Starting phenix.real_space_refine on Thu Jul 25 18:26:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jn5_36433/07_2024/8jn5_36433.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jn5_36433/07_2024/8jn5_36433.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jn5_36433/07_2024/8jn5_36433.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jn5_36433/07_2024/8jn5_36433.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jn5_36433/07_2024/8jn5_36433.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jn5_36433/07_2024/8jn5_36433.cif" } resolution = 3.6 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 19172 2.51 5 N 5062 2.21 5 O 5768 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 GLU 13": "OE1" <-> "OE2" Residue "A GLU 49": "OE1" <-> "OE2" Residue "A ARG 57": "NH1" <-> "NH2" Residue "A ASP 71": "OD1" <-> "OD2" Residue "A ARG 73": "NH1" <-> "NH2" Residue "A ASP 87": "OD1" <-> "OD2" Residue "A TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 99": "NH1" <-> "NH2" Residue "A PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 123": "OE1" <-> "OE2" Residue "A TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 175": "OE1" <-> "OE2" Residue "A TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 182": "OE1" <-> "OE2" Residue "A ARG 186": "NH1" <-> "NH2" Residue "A ASP 190": "OD1" <-> "OD2" Residue "A ARG 208": "NH1" <-> "NH2" Residue "A GLU 225": "OE1" <-> "OE2" Residue "A GLU 247": "OE1" <-> "OE2" Residue "A ARG 284": "NH1" <-> "NH2" Residue "A PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 348": "NH1" <-> "NH2" Residue "A ASP 382": "OD1" <-> "OD2" Residue "A TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 401": "OE1" <-> "OE2" Residue "A ARG 405": "NH1" <-> "NH2" Residue "A ARG 409": "NH1" <-> "NH2" Residue "A PHE 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 30": "OE1" <-> "OE2" Residue "B ARG 38": "NH1" <-> "NH2" Residue "B PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 2": "NH1" <-> "NH2" Residue "C ARG 9": "NH1" <-> "NH2" Residue "C ASP 42": "OD1" <-> "OD2" Residue "C ARG 57": "NH1" <-> "NH2" Residue "C GLU 62": "OE1" <-> "OE2" Residue "C ASP 71": "OD1" <-> "OD2" Residue "C ARG 73": "NH1" <-> "NH2" Residue "C ARG 99": "NH1" <-> "NH2" Residue "C PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 123": "OE1" <-> "OE2" Residue "C GLU 133": "OE1" <-> "OE2" Residue "C GLU 170": "OE1" <-> "OE2" Residue "C TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 186": "NH1" <-> "NH2" Residue "C PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 193": "OE1" <-> "OE2" Residue "C ARG 208": "NH1" <-> "NH2" Residue "C PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 247": "OE1" <-> "OE2" Residue "C PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 405": "NH1" <-> "NH2" Residue "C ARG 409": "NH1" <-> "NH2" Residue "C PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 13": "OD1" <-> "OD2" Residue "D GLU 30": "OE1" <-> "OE2" Residue "D GLU 33": "OE1" <-> "OE2" Residue "D ARG 38": "NH1" <-> "NH2" Residue "D PHE 48": "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 GLU 49": "OE1" <-> "OE2" Residue "E ASP 71": "OD1" <-> "OD2" Residue "E ARG 73": "NH1" <-> "NH2" Residue "E ARG 99": "NH1" <-> "NH2" Residue "E PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 154": "OE1" <-> "OE2" Residue "E TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 182": "OE1" <-> "OE2" Residue "E ARG 186": "NH1" <-> "NH2" Residue "E GLU 193": "OE1" <-> "OE2" Residue "E ARG 208": "NH1" <-> "NH2" Residue "E GLU 225": "OE1" <-> "OE2" Residue "E PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 284": "NH1" <-> "NH2" Residue "E GLU 291": "OE1" <-> "OE2" Residue "E GLU 327": "OE1" <-> "OE2" Residue "E ASP 328": "OD1" <-> "OD2" Residue "E PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 339": "OD1" <-> "OD2" Residue "E ARG 348": "NH1" <-> "NH2" Residue "E GLU 360": "OE1" <-> "OE2" Residue "E GLU 366": "OE1" <-> "OE2" Residue "E GLU 368": "OE1" <-> "OE2" Residue "E ARG 405": "NH1" <-> "NH2" Residue "E ARG 409": "NH1" <-> "NH2" Residue "E ASP 419": "OD1" <-> "OD2" Residue "E TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 30": "OE1" <-> "OE2" Residue "F ARG 38": "NH1" <-> "NH2" Residue "F PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 3": "OE1" <-> "OE2" Residue "H ASP 10": "OD1" <-> "OD2" Residue "H TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 73": "OD1" <-> "OD2" Residue "H ARG 98": "NH1" <-> "NH2" Residue "L ASP 34": "OD1" <-> "OD2" Residue "L TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 66": "OD1" <-> "OD2" Residue "L PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 87": "OE1" <-> "OE2" Residue "L ASP 88": "OD1" <-> "OD2" 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 GLU 13": "OE1" <-> "OE2" Residue "O GLU 49": "OE1" <-> "OE2" Residue "O ARG 57": "NH1" <-> "NH2" Residue "O ASP 71": "OD1" <-> "OD2" Residue "O ARG 73": "NH1" <-> "NH2" Residue "O ASP 87": "OD1" <-> "OD2" Residue "O TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 99": "NH1" <-> "NH2" Residue "O PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 123": "OE1" <-> "OE2" Residue "O TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 175": "OE1" <-> "OE2" Residue "O TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 182": "OE1" <-> "OE2" Residue "O ARG 186": "NH1" <-> "NH2" Residue "O ASP 190": "OD1" <-> "OD2" Residue "O ARG 208": "NH1" <-> "NH2" Residue "O GLU 225": "OE1" <-> "OE2" Residue "O GLU 247": "OE1" <-> "OE2" Residue "O ARG 284": "NH1" <-> "NH2" Residue "O PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 348": "NH1" <-> "NH2" Residue "O ASP 382": "OD1" <-> "OD2" Residue "O TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 401": "OE1" <-> "OE2" Residue "O ARG 405": "NH1" <-> "NH2" Residue "O ARG 409": "NH1" <-> "NH2" Residue "O PHE 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 30": "OE1" <-> "OE2" Residue "P ARG 38": "NH1" <-> "NH2" Residue "P PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 2": "NH1" <-> "NH2" Residue "Q ARG 9": "NH1" <-> "NH2" Residue "Q ASP 42": "OD1" <-> "OD2" Residue "Q ARG 57": "NH1" <-> "NH2" Residue "Q GLU 62": "OE1" <-> "OE2" Residue "Q ASP 71": "OD1" <-> "OD2" Residue "Q ARG 73": "NH1" <-> "NH2" Residue "Q ARG 99": "NH1" <-> "NH2" Residue "Q PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 123": "OE1" <-> "OE2" Residue "Q GLU 133": "OE1" <-> "OE2" Residue "Q GLU 170": "OE1" <-> "OE2" Residue "Q TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 186": "NH1" <-> "NH2" Residue "Q PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 193": "OE1" <-> "OE2" Residue "Q ARG 208": "NH1" <-> "NH2" Residue "Q PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 247": "OE1" <-> "OE2" Residue "Q PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 405": "NH1" <-> "NH2" Residue "Q ARG 409": "NH1" <-> "NH2" Residue "Q PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 13": "OD1" <-> "OD2" Residue "R GLU 30": "OE1" <-> "OE2" Residue "R GLU 33": "OE1" <-> "OE2" Residue "R ARG 38": "NH1" <-> "NH2" Residue "R PHE 48": "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 GLU 49": "OE1" <-> "OE2" Residue "S ASP 71": "OD1" <-> "OD2" Residue "S ARG 73": "NH1" <-> "NH2" Residue "S ARG 99": "NH1" <-> "NH2" Residue "S PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 154": "OE1" <-> "OE2" Residue "S TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 182": "OE1" <-> "OE2" Residue "S ARG 186": "NH1" <-> "NH2" Residue "S GLU 193": "OE1" <-> "OE2" Residue "S ARG 208": "NH1" <-> "NH2" Residue "S GLU 225": "OE1" <-> "OE2" Residue "S PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 284": "NH1" <-> "NH2" Residue "S GLU 291": "OE1" <-> "OE2" Residue "S GLU 327": "OE1" <-> "OE2" Residue "S ASP 328": "OD1" <-> "OD2" Residue "S PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 339": "OD1" <-> "OD2" Residue "S ARG 348": "NH1" <-> "NH2" Residue "S GLU 360": "OE1" <-> "OE2" Residue "S GLU 366": "OE1" <-> "OE2" Residue "S GLU 368": "OE1" <-> "OE2" Residue "S ARG 405": "NH1" <-> "NH2" Residue "S ARG 409": "NH1" <-> "NH2" Residue "S ASP 419": "OD1" <-> "OD2" Residue "S TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 30": "OE1" <-> "OE2" Residue "T ARG 38": "NH1" <-> "NH2" Residue "T PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 3": "OE1" <-> "OE2" Residue "U ASP 10": "OD1" <-> "OD2" Residue "U TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 73": "OD1" <-> "OD2" Residue "U ARG 98": "NH1" <-> "NH2" Residue "V ASP 34": "OD1" <-> "OD2" Residue "V TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 66": "OD1" <-> "OD2" Residue "V PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 87": "OE1" <-> "OE2" Residue "V ASP 88": "OD1" <-> "OD2" Residue "V TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 30204 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "0" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "1" Number of atoms: 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: 15.06, per 1000 atoms: 0.50 Number of scatterers: 30204 At special positions: 0 Unit cell: (165.87, 241.11, 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 5768 8.00 N 5062 7.00 C 19172 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=2.03 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 105 " distance=2.03 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 116 " distance=2.04 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 283 " distance=2.04 Simple disulfide: pdb=" SG CYS C 3 " - pdb=" SG CYS C 30 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS E 60 " - pdb=" SG CYS E 121 " distance=2.04 Simple disulfide: pdb=" SG CYS E 92 " - pdb=" SG CYS E 116 " distance=2.04 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS O 74 " - pdb=" SG CYS O 105 " distance=2.03 Simple disulfide: pdb=" SG CYS O 92 " - pdb=" SG CYS O 116 " distance=2.04 Simple disulfide: pdb=" SG CYS O 183 " - pdb=" SG CYS O 283 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 3 " - pdb=" SG CYS Q 30 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS S 60 " - pdb=" SG CYS S 121 " distance=2.04 Simple disulfide: pdb=" SG CYS S 92 " - pdb=" SG CYS S 116 " distance=2.04 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=2.04 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 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 " 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: 11.28 Conformation dependent library (CDL) restraints added in 5.4 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 74 sheets defined 25.8% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.99 Creating SS restraints... 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 190 through 192 No H-bonds generated for 'chain 'A' and resid 190 through 192' Processing helix chain 'A' and resid 208 through 212 Processing helix chain 'A' and resid 231 through 235 removed outlier: 3.921A pdb=" N LEU A 234 " --> pdb=" O ARG A 231 " (cutoff:3.500A) removed outlier: 3.600A 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 242 through 244 No H-bonds generated for 'chain 'A' and resid 242 through 244' 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 Processing helix chain 'A' and resid 425 through 447 removed outlier: 3.805A pdb=" N SER A 429 " --> pdb=" O GLY A 425 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU A 430 " --> pdb=" O VAL A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 468 Processing helix chain 'A' and resid 470 through 490 Processing helix chain 'B' and resid 26 through 39 removed outlier: 4.183A pdb=" N VAL B 32 " --> pdb=" O GLN B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 removed outlier: 3.985A 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 100 through 104 Processing helix chain 'C' and resid 208 through 214 Processing helix chain 'C' and resid 231 through 235 removed outlier: 3.766A pdb=" N LEU C 234 " --> pdb=" O ARG C 231 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU C 235 " --> pdb=" O LYS C 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 231 through 235' Processing helix chain 'C' and resid 254 through 262 Processing helix chain 'C' and resid 394 through 414 Processing helix chain 'C' and resid 415 through 420 removed outlier: 3.760A pdb=" N TRP C 418 " --> pdb=" O ASP C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 447 removed outlier: 3.527A pdb=" N SER C 429 " --> pdb=" O GLY C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 467 removed outlier: 3.742A pdb=" N ILE C 455 " --> pdb=" O TRP C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 490 removed outlier: 4.140A pdb=" N ILE C 478 " --> pdb=" O SER C 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 26 removed outlier: 4.637A pdb=" N TRP D 26 " --> pdb=" O ALA D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 39 Processing helix chain 'D' and resid 40 through 54 removed outlier: 3.884A pdb=" N ILE D 44 " --> pdb=" O PRO D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 75 removed outlier: 3.578A pdb=" N LYS D 60 " --> pdb=" O SER D 56 " (cutoff:3.500A) Proline residue: D 72 - end of helix Processing helix chain 'E' and resid 82 through 86 Processing helix chain 'E' and resid 131 through 133 No H-bonds generated for 'chain 'E' and resid 131 through 133' Processing helix chain 'E' and resid 208 through 213 Processing helix chain 'E' and resid 231 through 236 removed outlier: 3.539A pdb=" N LEU E 234 " --> pdb=" O ARG E 231 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL E 236 " --> pdb=" O GLU E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 394 through 414 Processing helix chain 'E' and resid 415 through 420 Processing helix chain 'E' and resid 425 through 447 Processing helix chain 'E' and resid 450 through 467 removed outlier: 4.222A pdb=" N ILE E 455 " --> pdb=" O TRP E 451 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY E 456 " --> pdb=" O VAL E 452 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASN E 467 " --> pdb=" O TRP E 463 " (cutoff:3.500A) Processing helix chain 'E' and resid 471 through 491 Processing helix chain 'F' and resid 26 through 39 Processing helix chain 'F' and resid 41 through 53 removed outlier: 4.103A pdb=" N LEU F 45 " --> pdb=" O GLY F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 75 Proline residue: F 72 - end of helix Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.786A pdb=" N ASN H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'L' and resid 85 through 89 removed outlier: 3.846A pdb=" N VAL L 89 " --> pdb=" O ALA L 86 " (cutoff:3.500A) 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 190 through 192 No H-bonds generated for 'chain 'O' and resid 190 through 192' Processing helix chain 'O' and resid 208 through 212 Processing helix chain 'O' and resid 231 through 235 removed outlier: 3.921A pdb=" N LEU O 234 " --> pdb=" O ARG O 231 " (cutoff:3.500A) removed outlier: 3.600A 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 242 through 244 No H-bonds generated for 'chain 'O' and resid 242 through 244' 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 Processing helix chain 'O' and resid 425 through 447 removed outlier: 3.805A pdb=" N SER O 429 " --> pdb=" O GLY O 425 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU O 430 " --> pdb=" O VAL O 426 " (cutoff:3.500A) Processing helix chain 'O' and resid 450 through 468 Processing helix chain 'O' and resid 470 through 490 Processing helix chain 'P' and resid 26 through 39 removed outlier: 4.183A pdb=" N VAL P 32 " --> pdb=" O GLN P 28 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 53 removed outlier: 3.985A 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 100 through 104 Processing helix chain 'Q' and resid 208 through 214 Processing helix chain 'Q' and resid 231 through 235 removed outlier: 3.766A pdb=" N LEU Q 234 " --> pdb=" O ARG Q 231 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU Q 235 " --> pdb=" O LYS Q 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 231 through 235' Processing helix chain 'Q' and resid 254 through 262 Processing helix chain 'Q' and resid 394 through 414 Processing helix chain 'Q' and resid 415 through 420 removed outlier: 3.760A pdb=" N TRP Q 418 " --> pdb=" O ASP Q 415 " (cutoff:3.500A) Processing helix chain 'Q' and resid 425 through 447 removed outlier: 3.527A pdb=" N SER Q 429 " --> pdb=" O GLY Q 425 " (cutoff:3.500A) Processing helix chain 'Q' and resid 450 through 467 removed outlier: 3.742A pdb=" N ILE Q 455 " --> pdb=" O TRP Q 451 " (cutoff:3.500A) Processing helix chain 'Q' and resid 472 through 490 removed outlier: 4.140A pdb=" N ILE Q 478 " --> pdb=" O SER Q 474 " (cutoff:3.500A) Processing helix chain 'R' and resid 20 through 26 removed outlier: 4.637A pdb=" N TRP R 26 " --> pdb=" O ALA R 22 " (cutoff:3.500A) Processing helix chain 'R' and resid 26 through 39 Processing helix chain 'R' and resid 40 through 54 removed outlier: 3.884A pdb=" N ILE R 44 " --> pdb=" O PRO R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 75 removed outlier: 3.578A pdb=" N LYS R 60 " --> pdb=" O SER R 56 " (cutoff:3.500A) Proline residue: R 72 - end of helix Processing helix chain 'S' and resid 82 through 86 Processing helix chain 'S' and resid 131 through 133 No H-bonds generated for 'chain 'S' and resid 131 through 133' Processing helix chain 'S' and resid 208 through 213 Processing helix chain 'S' and resid 231 through 236 removed outlier: 3.539A pdb=" N LEU S 234 " --> pdb=" O ARG S 231 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL S 236 " --> pdb=" O GLU S 233 " (cutoff:3.500A) Processing helix chain 'S' and resid 394 through 414 Processing helix chain 'S' and resid 415 through 420 Processing helix chain 'S' and resid 425 through 447 Processing helix chain 'S' and resid 450 through 467 removed outlier: 4.222A pdb=" N ILE S 455 " --> pdb=" O TRP S 451 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY S 456 " --> pdb=" O VAL S 452 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASN S 467 " --> pdb=" O TRP S 463 " (cutoff:3.500A) Processing helix chain 'S' and resid 471 through 491 Processing helix chain 'T' and resid 26 through 39 Processing helix chain 'T' and resid 41 through 53 removed outlier: 4.103A pdb=" N LEU T 45 " --> pdb=" O GLY T 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 57 through 75 Proline residue: T 72 - end of helix Processing helix chain 'U' and resid 28 through 32 removed outlier: 3.786A pdb=" N ASN U 31 " --> pdb=" O THR U 28 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR U 32 " --> pdb=" O PHE U 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 28 through 32' Processing helix chain 'V' and resid 85 through 89 removed outlier: 3.846A pdb=" N VAL V 89 " --> pdb=" O ALA V 86 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 23 through 26 Processing sheet with id=2, first strand: chain 'A' and resid 31 through 35 removed outlier: 3.852A pdb=" N LEU A 41 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ALA A 35 " --> pdb=" O PRO A 39 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 31 through 35 removed outlier: 3.852A pdb=" N LEU A 41 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ALA A 35 " --> pdb=" O PRO A 39 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'A' and resid 59 through 60 Processing sheet with id=5, first strand: chain 'A' and resid 63 through 72 removed outlier: 4.728A pdb=" N ILE A 68 " --> pdb=" O CYS A 116 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N CYS A 116 " --> pdb=" O ILE A 68 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N THR A 70 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL A 114 " --> pdb=" O THR A 70 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N SER A 72 " --> pdb=" O SER A 112 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N SER A 112 " --> pdb=" O SER A 72 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'A' and resid 63 through 72 removed outlier: 4.728A pdb=" N ILE A 68 " --> pdb=" O CYS A 116 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N CYS A 116 " --> pdb=" O ILE A 68 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N THR A 70 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL A 114 " --> pdb=" O THR A 70 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N SER A 72 " --> pdb=" O SER A 112 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N SER A 112 " --> pdb=" O SER A 72 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'A' and resid 171 through 173 removed outlier: 3.635A pdb=" N ALA A 171 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 179 " --> pdb=" O ALA A 171 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'A' and resid 194 through 195 Processing sheet with id=9, first strand: chain 'A' and resid 237 through 240 removed outlier: 3.705A pdb=" N GLU A 247 " --> pdb=" O LYS A 239 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'A' and resid 298 through 299 removed outlier: 6.706A pdb=" N ALA A 298 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N CYS A 331 " --> pdb=" O VAL A 356 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'A' and resid 304 through 306 Processing sheet with id=12, first strand: chain 'A' and resid 311 through 312 removed outlier: 4.204A pdb=" N SER A 311 " --> pdb=" O LEU A 319 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU A 368 " --> pdb=" O ARG A 348 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG A 348 " --> pdb=" O GLU A 368 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'A' and resid 335 through 339 removed outlier: 3.657A pdb=" N TRP A 389 " --> pdb=" O SER A 374 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'C' and resid 21 through 26 Processing sheet with id=15, first strand: chain 'C' and resid 41 through 45 removed outlier: 3.501A pdb=" N ILE C 141 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL C 158 " --> pdb=" O ILE C 141 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'C' and resid 49 through 50 Processing sheet with id=17, first strand: chain 'C' and resid 54 through 60 removed outlier: 5.495A pdb=" N THR C 55 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N VAL C 129 " --> pdb=" O THR C 55 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA C 203 " --> pdb=" O ILE C 268 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR C 266 " --> pdb=" O MET C 205 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'C' and resid 63 through 73 removed outlier: 5.493A pdb=" N ILE C 65 " --> pdb=" O GLN C 120 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N GLN C 120 " --> pdb=" O ILE C 65 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ASN C 67 " --> pdb=" O LYS C 118 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LYS C 118 " --> pdb=" O ASN C 67 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER C 112 " --> pdb=" O ARG C 73 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR C 115 " --> pdb=" O LYS C 93 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS C 93 " --> pdb=" O THR C 115 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'C' and resid 169 through 172 removed outlier: 3.766A pdb=" N THR C 178 " --> pdb=" O LYS C 289 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS C 289 " --> pdb=" O THR C 178 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'C' and resid 237 through 240 Processing sheet with id=21, first strand: chain 'C' and resid 304 through 306 removed outlier: 3.503A pdb=" N VAL C 322 " --> pdb=" O VAL C 363 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'C' and resid 336 through 338 removed outlier: 3.531A pdb=" N TRP C 389 " --> pdb=" O SER C 374 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.833A pdb=" N ASP E 10 " --> pdb=" O CYS E 30 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU E 41 " --> pdb=" O THR E 33 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR E 138 " --> pdb=" O GLN E 46 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N THR E 48 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LYS E 136 " --> pdb=" O THR E 48 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'E' and resid 20 through 26 removed outlier: 3.947A pdb=" N ARG E 284 " --> pdb=" O GLU E 182 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY E 180 " --> pdb=" O LYS E 286 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU E 181 " --> pdb=" O THR E 169 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR E 169 " --> pdb=" O LEU E 181 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'E' and resid 54 through 55 removed outlier: 3.668A pdb=" N LEU E 197 " --> pdb=" O TRP E 204 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TRP E 204 " --> pdb=" O LEU E 197 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ALA E 203 " --> pdb=" O ILE E 268 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N THR E 266 " --> pdb=" O MET E 205 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'E' and resid 59 through 72 removed outlier: 3.598A pdb=" N ILE E 61 " --> pdb=" O GLU E 123 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N GLU E 123 " --> pdb=" O ILE E 61 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLY E 63 " --> pdb=" O CYS E 121 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N CYS E 121 " --> pdb=" O GLY E 63 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ILE E 65 " --> pdb=" O PHE E 119 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N PHE E 119 " --> pdb=" O ILE E 65 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ASN E 67 " --> pdb=" O ALA E 117 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ALA E 117 " --> pdb=" O ASN E 67 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N THR E 69 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N THR E 115 " --> pdb=" O THR E 69 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ASP E 71 " --> pdb=" O LEU E 113 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU E 113 " --> pdb=" O ASP E 71 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'E' and resid 59 through 72 removed outlier: 3.598A pdb=" N ILE E 61 " --> pdb=" O GLU E 123 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N GLU E 123 " --> pdb=" O ILE E 61 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLY E 63 " --> pdb=" O CYS E 121 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N CYS E 121 " --> pdb=" O GLY E 63 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ILE E 65 " --> pdb=" O PHE E 119 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N PHE E 119 " --> pdb=" O ILE E 65 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ASN E 67 " --> pdb=" O ALA E 117 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ALA E 117 " --> pdb=" O ASN E 67 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N THR E 69 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N THR E 115 " --> pdb=" O THR E 69 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ASP E 71 " --> pdb=" O LEU E 113 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU E 113 " --> pdb=" O ASP E 71 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR E 95 " --> pdb=" O LEU E 113 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'E' and resid 172 through 173 removed outlier: 3.979A pdb=" N GLY E 177 " --> pdb=" O LEU E 173 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'E' and resid 239 through 241 removed outlier: 3.853A pdb=" N ALA E 241 " --> pdb=" O LYS E 245 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N LYS E 245 " --> pdb=" O ALA E 241 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'E' and resid 304 through 306 removed outlier: 3.650A pdb=" N VAL E 305 " --> pdb=" O GLU E 323 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'E' and resid 336 through 338 Processing sheet with id=32, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.530A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.557A pdb=" N ALA H 97 " --> pdb=" O HIS H 35 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=35, first strand: chain 'L' and resid 11 through 13 removed outlier: 5.833A pdb=" N LEU L 11 " --> pdb=" O GLU L 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=35 Processing sheet with id=36, first strand: chain 'L' and resid 30 through 31 removed outlier: 3.693A pdb=" N LYS L 36 " --> pdb=" O TRP L 31 " (cutoff:3.500A) Processing sheet with id=37, first strand: chain 'L' and resid 51 through 55 removed outlier: 6.745A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N TYR L 55 " --> pdb=" O LEU L 39 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU L 39 " --> pdb=" O TYR L 55 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN L 44 " --> pdb=" O LEU L 91 " (cutoff:3.500A) Processing sheet with id=38, first strand: chain 'O' and resid 23 through 26 Processing sheet with id=39, first strand: chain 'O' and resid 31 through 35 removed outlier: 3.852A pdb=" N LEU O 41 " --> pdb=" O THR O 33 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ALA O 35 " --> pdb=" O PRO O 39 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'O' and resid 31 through 35 removed outlier: 3.852A pdb=" N LEU O 41 " --> pdb=" O THR O 33 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ALA O 35 " --> pdb=" O PRO O 39 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'O' and resid 59 through 60 Processing sheet with id=42, first strand: chain 'O' and resid 63 through 72 removed outlier: 4.728A pdb=" N ILE O 68 " --> pdb=" O CYS O 116 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N CYS O 116 " --> pdb=" O ILE O 68 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N THR O 70 " --> pdb=" O VAL O 114 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL O 114 " --> pdb=" O THR O 70 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N SER O 72 " --> pdb=" O SER O 112 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N SER O 112 " --> pdb=" O SER O 72 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain 'O' and resid 63 through 72 removed outlier: 4.728A pdb=" N ILE O 68 " --> pdb=" O CYS O 116 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N CYS O 116 " --> pdb=" O ILE O 68 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N THR O 70 " --> pdb=" O VAL O 114 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL O 114 " --> pdb=" O THR O 70 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N SER O 72 " --> pdb=" O SER O 112 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N SER O 112 " --> pdb=" O SER O 72 " (cutoff:3.500A) Processing sheet with id=44, first strand: chain 'O' and resid 171 through 173 removed outlier: 3.635A pdb=" N ALA O 171 " --> pdb=" O LEU O 179 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU O 179 " --> pdb=" O ALA O 171 " (cutoff:3.500A) Processing sheet with id=45, first strand: chain 'O' and resid 194 through 195 Processing sheet with id=46, first strand: chain 'O' and resid 237 through 240 removed outlier: 3.705A pdb=" N GLU O 247 " --> pdb=" O LYS O 239 " (cutoff:3.500A) Processing sheet with id=47, first strand: chain 'O' and resid 298 through 299 removed outlier: 6.706A pdb=" N ALA O 298 " --> pdb=" O LYS O 332 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N CYS O 331 " --> pdb=" O VAL O 356 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'O' and resid 304 through 306 Processing sheet with id=49, first strand: chain 'O' and resid 311 through 312 removed outlier: 4.204A pdb=" N SER O 311 " --> pdb=" O LEU O 319 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU O 368 " --> pdb=" O ARG O 348 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG O 348 " --> pdb=" O GLU O 368 " (cutoff:3.500A) Processing sheet with id=50, first strand: chain 'O' and resid 335 through 339 removed outlier: 3.657A pdb=" N TRP O 389 " --> pdb=" O SER O 374 " (cutoff:3.500A) Processing sheet with id=51, first strand: chain 'Q' and resid 21 through 26 Processing sheet with id=52, first strand: chain 'Q' and resid 41 through 45 removed outlier: 3.501A pdb=" N ILE Q 141 " --> pdb=" O VAL Q 158 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL Q 158 " --> pdb=" O ILE Q 141 " (cutoff:3.500A) Processing sheet with id=53, first strand: chain 'Q' and resid 49 through 50 Processing sheet with id=54, first strand: chain 'Q' and resid 54 through 60 removed outlier: 5.495A pdb=" N THR Q 55 " --> pdb=" O VAL Q 129 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N VAL Q 129 " --> pdb=" O THR Q 55 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA Q 203 " --> pdb=" O ILE Q 268 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR Q 266 " --> pdb=" O MET Q 205 " (cutoff:3.500A) Processing sheet with id=55, first strand: chain 'Q' and resid 63 through 73 removed outlier: 5.493A pdb=" N ILE Q 65 " --> pdb=" O GLN Q 120 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N GLN Q 120 " --> pdb=" O ILE Q 65 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ASN Q 67 " --> pdb=" O LYS Q 118 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LYS Q 118 " --> pdb=" O ASN Q 67 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER Q 112 " --> pdb=" O ARG Q 73 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR Q 115 " --> pdb=" O LYS Q 93 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS Q 93 " --> pdb=" O THR Q 115 " (cutoff:3.500A) Processing sheet with id=56, first strand: chain 'Q' and resid 169 through 172 removed outlier: 3.766A pdb=" N THR Q 178 " --> pdb=" O LYS Q 289 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS Q 289 " --> pdb=" O THR Q 178 " (cutoff:3.500A) Processing sheet with id=57, first strand: chain 'Q' and resid 237 through 240 Processing sheet with id=58, first strand: chain 'Q' and resid 304 through 306 removed outlier: 3.503A pdb=" N VAL Q 322 " --> pdb=" O VAL Q 363 " (cutoff:3.500A) Processing sheet with id=59, first strand: chain 'Q' and resid 336 through 338 removed outlier: 3.531A pdb=" N TRP Q 389 " --> pdb=" O SER Q 374 " (cutoff:3.500A) Processing sheet with id=60, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.833A pdb=" N ASP S 10 " --> pdb=" O CYS S 30 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU S 41 " --> pdb=" O THR S 33 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR S 138 " --> pdb=" O GLN S 46 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N THR S 48 " --> pdb=" O LYS S 136 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LYS S 136 " --> pdb=" O THR S 48 " (cutoff:3.500A) Processing sheet with id=61, first strand: chain 'S' and resid 20 through 26 removed outlier: 3.947A pdb=" N ARG S 284 " --> pdb=" O GLU S 182 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY S 180 " --> pdb=" O LYS S 286 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU S 181 " --> pdb=" O THR S 169 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR S 169 " --> pdb=" O LEU S 181 " (cutoff:3.500A) Processing sheet with id=62, first strand: chain 'S' and resid 54 through 55 removed outlier: 3.668A pdb=" N LEU S 197 " --> pdb=" O TRP S 204 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TRP S 204 " --> pdb=" O LEU S 197 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ALA S 203 " --> pdb=" O ILE S 268 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N THR S 266 " --> pdb=" O MET S 205 " (cutoff:3.500A) Processing sheet with id=63, first strand: chain 'S' and resid 59 through 72 removed outlier: 3.598A pdb=" N ILE S 61 " --> pdb=" O GLU S 123 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N GLU S 123 " --> pdb=" O ILE S 61 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLY S 63 " --> pdb=" O CYS S 121 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N CYS S 121 " --> pdb=" O GLY S 63 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ILE S 65 " --> pdb=" O PHE S 119 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N PHE S 119 " --> pdb=" O ILE S 65 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ASN S 67 " --> pdb=" O ALA S 117 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ALA S 117 " --> pdb=" O ASN S 67 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N THR S 69 " --> pdb=" O THR S 115 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N THR S 115 " --> pdb=" O THR S 69 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ASP S 71 " --> pdb=" O LEU S 113 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU S 113 " --> pdb=" O ASP S 71 " (cutoff:3.500A) Processing sheet with id=64, first strand: chain 'S' and resid 59 through 72 removed outlier: 3.598A pdb=" N ILE S 61 " --> pdb=" O GLU S 123 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N GLU S 123 " --> pdb=" O ILE S 61 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLY S 63 " --> pdb=" O CYS S 121 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N CYS S 121 " --> pdb=" O GLY S 63 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ILE S 65 " --> pdb=" O PHE S 119 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N PHE S 119 " --> pdb=" O ILE S 65 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ASN S 67 " --> pdb=" O ALA S 117 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ALA S 117 " --> pdb=" O ASN S 67 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N THR S 69 " --> pdb=" O THR S 115 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N THR S 115 " --> pdb=" O THR S 69 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ASP S 71 " --> pdb=" O LEU S 113 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU S 113 " --> pdb=" O ASP S 71 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR S 95 " --> pdb=" O LEU S 113 " (cutoff:3.500A) Processing sheet with id=65, first strand: chain 'S' and resid 172 through 173 removed outlier: 3.979A pdb=" N GLY S 177 " --> pdb=" O LEU S 173 " (cutoff:3.500A) Processing sheet with id=66, first strand: chain 'S' and resid 239 through 241 removed outlier: 3.853A pdb=" N ALA S 241 " --> pdb=" O LYS S 245 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N LYS S 245 " --> pdb=" O ALA S 241 " (cutoff:3.500A) Processing sheet with id=67, first strand: chain 'S' and resid 304 through 306 removed outlier: 3.650A pdb=" N VAL S 305 " --> pdb=" O GLU S 323 " (cutoff:3.500A) Processing sheet with id=68, first strand: chain 'S' and resid 336 through 338 Processing sheet with id=69, first strand: chain 'U' and resid 3 through 7 removed outlier: 3.530A pdb=" N THR U 78 " --> pdb=" O ASP U 73 " (cutoff:3.500A) Processing sheet with id=70, first strand: chain 'U' and resid 11 through 12 removed outlier: 3.557A pdb=" N ALA U 97 " --> pdb=" O HIS U 35 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N TRP U 36 " --> pdb=" O VAL U 48 " (cutoff:3.500A) Processing sheet with id=71, first strand: chain 'V' and resid 5 through 6 Processing sheet with id=72, first strand: chain 'V' and resid 11 through 13 removed outlier: 5.833A pdb=" N LEU V 11 " --> pdb=" O GLU V 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=72 Processing sheet with id=73, first strand: chain 'V' and resid 30 through 31 removed outlier: 3.693A pdb=" N LYS V 36 " --> pdb=" O TRP V 31 " (cutoff:3.500A) Processing sheet with id=74, first strand: chain 'V' and resid 51 through 55 removed outlier: 6.745A pdb=" N TRP V 41 " --> pdb=" O LEU V 53 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N TYR V 55 " --> pdb=" O LEU V 39 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU V 39 " --> pdb=" O TYR V 55 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN V 44 " --> pdb=" O LEU V 91 " (cutoff:3.500A) 1120 hydrogen bonds defined for protein. 3036 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: 10.63 Time building geometry restraints manager: 12.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 9622 1.35 - 1.48: 7550 1.48 - 1.60: 13324 1.60 - 1.73: 0 1.73 - 1.85: 318 Bond restraints: 30814 Sorted by residual: bond pdb=" C1 BMA Y 5 " pdb=" O5 BMA Y 5 " ideal model delta sigma weight residual 1.410 1.451 -0.041 2.00e-02 2.50e+03 4.21e+00 bond pdb=" C1 BMA J 5 " pdb=" O5 BMA J 5 " ideal model delta sigma weight residual 1.410 1.451 -0.041 2.00e-02 2.50e+03 4.21e+00 bond pdb=" C1 BMA J 5 " pdb=" C2 BMA J 5 " ideal model delta sigma weight residual 1.519 1.559 -0.040 2.00e-02 2.50e+03 3.96e+00 bond pdb=" C1 BMA Y 5 " pdb=" C2 BMA Y 5 " ideal model delta sigma weight residual 1.519 1.559 -0.040 2.00e-02 2.50e+03 3.96e+00 bond pdb=" C5 MAN G 4 " pdb=" O5 MAN G 4 " ideal model delta sigma weight residual 1.418 1.455 -0.037 2.00e-02 2.50e+03 3.33e+00 ... (remaining 30809 not shown) Histogram of bond angle deviations from ideal: 99.44 - 106.36: 782 106.36 - 113.28: 17688 113.28 - 120.20: 9968 120.20 - 127.12: 12932 127.12 - 134.05: 406 Bond angle restraints: 41776 Sorted by residual: angle pdb=" CA PRO C 330 " pdb=" C PRO C 330 " pdb=" N CYS C 331 " ideal model delta sigma weight residual 114.58 118.44 -3.86 1.16e+00 7.43e-01 1.10e+01 angle pdb=" CA PRO Q 330 " pdb=" C PRO Q 330 " pdb=" N CYS Q 331 " ideal model delta sigma weight residual 114.58 118.44 -3.86 1.16e+00 7.43e-01 1.10e+01 angle pdb=" C LEU Q 292 " pdb=" N LYS Q 293 " pdb=" CA LYS Q 293 " ideal model delta sigma weight residual 121.54 127.49 -5.95 1.91e+00 2.74e-01 9.70e+00 angle pdb=" C LEU C 292 " pdb=" N LYS C 293 " pdb=" CA LYS C 293 " ideal model delta sigma weight residual 121.54 127.49 -5.95 1.91e+00 2.74e-01 9.70e+00 angle pdb=" N GLY L 107 " pdb=" CA GLY L 107 " pdb=" C GLY L 107 " ideal model delta sigma weight residual 110.97 115.66 -4.69 1.56e+00 4.11e-01 9.04e+00 ... (remaining 41771 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.79: 17696 23.79 - 47.57: 798 47.57 - 71.36: 136 71.36 - 95.15: 92 95.15 - 118.94: 56 Dihedral angle restraints: 18778 sinusoidal: 7840 harmonic: 10938 Sorted by residual: dihedral pdb=" CB CYS O 3 " pdb=" SG CYS O 3 " pdb=" SG CYS O 30 " pdb=" CB CYS O 30 " ideal model delta sinusoidal sigma weight residual -86.00 -165.42 79.42 1 1.00e+01 1.00e-02 7.84e+01 dihedral pdb=" CB CYS A 3 " pdb=" SG CYS A 3 " pdb=" SG CYS A 30 " pdb=" CB CYS A 30 " ideal model delta sinusoidal sigma weight residual -86.00 -165.42 79.42 1 1.00e+01 1.00e-02 7.84e+01 dihedral pdb=" CB CYS A 60 " pdb=" SG CYS A 60 " pdb=" SG CYS A 121 " pdb=" CB CYS A 121 " ideal model delta sinusoidal sigma weight residual -86.00 -27.97 -58.03 1 1.00e+01 1.00e-02 4.52e+01 ... (remaining 18775 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 4056 0.056 - 0.111: 742 0.111 - 0.167: 112 0.167 - 0.223: 6 0.223 - 0.278: 12 Chirality restraints: 4928 Sorted by residual: chirality pdb=" C5 BMA J 5 " pdb=" C4 BMA J 5 " pdb=" C6 BMA J 5 " pdb=" O5 BMA J 5 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" C5 BMA Y 5 " pdb=" C4 BMA Y 5 " pdb=" C6 BMA Y 5 " pdb=" O5 BMA Y 5 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" C5 BMA W 5 " pdb=" C4 BMA W 5 " pdb=" C6 BMA W 5 " pdb=" O5 BMA W 5 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 4925 not shown) Planarity restraints: 5204 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 57 " -0.181 9.50e-02 1.11e+02 8.13e-02 4.15e+00 pdb=" NE ARG A 57 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 57 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 57 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 57 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG O 57 " -0.181 9.50e-02 1.11e+02 8.13e-02 4.15e+00 pdb=" NE ARG O 57 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG O 57 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG O 57 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG O 57 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR E 163 " 0.032 5.00e-02 4.00e+02 4.81e-02 3.71e+00 pdb=" N PRO E 164 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO E 164 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 164 " 0.027 5.00e-02 4.00e+02 ... (remaining 5201 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 659 2.68 - 3.24: 29533 3.24 - 3.79: 44634 3.79 - 4.35: 57553 4.35 - 4.90: 97718 Nonbonded interactions: 230097 Sorted by model distance: nonbonded pdb=" OG1 THR C 48 " pdb=" O ILE C 276 " model vdw 2.130 2.440 nonbonded pdb=" OG1 THR Q 48 " pdb=" O ILE Q 276 " model vdw 2.130 2.440 nonbonded pdb=" OG SER O 167 " pdb=" O CYS O 183 " model vdw 2.131 2.440 nonbonded pdb=" OG SER A 167 " pdb=" O CYS A 183 " model vdw 2.131 2.440 nonbonded pdb=" OD1 ASP H 62 " pdb=" O3 MAN J 4 " model vdw 2.146 2.440 ... (remaining 230092 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 'K' selection = chain 'M' selection = chain 'Z' } ncs_group { reference = chain '1' selection = chain 'I' selection = chain 'N' selection = chain 'X' } 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: 0.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.030 Check model and map are aligned: 0.220 Set scattering table: 0.270 Process input model: 74.920 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.240 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 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 0.044 30814 Z= 0.269 Angle : 0.758 9.679 41776 Z= 0.423 Chirality : 0.046 0.278 4928 Planarity : 0.004 0.081 5192 Dihedral : 16.432 118.936 11704 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % 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: -1.68 (0.13), residues: 3846 helix: 1.02 (0.18), residues: 850 sheet: -1.82 (0.16), residues: 998 loop : -1.69 (0.13), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 20 HIS 0.005 0.001 HIS E 259 PHE 0.020 0.001 PHE P 42 TYR 0.011 0.001 TYR F 52 ARG 0.006 0.000 ARG A 57 *********************** 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 1306 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1306 time to evaluate : 3.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO B 72 " (corrupted residue). Skipping it. Corrupt residue: chain: B residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO P 72 " (corrupted residue). Skipping it. Corrupt residue: chain: P residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.7788 (t) cc_final: 0.7511 (p) REVERT: A 38 LYS cc_start: 0.9235 (mmtt) cc_final: 0.8959 (mmtm) REVERT: A 61 ILE cc_start: 0.8089 (pt) cc_final: 0.7682 (pt) REVERT: A 82 LEU cc_start: 0.8554 (mt) cc_final: 0.8080 (mm) REVERT: A 98 ASP cc_start: 0.8157 (p0) cc_final: 0.7808 (p0) REVERT: A 201 ASN cc_start: 0.6616 (m-40) cc_final: 0.6263 (t0) REVERT: A 234 LEU cc_start: 0.8560 (mt) cc_final: 0.8322 (mp) REVERT: A 287 MET cc_start: 0.8176 (mtp) cc_final: 0.7941 (mtp) REVERT: A 400 PHE cc_start: 0.7321 (m-10) cc_final: 0.6942 (m-10) REVERT: A 453 MET cc_start: 0.7699 (tpt) cc_final: 0.7333 (tpp) REVERT: B 26 TRP cc_start: 0.6803 (m100) cc_final: 0.6586 (m-90) REVERT: B 45 LEU cc_start: 0.8971 (tp) cc_final: 0.8386 (tt) REVERT: B 74 MET cc_start: 0.5698 (mmp) cc_final: 0.4684 (mmp) REVERT: C 15 LEU cc_start: 0.7984 (pp) cc_final: 0.7648 (pt) REVERT: C 26 GLU cc_start: 0.7794 (tt0) cc_final: 0.7515 (tt0) REVERT: C 131 GLN cc_start: 0.7757 (mt0) cc_final: 0.7379 (mt0) REVERT: C 400 PHE cc_start: 0.8133 (m-10) cc_final: 0.7499 (t80) REVERT: C 443 THR cc_start: 0.8300 (m) cc_final: 0.7968 (p) REVERT: D 14 THR cc_start: 0.8262 (p) cc_final: 0.7805 (m) REVERT: D 65 ILE cc_start: 0.9369 (mm) cc_final: 0.9150 (mm) REVERT: E 42 ASP cc_start: 0.8353 (m-30) cc_final: 0.8085 (m-30) REVERT: E 184 SER cc_start: 0.8968 (t) cc_final: 0.8726 (m) REVERT: E 199 MET cc_start: 0.8301 (ttp) cc_final: 0.8077 (ttm) REVERT: E 251 LEU cc_start: 0.8428 (tt) cc_final: 0.8041 (tt) REVERT: E 293 LYS cc_start: 0.8495 (ttpp) cc_final: 0.8230 (tttm) REVERT: E 409 ARG cc_start: 0.8720 (ttm110) cc_final: 0.8517 (ttm-80) REVERT: E 436 GLN cc_start: 0.7979 (mt0) cc_final: 0.7589 (mt0) REVERT: E 442 TYR cc_start: 0.8829 (t80) cc_final: 0.8305 (t80) REVERT: E 447 SER cc_start: 0.8992 (t) cc_final: 0.8731 (t) REVERT: E 484 THR cc_start: 0.8923 (m) cc_final: 0.8553 (p) REVERT: F 12 LEU cc_start: 0.8017 (pp) cc_final: 0.7760 (pp) REVERT: F 16 THR cc_start: 0.8846 (t) cc_final: 0.8586 (m) REVERT: F 32 VAL cc_start: 0.9054 (t) cc_final: 0.8789 (t) REVERT: H 57 ASP cc_start: 0.7357 (t0) cc_final: 0.7005 (t0) REVERT: H 94 TYR cc_start: 0.8314 (m-10) cc_final: 0.7633 (m-80) REVERT: H 110 ASP cc_start: 0.7907 (m-30) cc_final: 0.7675 (m-30) REVERT: L 2 ILE cc_start: 0.8898 (mt) cc_final: 0.8530 (mt) REVERT: L 55 TYR cc_start: 0.8512 (p90) cc_final: 0.8149 (p90) REVERT: O 6 VAL cc_start: 0.7813 (t) cc_final: 0.7543 (p) REVERT: O 38 LYS cc_start: 0.9235 (mmtt) cc_final: 0.8963 (mmtm) REVERT: O 61 ILE cc_start: 0.8075 (pt) cc_final: 0.7676 (pt) REVERT: O 82 LEU cc_start: 0.8520 (mt) cc_final: 0.8052 (mm) REVERT: O 98 ASP cc_start: 0.8157 (p0) cc_final: 0.7806 (p0) REVERT: O 201 ASN cc_start: 0.6575 (m-40) cc_final: 0.6231 (t0) REVERT: O 287 MET cc_start: 0.8173 (mtp) cc_final: 0.7962 (mtp) REVERT: O 400 PHE cc_start: 0.7312 (m-10) cc_final: 0.6912 (m-10) REVERT: O 453 MET cc_start: 0.7706 (tpt) cc_final: 0.7309 (tpp) REVERT: P 26 TRP cc_start: 0.6784 (m100) cc_final: 0.6577 (m-90) REVERT: P 45 LEU cc_start: 0.8975 (tp) cc_final: 0.8403 (tt) REVERT: P 74 MET cc_start: 0.5723 (mmp) cc_final: 0.4290 (mmp) REVERT: Q 15 LEU cc_start: 0.7990 (pp) cc_final: 0.7661 (pt) REVERT: Q 26 GLU cc_start: 0.7782 (tt0) cc_final: 0.7506 (tt0) REVERT: Q 131 GLN cc_start: 0.7758 (mt0) cc_final: 0.7354 (mt0) REVERT: Q 182 GLU cc_start: 0.6552 (tt0) cc_final: 0.6338 (tp30) REVERT: Q 400 PHE cc_start: 0.8139 (m-10) cc_final: 0.7500 (t80) REVERT: Q 443 THR cc_start: 0.8308 (m) cc_final: 0.7970 (p) REVERT: R 14 THR cc_start: 0.8272 (p) cc_final: 0.7817 (m) REVERT: R 35 TRP cc_start: 0.9005 (t60) cc_final: 0.8797 (t60) REVERT: R 65 ILE cc_start: 0.9372 (mm) cc_final: 0.9159 (mm) REVERT: S 36 LYS cc_start: 0.8432 (tptt) cc_final: 0.8155 (tppt) REVERT: S 42 ASP cc_start: 0.8344 (m-30) cc_final: 0.8077 (m-30) REVERT: S 184 SER cc_start: 0.8967 (t) cc_final: 0.8730 (m) REVERT: S 251 LEU cc_start: 0.8427 (tt) cc_final: 0.8034 (tt) REVERT: S 293 LYS cc_start: 0.8572 (ttpp) cc_final: 0.8353 (tttt) REVERT: S 436 GLN cc_start: 0.7975 (mt0) cc_final: 0.7593 (mt0) REVERT: S 442 TYR cc_start: 0.8838 (t80) cc_final: 0.8311 (t80) REVERT: S 447 SER cc_start: 0.8994 (t) cc_final: 0.8733 (t) REVERT: S 484 THR cc_start: 0.8927 (m) cc_final: 0.8565 (p) REVERT: T 12 LEU cc_start: 0.8004 (pp) cc_final: 0.7745 (pp) REVERT: T 16 THR cc_start: 0.8819 (t) cc_final: 0.8565 (m) REVERT: T 32 VAL cc_start: 0.9057 (t) cc_final: 0.8798 (t) REVERT: U 57 ASP cc_start: 0.7355 (t0) cc_final: 0.7047 (t0) REVERT: U 94 TYR cc_start: 0.8319 (m-10) cc_final: 0.7642 (m-80) REVERT: U 110 ASP cc_start: 0.7897 (m-30) cc_final: 0.7667 (m-30) REVERT: V 2 ILE cc_start: 0.8899 (mt) cc_final: 0.8532 (mt) REVERT: V 55 TYR cc_start: 0.8515 (p90) cc_final: 0.8151 (p90) outliers start: 0 outliers final: 0 residues processed: 1306 average time/residue: 0.4213 time to fit residues: 854.5700 Evaluate side-chains 874 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 874 time to evaluate : 3.248 ------------------------------------------------------------------------------- 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: 20.0000 chunk 160 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 chunk 195 optimal weight: 0.9980 chunk 154 optimal weight: 0.0000 chunk 299 optimal weight: 6.9990 chunk 115 optimal weight: 30.0000 chunk 182 optimal weight: 20.0000 chunk 222 optimal weight: 9.9990 chunk 346 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN ** D 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 GLN E 428 ASN ** F 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 GLN ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 44 GLN L 99 HIS ** O 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 302 ASN ** Q 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 388 ASN ** R 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 314 GLN S 428 ASN ** T 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 100 GLN ** V 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 44 GLN V 85 GLN V 99 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 30814 Z= 0.279 Angle : 0.701 9.740 41776 Z= 0.356 Chirality : 0.045 0.230 4928 Planarity : 0.004 0.051 5192 Dihedral : 13.676 113.620 4876 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 4.28 % Allowed : 13.59 % Favored : 82.12 % 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: -1.69 (0.13), residues: 3846 helix: 0.97 (0.18), residues: 882 sheet: -1.72 (0.15), residues: 1086 loop : -1.75 (0.13), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 20 HIS 0.006 0.001 HIS O 94 PHE 0.022 0.002 PHE P 42 TYR 0.018 0.002 TYR U 111 ARG 0.006 0.001 ARG S 2 *********************** 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 1023 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 885 time to evaluate : 3.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO B 72 " (corrupted residue). Skipping it. Corrupt residue: chain: B residue: PRO 72 >>> skipping 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 TARDY: cannot create tardy model for: "PRO P 72 " (corrupted residue). Skipping it. Corrupt residue: chain: P residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.7765 (t) cc_final: 0.7532 (p) REVERT: A 38 LYS cc_start: 0.9218 (mmtt) cc_final: 0.9014 (mmtm) REVERT: A 82 LEU cc_start: 0.8725 (mt) cc_final: 0.8495 (mm) REVERT: A 98 ASP cc_start: 0.8106 (p0) cc_final: 0.7827 (p0) REVERT: A 181 LEU cc_start: 0.8396 (tp) cc_final: 0.7942 (tp) REVERT: A 287 MET cc_start: 0.8176 (mtp) cc_final: 0.7832 (mtp) REVERT: A 299 MET cc_start: 0.6802 (mmm) cc_final: 0.5508 (mtm) REVERT: B 26 TRP cc_start: 0.6606 (m100) cc_final: 0.6234 (m-90) REVERT: B 28 GLN cc_start: 0.8115 (tp-100) cc_final: 0.7643 (tp40) REVERT: B 45 LEU cc_start: 0.8885 (tp) cc_final: 0.8331 (tt) REVERT: B 61 VAL cc_start: 0.9252 (t) cc_final: 0.9045 (p) REVERT: C 182 GLU cc_start: 0.6806 (tp30) cc_final: 0.6480 (tp30) REVERT: C 199 MET cc_start: 0.8210 (ptm) cc_final: 0.7999 (ptm) REVERT: C 380 ILE cc_start: 0.7862 (OUTLIER) cc_final: 0.7647 (tt) REVERT: C 400 PHE cc_start: 0.7764 (m-10) cc_final: 0.7464 (t80) REVERT: C 443 THR cc_start: 0.8383 (m) cc_final: 0.8064 (p) REVERT: C 480 ILE cc_start: 0.8119 (mm) cc_final: 0.7907 (mm) REVERT: D 14 THR cc_start: 0.8327 (p) cc_final: 0.7831 (m) REVERT: D 74 MET cc_start: 0.8033 (tpp) cc_final: 0.7435 (mmm) REVERT: E 8 ASN cc_start: 0.7621 (t0) cc_final: 0.7352 (t0) REVERT: E 108 PHE cc_start: 0.8529 (m-80) cc_final: 0.8151 (m-80) REVERT: E 199 MET cc_start: 0.8300 (ttp) cc_final: 0.8043 (ttm) REVERT: E 251 LEU cc_start: 0.8269 (tt) cc_final: 0.7744 (tt) REVERT: E 295 MET cc_start: 0.7426 (tpt) cc_final: 0.6125 (tmm) REVERT: E 335 PHE cc_start: 0.8047 (OUTLIER) cc_final: 0.6573 (m-80) REVERT: E 484 THR cc_start: 0.8938 (m) cc_final: 0.8576 (p) REVERT: F 13 ASP cc_start: 0.7081 (p0) cc_final: 0.6784 (m-30) REVERT: F 16 THR cc_start: 0.8887 (t) cc_final: 0.8629 (m) REVERT: F 37 LEU cc_start: 0.8824 (tp) cc_final: 0.8572 (mt) REVERT: H 37 LEU cc_start: 0.8798 (mt) cc_final: 0.8560 (mt) REVERT: H 47 TRP cc_start: 0.8050 (t60) cc_final: 0.7656 (t60) REVERT: H 110 ASP cc_start: 0.7842 (m-30) cc_final: 0.7595 (m-30) REVERT: H 117 LEU cc_start: 0.7784 (tt) cc_final: 0.7359 (tp) REVERT: L 2 ILE cc_start: 0.8606 (mt) cc_final: 0.8389 (mt) REVERT: L 48 GLN cc_start: 0.6363 (mp10) cc_final: 0.5852 (mp10) REVERT: L 55 TYR cc_start: 0.8509 (p90) cc_final: 0.8227 (p90) REVERT: L 93 TYR cc_start: 0.8801 (m-10) cc_final: 0.8291 (m-10) REVERT: L 109 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.8047 (mtp85) REVERT: O 6 VAL cc_start: 0.7776 (t) cc_final: 0.7555 (p) REVERT: O 82 LEU cc_start: 0.8708 (mt) cc_final: 0.8450 (mm) REVERT: O 98 ASP cc_start: 0.8099 (p0) cc_final: 0.7824 (p0) REVERT: O 181 LEU cc_start: 0.8440 (tp) cc_final: 0.7965 (tp) REVERT: O 201 ASN cc_start: 0.6760 (m-40) cc_final: 0.6280 (t0) REVERT: O 287 MET cc_start: 0.8182 (mtp) cc_final: 0.7848 (mtp) REVERT: O 299 MET cc_start: 0.6795 (mmm) cc_final: 0.5492 (mtm) REVERT: P 26 TRP cc_start: 0.6592 (m100) cc_final: 0.6236 (m-90) REVERT: P 28 GLN cc_start: 0.8120 (tp-100) cc_final: 0.7217 (tp40) REVERT: Q 182 GLU cc_start: 0.6445 (tt0) cc_final: 0.6225 (tp30) REVERT: Q 199 MET cc_start: 0.8220 (ptm) cc_final: 0.7989 (ptm) REVERT: Q 220 SER cc_start: 0.7749 (p) cc_final: 0.7501 (p) REVERT: Q 380 ILE cc_start: 0.7861 (OUTLIER) cc_final: 0.7648 (tt) REVERT: Q 400 PHE cc_start: 0.7770 (m-10) cc_final: 0.7470 (t80) REVERT: Q 443 THR cc_start: 0.8396 (m) cc_final: 0.8045 (p) REVERT: Q 480 ILE cc_start: 0.8112 (mm) cc_final: 0.7902 (mm) REVERT: R 14 THR cc_start: 0.8350 (p) cc_final: 0.7837 (m) REVERT: R 35 TRP cc_start: 0.9022 (t60) cc_final: 0.8796 (t60) REVERT: R 74 MET cc_start: 0.8051 (tpp) cc_final: 0.7582 (mmm) REVERT: S 108 PHE cc_start: 0.8514 (m-80) cc_final: 0.8190 (m-80) REVERT: S 251 LEU cc_start: 0.8265 (tt) cc_final: 0.7749 (tt) REVERT: S 295 MET cc_start: 0.7481 (tpt) cc_final: 0.6136 (tmm) REVERT: S 335 PHE cc_start: 0.7957 (OUTLIER) cc_final: 0.6833 (m-80) REVERT: S 447 SER cc_start: 0.8960 (t) cc_final: 0.8661 (t) REVERT: S 484 THR cc_start: 0.8945 (m) cc_final: 0.8578 (p) REVERT: T 13 ASP cc_start: 0.7069 (p0) cc_final: 0.6769 (m-30) REVERT: T 16 THR cc_start: 0.8845 (t) cc_final: 0.8621 (m) REVERT: T 32 VAL cc_start: 0.9054 (t) cc_final: 0.8846 (t) REVERT: U 37 LEU cc_start: 0.8801 (mt) cc_final: 0.8561 (mt) REVERT: U 47 TRP cc_start: 0.8049 (t60) cc_final: 0.7656 (t60) REVERT: U 110 ASP cc_start: 0.7828 (m-30) cc_final: 0.7566 (m-30) REVERT: U 117 LEU cc_start: 0.7785 (tt) cc_final: 0.7355 (tp) REVERT: V 2 ILE cc_start: 0.8604 (mt) cc_final: 0.8391 (mt) REVERT: V 48 GLN cc_start: 0.6384 (mp10) cc_final: 0.5860 (mp10) REVERT: V 55 TYR cc_start: 0.8512 (p90) cc_final: 0.8232 (p90) REVERT: V 93 TYR cc_start: 0.8806 (m-10) cc_final: 0.8292 (m-10) REVERT: V 109 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.8049 (mtp85) outliers start: 138 outliers final: 93 residues processed: 963 average time/residue: 0.3737 time to fit residues: 587.4988 Evaluate side-chains 908 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 809 time to evaluate : 3.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 318 ILE Chi-restraints excluded: chain E residue 335 PHE Chi-restraints excluded: chain E residue 451 TRP Chi-restraints excluded: chain E residue 455 ILE Chi-restraints excluded: chain E residue 468 SER Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain L residue 109 ARG Chi-restraints excluded: chain O residue 26 GLU Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 51 THR Chi-restraints excluded: chain O residue 187 THR Chi-restraints excluded: chain O residue 198 THR Chi-restraints excluded: chain O residue 237 THR Chi-restraints excluded: chain O residue 253 SER Chi-restraints excluded: chain O residue 275 SER Chi-restraints excluded: chain O residue 286 LYS Chi-restraints excluded: chain O residue 337 THR Chi-restraints excluded: chain O residue 365 ILE Chi-restraints excluded: chain O residue 413 LEU Chi-restraints excluded: chain O residue 423 VAL Chi-restraints excluded: chain O residue 455 ILE Chi-restraints excluded: chain O residue 459 VAL Chi-restraints excluded: chain O residue 461 LEU Chi-restraints excluded: chain O residue 466 LEU Chi-restraints excluded: chain P residue 14 THR Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 73 SER Chi-restraints excluded: chain Q residue 43 ILE Chi-restraints excluded: chain Q residue 48 THR Chi-restraints excluded: chain Q residue 113 LEU Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain Q residue 313 THR Chi-restraints excluded: chain Q residue 357 THR Chi-restraints excluded: chain Q residue 380 ILE Chi-restraints excluded: chain Q residue 491 VAL Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 41 LEU Chi-restraints excluded: chain S residue 64 LYS Chi-restraints excluded: chain S residue 142 THR Chi-restraints excluded: chain S residue 179 LEU Chi-restraints excluded: chain S residue 181 LEU Chi-restraints excluded: chain S residue 187 THR Chi-restraints excluded: chain S residue 258 MET Chi-restraints excluded: chain S residue 266 THR Chi-restraints excluded: chain S residue 318 ILE Chi-restraints excluded: chain S residue 335 PHE Chi-restraints excluded: chain S residue 451 TRP Chi-restraints excluded: chain S residue 455 ILE Chi-restraints excluded: chain S residue 468 SER Chi-restraints excluded: chain S residue 485 LEU Chi-restraints excluded: chain T residue 8 VAL Chi-restraints excluded: chain T residue 14 THR Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 17 SER Chi-restraints excluded: chain U residue 63 SER Chi-restraints excluded: chain U residue 118 VAL Chi-restraints excluded: chain V residue 109 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 192 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 288 optimal weight: 20.0000 chunk 236 optimal weight: 5.9990 chunk 95 optimal weight: 20.0000 chunk 347 optimal weight: 20.0000 chunk 375 optimal weight: 2.9990 chunk 309 optimal weight: 9.9990 chunk 344 optimal weight: 4.9990 chunk 118 optimal weight: 10.0000 chunk 278 optimal weight: 4.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 144 HIS ** C 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN ** D 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 8 ASN ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 428 ASN H 100 GLN H 114 GLN L 27 GLN L 85 GLN Q 144 HIS ** Q 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 428 ASN ** T 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 39 HIS U 100 GLN U 114 GLN V 27 GLN V 85 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 30814 Z= 0.301 Angle : 0.706 9.843 41776 Z= 0.355 Chirality : 0.046 0.229 4928 Planarity : 0.004 0.045 5192 Dihedral : 11.799 115.028 4876 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 5.62 % Allowed : 16.29 % Favored : 78.09 % 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: -1.58 (0.13), residues: 3846 helix: 1.13 (0.18), residues: 870 sheet: -1.63 (0.15), residues: 1104 loop : -1.71 (0.13), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP S 20 HIS 0.007 0.001 HIS A 94 PHE 0.023 0.002 PHE D 64 TYR 0.020 0.002 TYR H 111 ARG 0.007 0.001 ARG E 409 *********************** 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 1010 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 829 time to evaluate : 3.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO B 72 " (corrupted residue). Skipping it. Corrupt residue: chain: B residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO P 72 " (corrupted residue). Skipping it. Corrupt residue: chain: P residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.7988 (t) cc_final: 0.7690 (p) REVERT: A 38 LYS cc_start: 0.9249 (mmtt) cc_final: 0.9026 (mmtm) REVERT: A 98 ASP cc_start: 0.8052 (p0) cc_final: 0.7793 (p0) REVERT: A 181 LEU cc_start: 0.8345 (tp) cc_final: 0.7957 (tp) REVERT: A 247 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7065 (pm20) REVERT: A 287 MET cc_start: 0.8202 (mtp) cc_final: 0.7893 (mtp) REVERT: A 299 MET cc_start: 0.6599 (mmm) cc_final: 0.5541 (mmm) REVERT: B 12 LEU cc_start: 0.6273 (OUTLIER) cc_final: 0.5784 (pp) REVERT: B 28 GLN cc_start: 0.8128 (tp-100) cc_final: 0.7255 (tp-100) REVERT: C 182 GLU cc_start: 0.7381 (tp30) cc_final: 0.6976 (tp30) REVERT: C 258 MET cc_start: 0.9073 (tpp) cc_final: 0.8709 (tpp) REVERT: C 380 ILE cc_start: 0.7862 (OUTLIER) cc_final: 0.7657 (tt) REVERT: C 389 TRP cc_start: 0.7604 (t-100) cc_final: 0.7119 (t-100) REVERT: C 400 PHE cc_start: 0.7750 (m-10) cc_final: 0.7483 (t80) REVERT: C 436 GLN cc_start: 0.8695 (tm-30) cc_final: 0.8225 (tt0) REVERT: C 480 ILE cc_start: 0.8225 (mm) cc_final: 0.8017 (mm) REVERT: D 42 PHE cc_start: 0.8707 (t80) cc_final: 0.8062 (t80) REVERT: D 74 MET cc_start: 0.8156 (tpp) cc_final: 0.7833 (mmm) REVERT: E 8 ASN cc_start: 0.7727 (t0) cc_final: 0.7237 (t0) REVERT: E 20 TRP cc_start: 0.7449 (p90) cc_final: 0.6120 (p90) REVERT: E 108 PHE cc_start: 0.8561 (m-80) cc_final: 0.8204 (m-80) REVERT: E 181 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8556 (pp) REVERT: E 251 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8305 (tp) REVERT: E 270 ASN cc_start: 0.6629 (t0) cc_final: 0.6423 (t0) REVERT: E 320 ILE cc_start: 0.9431 (mm) cc_final: 0.9117 (mt) REVERT: E 447 SER cc_start: 0.8946 (t) cc_final: 0.8719 (t) REVERT: E 484 THR cc_start: 0.8930 (m) cc_final: 0.8607 (p) REVERT: F 16 THR cc_start: 0.8839 (t) cc_final: 0.8628 (m) REVERT: H 47 TRP cc_start: 0.8113 (t60) cc_final: 0.7664 (t60) REVERT: H 114 GLN cc_start: 0.7759 (tp40) cc_final: 0.7320 (tp40) REVERT: L 45 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8293 (mttp) REVERT: L 48 GLN cc_start: 0.7051 (mp10) cc_final: 0.6440 (mp10) REVERT: L 109 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7768 (mtp85) REVERT: O 6 VAL cc_start: 0.7984 (t) cc_final: 0.7710 (p) REVERT: O 98 ASP cc_start: 0.8060 (p0) cc_final: 0.7784 (p0) REVERT: O 181 LEU cc_start: 0.8375 (tp) cc_final: 0.7991 (tp) REVERT: O 201 ASN cc_start: 0.6819 (m-40) cc_final: 0.6129 (t0) REVERT: O 247 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7106 (pm20) REVERT: O 287 MET cc_start: 0.8242 (mtp) cc_final: 0.7938 (mtp) REVERT: O 299 MET cc_start: 0.6579 (mmm) cc_final: 0.5509 (mmm) REVERT: O 460 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7668 (mp) REVERT: P 12 LEU cc_start: 0.6506 (OUTLIER) cc_final: 0.6101 (pp) REVERT: P 28 GLN cc_start: 0.7768 (tp-100) cc_final: 0.7415 (tp-100) REVERT: Q 258 MET cc_start: 0.9087 (tpp) cc_final: 0.8708 (tpp) REVERT: Q 380 ILE cc_start: 0.7857 (OUTLIER) cc_final: 0.7650 (tt) REVERT: Q 389 TRP cc_start: 0.7605 (t-100) cc_final: 0.7117 (t-100) REVERT: Q 400 PHE cc_start: 0.7753 (m-10) cc_final: 0.7491 (t80) REVERT: Q 436 GLN cc_start: 0.8701 (tm-30) cc_final: 0.8219 (tt0) REVERT: Q 480 ILE cc_start: 0.8213 (mm) cc_final: 0.8012 (mm) REVERT: R 35 TRP cc_start: 0.8994 (t60) cc_final: 0.8766 (t60) REVERT: R 42 PHE cc_start: 0.8720 (t80) cc_final: 0.8061 (t80) REVERT: R 74 MET cc_start: 0.8186 (tpp) cc_final: 0.7816 (mmm) REVERT: S 8 ASN cc_start: 0.7339 (t0) cc_final: 0.6794 (t0) REVERT: S 20 TRP cc_start: 0.7476 (p90) cc_final: 0.6131 (p90) REVERT: S 108 PHE cc_start: 0.8550 (m-80) cc_final: 0.8227 (m-80) REVERT: S 442 TYR cc_start: 0.8817 (t80) cc_final: 0.8281 (t80) REVERT: S 484 THR cc_start: 0.8938 (m) cc_final: 0.8593 (p) REVERT: T 16 THR cc_start: 0.8808 (t) cc_final: 0.8586 (m) REVERT: U 47 TRP cc_start: 0.8117 (t60) cc_final: 0.7670 (t60) REVERT: U 73 ASP cc_start: 0.8153 (p0) cc_final: 0.7908 (p0) REVERT: U 114 GLN cc_start: 0.7758 (tp40) cc_final: 0.7319 (tp40) REVERT: V 45 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8301 (mttp) REVERT: V 48 GLN cc_start: 0.7055 (mp10) cc_final: 0.6440 (mp10) REVERT: V 109 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7768 (mtp85) outliers start: 181 outliers final: 119 residues processed: 942 average time/residue: 0.3862 time to fit residues: 597.7562 Evaluate side-chains 903 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 771 time to evaluate : 3.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 451 TRP Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 242 HIS Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 255 GLU Chi-restraints excluded: chain E residue 258 MET Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 313 THR Chi-restraints excluded: chain E residue 318 ILE Chi-restraints excluded: chain E residue 451 TRP Chi-restraints excluded: chain E residue 468 SER Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 109 ARG Chi-restraints excluded: chain O residue 26 GLU Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 51 THR Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain O residue 121 CYS Chi-restraints excluded: chain O residue 130 VAL Chi-restraints excluded: chain O residue 187 THR Chi-restraints excluded: chain O residue 195 ILE Chi-restraints excluded: chain O residue 198 THR Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain O residue 237 THR Chi-restraints excluded: chain O residue 247 GLU Chi-restraints excluded: chain O residue 275 SER Chi-restraints excluded: chain O residue 286 LYS Chi-restraints excluded: chain O residue 365 ILE Chi-restraints excluded: chain O residue 413 LEU Chi-restraints excluded: chain O residue 423 VAL Chi-restraints excluded: chain O residue 429 SER Chi-restraints excluded: chain O residue 451 TRP Chi-restraints excluded: chain O residue 452 VAL Chi-restraints excluded: chain O residue 455 ILE Chi-restraints excluded: chain O residue 459 VAL Chi-restraints excluded: chain O residue 460 LEU Chi-restraints excluded: chain O residue 461 LEU Chi-restraints excluded: chain O residue 466 LEU Chi-restraints excluded: chain P residue 12 LEU Chi-restraints excluded: chain P residue 14 THR Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 73 SER Chi-restraints excluded: chain Q residue 10 ASP Chi-restraints excluded: chain Q residue 43 ILE Chi-restraints excluded: chain Q residue 48 THR Chi-restraints excluded: chain Q residue 113 LEU Chi-restraints excluded: chain Q residue 158 VAL Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain Q residue 313 THR Chi-restraints excluded: chain Q residue 357 THR Chi-restraints excluded: chain Q residue 358 LYS Chi-restraints excluded: chain Q residue 380 ILE Chi-restraints excluded: chain Q residue 466 LEU Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain S residue 41 LEU Chi-restraints excluded: chain S residue 64 LYS Chi-restraints excluded: chain S residue 79 GLU Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 179 LEU Chi-restraints excluded: chain S residue 181 LEU Chi-restraints excluded: chain S residue 187 THR Chi-restraints excluded: chain S residue 242 HIS Chi-restraints excluded: chain S residue 255 GLU Chi-restraints excluded: chain S residue 258 MET Chi-restraints excluded: chain S residue 266 THR Chi-restraints excluded: chain S residue 313 THR Chi-restraints excluded: chain S residue 318 ILE Chi-restraints excluded: chain S residue 451 TRP Chi-restraints excluded: chain S residue 468 SER Chi-restraints excluded: chain S residue 485 LEU Chi-restraints excluded: chain T residue 8 VAL Chi-restraints excluded: chain T residue 14 THR Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 17 SER Chi-restraints excluded: chain U residue 25 SER Chi-restraints excluded: chain U residue 53 SER Chi-restraints excluded: chain U residue 63 SER Chi-restraints excluded: chain U residue 83 MET Chi-restraints excluded: chain V residue 45 LYS Chi-restraints excluded: chain V residue 109 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 343 optimal weight: 6.9990 chunk 261 optimal weight: 30.0000 chunk 180 optimal weight: 20.0000 chunk 38 optimal weight: 20.0000 chunk 165 optimal weight: 20.0000 chunk 233 optimal weight: 10.0000 chunk 348 optimal weight: 9.9990 chunk 369 optimal weight: 8.9990 chunk 182 optimal weight: 7.9990 chunk 330 optimal weight: 20.0000 chunk 99 optimal weight: 6.9990 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 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN ** D 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 8 ASN ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 242 HIS E 246 GLN E 259 HIS E 302 ASN E 428 ASN F 39 HIS ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 GLN L 85 GLN O 86 GLN ** O 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 17 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 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 242 HIS S 246 GLN S 259 HIS ** T 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 100 GLN V 85 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 30814 Z= 0.389 Angle : 0.753 9.962 41776 Z= 0.377 Chirality : 0.047 0.283 4928 Planarity : 0.005 0.050 5192 Dihedral : 11.148 117.557 4876 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 6.92 % Allowed : 18.84 % Favored : 74.24 % 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: -1.75 (0.13), residues: 3846 helix: 0.95 (0.18), residues: 876 sheet: -1.72 (0.15), residues: 1106 loop : -1.81 (0.13), residues: 1864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP Q 218 HIS 0.010 0.002 HIS O 94 PHE 0.021 0.002 PHE T 48 TYR 0.021 0.002 TYR U 111 ARG 0.007 0.001 ARG O 9 *********************** 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 999 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 776 time to evaluate : 3.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO B 72 " (corrupted residue). Skipping it. Corrupt residue: chain: B residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO P 72 " (corrupted residue). Skipping it. Corrupt residue: chain: P residue: PRO 72 >>> skipping revert: symmetry clash REVERT: A 6 VAL cc_start: 0.8127 (t) cc_final: 0.7748 (p) REVERT: A 38 LYS cc_start: 0.9287 (mmtt) cc_final: 0.9041 (mmtm) REVERT: A 48 THR cc_start: 0.9021 (OUTLIER) cc_final: 0.8774 (t) REVERT: A 57 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.7157 (ttm110) REVERT: A 98 ASP cc_start: 0.8045 (p0) cc_final: 0.7741 (p0) REVERT: A 181 LEU cc_start: 0.8466 (tp) cc_final: 0.8046 (tp) REVERT: A 201 ASN cc_start: 0.6608 (m-40) cc_final: 0.5694 (t0) REVERT: A 238 PHE cc_start: 0.8803 (OUTLIER) cc_final: 0.8000 (m-10) REVERT: A 287 MET cc_start: 0.8265 (mtp) cc_final: 0.7856 (mtp) REVERT: A 299 MET cc_start: 0.6482 (mmm) cc_final: 0.5630 (mmm) REVERT: A 400 PHE cc_start: 0.7339 (m-10) cc_final: 0.7014 (m-10) REVERT: B 12 LEU cc_start: 0.6371 (OUTLIER) cc_final: 0.5774 (pp) REVERT: B 28 GLN cc_start: 0.7414 (tp-100) cc_final: 0.7137 (tp-100) REVERT: B 68 MET cc_start: 0.7912 (tpt) cc_final: 0.7654 (tpt) REVERT: C 23 VAL cc_start: 0.9208 (m) cc_final: 0.9003 (m) REVERT: C 182 GLU cc_start: 0.6975 (tp30) cc_final: 0.6736 (tp30) REVERT: C 213 ASP cc_start: 0.7540 (m-30) cc_final: 0.7305 (m-30) REVERT: C 258 MET cc_start: 0.9099 (tpp) cc_final: 0.8848 (tpp) REVERT: C 293 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8606 (pptt) REVERT: C 368 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8208 (pm20) REVERT: C 380 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7677 (tt) REVERT: C 400 PHE cc_start: 0.7771 (m-10) cc_final: 0.7509 (t80) REVERT: D 18 THR cc_start: 0.8839 (OUTLIER) cc_final: 0.8237 (t) REVERT: D 42 PHE cc_start: 0.8735 (t80) cc_final: 0.8160 (t80) REVERT: D 74 MET cc_start: 0.8332 (tpp) cc_final: 0.7811 (mmm) REVERT: E 8 ASN cc_start: 0.7872 (t0) cc_final: 0.7472 (t0) REVERT: E 20 TRP cc_start: 0.7606 (p90) cc_final: 0.6360 (p90) REVERT: E 108 PHE cc_start: 0.8635 (m-80) cc_final: 0.8287 (m-80) REVERT: E 176 TYR cc_start: 0.8777 (m-80) cc_final: 0.8418 (m-80) REVERT: E 181 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8672 (pp) REVERT: E 259 HIS cc_start: 0.8470 (OUTLIER) cc_final: 0.6713 (t-90) REVERT: E 320 ILE cc_start: 0.9423 (mm) cc_final: 0.9125 (mt) REVERT: E 410 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.7991 (mtp) REVERT: E 447 SER cc_start: 0.9186 (t) cc_final: 0.8431 (p) REVERT: E 484 THR cc_start: 0.8994 (m) cc_final: 0.8718 (p) REVERT: H 3 GLU cc_start: 0.6353 (mm-30) cc_final: 0.6067 (mm-30) REVERT: H 47 TRP cc_start: 0.8101 (t60) cc_final: 0.7496 (t60) REVERT: H 65 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7116 (mtmt) REVERT: H 73 ASP cc_start: 0.8153 (p0) cc_final: 0.7946 (p0) REVERT: H 114 GLN cc_start: 0.7762 (tp40) cc_final: 0.7263 (tp-100) REVERT: O 6 VAL cc_start: 0.8130 (t) cc_final: 0.7762 (p) REVERT: O 57 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.7201 (ttm110) REVERT: O 98 ASP cc_start: 0.8047 (p0) cc_final: 0.7755 (p0) REVERT: O 181 LEU cc_start: 0.8502 (tp) cc_final: 0.8105 (tp) REVERT: O 238 PHE cc_start: 0.8783 (OUTLIER) cc_final: 0.8060 (m-10) REVERT: O 287 MET cc_start: 0.8176 (mtp) cc_final: 0.7849 (mtp) REVERT: O 299 MET cc_start: 0.6468 (mmm) cc_final: 0.5640 (mmm) REVERT: O 400 PHE cc_start: 0.7297 (m-10) cc_final: 0.6967 (m-10) REVERT: O 432 LYS cc_start: 0.8472 (tptm) cc_final: 0.8195 (tptp) REVERT: P 12 LEU cc_start: 0.6351 (OUTLIER) cc_final: 0.5769 (pp) REVERT: P 28 GLN cc_start: 0.7389 (tp-100) cc_final: 0.6909 (tp-100) REVERT: P 68 MET cc_start: 0.7909 (tpt) cc_final: 0.7651 (tpt) REVERT: Q 23 VAL cc_start: 0.9317 (m) cc_final: 0.9113 (m) REVERT: Q 258 MET cc_start: 0.9109 (tpp) cc_final: 0.8852 (tpp) REVERT: Q 293 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8574 (pptt) REVERT: Q 380 ILE cc_start: 0.7896 (OUTLIER) cc_final: 0.7679 (tt) REVERT: Q 400 PHE cc_start: 0.7779 (m-10) cc_final: 0.7510 (t80) REVERT: R 18 THR cc_start: 0.8831 (OUTLIER) cc_final: 0.8242 (t) REVERT: R 35 TRP cc_start: 0.9034 (t60) cc_final: 0.8792 (t60) REVERT: R 42 PHE cc_start: 0.8744 (t80) cc_final: 0.8126 (t80) REVERT: R 74 MET cc_start: 0.8329 (tpp) cc_final: 0.7816 (mmm) REVERT: S 8 ASN cc_start: 0.7696 (t0) cc_final: 0.7246 (t0) REVERT: S 20 TRP cc_start: 0.7615 (p90) cc_final: 0.6363 (p90) REVERT: S 108 PHE cc_start: 0.8626 (m-80) cc_final: 0.8268 (m-80) REVERT: S 122 LEU cc_start: 0.7026 (OUTLIER) cc_final: 0.6651 (tp) REVERT: S 176 TYR cc_start: 0.8759 (m-80) cc_final: 0.8392 (m-80) REVERT: S 250 VAL cc_start: 0.8610 (t) cc_final: 0.8409 (m) REVERT: S 259 HIS cc_start: 0.8469 (OUTLIER) cc_final: 0.6647 (t-90) REVERT: S 484 THR cc_start: 0.9007 (m) cc_final: 0.8729 (p) REVERT: U 3 GLU cc_start: 0.6376 (mm-30) cc_final: 0.6100 (mm-30) REVERT: U 47 TRP cc_start: 0.8098 (t60) cc_final: 0.7445 (t60) REVERT: U 65 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7118 (mtmt) REVERT: U 114 GLN cc_start: 0.7762 (tp40) cc_final: 0.7258 (tp-100) outliers start: 223 outliers final: 151 residues processed: 927 average time/residue: 0.3978 time to fit residues: 609.0353 Evaluate side-chains 914 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 742 time to evaluate : 3.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 451 TRP Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 26 TRP Chi-restraints excluded: chain B residue 34 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 43 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 293 LYS Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 365 ILE Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 242 HIS Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain E residue 255 GLU Chi-restraints excluded: chain E residue 258 MET Chi-restraints excluded: chain E residue 259 HIS Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 313 THR Chi-restraints excluded: chain E residue 318 ILE Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 410 MET Chi-restraints excluded: chain E residue 451 TRP Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain O residue 26 GLU Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 51 THR Chi-restraints excluded: chain O residue 57 ARG Chi-restraints excluded: chain O residue 121 CYS Chi-restraints excluded: chain O residue 130 VAL Chi-restraints excluded: chain O residue 187 THR Chi-restraints excluded: chain O residue 195 ILE Chi-restraints excluded: chain O residue 198 THR Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain O residue 234 LEU Chi-restraints excluded: chain O residue 237 THR Chi-restraints excluded: chain O residue 238 PHE Chi-restraints excluded: chain O residue 253 SER Chi-restraints excluded: chain O residue 266 THR Chi-restraints excluded: chain O residue 275 SER Chi-restraints excluded: chain O residue 286 LYS Chi-restraints excluded: chain O residue 337 THR Chi-restraints excluded: chain O residue 338 GLU Chi-restraints excluded: chain O residue 365 ILE Chi-restraints excluded: chain O residue 413 LEU Chi-restraints excluded: chain O residue 423 VAL Chi-restraints excluded: chain O residue 429 SER Chi-restraints excluded: chain O residue 451 TRP Chi-restraints excluded: chain O residue 452 VAL Chi-restraints excluded: chain O residue 455 ILE Chi-restraints excluded: chain O residue 461 LEU Chi-restraints excluded: chain O residue 466 LEU Chi-restraints excluded: chain P residue 12 LEU Chi-restraints excluded: chain P residue 14 THR Chi-restraints excluded: chain P residue 34 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 43 ILE Chi-restraints excluded: chain Q residue 48 THR Chi-restraints excluded: chain Q residue 91 VAL Chi-restraints excluded: chain Q residue 113 LEU Chi-restraints excluded: chain Q residue 158 VAL Chi-restraints excluded: chain Q residue 187 THR Chi-restraints excluded: chain Q residue 201 ASN Chi-restraints excluded: chain Q residue 236 VAL Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain Q residue 293 LYS Chi-restraints excluded: chain Q residue 313 THR Chi-restraints excluded: chain Q residue 356 VAL Chi-restraints excluded: chain Q residue 357 THR Chi-restraints excluded: chain Q residue 358 LYS Chi-restraints excluded: chain Q residue 377 VAL Chi-restraints excluded: chain Q residue 380 ILE Chi-restraints excluded: chain Q residue 461 LEU Chi-restraints excluded: chain Q residue 462 THR Chi-restraints excluded: chain Q residue 466 LEU Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain S residue 10 ASP Chi-restraints excluded: chain S residue 122 LEU Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 142 THR Chi-restraints excluded: chain S residue 179 LEU Chi-restraints excluded: chain S residue 181 LEU Chi-restraints excluded: chain S residue 187 THR Chi-restraints excluded: chain S residue 242 HIS Chi-restraints excluded: chain S residue 255 GLU Chi-restraints excluded: chain S residue 258 MET Chi-restraints excluded: chain S residue 259 HIS Chi-restraints excluded: chain S residue 266 THR Chi-restraints excluded: chain S residue 305 VAL Chi-restraints excluded: chain S residue 313 THR Chi-restraints excluded: chain S residue 318 ILE Chi-restraints excluded: chain S residue 356 VAL Chi-restraints excluded: chain S residue 447 SER Chi-restraints excluded: chain S residue 451 TRP Chi-restraints excluded: chain S residue 464 ILE Chi-restraints excluded: chain S residue 485 LEU Chi-restraints excluded: chain T residue 8 VAL Chi-restraints excluded: chain T residue 14 THR Chi-restraints excluded: chain U residue 17 SER Chi-restraints excluded: chain U residue 25 SER Chi-restraints excluded: chain U residue 53 SER Chi-restraints excluded: chain U residue 63 SER Chi-restraints excluded: chain U residue 65 LYS Chi-restraints excluded: chain U residue 83 MET Chi-restraints excluded: chain V residue 13 VAL Chi-restraints excluded: chain V residue 84 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 307 optimal weight: 9.9990 chunk 209 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 274 optimal weight: 20.0000 chunk 152 optimal weight: 30.0000 chunk 315 optimal weight: 0.0470 chunk 255 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 188 optimal weight: 7.9990 chunk 331 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 overall best weight: 3.5884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 8 ASN ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 428 ASN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 GLN ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 85 GLN ** O 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 302 ASN ** O 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 17 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 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 302 ASN ** T 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 100 GLN ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 85 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30814 Z= 0.225 Angle : 0.667 9.822 41776 Z= 0.331 Chirality : 0.044 0.240 4928 Planarity : 0.004 0.043 5192 Dihedral : 10.525 116.433 4876 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 5.83 % Allowed : 21.38 % Favored : 72.78 % 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: -1.54 (0.13), residues: 3846 helix: 1.22 (0.18), residues: 876 sheet: -1.61 (0.15), residues: 1094 loop : -1.73 (0.13), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 229 HIS 0.013 0.001 HIS E 259 PHE 0.019 0.002 PHE F 48 TYR 0.023 0.001 TYR L 55 ARG 0.006 0.001 ARG A 348 *********************** 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 986 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 798 time to evaluate : 3.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO B 72 " (corrupted residue). Skipping it. Corrupt residue: chain: B residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO P 72 " (corrupted residue). Skipping it. Corrupt residue: chain: P residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.7950 (t) cc_final: 0.7573 (p) REVERT: A 38 LYS cc_start: 0.9272 (mmtt) cc_final: 0.9048 (mmtm) REVERT: A 48 THR cc_start: 0.8867 (OUTLIER) cc_final: 0.8644 (t) REVERT: A 57 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.7413 (ttm110) REVERT: A 98 ASP cc_start: 0.8039 (p0) cc_final: 0.7748 (p0) REVERT: A 181 LEU cc_start: 0.8364 (tp) cc_final: 0.8020 (tp) REVERT: A 201 ASN cc_start: 0.6543 (m-40) cc_final: 0.5651 (t0) REVERT: A 287 MET cc_start: 0.8189 (mtp) cc_final: 0.7836 (mtp) REVERT: A 299 MET cc_start: 0.6408 (mmm) cc_final: 0.5652 (mmm) REVERT: B 12 LEU cc_start: 0.6018 (OUTLIER) cc_final: 0.5508 (pp) REVERT: B 26 TRP cc_start: 0.6303 (OUTLIER) cc_final: 0.5953 (m-90) REVERT: B 28 GLN cc_start: 0.7368 (tp-100) cc_final: 0.7057 (tp-100) REVERT: C 182 GLU cc_start: 0.7081 (tp30) cc_final: 0.6723 (tp30) REVERT: C 293 LYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8508 (pptt) REVERT: C 358 LYS cc_start: 0.7625 (OUTLIER) cc_final: 0.7052 (tppt) REVERT: C 360 GLU cc_start: 0.7005 (mm-30) cc_final: 0.6784 (mm-30) REVERT: C 380 ILE cc_start: 0.7818 (OUTLIER) cc_final: 0.7605 (tt) REVERT: C 400 PHE cc_start: 0.7707 (m-10) cc_final: 0.7492 (t80) REVERT: C 436 GLN cc_start: 0.8176 (tm-30) cc_final: 0.7684 (tm-30) REVERT: D 18 THR cc_start: 0.8783 (p) cc_final: 0.8195 (t) REVERT: D 42 PHE cc_start: 0.8708 (t80) cc_final: 0.8082 (t80) REVERT: D 74 MET cc_start: 0.8330 (tpp) cc_final: 0.8030 (mmm) REVERT: E 20 TRP cc_start: 0.7499 (p90) cc_final: 0.6318 (p90) REVERT: E 108 PHE cc_start: 0.8581 (m-80) cc_final: 0.8244 (m-80) REVERT: E 122 LEU cc_start: 0.6908 (OUTLIER) cc_final: 0.6491 (tp) REVERT: E 176 TYR cc_start: 0.8817 (m-80) cc_final: 0.8435 (m-80) REVERT: E 181 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8649 (pp) REVERT: E 286 LYS cc_start: 0.8462 (ptpt) cc_final: 0.8147 (ptpp) REVERT: E 320 ILE cc_start: 0.9401 (mm) cc_final: 0.9121 (mt) REVERT: E 410 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.7947 (mtp) REVERT: E 442 TYR cc_start: 0.8852 (t80) cc_final: 0.8328 (t80) REVERT: E 484 THR cc_start: 0.8961 (m) cc_final: 0.8645 (p) REVERT: H 3 GLU cc_start: 0.6205 (mm-30) cc_final: 0.5917 (mm-30) REVERT: H 47 TRP cc_start: 0.8011 (t60) cc_final: 0.7463 (t60) REVERT: H 65 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7190 (mtmt) REVERT: H 114 GLN cc_start: 0.7678 (tp40) cc_final: 0.7109 (tp-100) REVERT: O 6 VAL cc_start: 0.7951 (t) cc_final: 0.7593 (p) REVERT: O 57 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.7397 (ttm110) REVERT: O 98 ASP cc_start: 0.8038 (p0) cc_final: 0.7756 (p0) REVERT: O 181 LEU cc_start: 0.8407 (tp) cc_final: 0.8067 (tp) REVERT: O 287 MET cc_start: 0.8090 (mtp) cc_final: 0.7826 (mtp) REVERT: O 299 MET cc_start: 0.6404 (mmm) cc_final: 0.5571 (mmm) REVERT: O 432 LYS cc_start: 0.8297 (tptm) cc_final: 0.8063 (tttm) REVERT: P 12 LEU cc_start: 0.6002 (OUTLIER) cc_final: 0.5484 (pp) REVERT: P 28 GLN cc_start: 0.7397 (tp-100) cc_final: 0.7071 (tp-100) REVERT: Q 293 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8523 (pptt) REVERT: Q 358 LYS cc_start: 0.7493 (OUTLIER) cc_final: 0.7007 (tppt) REVERT: Q 360 GLU cc_start: 0.7007 (mm-30) cc_final: 0.6782 (mm-30) REVERT: Q 380 ILE cc_start: 0.7825 (OUTLIER) cc_final: 0.7613 (tt) REVERT: Q 400 PHE cc_start: 0.7712 (m-10) cc_final: 0.7496 (t80) REVERT: Q 436 GLN cc_start: 0.8173 (tm-30) cc_final: 0.7675 (tm-30) REVERT: R 18 THR cc_start: 0.8778 (p) cc_final: 0.8216 (t) REVERT: R 35 TRP cc_start: 0.8971 (t60) cc_final: 0.8559 (t60) REVERT: R 42 PHE cc_start: 0.8715 (t80) cc_final: 0.8076 (t80) REVERT: R 74 MET cc_start: 0.8327 (tpp) cc_final: 0.8003 (mmm) REVERT: S 8 ASN cc_start: 0.8064 (t0) cc_final: 0.7639 (t0) REVERT: S 20 TRP cc_start: 0.7501 (p90) cc_final: 0.6313 (p90) REVERT: S 108 PHE cc_start: 0.8579 (m-80) cc_final: 0.8233 (m-80) REVERT: S 176 TYR cc_start: 0.8811 (m-80) cc_final: 0.8498 (m-80) REVERT: S 250 VAL cc_start: 0.8638 (t) cc_final: 0.8422 (m) REVERT: S 270 ASN cc_start: 0.6380 (t0) cc_final: 0.6055 (t0) REVERT: S 442 TYR cc_start: 0.8853 (t80) cc_final: 0.8320 (t80) REVERT: S 484 THR cc_start: 0.8970 (m) cc_final: 0.8665 (p) REVERT: U 3 GLU cc_start: 0.6232 (mm-30) cc_final: 0.5941 (mm-30) REVERT: U 47 TRP cc_start: 0.8011 (t60) cc_final: 0.7470 (t60) REVERT: U 65 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7123 (mtmt) REVERT: U 114 GLN cc_start: 0.7675 (tp40) cc_final: 0.7133 (tp-100) outliers start: 188 outliers final: 142 residues processed: 924 average time/residue: 0.3768 time to fit residues: 568.1172 Evaluate side-chains 903 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 744 time to evaluate : 3.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 451 TRP Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 26 TRP 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 43 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 293 LYS Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 242 HIS Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain E residue 258 MET Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 318 ILE Chi-restraints excluded: chain E residue 336 SER Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 410 MET Chi-restraints excluded: chain E residue 451 TRP Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 76 ASP Chi-restraints excluded: chain O residue 16 SER Chi-restraints excluded: chain O residue 26 GLU Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 51 THR Chi-restraints excluded: chain O residue 57 ARG Chi-restraints excluded: chain O residue 121 CYS Chi-restraints excluded: chain O residue 130 VAL Chi-restraints excluded: chain O residue 187 THR Chi-restraints excluded: chain O residue 195 ILE Chi-restraints excluded: chain O residue 198 THR Chi-restraints excluded: chain O residue 237 THR Chi-restraints excluded: chain O residue 275 SER Chi-restraints excluded: chain O residue 283 CYS Chi-restraints excluded: chain O residue 302 ASN Chi-restraints excluded: chain O residue 337 THR Chi-restraints excluded: chain O residue 338 GLU Chi-restraints excluded: chain O residue 365 ILE Chi-restraints excluded: chain O residue 387 ILE Chi-restraints excluded: chain O residue 413 LEU Chi-restraints excluded: chain O residue 423 VAL Chi-restraints excluded: chain O residue 429 SER Chi-restraints excluded: chain O residue 451 TRP Chi-restraints excluded: chain O residue 452 VAL Chi-restraints excluded: chain O residue 455 ILE Chi-restraints excluded: chain O residue 461 LEU Chi-restraints excluded: chain O residue 466 LEU Chi-restraints excluded: chain O residue 484 THR Chi-restraints excluded: chain P residue 12 LEU Chi-restraints excluded: chain P residue 14 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 43 ILE Chi-restraints excluded: chain Q residue 48 THR Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 91 VAL Chi-restraints excluded: chain Q residue 107 LEU Chi-restraints excluded: chain Q residue 113 LEU Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain Q residue 158 VAL Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain Q residue 293 LYS Chi-restraints excluded: chain Q residue 313 THR Chi-restraints excluded: chain Q residue 356 VAL Chi-restraints excluded: chain Q residue 357 THR Chi-restraints excluded: chain Q residue 358 LYS Chi-restraints excluded: chain Q residue 380 ILE Chi-restraints excluded: chain Q residue 461 LEU Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain S residue 10 ASP Chi-restraints excluded: chain S residue 41 LEU Chi-restraints excluded: chain S residue 64 LYS Chi-restraints excluded: chain S residue 79 GLU Chi-restraints excluded: chain S residue 91 VAL Chi-restraints excluded: chain S residue 92 CYS Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 142 THR Chi-restraints excluded: chain S residue 181 LEU Chi-restraints excluded: chain S residue 187 THR Chi-restraints excluded: chain S residue 242 HIS Chi-restraints excluded: chain S residue 255 GLU Chi-restraints excluded: chain S residue 258 MET Chi-restraints excluded: chain S residue 266 THR Chi-restraints excluded: chain S residue 318 ILE Chi-restraints excluded: chain S residue 336 SER Chi-restraints excluded: chain S residue 356 VAL Chi-restraints excluded: chain S residue 451 TRP Chi-restraints excluded: chain S residue 485 LEU Chi-restraints excluded: chain T residue 8 VAL Chi-restraints excluded: chain T residue 14 THR Chi-restraints excluded: chain T residue 16 THR Chi-restraints excluded: chain T residue 58 THR Chi-restraints excluded: chain U residue 22 CYS Chi-restraints excluded: chain U residue 53 SER Chi-restraints excluded: chain U residue 63 SER Chi-restraints excluded: chain U residue 65 LYS Chi-restraints excluded: chain U residue 83 MET Chi-restraints excluded: chain U residue 91 THR Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 76 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 124 optimal weight: 10.0000 chunk 332 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 chunk 216 optimal weight: 0.9990 chunk 91 optimal weight: 0.0670 chunk 369 optimal weight: 10.0000 chunk 306 optimal weight: 10.0000 chunk 171 optimal weight: 0.9990 chunk 30 optimal weight: 9.9990 chunk 122 optimal weight: 20.0000 chunk 194 optimal weight: 20.0000 overall best weight: 2.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 46 GLN D 17 GLN ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 428 ASN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 GLN ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 85 GLN O 383 ASN R 17 GLN ** R 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 428 ASN ** T 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 100 GLN ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 85 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 30814 Z= 0.189 Angle : 0.653 13.905 41776 Z= 0.320 Chirality : 0.043 0.254 4928 Planarity : 0.004 0.044 5192 Dihedral : 10.024 114.284 4876 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 5.68 % Allowed : 22.44 % Favored : 71.88 % 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: -1.42 (0.13), residues: 3846 helix: 1.34 (0.18), residues: 876 sheet: -1.49 (0.15), residues: 1080 loop : -1.71 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP S 20 HIS 0.005 0.001 HIS O 94 PHE 0.019 0.001 PHE F 48 TYR 0.019 0.001 TYR H 111 ARG 0.007 0.000 ARG A 348 *********************** 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 973 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 790 time to evaluate : 3.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO B 72 " (corrupted residue). Skipping it. Corrupt residue: chain: B residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO P 72 " (corrupted residue). Skipping it. Corrupt residue: chain: P residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.7893 (t) cc_final: 0.7521 (p) REVERT: A 38 LYS cc_start: 0.9265 (mmtt) cc_final: 0.9059 (mmtm) REVERT: A 48 THR cc_start: 0.8855 (OUTLIER) cc_final: 0.8636 (t) REVERT: A 57 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.7412 (ttm110) REVERT: A 98 ASP cc_start: 0.8045 (p0) cc_final: 0.7699 (p0) REVERT: A 181 LEU cc_start: 0.8307 (tp) cc_final: 0.7965 (tp) REVERT: A 201 ASN cc_start: 0.6683 (m-40) cc_final: 0.5624 (t0) REVERT: A 287 MET cc_start: 0.8178 (mtp) cc_final: 0.7835 (mtp) REVERT: A 299 MET cc_start: 0.6536 (mmm) cc_final: 0.5691 (mmm) REVERT: B 12 LEU cc_start: 0.6274 (OUTLIER) cc_final: 0.5929 (pp) REVERT: B 26 TRP cc_start: 0.6267 (OUTLIER) cc_final: 0.5842 (m-90) REVERT: B 28 GLN cc_start: 0.7360 (tp-100) cc_final: 0.7151 (tp-100) REVERT: C 258 MET cc_start: 0.8801 (tpp) cc_final: 0.8327 (tpp) REVERT: C 293 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8169 (pptt) REVERT: C 358 LYS cc_start: 0.7384 (OUTLIER) cc_final: 0.6874 (tppt) REVERT: C 360 GLU cc_start: 0.6903 (mm-30) cc_final: 0.6688 (mm-30) REVERT: C 380 ILE cc_start: 0.7779 (OUTLIER) cc_final: 0.7561 (tt) REVERT: C 436 GLN cc_start: 0.8055 (tm-30) cc_final: 0.7757 (tt0) REVERT: D 18 THR cc_start: 0.8752 (p) cc_final: 0.8158 (t) REVERT: D 42 PHE cc_start: 0.8657 (t80) cc_final: 0.7975 (t80) REVERT: D 74 MET cc_start: 0.8543 (tpp) cc_final: 0.7745 (mmm) REVERT: E 20 TRP cc_start: 0.7450 (p90) cc_final: 0.6326 (p90) REVERT: E 108 PHE cc_start: 0.8568 (m-80) cc_final: 0.8244 (m-80) REVERT: E 122 LEU cc_start: 0.6865 (OUTLIER) cc_final: 0.6475 (tp) REVERT: E 176 TYR cc_start: 0.8716 (m-80) cc_final: 0.8410 (m-80) REVERT: E 181 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8684 (pp) REVERT: E 286 LYS cc_start: 0.8423 (ptpt) cc_final: 0.8016 (ptpp) REVERT: E 320 ILE cc_start: 0.9393 (mm) cc_final: 0.9130 (mt) REVERT: E 401 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7640 (mm-30) REVERT: E 410 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.7858 (mtp) REVERT: E 442 TYR cc_start: 0.8866 (t80) cc_final: 0.8314 (t80) REVERT: E 484 THR cc_start: 0.8931 (m) cc_final: 0.8490 (p) REVERT: H 3 GLU cc_start: 0.6231 (mm-30) cc_final: 0.5939 (mm-30) REVERT: H 47 TRP cc_start: 0.8074 (t60) cc_final: 0.7643 (t60) REVERT: H 65 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7193 (mtmt) REVERT: H 95 TYR cc_start: 0.8601 (m-80) cc_final: 0.8312 (m-80) REVERT: H 111 TYR cc_start: 0.8039 (m-80) cc_final: 0.7740 (m-10) REVERT: H 114 GLN cc_start: 0.7659 (tp40) cc_final: 0.7427 (tp-100) REVERT: L 48 GLN cc_start: 0.6722 (mp10) cc_final: 0.6434 (mp10) REVERT: L 109 ARG cc_start: 0.8556 (mtp85) cc_final: 0.8216 (mtp85) REVERT: O 6 VAL cc_start: 0.7903 (t) cc_final: 0.7540 (p) REVERT: O 57 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.7479 (ttm110) REVERT: O 98 ASP cc_start: 0.8047 (p0) cc_final: 0.7709 (p0) REVERT: O 181 LEU cc_start: 0.8349 (tp) cc_final: 0.8025 (tp) REVERT: O 287 MET cc_start: 0.8153 (mtp) cc_final: 0.7932 (mtp) REVERT: O 299 MET cc_start: 0.6485 (mmm) cc_final: 0.5703 (mmm) REVERT: P 12 LEU cc_start: 0.6359 (OUTLIER) cc_final: 0.5999 (pp) REVERT: P 28 GLN cc_start: 0.7379 (tp-100) cc_final: 0.7073 (tp-100) REVERT: Q 258 MET cc_start: 0.8810 (tpp) cc_final: 0.8311 (tpp) REVERT: Q 293 LYS cc_start: 0.9186 (OUTLIER) cc_final: 0.8187 (pptt) REVERT: Q 358 LYS cc_start: 0.7438 (OUTLIER) cc_final: 0.7103 (tppt) REVERT: Q 360 GLU cc_start: 0.6899 (mm-30) cc_final: 0.6679 (mm-30) REVERT: Q 380 ILE cc_start: 0.7786 (OUTLIER) cc_final: 0.7566 (tt) REVERT: Q 436 GLN cc_start: 0.8054 (tm-30) cc_final: 0.7743 (tt0) REVERT: R 18 THR cc_start: 0.8750 (p) cc_final: 0.8183 (t) REVERT: R 35 TRP cc_start: 0.8965 (t60) cc_final: 0.8717 (t60) REVERT: R 42 PHE cc_start: 0.8686 (t80) cc_final: 0.7970 (t80) REVERT: R 74 MET cc_start: 0.8405 (tpp) cc_final: 0.8123 (mmm) REVERT: S 8 ASN cc_start: 0.8042 (t0) cc_final: 0.7671 (t0) REVERT: S 20 TRP cc_start: 0.7447 (p90) cc_final: 0.6314 (p90) REVERT: S 108 PHE cc_start: 0.8565 (m-80) cc_final: 0.8233 (m-80) REVERT: S 176 TYR cc_start: 0.8798 (m-80) cc_final: 0.8377 (m-80) REVERT: S 250 VAL cc_start: 0.8606 (t) cc_final: 0.8364 (m) REVERT: S 270 ASN cc_start: 0.6367 (t0) cc_final: 0.6020 (t0) REVERT: S 286 LYS cc_start: 0.8345 (ptpt) cc_final: 0.8025 (ptpp) REVERT: S 293 LYS cc_start: 0.8429 (tttt) cc_final: 0.8153 (ttpt) REVERT: S 442 TYR cc_start: 0.8874 (t80) cc_final: 0.8319 (t80) REVERT: S 484 THR cc_start: 0.8945 (m) cc_final: 0.8504 (p) REVERT: U 3 GLU cc_start: 0.6255 (mm-30) cc_final: 0.5962 (mm-30) REVERT: U 47 TRP cc_start: 0.8076 (t60) cc_final: 0.7632 (t60) REVERT: U 65 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7198 (mtmt) REVERT: U 95 TYR cc_start: 0.8595 (m-80) cc_final: 0.8279 (m-80) REVERT: U 114 GLN cc_start: 0.7651 (tp40) cc_final: 0.7437 (tp-100) REVERT: V 48 GLN cc_start: 0.6737 (mp10) cc_final: 0.6012 (mp10) outliers start: 183 outliers final: 120 residues processed: 911 average time/residue: 0.4343 time to fit residues: 652.0621 Evaluate side-chains 883 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 746 time to evaluate : 3.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 26 TRP Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 293 LYS Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 242 HIS Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain E residue 258 MET Chi-restraints excluded: chain E residue 318 ILE Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 410 MET Chi-restraints excluded: chain E residue 428 ASN Chi-restraints excluded: chain E residue 451 TRP Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 76 ASP Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain O residue 26 GLU Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 51 THR Chi-restraints excluded: chain O residue 57 ARG Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain O residue 121 CYS Chi-restraints excluded: chain O residue 130 VAL Chi-restraints excluded: chain O residue 195 ILE Chi-restraints excluded: chain O residue 237 THR Chi-restraints excluded: chain O residue 266 THR Chi-restraints excluded: chain O residue 283 CYS Chi-restraints excluded: chain O residue 337 THR Chi-restraints excluded: chain O residue 338 GLU Chi-restraints excluded: chain O residue 365 ILE Chi-restraints excluded: chain O residue 413 LEU Chi-restraints excluded: chain O residue 423 VAL Chi-restraints excluded: chain O residue 429 SER Chi-restraints excluded: chain O residue 452 VAL Chi-restraints excluded: chain O residue 460 LEU Chi-restraints excluded: chain O residue 466 LEU Chi-restraints excluded: chain P residue 12 LEU Chi-restraints excluded: chain P residue 14 THR Chi-restraints excluded: chain P residue 67 LEU Chi-restraints excluded: chain Q residue 10 ASP Chi-restraints excluded: chain Q residue 48 THR Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 107 LEU Chi-restraints excluded: chain Q residue 113 LEU Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain Q residue 158 VAL Chi-restraints excluded: chain Q residue 236 VAL Chi-restraints excluded: chain Q residue 293 LYS Chi-restraints excluded: chain Q residue 313 THR Chi-restraints excluded: chain Q residue 356 VAL Chi-restraints excluded: chain Q residue 357 THR Chi-restraints excluded: chain Q residue 358 LYS Chi-restraints excluded: chain Q residue 365 ILE Chi-restraints excluded: chain Q residue 371 PHE Chi-restraints excluded: chain Q residue 380 ILE Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain S residue 10 ASP Chi-restraints excluded: chain S residue 41 LEU Chi-restraints excluded: chain S residue 79 GLU Chi-restraints excluded: chain S residue 92 CYS Chi-restraints excluded: chain S residue 130 VAL Chi-restraints excluded: chain S residue 142 THR Chi-restraints excluded: chain S residue 181 LEU Chi-restraints excluded: chain S residue 187 THR Chi-restraints excluded: chain S residue 242 HIS Chi-restraints excluded: chain S residue 258 MET Chi-restraints excluded: chain S residue 318 ILE Chi-restraints excluded: chain S residue 336 SER Chi-restraints excluded: chain S residue 356 VAL Chi-restraints excluded: chain S residue 451 TRP Chi-restraints excluded: chain S residue 485 LEU Chi-restraints excluded: chain T residue 14 THR Chi-restraints excluded: chain U residue 22 CYS Chi-restraints excluded: chain U residue 53 SER Chi-restraints excluded: chain U residue 63 SER Chi-restraints excluded: chain U residue 65 LYS Chi-restraints excluded: chain U residue 83 MET Chi-restraints excluded: chain U residue 91 THR Chi-restraints excluded: chain V residue 76 ASP Chi-restraints excluded: chain V residue 84 VAL 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: 8.9990 chunk 210 optimal weight: 0.9980 chunk 269 optimal weight: 9.9990 chunk 209 optimal weight: 4.9990 chunk 311 optimal weight: 0.9990 chunk 206 optimal weight: 6.9990 chunk 368 optimal weight: 30.0000 chunk 230 optimal weight: 10.0000 chunk 224 optimal weight: 9.9990 chunk 169 optimal weight: 10.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 GLN ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 GLN ** D 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 8 ASN ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 GLN ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 85 GLN ** O 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 209 GLN ** O 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 17 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 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 428 ASN ** T 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 100 GLN ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 85 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 30814 Z= 0.248 Angle : 0.676 14.397 41776 Z= 0.333 Chirality : 0.044 0.283 4928 Planarity : 0.004 0.044 5192 Dihedral : 9.802 113.661 4876 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 6.21 % Allowed : 22.19 % Favored : 71.60 % 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: -1.39 (0.13), residues: 3846 helix: 1.28 (0.18), residues: 876 sheet: -1.42 (0.15), residues: 1068 loop : -1.68 (0.13), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP Q 218 HIS 0.005 0.001 HIS O 94 PHE 0.021 0.002 PHE E 475 TYR 0.016 0.001 TYR H 111 ARG 0.007 0.001 ARG O 348 *********************** 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 962 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 762 time to evaluate : 3.276 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO B 72 " (corrupted residue). Skipping it. Corrupt residue: chain: B residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO P 72 " (corrupted residue). Skipping it. Corrupt residue: chain: P residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.7938 (t) cc_final: 0.7549 (p) REVERT: A 38 LYS cc_start: 0.9267 (mmtt) cc_final: 0.9055 (mmtm) REVERT: A 57 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.7426 (ttm110) REVERT: A 98 ASP cc_start: 0.8064 (p0) cc_final: 0.7745 (p0) REVERT: A 168 THR cc_start: 0.9042 (OUTLIER) cc_final: 0.8553 (p) REVERT: A 181 LEU cc_start: 0.8364 (tp) cc_final: 0.7957 (tp) REVERT: A 201 ASN cc_start: 0.6701 (m-40) cc_final: 0.5619 (t0) REVERT: A 287 MET cc_start: 0.8184 (mtp) cc_final: 0.7831 (mtp) REVERT: A 299 MET cc_start: 0.6584 (mmm) cc_final: 0.5776 (mmm) REVERT: A 390 TYR cc_start: 0.8652 (t80) cc_final: 0.8250 (t80) REVERT: B 12 LEU cc_start: 0.6020 (OUTLIER) cc_final: 0.5521 (pp) REVERT: B 28 GLN cc_start: 0.7456 (tp-100) cc_final: 0.7217 (tp-100) REVERT: B 69 LEU cc_start: 0.8350 (tp) cc_final: 0.7841 (mp) REVERT: C 25 LEU cc_start: 0.8066 (mt) cc_final: 0.7831 (mp) REVERT: C 258 MET cc_start: 0.8810 (tpp) cc_final: 0.8345 (tpp) REVERT: C 293 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.7986 (pptt) REVERT: C 358 LYS cc_start: 0.7395 (OUTLIER) cc_final: 0.6993 (tppt) REVERT: C 380 ILE cc_start: 0.7791 (mt) cc_final: 0.7570 (tt) REVERT: D 18 THR cc_start: 0.8759 (p) cc_final: 0.8185 (t) REVERT: D 42 PHE cc_start: 0.8687 (t80) cc_final: 0.7938 (t80) REVERT: D 74 MET cc_start: 0.8564 (tpp) cc_final: 0.7770 (mmm) REVERT: E 20 TRP cc_start: 0.7486 (p90) cc_final: 0.6318 (p90) REVERT: E 108 PHE cc_start: 0.8605 (m-80) cc_final: 0.8284 (m-80) REVERT: E 122 LEU cc_start: 0.6841 (OUTLIER) cc_final: 0.6456 (tp) REVERT: E 176 TYR cc_start: 0.8737 (m-80) cc_final: 0.8369 (m-80) REVERT: E 181 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8734 (pp) REVERT: E 251 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.7970 (tt) REVERT: E 259 HIS cc_start: 0.9018 (OUTLIER) cc_final: 0.7334 (t70) REVERT: E 286 LYS cc_start: 0.8419 (ptpt) cc_final: 0.8022 (ptpp) REVERT: E 320 ILE cc_start: 0.9405 (mm) cc_final: 0.9138 (mt) REVERT: E 401 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7640 (mm-30) REVERT: E 410 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.7918 (mtp) REVERT: E 484 THR cc_start: 0.8915 (m) cc_final: 0.8563 (p) REVERT: H 3 GLU cc_start: 0.6293 (mm-30) cc_final: 0.6026 (mm-30) REVERT: H 47 TRP cc_start: 0.8117 (t60) cc_final: 0.7603 (t60) REVERT: H 65 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7225 (mtmt) REVERT: H 95 TYR cc_start: 0.8539 (m-80) cc_final: 0.8323 (m-80) REVERT: H 111 TYR cc_start: 0.8063 (m-80) cc_final: 0.7834 (m-10) REVERT: H 114 GLN cc_start: 0.7650 (tp40) cc_final: 0.7418 (tp-100) REVERT: L 48 GLN cc_start: 0.6899 (mp10) cc_final: 0.6531 (mp10) REVERT: O 6 VAL cc_start: 0.7947 (t) cc_final: 0.7568 (p) REVERT: O 57 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.7429 (ttm110) REVERT: O 98 ASP cc_start: 0.8066 (p0) cc_final: 0.7764 (p0) REVERT: O 168 THR cc_start: 0.9040 (OUTLIER) cc_final: 0.8558 (p) REVERT: O 181 LEU cc_start: 0.8319 (tp) cc_final: 0.7988 (tp) REVERT: O 190 ASP cc_start: 0.8097 (t0) cc_final: 0.7844 (t0) REVERT: O 193 GLU cc_start: 0.6297 (pt0) cc_final: 0.5954 (pt0) REVERT: O 238 PHE cc_start: 0.8559 (OUTLIER) cc_final: 0.7815 (m-10) REVERT: O 287 MET cc_start: 0.8171 (mtp) cc_final: 0.7950 (mtp) REVERT: O 299 MET cc_start: 0.6546 (mmm) cc_final: 0.5769 (mmm) REVERT: O 390 TYR cc_start: 0.8680 (t80) cc_final: 0.8277 (t80) REVERT: P 12 LEU cc_start: 0.6442 (OUTLIER) cc_final: 0.5976 (pp) REVERT: P 28 GLN cc_start: 0.7412 (tp-100) cc_final: 0.7087 (tp-100) REVERT: Q 25 LEU cc_start: 0.8065 (mt) cc_final: 0.7807 (mp) REVERT: Q 258 MET cc_start: 0.8803 (tpp) cc_final: 0.8340 (tpp) REVERT: Q 293 LYS cc_start: 0.9255 (OUTLIER) cc_final: 0.8187 (pptt) REVERT: Q 358 LYS cc_start: 0.7459 (OUTLIER) cc_final: 0.7199 (tppt) REVERT: Q 380 ILE cc_start: 0.7798 (mt) cc_final: 0.7572 (tt) REVERT: R 18 THR cc_start: 0.8783 (p) cc_final: 0.8207 (t) REVERT: R 35 TRP cc_start: 0.8974 (t60) cc_final: 0.8699 (t60) REVERT: R 42 PHE cc_start: 0.8693 (t80) cc_final: 0.7860 (t80) REVERT: R 74 MET cc_start: 0.8459 (tpp) cc_final: 0.8247 (mmm) REVERT: S 8 ASN cc_start: 0.8120 (t0) cc_final: 0.7674 (t0) REVERT: S 20 TRP cc_start: 0.7487 (p90) cc_final: 0.6347 (p90) REVERT: S 108 PHE cc_start: 0.8604 (m-80) cc_final: 0.8278 (m-80) REVERT: S 176 TYR cc_start: 0.8956 (m-80) cc_final: 0.8570 (m-80) REVERT: S 250 VAL cc_start: 0.8625 (t) cc_final: 0.8393 (m) REVERT: S 259 HIS cc_start: 0.9010 (OUTLIER) cc_final: 0.7292 (t70) REVERT: S 270 ASN cc_start: 0.6412 (t0) cc_final: 0.6068 (t0) REVERT: S 286 LYS cc_start: 0.8344 (ptpt) cc_final: 0.8008 (ptpp) REVERT: S 484 THR cc_start: 0.8918 (m) cc_final: 0.8576 (p) REVERT: U 3 GLU cc_start: 0.6509 (mm-30) cc_final: 0.6240 (mm-30) REVERT: U 47 TRP cc_start: 0.8110 (t60) cc_final: 0.7593 (t60) REVERT: U 65 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7200 (mtmt) REVERT: U 95 TYR cc_start: 0.8531 (m-80) cc_final: 0.8307 (m-80) REVERT: U 114 GLN cc_start: 0.7665 (tp40) cc_final: 0.7430 (tp-100) outliers start: 200 outliers final: 144 residues processed: 903 average time/residue: 0.3723 time to fit residues: 549.6675 Evaluate side-chains 897 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 734 time to evaluate : 3.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 26 TRP Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 30 CYS Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 293 LYS Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain E residue 8 ASN Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 242 HIS Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 258 MET Chi-restraints excluded: chain E residue 259 HIS Chi-restraints excluded: chain E residue 318 ILE Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 410 MET Chi-restraints excluded: chain E residue 451 TRP Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 76 ASP Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain O residue 16 SER Chi-restraints excluded: chain O residue 26 GLU Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 57 ARG Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain O residue 121 CYS Chi-restraints excluded: chain O residue 130 VAL Chi-restraints excluded: chain O residue 168 THR Chi-restraints excluded: chain O residue 187 THR Chi-restraints excluded: chain O residue 195 ILE Chi-restraints excluded: chain O residue 237 THR Chi-restraints excluded: chain O residue 238 PHE Chi-restraints excluded: chain O residue 266 THR Chi-restraints excluded: chain O residue 283 CYS Chi-restraints excluded: chain O residue 320 ILE Chi-restraints excluded: chain O residue 337 THR Chi-restraints excluded: chain O residue 338 GLU Chi-restraints excluded: chain O residue 365 ILE Chi-restraints excluded: chain O residue 387 ILE Chi-restraints excluded: chain O residue 413 LEU Chi-restraints excluded: chain O residue 423 VAL Chi-restraints excluded: chain O residue 429 SER Chi-restraints excluded: chain O residue 466 LEU Chi-restraints excluded: chain P residue 12 LEU Chi-restraints excluded: chain P residue 14 THR Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 67 LEU Chi-restraints excluded: chain Q residue 10 ASP Chi-restraints excluded: chain Q residue 30 CYS Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 48 THR Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 107 LEU Chi-restraints excluded: chain Q residue 113 LEU Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain Q residue 158 VAL Chi-restraints excluded: chain Q residue 236 VAL Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain Q residue 293 LYS Chi-restraints excluded: chain Q residue 313 THR Chi-restraints excluded: chain Q residue 356 VAL Chi-restraints excluded: chain Q residue 357 THR Chi-restraints excluded: chain Q residue 358 LYS Chi-restraints excluded: chain Q residue 371 PHE Chi-restraints excluded: chain Q residue 466 LEU Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain S residue 10 ASP Chi-restraints excluded: chain S residue 41 LEU Chi-restraints excluded: chain S residue 79 GLU Chi-restraints excluded: chain S residue 92 CYS Chi-restraints excluded: chain S residue 125 ILE Chi-restraints excluded: chain S residue 130 VAL Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain S residue 181 LEU Chi-restraints excluded: chain S residue 187 THR Chi-restraints excluded: chain S residue 242 HIS Chi-restraints excluded: chain S residue 258 MET Chi-restraints excluded: chain S residue 259 HIS Chi-restraints excluded: chain S residue 266 THR Chi-restraints excluded: chain S residue 318 ILE Chi-restraints excluded: chain S residue 336 SER Chi-restraints excluded: chain S residue 356 VAL Chi-restraints excluded: chain S residue 451 TRP Chi-restraints excluded: chain S residue 464 ILE Chi-restraints excluded: chain S residue 485 LEU Chi-restraints excluded: chain T residue 10 MET Chi-restraints excluded: chain T residue 14 THR Chi-restraints excluded: chain T residue 16 THR Chi-restraints excluded: chain T residue 58 THR Chi-restraints excluded: chain U residue 22 CYS Chi-restraints excluded: chain U residue 25 SER Chi-restraints excluded: chain U residue 53 SER Chi-restraints excluded: chain U residue 63 SER Chi-restraints excluded: chain U residue 65 LYS Chi-restraints excluded: chain U residue 83 MET Chi-restraints excluded: chain U residue 91 THR Chi-restraints excluded: chain V residue 76 ASP Chi-restraints excluded: chain V residue 84 VAL Chi-restraints excluded: chain V residue 100 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 227 optimal weight: 8.9990 chunk 147 optimal weight: 10.0000 chunk 219 optimal weight: 10.0000 chunk 110 optimal weight: 20.0000 chunk 72 optimal weight: 4.9990 chunk 71 optimal weight: 30.0000 chunk 234 optimal weight: 6.9990 chunk 250 optimal weight: 9.9990 chunk 182 optimal weight: 0.0270 chunk 34 optimal weight: 10.0000 chunk 289 optimal weight: 20.0000 overall best weight: 6.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 17 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 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 GLN ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 85 GLN ** O 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 17 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 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 428 ASN ** T 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 100 GLN ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 85 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 30814 Z= 0.315 Angle : 0.707 13.208 41776 Z= 0.351 Chirality : 0.045 0.301 4928 Planarity : 0.004 0.060 5192 Dihedral : 9.722 113.589 4876 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 6.42 % Allowed : 22.66 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.42 (0.13), residues: 3846 helix: 1.22 (0.18), residues: 876 sheet: -1.43 (0.15), residues: 1072 loop : -1.67 (0.13), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP O 20 HIS 0.004 0.001 HIS Q 149 PHE 0.022 0.002 PHE S 475 TYR 0.024 0.001 TYR L 55 ARG 0.007 0.001 ARG A 348 *********************** 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 952 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 745 time to evaluate : 3.391 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO B 72 " (corrupted residue). Skipping it. Corrupt residue: chain: B residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO P 72 " (corrupted residue). Skipping it. Corrupt residue: chain: P residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.7948 (t) cc_final: 0.7556 (p) REVERT: A 38 LYS cc_start: 0.9277 (mmtt) cc_final: 0.9052 (mmtm) REVERT: A 57 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.7378 (ttm110) REVERT: A 98 ASP cc_start: 0.8073 (p0) cc_final: 0.7788 (p0) REVERT: A 168 THR cc_start: 0.9042 (OUTLIER) cc_final: 0.8538 (p) REVERT: A 181 LEU cc_start: 0.8434 (tp) cc_final: 0.8047 (tp) REVERT: A 196 LEU cc_start: 0.7448 (mt) cc_final: 0.7140 (mt) REVERT: A 201 ASN cc_start: 0.6603 (m-40) cc_final: 0.5624 (t0) REVERT: A 238 PHE cc_start: 0.8678 (OUTLIER) cc_final: 0.7840 (m-10) REVERT: A 287 MET cc_start: 0.8179 (mtp) cc_final: 0.7826 (mtp) REVERT: A 299 MET cc_start: 0.6592 (mmm) cc_final: 0.6064 (mtt) REVERT: A 371 PHE cc_start: 0.9228 (OUTLIER) cc_final: 0.8691 (t80) REVERT: A 390 TYR cc_start: 0.8754 (t80) cc_final: 0.8238 (t80) REVERT: B 12 LEU cc_start: 0.6156 (OUTLIER) cc_final: 0.5636 (pp) REVERT: B 28 GLN cc_start: 0.7387 (tp-100) cc_final: 0.6812 (tp-100) REVERT: C 23 VAL cc_start: 0.9184 (m) cc_final: 0.8970 (m) REVERT: C 25 LEU cc_start: 0.8173 (mt) cc_final: 0.7914 (mp) REVERT: C 192 ASN cc_start: 0.8776 (t0) cc_final: 0.8516 (t0) REVERT: C 258 MET cc_start: 0.8826 (tpp) cc_final: 0.8364 (tpp) REVERT: C 293 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8187 (pptt) REVERT: C 358 LYS cc_start: 0.7776 (OUTLIER) cc_final: 0.7372 (tppt) REVERT: C 380 ILE cc_start: 0.7823 (mt) cc_final: 0.7595 (tt) REVERT: C 436 GLN cc_start: 0.8193 (tm-30) cc_final: 0.7962 (tt0) REVERT: D 42 PHE cc_start: 0.8719 (t80) cc_final: 0.8068 (t80) REVERT: D 69 LEU cc_start: 0.8554 (mt) cc_final: 0.8221 (mt) REVERT: D 74 MET cc_start: 0.8592 (tpp) cc_final: 0.7866 (mmm) REVERT: E 8 ASN cc_start: 0.8131 (t0) cc_final: 0.7740 (t0) REVERT: E 20 TRP cc_start: 0.7565 (p90) cc_final: 0.6319 (p90) REVERT: E 108 PHE cc_start: 0.8642 (m-80) cc_final: 0.8287 (m-80) REVERT: E 122 LEU cc_start: 0.6836 (OUTLIER) cc_final: 0.6460 (tp) REVERT: E 176 TYR cc_start: 0.8760 (m-80) cc_final: 0.8395 (m-80) REVERT: E 181 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8715 (pp) REVERT: E 251 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.7978 (tt) REVERT: E 259 HIS cc_start: 0.9070 (OUTLIER) cc_final: 0.7126 (t70) REVERT: E 286 LYS cc_start: 0.8419 (ptpt) cc_final: 0.8028 (mtmm) REVERT: E 320 ILE cc_start: 0.9416 (mm) cc_final: 0.9159 (mt) REVERT: E 401 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7643 (mm-30) REVERT: E 410 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.8097 (mtp) REVERT: E 442 TYR cc_start: 0.8871 (t80) cc_final: 0.8359 (t80) REVERT: E 484 THR cc_start: 0.8941 (m) cc_final: 0.8649 (p) REVERT: H 3 GLU cc_start: 0.6359 (mm-30) cc_final: 0.6090 (mm-30) REVERT: H 47 TRP cc_start: 0.8029 (t60) cc_final: 0.7390 (t60) REVERT: H 65 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7261 (mtmt) REVERT: H 111 TYR cc_start: 0.8195 (m-80) cc_final: 0.7973 (m-10) REVERT: H 114 GLN cc_start: 0.7514 (tp40) cc_final: 0.7288 (tp-100) REVERT: L 45 LYS cc_start: 0.8776 (mttp) cc_final: 0.8330 (mptp) REVERT: O 6 VAL cc_start: 0.7965 (t) cc_final: 0.7603 (p) REVERT: O 53 LEU cc_start: 0.8112 (mt) cc_final: 0.7883 (mt) REVERT: O 57 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.7373 (ttm110) REVERT: O 98 ASP cc_start: 0.8075 (p0) cc_final: 0.7797 (p0) REVERT: O 168 THR cc_start: 0.9044 (OUTLIER) cc_final: 0.8548 (p) REVERT: O 181 LEU cc_start: 0.8397 (tp) cc_final: 0.8084 (tp) REVERT: O 196 LEU cc_start: 0.7699 (mt) cc_final: 0.7365 (mt) REVERT: O 238 PHE cc_start: 0.8669 (OUTLIER) cc_final: 0.7876 (m-10) REVERT: O 287 MET cc_start: 0.8181 (mtp) cc_final: 0.7964 (mtp) REVERT: O 299 MET cc_start: 0.6573 (mmm) cc_final: 0.6073 (mtt) REVERT: O 371 PHE cc_start: 0.9266 (OUTLIER) cc_final: 0.8727 (t80) REVERT: O 390 TYR cc_start: 0.8757 (t80) cc_final: 0.8242 (t80) REVERT: P 12 LEU cc_start: 0.5963 (OUTLIER) cc_final: 0.5386 (pp) REVERT: P 28 GLN cc_start: 0.7419 (tp-100) cc_final: 0.7076 (tp-100) REVERT: Q 25 LEU cc_start: 0.8170 (mt) cc_final: 0.7875 (mp) REVERT: Q 258 MET cc_start: 0.8824 (tpp) cc_final: 0.8363 (tpp) REVERT: Q 293 LYS cc_start: 0.9103 (OUTLIER) cc_final: 0.8574 (pptt) REVERT: Q 380 ILE cc_start: 0.7824 (mt) cc_final: 0.7596 (tt) REVERT: Q 436 GLN cc_start: 0.8194 (tm-30) cc_final: 0.7953 (tt0) REVERT: R 35 TRP cc_start: 0.8975 (t60) cc_final: 0.8732 (t60) REVERT: R 42 PHE cc_start: 0.8707 (t80) cc_final: 0.8049 (t80) REVERT: R 74 MET cc_start: 0.8610 (tpp) cc_final: 0.8201 (mmm) REVERT: S 8 ASN cc_start: 0.8278 (t0) cc_final: 0.7866 (t0) REVERT: S 20 TRP cc_start: 0.7564 (p90) cc_final: 0.6405 (p90) REVERT: S 108 PHE cc_start: 0.8647 (m-80) cc_final: 0.8288 (m-80) REVERT: S 176 TYR cc_start: 0.8860 (m-80) cc_final: 0.8497 (m-80) REVERT: S 250 VAL cc_start: 0.8645 (t) cc_final: 0.8434 (m) REVERT: S 259 HIS cc_start: 0.8950 (OUTLIER) cc_final: 0.7045 (t70) REVERT: S 270 ASN cc_start: 0.6480 (t0) cc_final: 0.6144 (t0) REVERT: S 286 LYS cc_start: 0.8410 (ptpt) cc_final: 0.8021 (mtmm) REVERT: S 442 TYR cc_start: 0.8880 (t80) cc_final: 0.8367 (t80) REVERT: S 484 THR cc_start: 0.8951 (m) cc_final: 0.8662 (p) REVERT: U 3 GLU cc_start: 0.6344 (mm-30) cc_final: 0.6051 (mm-30) REVERT: U 47 TRP cc_start: 0.8022 (t60) cc_final: 0.7391 (t60) REVERT: U 65 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7248 (mtmt) REVERT: U 111 TYR cc_start: 0.8084 (m-80) cc_final: 0.7806 (m-10) REVERT: U 114 GLN cc_start: 0.7531 (tp40) cc_final: 0.7301 (tp-100) outliers start: 207 outliers final: 163 residues processed: 890 average time/residue: 0.3678 time to fit residues: 537.9867 Evaluate side-chains 905 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 721 time to evaluate : 3.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 30 CYS Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 293 LYS Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 242 HIS Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 258 MET Chi-restraints excluded: chain E residue 259 HIS Chi-restraints excluded: chain E residue 318 ILE Chi-restraints excluded: chain E residue 336 SER Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 410 MET Chi-restraints excluded: chain E residue 451 TRP Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 76 ASP Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain O residue 26 GLU Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 57 ARG Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain O residue 121 CYS Chi-restraints excluded: chain O residue 130 VAL Chi-restraints excluded: chain O residue 168 THR Chi-restraints excluded: chain O residue 187 THR Chi-restraints excluded: chain O residue 195 ILE Chi-restraints excluded: chain O residue 198 THR Chi-restraints excluded: chain O residue 233 GLU Chi-restraints excluded: chain O residue 237 THR Chi-restraints excluded: chain O residue 238 PHE Chi-restraints excluded: chain O residue 266 THR Chi-restraints excluded: chain O residue 275 SER Chi-restraints excluded: chain O residue 283 CYS Chi-restraints excluded: chain O residue 320 ILE Chi-restraints excluded: chain O residue 337 THR Chi-restraints excluded: chain O residue 338 GLU Chi-restraints excluded: chain O residue 365 ILE Chi-restraints excluded: chain O residue 371 PHE Chi-restraints excluded: chain O residue 387 ILE Chi-restraints excluded: chain O residue 413 LEU Chi-restraints excluded: chain O residue 423 VAL Chi-restraints excluded: chain O residue 429 SER Chi-restraints excluded: chain O residue 433 MET Chi-restraints excluded: chain O residue 466 LEU Chi-restraints excluded: chain O residue 484 THR Chi-restraints excluded: chain P residue 12 LEU Chi-restraints excluded: chain P residue 14 THR Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 49 LEU Chi-restraints excluded: chain P residue 67 LEU Chi-restraints excluded: chain Q residue 10 ASP Chi-restraints excluded: chain Q residue 30 CYS Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 48 THR Chi-restraints excluded: chain Q residue 59 LEU Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 107 LEU Chi-restraints excluded: chain Q residue 113 LEU Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain Q residue 158 VAL Chi-restraints excluded: chain Q residue 195 ILE Chi-restraints excluded: chain Q residue 236 VAL Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain Q residue 293 LYS Chi-restraints excluded: chain Q residue 313 THR Chi-restraints excluded: chain Q residue 356 VAL Chi-restraints excluded: chain Q residue 357 THR Chi-restraints excluded: chain Q residue 371 PHE Chi-restraints excluded: chain Q residue 377 VAL Chi-restraints excluded: chain Q residue 466 LEU Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain S residue 10 ASP Chi-restraints excluded: chain S residue 41 LEU Chi-restraints excluded: chain S residue 79 GLU Chi-restraints excluded: chain S residue 91 VAL Chi-restraints excluded: chain S residue 92 CYS Chi-restraints excluded: chain S residue 125 ILE Chi-restraints excluded: chain S residue 130 VAL Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 142 THR Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain S residue 181 LEU Chi-restraints excluded: chain S residue 187 THR Chi-restraints excluded: chain S residue 242 HIS Chi-restraints excluded: chain S residue 258 MET Chi-restraints excluded: chain S residue 259 HIS Chi-restraints excluded: chain S residue 266 THR Chi-restraints excluded: chain S residue 318 ILE Chi-restraints excluded: chain S residue 336 SER Chi-restraints excluded: chain S residue 356 VAL Chi-restraints excluded: chain S residue 428 ASN Chi-restraints excluded: chain S residue 451 TRP Chi-restraints excluded: chain S residue 464 ILE Chi-restraints excluded: chain S residue 485 LEU Chi-restraints excluded: chain T residue 14 THR Chi-restraints excluded: chain T residue 16 THR Chi-restraints excluded: chain T residue 58 THR Chi-restraints excluded: chain U residue 17 SER Chi-restraints excluded: chain U residue 22 CYS Chi-restraints excluded: chain U residue 25 SER Chi-restraints excluded: chain U residue 53 SER Chi-restraints excluded: chain U residue 63 SER Chi-restraints excluded: chain U residue 65 LYS Chi-restraints excluded: chain U residue 83 MET Chi-restraints excluded: chain U residue 91 THR Chi-restraints excluded: chain V residue 13 VAL Chi-restraints excluded: chain V residue 76 ASP Chi-restraints excluded: chain V residue 84 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 334 optimal weight: 20.0000 chunk 352 optimal weight: 9.9990 chunk 321 optimal weight: 7.9990 chunk 343 optimal weight: 30.0000 chunk 206 optimal weight: 0.2980 chunk 149 optimal weight: 9.9990 chunk 269 optimal weight: 8.9990 chunk 105 optimal weight: 8.9990 chunk 310 optimal weight: 40.0000 chunk 324 optimal weight: 0.9990 chunk 341 optimal weight: 10.0000 overall best weight: 5.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 ASN ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 17 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 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 GLN ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 85 GLN ** O 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 353 ASN ** R 17 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 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 100 GLN V 27 GLN ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 85 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 30814 Z= 0.284 Angle : 0.697 12.437 41776 Z= 0.344 Chirality : 0.044 0.278 4928 Planarity : 0.004 0.048 5192 Dihedral : 9.550 112.518 4876 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 6.42 % Allowed : 23.18 % Favored : 70.39 % 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: -1.43 (0.13), residues: 3846 helix: 1.18 (0.18), residues: 882 sheet: -1.41 (0.15), residues: 1072 loop : -1.69 (0.13), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP O 20 HIS 0.005 0.001 HIS A 94 PHE 0.032 0.002 PHE T 48 TYR 0.019 0.001 TYR H 111 ARG 0.009 0.001 ARG O 348 *********************** 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 949 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 742 time to evaluate : 3.541 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PRO B 72 " (corrupted residue). Skipping it. Corrupt residue: chain: B residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO P 72 " (corrupted residue). Skipping it. Corrupt residue: chain: P residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.9278 (mmtt) cc_final: 0.9052 (mmtm) REVERT: A 57 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.7427 (ttm110) REVERT: A 98 ASP cc_start: 0.8066 (p0) cc_final: 0.7802 (p0) REVERT: A 168 THR cc_start: 0.9073 (OUTLIER) cc_final: 0.8579 (p) REVERT: A 181 LEU cc_start: 0.8424 (tp) cc_final: 0.8053 (tp) REVERT: A 196 LEU cc_start: 0.7688 (mt) cc_final: 0.7426 (mt) REVERT: A 201 ASN cc_start: 0.6372 (m-40) cc_final: 0.5547 (t0) REVERT: A 238 PHE cc_start: 0.8672 (OUTLIER) cc_final: 0.7896 (m-10) REVERT: A 287 MET cc_start: 0.8171 (mtp) cc_final: 0.7832 (mtp) REVERT: A 299 MET cc_start: 0.6542 (mmm) cc_final: 0.6100 (mtt) REVERT: A 371 PHE cc_start: 0.9236 (OUTLIER) cc_final: 0.8688 (t80) REVERT: A 390 TYR cc_start: 0.8735 (t80) cc_final: 0.8276 (t80) REVERT: B 12 LEU cc_start: 0.6468 (OUTLIER) cc_final: 0.5966 (pp) REVERT: B 28 GLN cc_start: 0.7358 (tp-100) cc_final: 0.6856 (tp-100) REVERT: B 69 LEU cc_start: 0.8399 (tp) cc_final: 0.7862 (mp) REVERT: C 23 VAL cc_start: 0.9188 (m) cc_final: 0.8982 (m) REVERT: C 25 LEU cc_start: 0.8150 (mt) cc_final: 0.7891 (mp) REVERT: C 182 GLU cc_start: 0.7116 (tp30) cc_final: 0.6471 (tp30) REVERT: C 192 ASN cc_start: 0.8718 (t0) cc_final: 0.8449 (t0) REVERT: C 258 MET cc_start: 0.8816 (tpp) cc_final: 0.8366 (tpp) REVERT: C 293 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8167 (pptt) REVERT: C 358 LYS cc_start: 0.7776 (OUTLIER) cc_final: 0.7380 (tppt) REVERT: C 380 ILE cc_start: 0.7809 (mt) cc_final: 0.7589 (tt) REVERT: C 436 GLN cc_start: 0.8208 (tm-30) cc_final: 0.7799 (tm-30) REVERT: D 42 PHE cc_start: 0.8708 (t80) cc_final: 0.8080 (t80) REVERT: D 69 LEU cc_start: 0.8520 (mt) cc_final: 0.8225 (mt) REVERT: D 73 SER cc_start: 0.7439 (OUTLIER) cc_final: 0.7105 (t) REVERT: D 74 MET cc_start: 0.8592 (tpp) cc_final: 0.7899 (mmm) REVERT: E 8 ASN cc_start: 0.8370 (t0) cc_final: 0.8063 (t0) REVERT: E 20 TRP cc_start: 0.7566 (p90) cc_final: 0.6315 (p90) REVERT: E 108 PHE cc_start: 0.8649 (m-80) cc_final: 0.8033 (m-80) REVERT: E 122 LEU cc_start: 0.6769 (OUTLIER) cc_final: 0.6402 (tp) REVERT: E 176 TYR cc_start: 0.8743 (m-80) cc_final: 0.8374 (m-80) REVERT: E 181 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8746 (pp) REVERT: E 251 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.7968 (tt) REVERT: E 259 HIS cc_start: 0.9047 (OUTLIER) cc_final: 0.7024 (t70) REVERT: E 286 LYS cc_start: 0.8402 (ptpt) cc_final: 0.8054 (mtmm) REVERT: E 320 ILE cc_start: 0.9410 (mm) cc_final: 0.9156 (mt) REVERT: E 401 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7773 (mm-30) REVERT: E 410 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.8081 (mtp) REVERT: E 442 TYR cc_start: 0.8901 (t80) cc_final: 0.8391 (t80) REVERT: E 484 THR cc_start: 0.8947 (m) cc_final: 0.8653 (p) REVERT: H 3 GLU cc_start: 0.6414 (mm-30) cc_final: 0.6203 (mm-30) REVERT: H 47 TRP cc_start: 0.8058 (t60) cc_final: 0.7416 (t60) REVERT: H 65 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7227 (mtmt) REVERT: H 111 TYR cc_start: 0.8110 (m-80) cc_final: 0.7760 (m-10) REVERT: H 114 GLN cc_start: 0.7654 (tp40) cc_final: 0.7407 (tp-100) REVERT: O 57 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.7358 (ttm110) REVERT: O 98 ASP cc_start: 0.8067 (p0) cc_final: 0.7810 (p0) REVERT: O 168 THR cc_start: 0.9071 (OUTLIER) cc_final: 0.8588 (p) REVERT: O 181 LEU cc_start: 0.8375 (tp) cc_final: 0.8090 (tp) REVERT: O 201 ASN cc_start: 0.6935 (m-40) cc_final: 0.6296 (t0) REVERT: O 238 PHE cc_start: 0.8659 (OUTLIER) cc_final: 0.7893 (m-10) REVERT: O 287 MET cc_start: 0.8165 (mtp) cc_final: 0.7949 (mtp) REVERT: O 299 MET cc_start: 0.6543 (mmm) cc_final: 0.6097 (mtt) REVERT: O 371 PHE cc_start: 0.9255 (OUTLIER) cc_final: 0.8691 (t80) REVERT: O 390 TYR cc_start: 0.8714 (t80) cc_final: 0.8251 (t80) REVERT: P 12 LEU cc_start: 0.6436 (OUTLIER) cc_final: 0.5984 (pp) REVERT: P 28 GLN cc_start: 0.7338 (tp-100) cc_final: 0.6757 (tp-100) REVERT: Q 23 VAL cc_start: 0.9194 (m) cc_final: 0.8994 (m) REVERT: Q 25 LEU cc_start: 0.8155 (mt) cc_final: 0.7896 (mp) REVERT: Q 192 ASN cc_start: 0.8649 (t0) cc_final: 0.8363 (t0) REVERT: Q 258 MET cc_start: 0.8826 (tpp) cc_final: 0.8368 (tpp) REVERT: Q 293 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8186 (pptt) REVERT: Q 380 ILE cc_start: 0.7818 (mt) cc_final: 0.7592 (tt) REVERT: Q 436 GLN cc_start: 0.8190 (tm-30) cc_final: 0.7833 (tm-30) REVERT: R 35 TRP cc_start: 0.8966 (t60) cc_final: 0.8729 (t60) REVERT: R 42 PHE cc_start: 0.8703 (t80) cc_final: 0.8062 (t80) REVERT: R 74 MET cc_start: 0.8526 (tpp) cc_final: 0.7675 (mmm) REVERT: S 8 ASN cc_start: 0.8141 (t0) cc_final: 0.7848 (t0) REVERT: S 20 TRP cc_start: 0.7554 (p90) cc_final: 0.6342 (p90) REVERT: S 108 PHE cc_start: 0.8646 (m-80) cc_final: 0.8017 (m-80) REVERT: S 176 TYR cc_start: 0.8860 (m-80) cc_final: 0.8462 (m-80) REVERT: S 250 VAL cc_start: 0.8579 (t) cc_final: 0.8354 (m) REVERT: S 259 HIS cc_start: 0.8904 (OUTLIER) cc_final: 0.6922 (t70) REVERT: S 286 LYS cc_start: 0.8400 (ptpt) cc_final: 0.8049 (mtmm) REVERT: S 428 ASN cc_start: 0.8008 (m-40) cc_final: 0.7788 (t0) REVERT: S 442 TYR cc_start: 0.8913 (t80) cc_final: 0.8398 (t80) REVERT: S 484 THR cc_start: 0.8955 (m) cc_final: 0.8666 (p) REVERT: U 3 GLU cc_start: 0.6609 (mm-30) cc_final: 0.6394 (mm-30) REVERT: U 47 TRP cc_start: 0.8051 (t60) cc_final: 0.7406 (t60) REVERT: U 65 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7910 (mtpp) REVERT: U 111 TYR cc_start: 0.8239 (m-80) cc_final: 0.7899 (m-10) REVERT: U 114 GLN cc_start: 0.7663 (tp40) cc_final: 0.7417 (tp-100) outliers start: 207 outliers final: 166 residues processed: 892 average time/residue: 0.3700 time to fit residues: 542.8220 Evaluate side-chains 916 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 728 time to evaluate : 3.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 30 CYS Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 293 LYS Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 242 HIS Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 258 MET Chi-restraints excluded: chain E residue 259 HIS Chi-restraints excluded: chain E residue 318 ILE Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 410 MET Chi-restraints excluded: chain E residue 451 TRP Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 76 ASP Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain O residue 26 GLU Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 51 THR Chi-restraints excluded: chain O residue 57 ARG Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain O residue 121 CYS Chi-restraints excluded: chain O residue 130 VAL Chi-restraints excluded: chain O residue 168 THR Chi-restraints excluded: chain O residue 187 THR Chi-restraints excluded: chain O residue 195 ILE Chi-restraints excluded: chain O residue 198 THR Chi-restraints excluded: chain O residue 237 THR Chi-restraints excluded: chain O residue 238 PHE Chi-restraints excluded: chain O residue 266 THR Chi-restraints excluded: chain O residue 275 SER Chi-restraints excluded: chain O residue 283 CYS Chi-restraints excluded: chain O residue 320 ILE Chi-restraints excluded: chain O residue 337 THR Chi-restraints excluded: chain O residue 338 GLU Chi-restraints excluded: chain O residue 365 ILE Chi-restraints excluded: chain O residue 371 PHE Chi-restraints excluded: chain O residue 387 ILE Chi-restraints excluded: chain O residue 413 LEU Chi-restraints excluded: chain O residue 423 VAL Chi-restraints excluded: chain O residue 429 SER Chi-restraints excluded: chain O residue 433 MET Chi-restraints excluded: chain O residue 466 LEU Chi-restraints excluded: chain O residue 484 THR Chi-restraints excluded: chain P residue 12 LEU Chi-restraints excluded: chain P residue 14 THR Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 67 LEU Chi-restraints excluded: chain Q residue 10 ASP Chi-restraints excluded: chain Q residue 30 CYS Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 48 THR Chi-restraints excluded: chain Q residue 59 LEU Chi-restraints excluded: chain Q residue 65 ILE Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 107 LEU Chi-restraints excluded: chain Q residue 113 LEU Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain Q residue 158 VAL Chi-restraints excluded: chain Q residue 201 ASN Chi-restraints excluded: chain Q residue 236 VAL Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain Q residue 293 LYS Chi-restraints excluded: chain Q residue 313 THR Chi-restraints excluded: chain Q residue 356 VAL Chi-restraints excluded: chain Q residue 357 THR Chi-restraints excluded: chain Q residue 371 PHE Chi-restraints excluded: chain Q residue 466 LEU Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain R residue 34 THR Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain S residue 10 ASP Chi-restraints excluded: chain S residue 41 LEU Chi-restraints excluded: chain S residue 79 GLU Chi-restraints excluded: chain S residue 91 VAL Chi-restraints excluded: chain S residue 92 CYS Chi-restraints excluded: chain S residue 125 ILE Chi-restraints excluded: chain S residue 130 VAL Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 142 THR Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain S residue 163 THR Chi-restraints excluded: chain S residue 181 LEU Chi-restraints excluded: chain S residue 187 THR Chi-restraints excluded: chain S residue 242 HIS Chi-restraints excluded: chain S residue 258 MET Chi-restraints excluded: chain S residue 259 HIS Chi-restraints excluded: chain S residue 266 THR Chi-restraints excluded: chain S residue 313 THR Chi-restraints excluded: chain S residue 318 ILE Chi-restraints excluded: chain S residue 356 VAL Chi-restraints excluded: chain S residue 451 TRP Chi-restraints excluded: chain S residue 464 ILE Chi-restraints excluded: chain S residue 485 LEU Chi-restraints excluded: chain T residue 14 THR Chi-restraints excluded: chain T residue 16 THR Chi-restraints excluded: chain T residue 58 THR Chi-restraints excluded: chain U residue 17 SER Chi-restraints excluded: chain U residue 22 CYS Chi-restraints excluded: chain U residue 25 SER Chi-restraints excluded: chain U residue 53 SER Chi-restraints excluded: chain U residue 63 SER Chi-restraints excluded: chain U residue 65 LYS Chi-restraints excluded: chain U residue 83 MET Chi-restraints excluded: chain U residue 91 THR Chi-restraints excluded: chain V residue 13 VAL Chi-restraints excluded: chain V residue 76 ASP Chi-restraints excluded: chain V residue 84 VAL Chi-restraints excluded: chain V residue 100 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: 8.9990 chunk 221 optimal weight: 20.0000 chunk 172 optimal weight: 5.9990 chunk 252 optimal weight: 20.0000 chunk 380 optimal weight: 9.9990 chunk 350 optimal weight: 8.9990 chunk 303 optimal weight: 9.9990 chunk 31 optimal weight: 0.9980 chunk 234 optimal weight: 5.9990 chunk 185 optimal weight: 8.9990 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 ASN ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 17 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 134 ASN ** E 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 150 GLN E 242 HIS ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 GLN L 27 GLN ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 353 ASN ** Q 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 17 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 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 242 HIS S 428 ASN ** T 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 100 GLN V 51 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 30814 Z= 0.313 Angle : 0.722 16.884 41776 Z= 0.357 Chirality : 0.045 0.309 4928 Planarity : 0.004 0.046 5192 Dihedral : 9.457 110.776 4876 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 6.33 % Allowed : 23.56 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.50 (0.13), residues: 3846 helix: 1.09 (0.18), residues: 888 sheet: -1.50 (0.15), residues: 1072 loop : -1.70 (0.13), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 35 HIS 0.004 0.001 HIS C 149 PHE 0.019 0.002 PHE S 475 TYR 0.019 0.001 TYR H 111 ARG 0.008 0.001 ARG A 348 ********************** 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 941 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 737 time to evaluate : 3.444 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PRO B 72 " (corrupted residue). Skipping it. Corrupt residue: chain: B residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO P 72 " (corrupted residue). Skipping it. Corrupt residue: chain: P residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.9274 (mmtt) cc_final: 0.9048 (mmtm) REVERT: A 57 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.7429 (ttm110) REVERT: A 98 ASP cc_start: 0.8051 (p0) cc_final: 0.7767 (p0) REVERT: A 168 THR cc_start: 0.9062 (OUTLIER) cc_final: 0.8552 (p) REVERT: A 181 LEU cc_start: 0.8449 (tp) cc_final: 0.8084 (tp) REVERT: A 196 LEU cc_start: 0.7703 (mt) cc_final: 0.7472 (mt) REVERT: A 201 ASN cc_start: 0.6924 (m-40) cc_final: 0.5990 (t0) REVERT: A 238 PHE cc_start: 0.8752 (OUTLIER) cc_final: 0.7955 (m-10) REVERT: A 287 MET cc_start: 0.8169 (mtp) cc_final: 0.7831 (mtp) REVERT: A 299 MET cc_start: 0.6525 (mmm) cc_final: 0.6111 (mtt) REVERT: A 371 PHE cc_start: 0.9234 (OUTLIER) cc_final: 0.8609 (t80) REVERT: A 390 TYR cc_start: 0.8610 (t80) cc_final: 0.8246 (t80) REVERT: A 477 CYS cc_start: 0.7368 (OUTLIER) cc_final: 0.7072 (t) REVERT: B 12 LEU cc_start: 0.6768 (OUTLIER) cc_final: 0.6291 (pp) REVERT: B 28 GLN cc_start: 0.7337 (tp-100) cc_final: 0.6855 (tp-100) REVERT: B 69 LEU cc_start: 0.8426 (tp) cc_final: 0.7910 (mp) REVERT: C 23 VAL cc_start: 0.9213 (m) cc_final: 0.8996 (m) REVERT: C 25 LEU cc_start: 0.8232 (mt) cc_final: 0.7919 (mp) REVERT: C 182 GLU cc_start: 0.7142 (tp30) cc_final: 0.6476 (tp30) REVERT: C 192 ASN cc_start: 0.8749 (t0) cc_final: 0.8484 (t0) REVERT: C 258 MET cc_start: 0.8819 (tpp) cc_final: 0.8371 (tpp) REVERT: C 293 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8063 (pptt) REVERT: C 358 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.7400 (tppt) REVERT: C 380 ILE cc_start: 0.7830 (mt) cc_final: 0.7601 (tt) REVERT: D 42 PHE cc_start: 0.8718 (t80) cc_final: 0.8085 (t80) REVERT: D 69 LEU cc_start: 0.8542 (mt) cc_final: 0.8254 (mt) REVERT: D 73 SER cc_start: 0.7415 (OUTLIER) cc_final: 0.6975 (t) REVERT: D 74 MET cc_start: 0.8522 (tpp) cc_final: 0.7794 (mmm) REVERT: E 8 ASN cc_start: 0.8397 (t0) cc_final: 0.8091 (t0) REVERT: E 20 TRP cc_start: 0.7614 (p90) cc_final: 0.6325 (p90) REVERT: E 108 PHE cc_start: 0.8673 (m-80) cc_final: 0.8067 (m-80) REVERT: E 122 LEU cc_start: 0.7141 (OUTLIER) cc_final: 0.6763 (tp) REVERT: E 176 TYR cc_start: 0.8764 (m-80) cc_final: 0.8387 (m-80) REVERT: E 181 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8757 (pp) REVERT: E 251 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.7963 (tt) REVERT: E 259 HIS cc_start: 0.8942 (OUTLIER) cc_final: 0.6926 (t70) REVERT: E 286 LYS cc_start: 0.8395 (ptpt) cc_final: 0.7968 (mtmt) REVERT: E 320 ILE cc_start: 0.9412 (mm) cc_final: 0.9158 (mt) REVERT: E 401 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7783 (mm-30) REVERT: E 410 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.8081 (mtp) REVERT: E 442 TYR cc_start: 0.8926 (t80) cc_final: 0.8419 (t80) REVERT: E 473 MET cc_start: 0.4753 (pmm) cc_final: 0.3469 (mtm) REVERT: E 484 THR cc_start: 0.8943 (m) cc_final: 0.8652 (p) REVERT: H 47 TRP cc_start: 0.8112 (t60) cc_final: 0.7364 (t60) REVERT: H 65 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.7935 (mtpp) REVERT: H 111 TYR cc_start: 0.8195 (m-80) cc_final: 0.7872 (m-10) REVERT: O 57 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.7430 (ttm110) REVERT: O 98 ASP cc_start: 0.8053 (p0) cc_final: 0.7777 (p0) REVERT: O 168 THR cc_start: 0.9064 (OUTLIER) cc_final: 0.8561 (p) REVERT: O 181 LEU cc_start: 0.8403 (tp) cc_final: 0.8125 (tp) REVERT: O 196 LEU cc_start: 0.7205 (mt) cc_final: 0.6743 (mp) REVERT: O 201 ASN cc_start: 0.6981 (m-40) cc_final: 0.6305 (t0) REVERT: O 238 PHE cc_start: 0.8715 (OUTLIER) cc_final: 0.7929 (m-10) REVERT: O 287 MET cc_start: 0.8160 (mtp) cc_final: 0.7942 (mtp) REVERT: O 299 MET cc_start: 0.6473 (mmm) cc_final: 0.6109 (mtt) REVERT: O 371 PHE cc_start: 0.9258 (OUTLIER) cc_final: 0.8600 (t80) REVERT: O 390 TYR cc_start: 0.8592 (t80) cc_final: 0.8268 (t80) REVERT: P 12 LEU cc_start: 0.6585 (OUTLIER) cc_final: 0.5949 (pp) REVERT: P 28 GLN cc_start: 0.7417 (tp-100) cc_final: 0.7114 (tp-100) REVERT: Q 23 VAL cc_start: 0.9217 (m) cc_final: 0.9005 (m) REVERT: Q 25 LEU cc_start: 0.8237 (mt) cc_final: 0.7921 (mp) REVERT: Q 213 ASP cc_start: 0.7032 (m-30) cc_final: 0.6831 (m-30) REVERT: Q 258 MET cc_start: 0.8823 (tpp) cc_final: 0.8376 (tpp) REVERT: Q 293 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8071 (pptt) REVERT: Q 380 ILE cc_start: 0.7839 (mt) cc_final: 0.7605 (tt) REVERT: Q 436 GLN cc_start: 0.8219 (tm-30) cc_final: 0.7870 (tt0) REVERT: R 35 TRP cc_start: 0.9022 (t60) cc_final: 0.8797 (t60) REVERT: R 42 PHE cc_start: 0.8715 (t80) cc_final: 0.8064 (t80) REVERT: R 69 LEU cc_start: 0.8439 (mt) cc_final: 0.8174 (mt) REVERT: R 74 MET cc_start: 0.8563 (tpp) cc_final: 0.8083 (mmm) REVERT: S 8 ASN cc_start: 0.8198 (t0) cc_final: 0.7896 (t0) REVERT: S 20 TRP cc_start: 0.7520 (p90) cc_final: 0.6221 (p90) REVERT: S 108 PHE cc_start: 0.8662 (m-80) cc_final: 0.8045 (m-80) REVERT: S 176 TYR cc_start: 0.8797 (m-80) cc_final: 0.8389 (m-80) REVERT: S 250 VAL cc_start: 0.8584 (t) cc_final: 0.8374 (m) REVERT: S 259 HIS cc_start: 0.8910 (OUTLIER) cc_final: 0.6907 (t70) REVERT: S 270 ASN cc_start: 0.6563 (t0) cc_final: 0.6360 (t0) REVERT: S 286 LYS cc_start: 0.8398 (ptpt) cc_final: 0.8007 (mtmt) REVERT: S 442 TYR cc_start: 0.8941 (t80) cc_final: 0.8437 (t80) REVERT: S 484 THR cc_start: 0.8953 (m) cc_final: 0.8673 (p) REVERT: U 47 TRP cc_start: 0.8090 (t60) cc_final: 0.7381 (t60) REVERT: U 65 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.7934 (mtpp) REVERT: U 90 ASP cc_start: 0.7062 (t0) cc_final: 0.6761 (t0) REVERT: U 111 TYR cc_start: 0.8277 (m-80) cc_final: 0.7947 (m-10) outliers start: 204 outliers final: 168 residues processed: 887 average time/residue: 0.3909 time to fit residues: 568.5475 Evaluate side-chains 910 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 719 time to evaluate : 3.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 30 CYS Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 293 LYS Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 242 HIS Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 258 MET Chi-restraints excluded: chain E residue 259 HIS Chi-restraints excluded: chain E residue 318 ILE Chi-restraints excluded: chain E residue 336 SER Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 410 MET Chi-restraints excluded: chain E residue 451 TRP Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 76 ASP Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain O residue 26 GLU Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 57 ARG Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain O residue 121 CYS Chi-restraints excluded: chain O residue 130 VAL Chi-restraints excluded: chain O residue 168 THR Chi-restraints excluded: chain O residue 187 THR Chi-restraints excluded: chain O residue 195 ILE Chi-restraints excluded: chain O residue 198 THR Chi-restraints excluded: chain O residue 233 GLU Chi-restraints excluded: chain O residue 238 PHE Chi-restraints excluded: chain O residue 266 THR Chi-restraints excluded: chain O residue 275 SER Chi-restraints excluded: chain O residue 283 CYS Chi-restraints excluded: chain O residue 320 ILE Chi-restraints excluded: chain O residue 337 THR Chi-restraints excluded: chain O residue 338 GLU Chi-restraints excluded: chain O residue 365 ILE Chi-restraints excluded: chain O residue 371 PHE Chi-restraints excluded: chain O residue 387 ILE Chi-restraints excluded: chain O residue 413 LEU Chi-restraints excluded: chain O residue 423 VAL Chi-restraints excluded: chain O residue 429 SER Chi-restraints excluded: chain O residue 433 MET Chi-restraints excluded: chain O residue 452 VAL Chi-restraints excluded: chain O residue 466 LEU Chi-restraints excluded: chain O residue 484 THR Chi-restraints excluded: chain P residue 12 LEU Chi-restraints excluded: chain P residue 14 THR Chi-restraints excluded: chain P residue 67 LEU Chi-restraints excluded: chain Q residue 10 ASP Chi-restraints excluded: chain Q residue 30 CYS Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 48 THR Chi-restraints excluded: chain Q residue 59 LEU Chi-restraints excluded: chain Q residue 65 ILE Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 107 LEU Chi-restraints excluded: chain Q residue 113 LEU Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain Q residue 158 VAL Chi-restraints excluded: chain Q residue 201 ASN Chi-restraints excluded: chain Q residue 236 VAL Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain Q residue 293 LYS Chi-restraints excluded: chain Q residue 313 THR Chi-restraints excluded: chain Q residue 356 VAL Chi-restraints excluded: chain Q residue 357 THR Chi-restraints excluded: chain Q residue 371 PHE Chi-restraints excluded: chain Q residue 466 LEU Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain R residue 34 THR Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain S residue 10 ASP Chi-restraints excluded: chain S residue 41 LEU Chi-restraints excluded: chain S residue 79 GLU Chi-restraints excluded: chain S residue 91 VAL Chi-restraints excluded: chain S residue 92 CYS Chi-restraints excluded: chain S residue 125 ILE Chi-restraints excluded: chain S residue 130 VAL Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain S residue 163 THR Chi-restraints excluded: chain S residue 181 LEU Chi-restraints excluded: chain S residue 187 THR Chi-restraints excluded: chain S residue 242 HIS Chi-restraints excluded: chain S residue 258 MET Chi-restraints excluded: chain S residue 259 HIS Chi-restraints excluded: chain S residue 266 THR Chi-restraints excluded: chain S residue 310 VAL Chi-restraints excluded: chain S residue 313 THR Chi-restraints excluded: chain S residue 318 ILE Chi-restraints excluded: chain S residue 356 VAL Chi-restraints excluded: chain S residue 428 ASN Chi-restraints excluded: chain S residue 451 TRP Chi-restraints excluded: chain S residue 464 ILE Chi-restraints excluded: chain S residue 485 LEU Chi-restraints excluded: chain T residue 14 THR Chi-restraints excluded: chain T residue 16 THR Chi-restraints excluded: chain T residue 58 THR Chi-restraints excluded: chain U residue 17 SER Chi-restraints excluded: chain U residue 22 CYS Chi-restraints excluded: chain U residue 25 SER Chi-restraints excluded: chain U residue 53 SER Chi-restraints excluded: chain U residue 63 SER Chi-restraints excluded: chain U residue 65 LYS Chi-restraints excluded: chain U residue 83 MET Chi-restraints excluded: chain U residue 91 THR Chi-restraints excluded: chain V residue 51 GLN Chi-restraints excluded: chain V residue 76 ASP Chi-restraints excluded: chain V residue 84 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 240 optimal weight: 4.9990 chunk 322 optimal weight: 0.0870 chunk 92 optimal weight: 10.0000 chunk 279 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 303 optimal weight: 20.0000 chunk 127 optimal weight: 10.0000 chunk 311 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 chunk 55 optimal weight: 0.9980 overall best weight: 2.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 ASN ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 17 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** ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 52 GLN O 353 ASN ** Q 353 ASN ** 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 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 100 GLN U 114 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.119991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.102916 restraints weight = 51951.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.105785 restraints weight = 25994.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.107696 restraints weight = 16116.770| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.346 30814 Z= 0.389 Angle : 0.966 59.200 41776 Z= 0.562 Chirality : 0.046 0.670 4928 Planarity : 0.005 0.105 5192 Dihedral : 9.455 110.731 4876 Min Nonbonded Distance : 1.696 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 6.33 % Allowed : 23.09 % Favored : 70.58 % Cbeta Deviations : 0.06 % 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: -1.52 (0.13), residues: 3846 helix: 1.06 (0.18), residues: 888 sheet: -1.50 (0.15), residues: 1072 loop : -1.70 (0.13), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 35 HIS 0.084 0.002 HIS S 242 PHE 0.018 0.002 PHE S 475 TYR 0.018 0.001 TYR H 111 ARG 0.006 0.001 ARG A 348 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8821.86 seconds wall clock time: 156 minutes 54.19 seconds (9414.19 seconds total)