: chain R residue 43 THR Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain S residue 10 ASP Chi-restraints excluded: chain S residue 49 GLU Chi-restraints excluded: chain S residue 91 VAL Chi-restraints excluded: chain S residue 107 LEU Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 205 MET Chi-restraints excluded: chain S residue 223 THR Chi-restraints excluded: chain S residue 234 LEU Chi-restraints excluded: chain S residue 236 VAL Chi-restraints excluded: chain S residue 237 THR Chi-restraints excluded: chain S residue 251 LEU Chi-restraints excluded: chain S residue 263 THR Chi-restraints excluded: chain S residue 301 THR Chi-restraints excluded: chain S residue 374 SER Chi-restraints excluded: chain S residue 382 ASP Chi-restraints excluded: chain S residue 416 THR Chi-restraints excluded: chain S residue 426 VAL Chi-restraints excluded: chain S residue 460 LEU Chi-restraints excluded: chain S residue 471 THR Chi-restraints excluded: chain T residue 1 SER Chi-restraints excluded: chain T residue 14 THR Chi-restraints excluded: chain T residue 47 LEU Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 58 THR Chi-restraints excluded: chain T residue 61 VAL Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 43 LYS Chi-restraints excluded: chain U residue 56 ASN Chi-restraints excluded: chain U residue 62 ASP Chi-restraints excluded: chain U residue 69 THR Chi-restraints excluded: chain U residue 102 VAL Chi-restraints excluded: chain U residue 107 TRP Chi-restraints excluded: chain V residue 14 THR Chi-restraints excluded: chain V residue 53 LEU Chi-restraints excluded: chain V residue 62 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 124 optimal weight: 8.9990 chunk 332 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 216 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 chunk 369 optimal weight: 7.9990 chunk 306 optimal weight: 30.0000 chunk 171 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 122 optimal weight: 20.0000 chunk 194 optimal weight: 0.9980 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 ASN ** B 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 ASN C 467 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 201 ASN Q 467 ASN ** R 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 30836 Z= 0.253 Angle : 0.612 8.504 41806 Z= 0.311 Chirality : 0.045 0.238 4938 Planarity : 0.004 0.049 5192 Dihedral : 7.584 58.947 4914 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 5.99 % Allowed : 19.89 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.06 (0.13), residues: 3846 helix: 1.59 (0.18), residues: 866 sheet: -1.04 (0.16), residues: 1024 loop : -1.60 (0.13), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 451 HIS 0.004 0.001 HIS A 207 PHE 0.025 0.002 PHE P 48 TYR 0.028 0.001 TYR V 55 ARG 0.006 0.000 ARG A 2 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 500 time to evaluate : 4.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.7324 (tm-30) cc_final: 0.6539 (tm-30) REVERT: A 236 VAL cc_start: 0.9296 (OUTLIER) cc_final: 0.9058 (p) REVERT: A 365 ILE cc_start: 0.9345 (OUTLIER) cc_final: 0.9134 (mm) REVERT: B 30 GLU cc_start: 0.7036 (pt0) cc_final: 0.6765 (pt0) REVERT: B 70 VAL cc_start: 0.9216 (t) cc_final: 0.8799 (p) REVERT: B 73 SER cc_start: 0.7871 (m) cc_final: 0.7567 (p) REVERT: C 415 ASP cc_start: 0.7777 (t0) cc_final: 0.7566 (m-30) REVERT: C 473 MET cc_start: 0.7480 (mmp) cc_final: 0.7153 (mtt) REVERT: C 482 ILE cc_start: 0.9045 (mm) cc_final: 0.8761 (mt) REVERT: C 486 TYR cc_start: 0.8230 (t80) cc_final: 0.7956 (t80) REVERT: E 27 HIS cc_start: 0.8673 (OUTLIER) cc_final: 0.7199 (t-90) REVERT: E 65 ILE cc_start: 0.9055 (OUTLIER) cc_final: 0.8682 (tp) REVERT: E 234 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7667 (pp) REVERT: E 364 ASN cc_start: 0.8908 (OUTLIER) cc_final: 0.8424 (p0) REVERT: H 6 GLU cc_start: 0.7379 (mm-30) cc_final: 0.6732 (mp0) REVERT: H 62 ASP cc_start: 0.8058 (OUTLIER) cc_final: 0.7839 (t0) REVERT: H 107 TRP cc_start: 0.8543 (OUTLIER) cc_final: 0.7571 (p90) REVERT: L 24 LYS cc_start: 0.8809 (tptp) cc_final: 0.8295 (mtpp) REVERT: O 13 GLU cc_start: 0.7321 (tm-30) cc_final: 0.6526 (tm-30) REVERT: O 205 MET cc_start: 0.7936 (ttm) cc_final: 0.7608 (mtp) REVERT: O 236 VAL cc_start: 0.9301 (OUTLIER) cc_final: 0.9083 (p) REVERT: P 30 GLU cc_start: 0.7084 (pt0) cc_final: 0.6790 (pt0) REVERT: P 70 VAL cc_start: 0.9199 (t) cc_final: 0.8781 (p) REVERT: P 73 SER cc_start: 0.7900 (m) cc_final: 0.7604 (p) REVERT: Q 415 ASP cc_start: 0.7773 (t0) cc_final: 0.7569 (m-30) REVERT: Q 473 MET cc_start: 0.7477 (mmp) cc_final: 0.7158 (mtt) REVERT: Q 482 ILE cc_start: 0.9044 (mm) cc_final: 0.8760 (mt) REVERT: Q 486 TYR cc_start: 0.8236 (t80) cc_final: 0.7961 (t80) REVERT: S 10 ASP cc_start: 0.8883 (OUTLIER) cc_final: 0.8673 (p0) REVERT: S 27 HIS cc_start: 0.8672 (OUTLIER) cc_final: 0.7245 (t-90) REVERT: S 65 ILE cc_start: 0.9061 (OUTLIER) cc_final: 0.8688 (tp) REVERT: S 234 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7703 (pp) REVERT: S 364 ASN cc_start: 0.9002 (OUTLIER) cc_final: 0.8562 (p0) REVERT: S 410 MET cc_start: 0.8039 (ttm) cc_final: 0.7778 (ttm) REVERT: U 6 GLU cc_start: 0.7394 (mm-30) cc_final: 0.6730 (mp0) REVERT: U 62 ASP cc_start: 0.8058 (OUTLIER) cc_final: 0.7837 (t0) REVERT: U 107 TRP cc_start: 0.8543 (OUTLIER) cc_final: 0.7562 (p90) REVERT: V 24 LYS cc_start: 0.8793 (tptp) cc_final: 0.8310 (mtpp) outliers start: 193 outliers final: 143 residues processed: 648 average time/residue: 0.3664 time to fit residues: 391.2878 Evaluate side-chains 635 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 476 time to evaluate : 3.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 364 ASN Chi-restraints excluded: chain E residue 374 SER Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 460 LEU Chi-restraints excluded: chain E residue 471 THR Chi-restraints excluded: chain E residue 480 ILE Chi-restraints excluded: chain F residue 1 SER Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 107 TRP Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 60 CYS Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 91 VAL Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 195 ILE Chi-restraints excluded: chain O residue 233 GLU Chi-restraints excluded: chain O residue 236 VAL Chi-restraints excluded: chain O residue 314 GLN Chi-restraints excluded: chain O residue 337 THR Chi-restraints excluded: chain O residue 364 ASN Chi-restraints excluded: chain O residue 376 ILE Chi-restraints excluded: chain O residue 399 MET Chi-restraints excluded: chain O residue 466 LEU Chi-restraints excluded: chain O residue 476 SER Chi-restraints excluded: chain P residue 17 GLN Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain Q residue 10 ASP Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 187 THR Chi-restraints excluded: chain Q residue 266 THR Chi-restraints excluded: chain Q residue 271 SER Chi-restraints excluded: chain Q residue 363 VAL Chi-restraints excluded: chain Q residue 371 PHE Chi-restraints excluded: chain Q residue 388 ASN Chi-restraints excluded: chain Q residue 423 VAL Chi-restraints excluded: chain Q residue 426 VAL Chi-restraints excluded: chain Q residue 430 LEU Chi-restraints excluded: chain Q residue 452 VAL Chi-restraints excluded: chain Q residue 455 ILE Chi-restraints excluded: chain Q residue 461 LEU Chi-restraints excluded: chain Q residue 464 ILE Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 74 MET Chi-restraints excluded: chain S residue 10 ASP Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 27 HIS Chi-restraints excluded: chain S residue 49 GLU Chi-restraints excluded: chain S residue 62 GLU Chi-restraints excluded: chain S residue 65 ILE Chi-restraints excluded: chain S residue 91 VAL Chi-restraints excluded: chain S residue 107 LEU Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 205 MET Chi-restraints excluded: chain S residue 206 VAL Chi-restraints excluded: chain S residue 223 THR Chi-restraints excluded: chain S residue 234 LEU Chi-restraints excluded: chain S residue 237 THR Chi-restraints excluded: chain S residue 251 LEU Chi-restraints excluded: chain S residue 266 THR Chi-restraints excluded: chain S residue 301 THR Chi-restraints excluded: chain S residue 356 VAL Chi-restraints excluded: chain S residue 364 ASN Chi-restraints excluded: chain S residue 374 SER Chi-restraints excluded: chain S residue 416 THR Chi-restraints excluded: chain S residue 426 VAL Chi-restraints excluded: chain S residue 460 LEU Chi-restraints excluded: chain S residue 471 THR Chi-restraints excluded: chain S residue 480 ILE Chi-restraints excluded: chain T residue 1 SER Chi-restraints excluded: chain T residue 14 THR Chi-restraints excluded: chain T residue 37 LEU Chi-restraints excluded: chain T residue 47 LEU Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 58 THR Chi-restraints excluded: chain T residue 61 VAL Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 43 LYS Chi-restraints excluded: chain U residue 56 ASN Chi-restraints excluded: chain U residue 62 ASP Chi-restraints excluded: chain U residue 87 THR Chi-restraints excluded: chain U residue 102 VAL Chi-restraints excluded: chain U residue 107 TRP Chi-restraints excluded: chain V residue 53 LEU Chi-restraints excluded: chain V residue 62 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 356 optimal weight: 6.9990 chunk 41 optimal weight: 20.0000 chunk 210 optimal weight: 1.9990 chunk 269 optimal weight: 10.0000 chunk 209 optimal weight: 10.0000 chunk 311 optimal weight: 7.9990 chunk 206 optimal weight: 0.0470 chunk 368 optimal weight: 30.0000 chunk 230 optimal weight: 5.9990 chunk 224 optimal weight: 3.9990 chunk 169 optimal weight: 20.0000 overall best weight: 3.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 HIS ** B 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 1 HIS ** O 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 435 HIS ** P 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 201 ASN ** R 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 77 GLN S 492 GLN V 1 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 30836 Z= 0.227 Angle : 0.600 8.997 41806 Z= 0.304 Chirality : 0.044 0.262 4938 Planarity : 0.004 0.054 5192 Dihedral : 7.288 59.967 4914 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 6.11 % Allowed : 19.80 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.99 (0.13), residues: 3846 helix: 1.69 (0.18), residues: 866 sheet: -0.98 (0.16), residues: 1024 loop : -1.59 (0.13), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 451 HIS 0.005 0.001 HIS O 242 PHE 0.021 0.001 PHE E 475 TYR 0.028 0.001 TYR V 55 ARG 0.007 0.000 ARG O 2 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 498 time to evaluate : 3.296 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 13 GLU cc_start: 0.7316 (tm-30) cc_final: 0.6510 (tm-30) REVERT: A 236 VAL cc_start: 0.9199 (OUTLIER) cc_final: 0.8980 (p) REVERT: A 365 ILE cc_start: 0.9330 (OUTLIER) cc_final: 0.9102 (mm) REVERT: A 457 ILE cc_start: 0.8741 (mm) cc_final: 0.8517 (mp) REVERT: B 30 GLU cc_start: 0.7001 (pt0) cc_final: 0.6730 (pt0) REVERT: B 70 VAL cc_start: 0.9230 (t) cc_final: 0.8828 (p) REVERT: B 73 SER cc_start: 0.7870 (m) cc_final: 0.7581 (p) REVERT: C 473 MET cc_start: 0.7445 (mmp) cc_final: 0.7107 (mtt) REVERT: C 482 ILE cc_start: 0.9038 (mm) cc_final: 0.8719 (mt) REVERT: C 486 TYR cc_start: 0.8345 (t80) cc_final: 0.8106 (t80) REVERT: E 27 HIS cc_start: 0.8570 (OUTLIER) cc_final: 0.7146 (t-90) REVERT: E 234 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7601 (pp) REVERT: E 364 ASN cc_start: 0.8875 (OUTLIER) cc_final: 0.8403 (p0) REVERT: H 62 ASP cc_start: 0.8085 (OUTLIER) cc_final: 0.7834 (t0) REVERT: H 107 TRP cc_start: 0.8538 (OUTLIER) cc_final: 0.7397 (p90) REVERT: L 24 LYS cc_start: 0.8478 (tptp) cc_final: 0.8149 (mtpp) REVERT: O 13 GLU cc_start: 0.7311 (tm-30) cc_final: 0.6500 (tm-30) REVERT: O 236 VAL cc_start: 0.9206 (OUTLIER) cc_final: 0.9005 (p) REVERT: P 30 GLU cc_start: 0.7053 (pt0) cc_final: 0.6761 (pt0) REVERT: P 70 VAL cc_start: 0.9247 (t) cc_final: 0.8816 (p) REVERT: P 73 SER cc_start: 0.7895 (m) cc_final: 0.7605 (p) REVERT: Q 473 MET cc_start: 0.7468 (mmp) cc_final: 0.7197 (mtt) REVERT: Q 482 ILE cc_start: 0.9036 (mm) cc_final: 0.8714 (mt) REVERT: Q 486 TYR cc_start: 0.8345 (t80) cc_final: 0.8108 (t80) REVERT: S 10 ASP cc_start: 0.8866 (OUTLIER) cc_final: 0.8621 (p0) REVERT: S 27 HIS cc_start: 0.8561 (OUTLIER) cc_final: 0.7234 (t-90) REVERT: S 234 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7620 (pp) REVERT: S 364 ASN cc_start: 0.8965 (OUTLIER) cc_final: 0.8548 (p0) REVERT: S 410 MET cc_start: 0.8026 (ttm) cc_final: 0.7749 (ttm) REVERT: U 62 ASP cc_start: 0.8094 (OUTLIER) cc_final: 0.7840 (t0) REVERT: U 107 TRP cc_start: 0.8546 (OUTLIER) cc_final: 0.7493 (p90) REVERT: V 24 LYS cc_start: 0.8448 (tptp) cc_final: 0.8176 (mtpp) outliers start: 197 outliers final: 149 residues processed: 641 average time/residue: 0.3861 time to fit residues: 407.3268 Evaluate side-chains 633 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 470 time to evaluate : 3.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 359 LYS Chi-restraints excluded: chain E residue 364 ASN Chi-restraints excluded: chain E residue 374 SER Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 471 THR Chi-restraints excluded: chain F residue 1 SER Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 107 TRP Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 95 MET Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 60 CYS Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 91 VAL Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 194 MET Chi-restraints excluded: chain O residue 195 ILE Chi-restraints excluded: chain O residue 233 GLU Chi-restraints excluded: chain O residue 236 VAL Chi-restraints excluded: chain O residue 258 MET Chi-restraints excluded: chain O residue 314 GLN Chi-restraints excluded: chain O residue 337 THR Chi-restraints excluded: chain O residue 339 ASP Chi-restraints excluded: chain O residue 364 ASN Chi-restraints excluded: chain O residue 376 ILE Chi-restraints excluded: chain O residue 399 MET Chi-restraints excluded: chain O residue 466 LEU Chi-restraints excluded: chain O residue 476 SER Chi-restraints excluded: chain P residue 17 GLN Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 67 LEU Chi-restraints excluded: chain Q residue 10 ASP Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 187 THR Chi-restraints excluded: chain Q residue 266 THR Chi-restraints excluded: chain Q residue 271 SER Chi-restraints excluded: chain Q residue 363 VAL Chi-restraints excluded: chain Q residue 371 PHE Chi-restraints excluded: chain Q residue 388 ASN Chi-restraints excluded: chain Q residue 400 PHE Chi-restraints excluded: chain Q residue 423 VAL Chi-restraints excluded: chain Q residue 426 VAL Chi-restraints excluded: chain Q residue 452 VAL Chi-restraints excluded: chain Q residue 455 ILE Chi-restraints excluded: chain Q residue 461 LEU Chi-restraints excluded: chain Q residue 485 LEU Chi-restraints excluded: chain R residue 63 ILE Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 74 MET Chi-restraints excluded: chain S residue 10 ASP Chi-restraints excluded: chain S residue 27 HIS Chi-restraints excluded: chain S residue 49 GLU Chi-restraints excluded: chain S residue 62 GLU Chi-restraints excluded: chain S residue 91 VAL Chi-restraints excluded: chain S residue 107 LEU Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 205 MET Chi-restraints excluded: chain S residue 206 VAL Chi-restraints excluded: chain S residue 223 THR Chi-restraints excluded: chain S residue 234 LEU Chi-restraints excluded: chain S residue 236 VAL Chi-restraints excluded: chain S residue 237 THR Chi-restraints excluded: chain S residue 251 LEU Chi-restraints excluded: chain S residue 266 THR Chi-restraints excluded: chain S residue 301 THR Chi-restraints excluded: chain S residue 356 VAL Chi-restraints excluded: chain S residue 364 ASN Chi-restraints excluded: chain S residue 374 SER Chi-restraints excluded: chain S residue 416 THR Chi-restraints excluded: chain S residue 423 VAL Chi-restraints excluded: chain S residue 426 VAL Chi-restraints excluded: chain S residue 471 THR Chi-restraints excluded: chain T residue 1 SER Chi-restraints excluded: chain T residue 14 THR Chi-restraints excluded: chain T residue 37 LEU Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 58 THR Chi-restraints excluded: chain T residue 61 VAL Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 43 LYS Chi-restraints excluded: chain U residue 56 ASN Chi-restraints excluded: chain U residue 62 ASP Chi-restraints excluded: chain U residue 69 THR Chi-restraints excluded: chain U residue 102 VAL Chi-restraints excluded: chain U residue 107 TRP Chi-restraints excluded: chain V residue 14 THR Chi-restraints excluded: chain V residue 53 LEU Chi-restraints excluded: chain V residue 62 SER Chi-restraints excluded: chain V residue 95 MET Chi-restraints excluded: chain V residue 102 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 227 optimal weight: 6.9990 chunk 147 optimal weight: 10.0000 chunk 219 optimal weight: 9.9990 chunk 110 optimal weight: 8.9990 chunk 72 optimal weight: 0.0060 chunk 71 optimal weight: 20.0000 chunk 234 optimal weight: 5.9990 chunk 250 optimal weight: 20.0000 chunk 182 optimal weight: 7.9990 chunk 34 optimal weight: 30.0000 chunk 289 optimal weight: 20.0000 overall best weight: 6.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 HIS ** B 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 435 HIS ** P 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 201 ASN ** R 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 144 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 30836 Z= 0.303 Angle : 0.634 9.015 41806 Z= 0.323 Chirality : 0.045 0.194 4938 Planarity : 0.004 0.062 5192 Dihedral : 7.245 59.732 4914 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 5.80 % Allowed : 19.99 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.02 (0.13), residues: 3846 helix: 1.67 (0.18), residues: 866 sheet: -1.05 (0.16), residues: 1036 loop : -1.57 (0.13), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 418 HIS 0.005 0.001 HIS C 259 PHE 0.025 0.002 PHE P 48 TYR 0.027 0.002 TYR L 55 ARG 0.006 0.001 ARG V 67 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 491 time to evaluate : 3.738 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 13 GLU cc_start: 0.7315 (tm-30) cc_final: 0.6499 (tm-30) REVERT: A 205 MET cc_start: 0.7810 (ttm) cc_final: 0.7323 (mtp) REVERT: A 236 VAL cc_start: 0.9302 (OUTLIER) cc_final: 0.9055 (p) REVERT: A 365 ILE cc_start: 0.9355 (OUTLIER) cc_final: 0.9131 (mm) REVERT: A 457 ILE cc_start: 0.8774 (mm) cc_final: 0.8492 (mp) REVERT: B 70 VAL cc_start: 0.9253 (t) cc_final: 0.8852 (p) REVERT: B 73 SER cc_start: 0.7886 (m) cc_final: 0.7595 (p) REVERT: C 473 MET cc_start: 0.7463 (mmp) cc_final: 0.7209 (mtt) REVERT: C 482 ILE cc_start: 0.9041 (mm) cc_final: 0.8727 (mt) REVERT: C 486 TYR cc_start: 0.8381 (t80) cc_final: 0.8137 (t80) REVERT: E 65 ILE cc_start: 0.9044 (OUTLIER) cc_final: 0.8662 (tp) REVERT: E 234 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7695 (pp) REVERT: E 364 ASN cc_start: 0.8982 (OUTLIER) cc_final: 0.8533 (p0) REVERT: H 62 ASP cc_start: 0.8133 (OUTLIER) cc_final: 0.7887 (t0) REVERT: H 107 TRP cc_start: 0.8566 (OUTLIER) cc_final: 0.7533 (p90) REVERT: L 24 LYS cc_start: 0.8394 (tptp) cc_final: 0.8110 (mtpp) REVERT: O 13 GLU cc_start: 0.7314 (tm-30) cc_final: 0.6493 (tm-30) REVERT: O 236 VAL cc_start: 0.9317 (OUTLIER) cc_final: 0.9087 (p) REVERT: P 70 VAL cc_start: 0.9243 (t) cc_final: 0.8789 (p) REVERT: P 73 SER cc_start: 0.7915 (m) cc_final: 0.7598 (p) REVERT: Q 473 MET cc_start: 0.7461 (mmp) cc_final: 0.7215 (mtt) REVERT: Q 482 ILE cc_start: 0.9040 (mm) cc_final: 0.8723 (mt) REVERT: Q 486 TYR cc_start: 0.8380 (t80) cc_final: 0.8139 (t80) REVERT: S 10 ASP cc_start: 0.8907 (OUTLIER) cc_final: 0.8662 (p0) REVERT: S 65 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8658 (tp) REVERT: S 234 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7749 (pp) REVERT: S 364 ASN cc_start: 0.9007 (OUTLIER) cc_final: 0.8555 (p0) REVERT: S 410 MET cc_start: 0.8111 (ttm) cc_final: 0.7806 (ttm) REVERT: U 62 ASP cc_start: 0.8141 (OUTLIER) cc_final: 0.7881 (t0) REVERT: U 107 TRP cc_start: 0.8563 (OUTLIER) cc_final: 0.7516 (p90) REVERT: V 24 LYS cc_start: 0.8360 (tptp) cc_final: 0.8139 (mtpp) outliers start: 187 outliers final: 157 residues processed: 630 average time/residue: 0.3828 time to fit residues: 398.4930 Evaluate side-chains 641 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 470 time to evaluate : 3.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 199 MET Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 359 LYS Chi-restraints excluded: chain E residue 364 ASN Chi-restraints excluded: chain E residue 374 SER Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 107 TRP Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 95 MET Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 60 CYS Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 91 VAL Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 194 MET Chi-restraints excluded: chain O residue 195 ILE Chi-restraints excluded: chain O residue 233 GLU Chi-restraints excluded: chain O residue 236 VAL Chi-restraints excluded: chain O residue 258 MET Chi-restraints excluded: chain O residue 314 GLN Chi-restraints excluded: chain O residue 337 THR Chi-restraints excluded: chain O residue 339 ASP Chi-restraints excluded: chain O residue 364 ASN Chi-restraints excluded: chain O residue 376 ILE Chi-restraints excluded: chain O residue 385 LEU Chi-restraints excluded: chain O residue 399 MET Chi-restraints excluded: chain O residue 460 LEU Chi-restraints excluded: chain O residue 466 LEU Chi-restraints excluded: chain O residue 476 SER Chi-restraints excluded: chain P residue 17 GLN Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 67 LEU Chi-restraints excluded: chain Q residue 10 ASP Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 187 THR Chi-restraints excluded: chain Q residue 199 MET Chi-restraints excluded: chain Q residue 266 THR Chi-restraints excluded: chain Q residue 271 SER Chi-restraints excluded: chain Q residue 363 VAL Chi-restraints excluded: chain Q residue 371 PHE Chi-restraints excluded: chain Q residue 388 ASN Chi-restraints excluded: chain Q residue 400 PHE Chi-restraints excluded: chain Q residue 423 VAL Chi-restraints excluded: chain Q residue 426 VAL Chi-restraints excluded: chain Q residue 452 VAL Chi-restraints excluded: chain Q residue 455 ILE Chi-restraints excluded: chain Q residue 461 LEU Chi-restraints excluded: chain Q residue 464 ILE Chi-restraints excluded: chain Q residue 485 LEU Chi-restraints excluded: chain R residue 63 ILE Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain S residue 10 ASP Chi-restraints excluded: chain S residue 27 HIS Chi-restraints excluded: chain S residue 49 GLU Chi-restraints excluded: chain S residue 62 GLU Chi-restraints excluded: chain S residue 65 ILE Chi-restraints excluded: chain S residue 91 VAL Chi-restraints excluded: chain S residue 107 LEU Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 205 MET Chi-restraints excluded: chain S residue 206 VAL Chi-restraints excluded: chain S residue 223 THR Chi-restraints excluded: chain S residue 234 LEU Chi-restraints excluded: chain S residue 236 VAL Chi-restraints excluded: chain S residue 237 THR Chi-restraints excluded: chain S residue 263 THR Chi-restraints excluded: chain S residue 266 THR Chi-restraints excluded: chain S residue 301 THR Chi-restraints excluded: chain S residue 356 VAL Chi-restraints excluded: chain S residue 364 ASN Chi-restraints excluded: chain S residue 374 SER Chi-restraints excluded: chain S residue 416 THR Chi-restraints excluded: chain S residue 423 VAL Chi-restraints excluded: chain S residue 426 VAL Chi-restraints excluded: chain T residue 14 THR Chi-restraints excluded: chain T residue 37 LEU Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 58 THR Chi-restraints excluded: chain T residue 61 VAL Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 43 LYS Chi-restraints excluded: chain U residue 56 ASN Chi-restraints excluded: chain U residue 62 ASP Chi-restraints excluded: chain U residue 69 THR Chi-restraints excluded: chain U residue 87 THR Chi-restraints excluded: chain U residue 102 VAL Chi-restraints excluded: chain U residue 107 TRP Chi-restraints excluded: chain V residue 14 THR Chi-restraints excluded: chain V residue 53 LEU Chi-restraints excluded: chain V residue 62 SER Chi-restraints excluded: chain V residue 95 MET Chi-restraints excluded: chain V residue 102 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 334 optimal weight: 5.9990 chunk 352 optimal weight: 9.9990 chunk 321 optimal weight: 0.0870 chunk 343 optimal weight: 9.9990 chunk 206 optimal weight: 20.0000 chunk 149 optimal weight: 10.0000 chunk 269 optimal weight: 1.9990 chunk 105 optimal weight: 10.0000 chunk 310 optimal weight: 0.0670 chunk 324 optimal weight: 4.9990 chunk 341 optimal weight: 1.9990 overall best weight: 1.8302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 HIS ** B 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN E 144 HIS E 492 GLN ** O 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 375 ASN O 388 ASN O 435 HIS ** P 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 201 ASN ** R 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 30836 Z= 0.170 Angle : 0.592 11.469 41806 Z= 0.299 Chirality : 0.043 0.196 4938 Planarity : 0.004 0.047 5192 Dihedral : 6.843 59.216 4914 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.28 % Allowed : 21.79 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.93 (0.13), residues: 3846 helix: 1.61 (0.18), residues: 872 sheet: -0.89 (0.16), residues: 1042 loop : -1.52 (0.13), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP V 31 HIS 0.005 0.001 HIS O 242 PHE 0.028 0.001 PHE D 64 TYR 0.029 0.001 TYR V 55 ARG 0.005 0.000 ARG V 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 505 time to evaluate : 3.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.7261 (tm-30) cc_final: 0.6627 (tm-30) REVERT: A 285 LEU cc_start: 0.9452 (OUTLIER) cc_final: 0.9039 (mt) REVERT: A 365 ILE cc_start: 0.9284 (OUTLIER) cc_final: 0.9053 (mm) REVERT: B 27 ARG cc_start: 0.7193 (ptt-90) cc_final: 0.6823 (ptt-90) REVERT: B 70 VAL cc_start: 0.9256 (t) cc_final: 0.8867 (p) REVERT: C 438 PHE cc_start: 0.7963 (m-10) cc_final: 0.7619 (m-80) REVERT: C 473 MET cc_start: 0.7107 (mmp) cc_final: 0.6629 (mtt) REVERT: C 482 ILE cc_start: 0.9158 (mm) cc_final: 0.8799 (mt) REVERT: E 234 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7216 (pp) REVERT: E 364 ASN cc_start: 0.8677 (OUTLIER) cc_final: 0.8229 (p0) REVERT: F 26 TRP cc_start: 0.8193 (m100) cc_final: 0.7747 (m-90) REVERT: H 62 ASP cc_start: 0.8109 (OUTLIER) cc_final: 0.7881 (t0) REVERT: H 73 ASP cc_start: 0.7369 (t0) cc_final: 0.7073 (t0) REVERT: H 107 TRP cc_start: 0.8528 (OUTLIER) cc_final: 0.7240 (p90) REVERT: L 87 GLU cc_start: 0.7312 (pp20) cc_final: 0.6986 (pp20) REVERT: O 13 GLU cc_start: 0.7285 (tm-30) cc_final: 0.6637 (tm-30) REVERT: O 176 TYR cc_start: 0.8747 (m-80) cc_final: 0.8408 (m-80) REVERT: O 199 MET cc_start: 0.8430 (ptp) cc_final: 0.7830 (ptm) REVERT: O 285 LEU cc_start: 0.9458 (OUTLIER) cc_final: 0.9059 (mt) REVERT: P 27 ARG cc_start: 0.7186 (ptt-90) cc_final: 0.6850 (ptt-90) REVERT: P 70 VAL cc_start: 0.9219 (t) cc_final: 0.8804 (p) REVERT: Q 438 PHE cc_start: 0.7956 (m-10) cc_final: 0.7623 (m-80) REVERT: Q 473 MET cc_start: 0.7102 (mmp) cc_final: 0.6327 (mtt) REVERT: Q 482 ILE cc_start: 0.9154 (mm) cc_final: 0.8792 (mt) REVERT: S 10 ASP cc_start: 0.8790 (OUTLIER) cc_final: 0.8547 (p0) REVERT: S 199 MET cc_start: 0.7878 (ttt) cc_final: 0.7281 (ttp) REVERT: S 234 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7181 (pp) REVERT: S 364 ASN cc_start: 0.8725 (OUTLIER) cc_final: 0.8263 (p0) REVERT: S 410 MET cc_start: 0.7963 (ttm) cc_final: 0.7701 (ttm) REVERT: T 26 TRP cc_start: 0.8191 (m100) cc_final: 0.7738 (m-90) REVERT: U 62 ASP cc_start: 0.8111 (OUTLIER) cc_final: 0.7875 (t0) REVERT: U 73 ASP cc_start: 0.7263 (t0) cc_final: 0.6927 (t0) REVERT: U 107 TRP cc_start: 0.8518 (OUTLIER) cc_final: 0.7325 (p90) REVERT: V 28 ILE cc_start: 0.8374 (OUTLIER) cc_final: 0.8110 (mp) REVERT: V 87 GLU cc_start: 0.7317 (pp20) cc_final: 0.6982 (pp20) outliers start: 138 outliers final: 100 residues processed: 606 average time/residue: 0.3918 time to fit residues: 388.0049 Evaluate side-chains 599 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 486 time to evaluate : 3.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 199 MET Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 364 ASN Chi-restraints excluded: chain E residue 374 SER Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 107 TRP Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 95 MET Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain O residue 60 CYS Chi-restraints excluded: chain O residue 91 VAL Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 194 MET Chi-restraints excluded: chain O residue 233 GLU Chi-restraints excluded: chain O residue 258 MET Chi-restraints excluded: chain O residue 285 LEU Chi-restraints excluded: chain O residue 314 GLN Chi-restraints excluded: chain O residue 337 THR Chi-restraints excluded: chain O residue 364 ASN Chi-restraints excluded: chain O residue 376 ILE Chi-restraints excluded: chain O residue 460 LEU Chi-restraints excluded: chain P residue 17 GLN Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain Q residue 10 ASP Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 187 THR Chi-restraints excluded: chain Q residue 199 MET Chi-restraints excluded: chain Q residue 266 THR Chi-restraints excluded: chain Q residue 271 SER Chi-restraints excluded: chain Q residue 363 VAL Chi-restraints excluded: chain Q residue 371 PHE Chi-restraints excluded: chain Q residue 388 ASN Chi-restraints excluded: chain Q residue 423 VAL Chi-restraints excluded: chain Q residue 426 VAL Chi-restraints excluded: chain Q residue 452 VAL Chi-restraints excluded: chain Q residue 455 ILE Chi-restraints excluded: chain Q residue 461 LEU Chi-restraints excluded: chain Q residue 485 LEU Chi-restraints excluded: chain R residue 63 ILE Chi-restraints excluded: chain S residue 10 ASP Chi-restraints excluded: chain S residue 27 HIS Chi-restraints excluded: chain S residue 49 GLU Chi-restraints excluded: chain S residue 107 LEU Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 205 MET Chi-restraints excluded: chain S residue 234 LEU Chi-restraints excluded: chain S residue 236 VAL Chi-restraints excluded: chain S residue 237 THR Chi-restraints excluded: chain S residue 266 THR Chi-restraints excluded: chain S residue 356 VAL Chi-restraints excluded: chain S residue 364 ASN Chi-restraints excluded: chain S residue 374 SER Chi-restraints excluded: chain S residue 423 VAL Chi-restraints excluded: chain S residue 471 THR Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 58 THR Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain U residue 43 LYS Chi-restraints excluded: chain U residue 56 ASN Chi-restraints excluded: chain U residue 62 ASP Chi-restraints excluded: chain U residue 102 VAL Chi-restraints excluded: chain U residue 107 TRP Chi-restraints excluded: chain V residue 14 THR Chi-restraints excluded: chain V residue 28 ILE Chi-restraints excluded: chain V residue 62 SER Chi-restraints excluded: chain V residue 95 MET Chi-restraints excluded: chain V residue 102 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 225 optimal weight: 40.0000 chunk 362 optimal weight: 30.0000 chunk 221 optimal weight: 20.0000 chunk 172 optimal weight: 4.9990 chunk 252 optimal weight: 10.0000 chunk 380 optimal weight: 10.0000 chunk 350 optimal weight: 10.0000 chunk 303 optimal weight: 8.9990 chunk 31 optimal weight: 9.9990 chunk 234 optimal weight: 6.9990 chunk 185 optimal weight: 8.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 GLN H 56 ASN ** O 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 201 ASN ** R 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 56 ASN ** U 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.119 30836 Z= 0.384 Angle : 0.682 10.169 41806 Z= 0.347 Chirality : 0.047 0.315 4938 Planarity : 0.004 0.052 5192 Dihedral : 7.046 55.426 4914 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 4.16 % Allowed : 22.41 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.02 (0.13), residues: 3846 helix: 1.54 (0.18), residues: 866 sheet: -0.96 (0.16), residues: 1042 loop : -1.56 (0.13), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 418 HIS 0.006 0.001 HIS A 207 PHE 0.026 0.002 PHE P 48 TYR 0.024 0.002 TYR V 55 ARG 0.009 0.001 ARG O 2 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 475 time to evaluate : 3.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.7280 (tm-30) cc_final: 0.6472 (tm-30) REVERT: A 205 MET cc_start: 0.7849 (ttm) cc_final: 0.7312 (mtp) REVERT: A 242 HIS cc_start: 0.8312 (OUTLIER) cc_final: 0.7723 (p-80) REVERT: A 285 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9017 (mt) REVERT: A 457 ILE cc_start: 0.8773 (mm) cc_final: 0.8515 (mp) REVERT: B 70 VAL cc_start: 0.9148 (t) cc_final: 0.8836 (p) REVERT: C 438 PHE cc_start: 0.7694 (m-10) cc_final: 0.7315 (m-80) REVERT: C 473 MET cc_start: 0.7211 (mmp) cc_final: 0.6620 (mtt) REVERT: C 482 ILE cc_start: 0.9114 (mm) cc_final: 0.8793 (mt) REVERT: E 27 HIS cc_start: 0.8585 (OUTLIER) cc_final: 0.7140 (t-90) REVERT: E 65 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8648 (tp) REVERT: E 234 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.7747 (pp) REVERT: E 364 ASN cc_start: 0.9012 (OUTLIER) cc_final: 0.8546 (p0) REVERT: F 10 MET cc_start: 0.8736 (ppp) cc_final: 0.8321 (ppp) REVERT: H 107 TRP cc_start: 0.8633 (OUTLIER) cc_final: 0.7601 (p90) REVERT: L 87 GLU cc_start: 0.7515 (pp20) cc_final: 0.7151 (pp20) REVERT: O 13 GLU cc_start: 0.7292 (tm-30) cc_final: 0.6468 (tm-30) REVERT: O 176 TYR cc_start: 0.8638 (m-80) cc_final: 0.8272 (m-80) REVERT: O 242 HIS cc_start: 0.8302 (OUTLIER) cc_final: 0.7685 (p-80) REVERT: O 285 LEU cc_start: 0.9427 (OUTLIER) cc_final: 0.9028 (mt) REVERT: P 70 VAL cc_start: 0.9136 (t) cc_final: 0.8806 (p) REVERT: Q 438 PHE cc_start: 0.7704 (m-10) cc_final: 0.7333 (m-80) REVERT: Q 473 MET cc_start: 0.7012 (mmp) cc_final: 0.6562 (mtt) REVERT: Q 482 ILE cc_start: 0.9102 (mm) cc_final: 0.8784 (mt) REVERT: S 10 ASP cc_start: 0.8933 (OUTLIER) cc_final: 0.8667 (p0) REVERT: S 27 HIS cc_start: 0.8588 (OUTLIER) cc_final: 0.7157 (t-90) REVERT: S 65 ILE cc_start: 0.9043 (OUTLIER) cc_final: 0.8648 (tp) REVERT: S 234 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.7811 (pp) REVERT: S 339 ASP cc_start: 0.6688 (OUTLIER) cc_final: 0.5763 (p0) REVERT: S 364 ASN cc_start: 0.9023 (OUTLIER) cc_final: 0.8546 (p0) REVERT: S 410 MET cc_start: 0.8145 (ttm) cc_final: 0.7825 (ttm) REVERT: T 10 MET cc_start: 0.8723 (ppp) cc_final: 0.8263 (ppp) REVERT: U 107 TRP cc_start: 0.8629 (OUTLIER) cc_final: 0.7605 (p90) REVERT: V 87 GLU cc_start: 0.7362 (pp20) cc_final: 0.7027 (pp20) outliers start: 134 outliers final: 106 residues processed: 577 average time/residue: 0.3773 time to fit residues: 359.0302 Evaluate side-chains 596 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 474 time to evaluate : 3.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 242 HIS Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 199 MET Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 364 ASN Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 471 THR Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 107 TRP Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 95 MET Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 60 CYS Chi-restraints excluded: chain O residue 91 VAL Chi-restraints excluded: chain O residue 194 MET Chi-restraints excluded: chain O residue 233 GLU Chi-restraints excluded: chain O residue 242 HIS Chi-restraints excluded: chain O residue 258 MET Chi-restraints excluded: chain O residue 285 LEU Chi-restraints excluded: chain O residue 314 GLN Chi-restraints excluded: chain O residue 337 THR Chi-restraints excluded: chain O residue 364 ASN Chi-restraints excluded: chain O residue 376 ILE Chi-restraints excluded: chain O residue 385 LEU Chi-restraints excluded: chain O residue 460 LEU Chi-restraints excluded: chain P residue 17 GLN Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain Q residue 10 ASP Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 187 THR Chi-restraints excluded: chain Q residue 199 MET Chi-restraints excluded: chain Q residue 266 THR Chi-restraints excluded: chain Q residue 271 SER Chi-restraints excluded: chain Q residue 363 VAL Chi-restraints excluded: chain Q residue 371 PHE Chi-restraints excluded: chain Q residue 388 ASN Chi-restraints excluded: chain Q residue 426 VAL Chi-restraints excluded: chain Q residue 452 VAL Chi-restraints excluded: chain Q residue 455 ILE Chi-restraints excluded: chain Q residue 461 LEU Chi-restraints excluded: chain Q residue 485 LEU Chi-restraints excluded: chain R residue 63 ILE Chi-restraints excluded: chain S residue 10 ASP Chi-restraints excluded: chain S residue 27 HIS Chi-restraints excluded: chain S residue 49 GLU Chi-restraints excluded: chain S residue 65 ILE Chi-restraints excluded: chain S residue 91 VAL Chi-restraints excluded: chain S residue 107 LEU Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 205 MET Chi-restraints excluded: chain S residue 234 LEU Chi-restraints excluded: chain S residue 236 VAL Chi-restraints excluded: chain S residue 237 THR Chi-restraints excluded: chain S residue 263 THR Chi-restraints excluded: chain S residue 266 THR Chi-restraints excluded: chain S residue 339 ASP Chi-restraints excluded: chain S residue 356 VAL Chi-restraints excluded: chain S residue 364 ASN Chi-restraints excluded: chain S residue 416 THR Chi-restraints excluded: chain S residue 423 VAL Chi-restraints excluded: chain S residue 485 LEU Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 58 THR Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain U residue 43 LYS Chi-restraints excluded: chain U residue 56 ASN Chi-restraints excluded: chain U residue 87 THR Chi-restraints excluded: chain U residue 102 VAL Chi-restraints excluded: chain U residue 107 TRP Chi-restraints excluded: chain V residue 14 THR Chi-restraints excluded: chain V residue 62 SER Chi-restraints excluded: chain V residue 95 MET Chi-restraints excluded: chain V residue 102 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 240 optimal weight: 9.9990 chunk 322 optimal weight: 4.9990 chunk 92 optimal weight: 8.9990 chunk 279 optimal weight: 9.9990 chunk 44 optimal weight: 7.9990 chunk 84 optimal weight: 8.9990 chunk 303 optimal weight: 0.8980 chunk 127 optimal weight: 7.9990 chunk 311 optimal weight: 0.7980 chunk 38 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 overall best weight: 4.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 201 ASN ** R 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 59 GLN ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.090321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.078081 restraints weight = 72562.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.080220 restraints weight = 37372.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.081610 restraints weight = 23558.343| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 30836 Z= 0.252 Angle : 0.624 10.765 41806 Z= 0.316 Chirality : 0.045 0.271 4938 Planarity : 0.004 0.046 5192 Dihedral : 6.869 54.240 4914 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.56 % Allowed : 22.35 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.95 (0.13), residues: 3846 helix: 1.59 (0.18), residues: 866 sheet: -0.89 (0.16), residues: 1042 loop : -1.52 (0.13), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP L 31 HIS 0.004 0.001 HIS O 242 PHE 0.021 0.001 PHE S 475 TYR 0.026 0.001 TYR V 55 ARG 0.007 0.001 ARG F 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6872.97 seconds wall clock time: 124 minutes 7.35 seconds (7447.35 seconds total)