Starting phenix.real_space_refine on Fri Mar 15 13:08:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u06_26255/03_2024/7u06_26255_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u06_26255/03_2024/7u06_26255.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u06_26255/03_2024/7u06_26255.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u06_26255/03_2024/7u06_26255.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u06_26255/03_2024/7u06_26255_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u06_26255/03_2024/7u06_26255_trim_updated.pdb" } resolution = 4.2 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= 0.004 sd= 0.716 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: 5 Type Number sf(0) Gaussians S 279 5.16 5 C 41051 2.51 5 N 10556 2.21 5 O 11974 1.98 5 H 60450 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 263": "OE1" <-> "OE2" Residue "C ASP 270": "OD1" <-> "OD2" Residue "C PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 91": "OE1" <-> "OE2" Residue "D PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 151": "OE1" <-> "OE2" Residue "E TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 113": "OE1" <-> "OE2" Residue "E PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 88": "OE1" <-> "OE2" Residue "F PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 69": "OE1" <-> "OE2" Residue "I ASP 133": "OD1" <-> "OD2" Residue "J GLU 35": "OE1" <-> "OE2" Residue "J PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ASP 82": "OD1" <-> "OD2" Residue "J TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "l PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "l TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 398": "OD1" <-> "OD2" Residue "B TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 573": "OE1" <-> "OE2" Residue "B PHE 599": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 611": "OE1" <-> "OE2" Residue "B GLU 630": "OE1" <-> "OE2" Residue "B GLU 640": "OE1" <-> "OE2" Residue "B GLU 650": "OE1" <-> "OE2" Residue "B TYR 652": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 672": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 682": "OD1" <-> "OD2" Residue "B ASP 710": "OD1" <-> "OD2" Residue "B ASP 739": "OD1" <-> "OD2" Residue "B PHE 783": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 830": "OD1" <-> "OD2" Residue "B GLU 833": "OE1" <-> "OE2" Residue "B ASP 851": "OD1" <-> "OD2" Residue "B PHE 853": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 877": "OE1" <-> "OE2" Residue "B GLU 963": "OE1" <-> "OE2" Residue "B GLU 1060": "OE1" <-> "OE2" Residue "B GLU 1062": "OE1" <-> "OE2" Residue "B PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 48": "OD1" <-> "OD2" Residue "A ASP 75": "OD1" <-> "OD2" Residue "A ASP 102": "OD1" <-> "OD2" Residue "A TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 105": "OD1" <-> "OD2" Residue "A GLU 115": "OE1" <-> "OE2" Residue "A GLU 135": "OE1" <-> "OE2" Residue "A GLU 144": "OE1" <-> "OE2" Residue "A PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 604": "OD1" <-> "OD2" Residue "A ASP 666": "OD1" <-> "OD2" Residue "A PHE 741": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 742": "OD1" <-> "OD2" Residue "A GLU 753": "OE1" <-> "OE2" Residue "A PHE 946": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 957": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1009": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 1060": "OD1" <-> "OD2" Residue "A TYR 1099": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "c GLU 146": "OE1" <-> "OE2" Residue "c PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "c TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "c PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d ASP 15": "OD1" <-> "OD2" Residue "d TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d GLU 91": "OE1" <-> "OE2" Residue "e TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e GLU 113": "OE1" <-> "OE2" Residue "e TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e GLU 206": "OE1" <-> "OE2" Residue "e PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f GLU 15": "OE1" <-> "OE2" Residue "f GLU 28": "OE1" <-> "OE2" Residue "f TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f ASP 186": "OD1" <-> "OD2" Residue "g GLU 131": "OE1" <-> "OE2" Residue "g PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "h TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "h PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "h ASP 104": "OD1" <-> "OD2" Residue "h PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "h GLU 109": "OE1" <-> "OE2" Residue "h ASP 193": "OD1" <-> "OD2" Residue "i GLU 15": "OE1" <-> "OE2" Residue "i GLU 81": "OE1" <-> "OE2" Residue "i ASP 186": "OD1" <-> "OD2" Residue "j PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "j TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "j PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "j TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "k TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "k TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "k PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b TYR 329": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b GLU 339": "OE1" <-> "OE2" Residue "b ASP 377": "OD1" <-> "OD2" Residue "b ASP 398": "OD1" <-> "OD2" Residue "b GLU 399": "OE1" <-> "OE2" Residue "b PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b ASP 486": "OD1" <-> "OD2" Residue "b PHE 505": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b ASP 574": "OD1" <-> "OD2" Residue "b GLU 605": "OE1" <-> "OE2" Residue "b PHE 638": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b GLU 644": "OE1" <-> "OE2" Residue "b PHE 645": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b GLU 671": "OE1" <-> "OE2" Residue "b PHE 722": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b GLU 723": "OE1" <-> "OE2" Residue "b TYR 730": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b PHE 755": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b TYR 766": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b ASP 830": "OD1" <-> "OD2" Residue "b TYR 839": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b GLU 963": "OE1" <-> "OE2" Residue "b PHE 982": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b PHE 985": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b PHE 986": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b ASP 1031": "OD1" <-> "OD2" Residue "b TYR 1034": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b PHE 1096": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a ASP 53": "OD1" <-> "OD2" Residue "a PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a ASP 75": "OD1" <-> "OD2" Residue "a PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a ASP 105": "OD1" <-> "OD2" Residue "a TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a ASP 152": "OD1" <-> "OD2" Residue "a ASP 163": "OD1" <-> "OD2" Residue "a TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a ASP 298": "OD1" <-> "OD2" Residue "a GLU 433": "OE1" <-> "OE2" Residue "a GLU 442": "OE1" <-> "OE2" Residue "a PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a TYR 493": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a GLU 504": "OE1" <-> "OE2" Residue "a GLU 627": "OE1" <-> "OE2" Residue "a GLU 656": "OE1" <-> "OE2" Residue "a ASP 666": "OD1" <-> "OD2" Residue "a GLU 675": "OE1" <-> "OE2" Residue "a ASP 742": "OD1" <-> "OD2" Residue "a ASP 751": "OD1" <-> "OD2" Residue "a GLU 776": "OE1" <-> "OE2" Residue "a GLU 797": "OE1" <-> "OE2" Residue "a PHE 873": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a PHE 946": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a TYR 968": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a ASP 1084": "OD1" <-> "OD2" Residue "a GLU 1111": "OE1" <-> "OE2" Residue "a ASP 1157": "OD1" <-> "OD2" Residue "a ASP 1178": "OD1" <-> "OD2" Residue "a GLU 1248": "OE1" <-> "OE2" Residue "a PHE 1279": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 124310 Number of models: 1 Model: "" Number of chains: 31 Chain: "C" Number of atoms: 4650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 4650 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 4 Chain: "D" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2344 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 5, 'TRANS': 140} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 3495 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 9, 'TRANS': 202} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 2975 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 5, 'TRANS': 178} Chain: "G" Number of atoms: 2544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 2544 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 2862 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 6, 'TRANS': 172} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "I" Number of atoms: 2964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 2964 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 5, 'TRANS': 177} Chain: "J" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 3350 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 7, 'TRANS': 202} Chain breaks: 2 Chain: "K" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2342 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 7, 'TRANS': 138} Chain breaks: 1 Chain: "l" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 2958 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 12974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 791, 12974 Classifications: {'peptide': 791} Link IDs: {'PTRANS': 17, 'TRANS': 773} Chain breaks: 4 Chain: "A" Number of atoms: 18239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1106, 18239 Classifications: {'peptide': 1106} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 55, 'TRANS': 1050} Chain breaks: 5 Chain: "c" Number of atoms: 4652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 4652 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 4 Chain: "d" Number of atoms: 2270 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 140, 2262 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 140, 2262 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 2271 Chain: "e" Number of atoms: 3430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 3430 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 9, 'TRANS': 197} Chain breaks: 1 Chain: "f" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 2996 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 5, 'TRANS': 180} Chain: "g" Number of atoms: 2518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 2518 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "h" Number of atoms: 2863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 2863 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 6, 'TRANS': 172} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "i" Number of atoms: 2971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 2971 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 5, 'TRANS': 178} Chain: "j" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 3350 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 7, 'TRANS': 202} Chain breaks: 2 Chain: "k" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2342 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 7, 'TRANS': 138} Chain breaks: 1 Chain: "b" Number of atoms: 12979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 791, 12979 Classifications: {'peptide': 791} Link IDs: {'PTRANS': 17, 'TRANS': 773} Chain breaks: 4 Chain: "a" Number of atoms: 18374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1114, 18374 Classifications: {'peptide': 1114} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 56, 'TRANS': 1057} Chain breaks: 6 Chain: "M" Number of atoms: 1235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1235 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 247} Link IDs: {'TRANS': 246} Chain breaks: 3 Unresolved non-hydrogen bonds: 494 Unresolved non-hydrogen angles: 741 Unresolved non-hydrogen dihedrals: 247 Planarities with less than four sites: {'UNK:plan-1': 247} Unresolved non-hydrogen planarities: 247 Chain: "m" Number of atoms: 1245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1245 Classifications: {'peptide': 249} Incomplete info: {'truncation_to_alanine': 249} Link IDs: {'TRANS': 248} Chain breaks: 3 Unresolved non-hydrogen bonds: 498 Unresolved non-hydrogen angles: 747 Unresolved non-hydrogen dihedrals: 249 Planarities with less than four sites: {'UNK:plan-1': 249} Unresolved non-hydrogen planarities: 249 Chain: "n" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 660 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 132} Link IDs: {'TRANS': 131} Chain breaks: 2 Unresolved non-hydrogen bonds: 264 Unresolved non-hydrogen angles: 396 Unresolved non-hydrogen dihedrals: 132 Planarities with less than four sites: {'UNK:plan-1': 132} Unresolved non-hydrogen planarities: 132 Chain: "N" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 660 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 132} Link IDs: {'TRANS': 131} Chain breaks: 2 Unresolved non-hydrogen bonds: 264 Unresolved non-hydrogen angles: 396 Unresolved non-hydrogen dihedrals: 132 Planarities with less than four sites: {'UNK:plan-1': 132} Unresolved non-hydrogen planarities: 132 Chain: "F" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "f" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "i" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 37.91, per 1000 atoms: 0.30 Number of scatterers: 124310 At special positions: 0 Unit cell: (340.816, 325.064, 176.136, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 279 16.00 O 11974 8.00 N 10556 7.00 C 41051 6.00 H 60450 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 68.11 Conformation dependent library (CDL) restraints added in 8.4 seconds 14524 Ramachandran restraints generated. 7262 Oldfield, 0 Emsley, 7262 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15732 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 194 helices and 73 sheets defined 39.9% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 43.60 Creating SS restraints... Processing helix chain 'C' and resid 138 through 146 removed outlier: 3.636A pdb=" N SER C 144 " --> pdb=" O ASP C 140 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU C 145 " --> pdb=" O LYS C 141 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N GLU C 146 " --> pdb=" O TYR C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 247 removed outlier: 4.124A pdb=" N LYS C 245 " --> pdb=" O GLU C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 498 removed outlier: 4.092A pdb=" N GLN C 487 " --> pdb=" O GLU C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 550 through 555 removed outlier: 3.657A pdb=" N ASN C 553 " --> pdb=" O GLU C 550 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY C 554 " --> pdb=" O VAL C 551 " (cutoff:3.500A) Processing helix chain 'c' and resid 138 through 146 Processing helix chain 'c' and resid 237 through 247 removed outlier: 3.579A pdb=" N GLU c 241 " --> pdb=" O SER c 237 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS c 245 " --> pdb=" O GLU c 241 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LYS c 246 " --> pdb=" O GLN c 242 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE c 247 " --> pdb=" O LEU c 243 " (cutoff:3.500A) Processing helix chain 'c' and resid 481 through 498 removed outlier: 3.567A pdb=" N GLN c 487 " --> pdb=" O GLU c 483 " (cutoff:3.500A) Processing helix chain 'c' and resid 550 through 555 removed outlier: 3.946A pdb=" N ASN c 553 " --> pdb=" O GLU c 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 48 removed outlier: 4.028A pdb=" N LYS D 35 " --> pdb=" O ASN D 31 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLU D 48 " --> pdb=" O LEU D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 96 removed outlier: 3.760A pdb=" N LEU D 95 " --> pdb=" O GLU D 91 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N SER D 96 " --> pdb=" O GLN D 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 91 through 96' Processing helix chain 'D' and resid 98 through 121 removed outlier: 3.621A pdb=" N GLN D 107 " --> pdb=" O GLU D 103 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS D 121 " --> pdb=" O ILE D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 146 removed outlier: 3.725A pdb=" N PHE D 145 " --> pdb=" O PHE D 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 37 removed outlier: 3.838A pdb=" N SER E 36 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N LEU E 37 " --> pdb=" O PHE E 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 32 through 37' Processing helix chain 'E' and resid 41 through 64 removed outlier: 4.461A pdb=" N MET E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N VAL E 53 " --> pdb=" O LEU E 49 " (cutoff:3.500A) Proline residue: E 54 - end of helix Processing helix chain 'E' and resid 100 through 111 removed outlier: 5.747A pdb=" N LEU E 104 " --> pdb=" O ARG E 100 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ILE E 105 " --> pdb=" O SER E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 135 removed outlier: 4.190A pdb=" N LYS E 133 " --> pdb=" O GLN E 129 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU E 134 " --> pdb=" O ILE E 130 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N SER E 135 " --> pdb=" O GLY E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 142 removed outlier: 3.650A pdb=" N SER E 141 " --> pdb=" O LEU E 137 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ASN E 142 " --> pdb=" O LEU E 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 137 through 142' Processing helix chain 'E' and resid 152 through 169 removed outlier: 6.027A pdb=" N ILE E 156 " --> pdb=" O ASP E 152 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N MET E 157 " --> pdb=" O LEU E 153 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL E 164 " --> pdb=" O ILE E 160 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N TRP E 165 " --> pdb=" O CYS E 161 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS E 166 " --> pdb=" O ARG E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 230 removed outlier: 3.770A pdb=" N GLU E 207 " --> pdb=" O ALA E 203 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU E 208 " --> pdb=" O LYS E 204 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS E 209 " --> pdb=" O ASN E 205 " (cutoff:3.500A) Proline residue: E 213 - end of helix removed outlier: 4.140A pdb=" N GLU E 216 " --> pdb=" O GLU E 212 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ILE E 217 " --> pdb=" O PRO E 213 " (cutoff:3.500A) Proline residue: E 218 - end of helix removed outlier: 3.763A pdb=" N LEU E 226 " --> pdb=" O ILE E 222 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N SER E 227 " --> pdb=" O ARG E 223 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N SER E 228 " --> pdb=" O GLY E 224 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU E 229 " --> pdb=" O VAL E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 237 removed outlier: 4.805A pdb=" N ILE E 237 " --> pdb=" O SER E 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 20 removed outlier: 4.175A pdb=" N GLY F 14 " --> pdb=" O LEU F 10 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ILE F 17 " --> pdb=" O MET F 13 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS F 19 " --> pdb=" O GLU F 15 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN F 20 " --> pdb=" O GLU F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 45 removed outlier: 4.118A pdb=" N TYR F 45 " --> pdb=" O LEU F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 75 removed outlier: 3.830A pdb=" N ASP F 54 " --> pdb=" O ASN F 50 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N HIS F 55 " --> pdb=" O LYS F 51 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N GLU F 69 " --> pdb=" O CYS F 65 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ASP F 70 " --> pdb=" O ARG F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 99 removed outlier: 4.548A pdb=" N ALA F 94 " --> pdb=" O LEU F 90 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N PHE F 95 " --> pdb=" O SER F 91 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N LYS F 96 " --> pdb=" O LYS F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 156 removed outlier: 3.993A pdb=" N CYS F 145 " --> pdb=" O SER F 141 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N MET F 154 " --> pdb=" O GLY F 150 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL F 155 " --> pdb=" O SER F 151 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLN F 156 " --> pdb=" O LEU F 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 59 removed outlier: 4.420A pdb=" N GLU G 38 " --> pdb=" O SER G 34 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N GLU G 39 " --> pdb=" O LYS G 35 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ASP G 40 " --> pdb=" O GLN G 36 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER G 53 " --> pdb=" O PHE G 49 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ILE G 54 " --> pdb=" O SER G 50 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N THR G 55 " --> pdb=" O LEU G 51 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER G 59 " --> pdb=" O THR G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 109 removed outlier: 3.844A pdb=" N LEU G 103 " --> pdb=" O TYR G 99 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS G 109 " --> pdb=" O TYR G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 158 Proline residue: G 155 - end of helix removed outlier: 5.022A pdb=" N ASN G 158 " --> pdb=" O ALA G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 118 removed outlier: 4.602A pdb=" N VAL G 115 " --> pdb=" O ILE G 110 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N ASN G 118 " --> pdb=" O LYS G 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 51 removed outlier: 3.647A pdb=" N TYR H 33 " --> pdb=" O ASN H 29 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU H 34 " --> pdb=" O SER H 30 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE H 35 " --> pdb=" O ASN H 31 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N SER H 48 " --> pdb=" O PHE H 44 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N GLN H 49 " --> pdb=" O ALA H 45 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N LEU H 50 " --> pdb=" O ILE H 46 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N THR H 51 " --> pdb=" O ALA H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 59 removed outlier: 3.769A pdb=" N GLN H 56 " --> pdb=" O PRO H 52 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LEU H 57 " --> pdb=" O LYS H 53 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N THR H 58 " --> pdb=" O ALA H 54 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN H 59 " --> pdb=" O LEU H 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 52 through 59' Processing helix chain 'H' and resid 61 through 66 removed outlier: 4.146A pdb=" N ASN H 65 " --> pdb=" O THR H 61 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N THR H 66 " --> pdb=" O ASN H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 66' Processing helix chain 'H' and resid 169 through 190 removed outlier: 4.075A pdb=" N GLN H 173 " --> pdb=" O ASN H 169 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 219 removed outlier: 4.960A pdb=" N ASP H 208 " --> pdb=" O SER H 204 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS H 213 " --> pdb=" O GLU H 209 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU H 218 " --> pdb=" O MET H 214 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLN H 219 " --> pdb=" O VAL H 215 " (cutoff:3.500A) Processing helix chain 'h' and resid 29 through 51 removed outlier: 3.805A pdb=" N TYR h 33 " --> pdb=" O ASN h 29 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU h 34 " --> pdb=" O SER h 30 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE h 35 " --> pdb=" O ASN h 31 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER h 48 " --> pdb=" O PHE h 44 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLN h 49 " --> pdb=" O ALA h 45 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LEU h 50 " --> pdb=" O ILE h 46 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N THR h 51 " --> pdb=" O ALA h 47 " (cutoff:3.500A) Processing helix chain 'h' and resid 52 through 59 removed outlier: 3.958A pdb=" N LEU h 57 " --> pdb=" O LYS h 53 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N THR h 58 " --> pdb=" O ALA h 54 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLN h 59 " --> pdb=" O LEU h 55 " (cutoff:3.500A) Processing helix chain 'h' and resid 61 through 66 removed outlier: 4.279A pdb=" N ASN h 65 " --> pdb=" O THR h 61 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N THR h 66 " --> pdb=" O ASN h 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 61 through 66' Processing helix chain 'h' and resid 169 through 190 removed outlier: 3.548A pdb=" N ASN h 177 " --> pdb=" O GLN h 173 " (cutoff:3.500A) Processing helix chain 'h' and resid 204 through 219 removed outlier: 4.185A pdb=" N ASP h 208 " --> pdb=" O SER h 204 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN h 217 " --> pdb=" O LYS h 213 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU h 218 " --> pdb=" O MET h 214 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLN h 219 " --> pdb=" O VAL h 215 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 20 removed outlier: 5.671A pdb=" N MET I 13 " --> pdb=" O SER I 9 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 46 removed outlier: 3.870A pdb=" N PHE I 30 " --> pdb=" O ASN I 26 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 68 removed outlier: 3.956A pdb=" N ARG I 66 " --> pdb=" O ASN I 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 75 removed outlier: 6.263A pdb=" N THR I 75 " --> pdb=" O PHE I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 99 removed outlier: 3.721A pdb=" N THR I 86 " --> pdb=" O ASN I 82 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N SER I 87 " --> pdb=" O LEU I 83 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA I 94 " --> pdb=" O LEU I 90 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N PHE I 95 " --> pdb=" O SER I 91 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LYS I 96 " --> pdb=" O LYS I 92 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE I 98 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU I 99 " --> pdb=" O PHE I 95 " (cutoff:3.500A) Processing helix chain 'I' and resid 131 through 136 removed outlier: 4.738A pdb=" N LYS I 136 " --> pdb=" O MET I 132 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 156 removed outlier: 4.536A pdb=" N CYS I 145 " --> pdb=" O SER I 141 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN I 156 " --> pdb=" O LEU I 152 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 48 removed outlier: 6.489A pdb=" N SER J 47 " --> pdb=" O SER J 43 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU J 48 " --> pdb=" O ARG J 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 43 through 48' Processing helix chain 'J' and resid 58 through 77 removed outlier: 3.933A pdb=" N MET J 62 " --> pdb=" O SER J 58 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG J 75 " --> pdb=" O SER J 71 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR J 76 " --> pdb=" O GLN J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 108 removed outlier: 3.810A pdb=" N ASN J 93 " --> pdb=" O ASP J 89 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE J 94 " --> pdb=" O TYR J 90 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARG J 97 " --> pdb=" O ASN J 93 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASN J 103 " --> pdb=" O LEU J 99 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER J 107 " --> pdb=" O ASN J 103 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL J 108 " --> pdb=" O PHE J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 166 removed outlier: 4.649A pdb=" N TYR J 165 " --> pdb=" O SER J 161 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ILE J 166 " --> pdb=" O LEU J 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 161 through 166' Processing helix chain 'J' and resid 175 through 192 removed outlier: 3.965A pdb=" N LEU J 187 " --> pdb=" O ILE J 183 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N TRP J 188 " --> pdb=" O HIS J 184 " (cutoff:3.500A) Processing helix chain 'J' and resid 230 through 245 removed outlier: 3.758A pdb=" N CYS J 234 " --> pdb=" O GLU J 230 " (cutoff:3.500A) Processing helix chain 'J' and resid 271 through 279 removed outlier: 4.431A pdb=" N GLY J 279 " --> pdb=" O LEU J 275 " (cutoff:3.500A) Processing helix chain 'j' and resid 43 through 48 removed outlier: 6.429A pdb=" N SER j 47 " --> pdb=" O SER j 43 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLU j 48 " --> pdb=" O ARG j 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 43 through 48' Processing helix chain 'j' and resid 58 through 77 removed outlier: 3.946A pdb=" N MET j 62 " --> pdb=" O SER j 58 " (cutoff:3.500A) Processing helix chain 'j' and resid 79 through 108 removed outlier: 3.599A pdb=" N ASN j 93 " --> pdb=" O ASP j 89 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE j 94 " --> pdb=" O TYR j 90 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY j 95 " --> pdb=" O GLY j 91 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE j 96 " --> pdb=" O HIS j 92 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ARG j 97 " --> pdb=" O ASN j 93 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLU j 100 " --> pdb=" O ILE j 96 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU j 101 " --> pdb=" O ARG j 97 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASN j 103 " --> pdb=" O LEU j 99 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL j 108 " --> pdb=" O PHE j 104 " (cutoff:3.500A) Processing helix chain 'j' and resid 161 through 166 removed outlier: 5.012A pdb=" N TYR j 165 " --> pdb=" O SER j 161 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ILE j 166 " --> pdb=" O LEU j 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 161 through 166' Processing helix chain 'j' and resid 175 through 192 removed outlier: 4.067A pdb=" N LEU j 187 " --> pdb=" O ILE j 183 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N TRP j 188 " --> pdb=" O HIS j 184 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER j 189 " --> pdb=" O GLY j 185 " (cutoff:3.500A) Processing helix chain 'j' and resid 230 through 245 removed outlier: 3.921A pdb=" N CYS j 234 " --> pdb=" O GLU j 230 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA j 244 " --> pdb=" O PHE j 240 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY j 245 " --> pdb=" O LEU j 241 " (cutoff:3.500A) Processing helix chain 'j' and resid 271 through 279 removed outlier: 3.928A pdb=" N GLY j 279 " --> pdb=" O LEU j 275 " (cutoff:3.500A) Processing helix chain 'K' and resid 30 through 52 removed outlier: 6.102A pdb=" N LYS K 34 " --> pdb=" O PRO K 30 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU K 35 " --> pdb=" O GLN K 31 " (cutoff:3.500A) Proline residue: K 38 - end of helix removed outlier: 4.025A pdb=" N ASP K 46 " --> pdb=" O HIS K 42 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE K 47 " --> pdb=" O ALA K 43 " (cutoff:3.500A) Processing helix chain 'K' and resid 126 through 147 removed outlier: 3.519A pdb=" N MET K 130 " --> pdb=" O ASP K 126 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG K 131 " --> pdb=" O ASP K 127 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASN K 147 " --> pdb=" O LYS K 143 " (cutoff:3.500A) Processing helix chain 'K' and resid 158 through 173 removed outlier: 3.561A pdb=" N ARG K 170 " --> pdb=" O ARG K 166 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LYS K 171 " --> pdb=" O THR K 167 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N HIS K 172 " --> pdb=" O LEU K 168 " (cutoff:3.500A) Processing helix chain 'k' and resid 30 through 52 removed outlier: 6.063A pdb=" N LYS k 34 " --> pdb=" O PRO k 30 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU k 35 " --> pdb=" O GLN k 31 " (cutoff:3.500A) Proline residue: k 38 - end of helix removed outlier: 3.872A pdb=" N ASP k 46 " --> pdb=" O HIS k 42 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ILE k 47 " --> pdb=" O ALA k 43 " (cutoff:3.500A) Processing helix chain 'k' and resid 126 through 147 removed outlier: 4.466A pdb=" N MET k 130 " --> pdb=" O ASP k 126 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ARG k 131 " --> pdb=" O ASP k 127 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET k 146 " --> pdb=" O VAL k 142 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ASN k 147 " --> pdb=" O LYS k 143 " (cutoff:3.500A) Processing helix chain 'k' and resid 158 through 173 Processing helix chain 'l' and resid 25 through 34 removed outlier: 3.867A pdb=" N ARG l 32 " --> pdb=" O ASN l 28 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N PHE l 33 " --> pdb=" O LEU l 29 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N THR l 34 " --> pdb=" O LEU l 30 " (cutoff:3.500A) Processing helix chain 'l' and resid 76 through 84 removed outlier: 4.082A pdb=" N SER l 80 " --> pdb=" O ARG l 76 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N TYR l 83 " --> pdb=" O THR l 79 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ARG l 84 " --> pdb=" O SER l 80 " (cutoff:3.500A) Processing helix chain 'l' and resid 97 through 115 removed outlier: 3.905A pdb=" N TYR l 101 " --> pdb=" O LYS l 97 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN l 103 " --> pdb=" O SER l 99 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N CYS l 104 " --> pdb=" O SER l 100 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ASN l 105 " --> pdb=" O TYR l 101 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N HIS l 106 " --> pdb=" O GLU l 102 " (cutoff:3.500A) Processing helix chain 'l' and resid 137 through 149 removed outlier: 3.611A pdb=" N GLU l 147 " --> pdb=" O ASN l 143 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASN l 148 " --> pdb=" O PHE l 144 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLN l 149 " --> pdb=" O ALA l 145 " (cutoff:3.500A) Processing helix chain 'l' and resid 161 through 179 removed outlier: 3.522A pdb=" N GLN l 176 " --> pdb=" O VAL l 172 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET l 177 " --> pdb=" O ALA l 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 317 removed outlier: 3.714A pdb=" N GLU B 316 " --> pdb=" O SER B 312 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR B 317 " --> pdb=" O ILE B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 339 removed outlier: 4.137A pdb=" N SER B 336 " --> pdb=" O THR B 332 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N TYR B 337 " --> pdb=" O SER B 333 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N PHE B 338 " --> pdb=" O MET B 334 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLU B 339 " --> pdb=" O LEU B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 371 removed outlier: 3.600A pdb=" N ASN B 362 " --> pdb=" O LEU B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 422 removed outlier: 3.700A pdb=" N PHE B 402 " --> pdb=" O ASP B 398 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 407 " --> pdb=" O GLN B 403 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 416 " --> pdb=" O GLU B 412 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N CYS B 420 " --> pdb=" O LEU B 416 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLU B 421 " --> pdb=" O PHE B 417 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLY B 422 " --> pdb=" O ASN B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 443 removed outlier: 5.294A pdb=" N VAL B 428 " --> pdb=" O ARG B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 463 removed outlier: 4.761A pdb=" N SER B 454 " --> pdb=" O SER B 450 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N CYS B 455 " --> pdb=" O LEU B 451 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N GLU B 457 " --> pdb=" O LEU B 453 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N TYR B 458 " --> pdb=" O SER B 454 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N TYR B 459 " --> pdb=" O CYS B 455 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N THR B 460 " --> pdb=" O TYR B 456 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLN B 461 " --> pdb=" O GLU B 457 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N THR B 462 " --> pdb=" O TYR B 458 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ASN B 463 " --> pdb=" O TYR B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 483 removed outlier: 3.583A pdb=" N CYS B 482 " --> pdb=" O SER B 478 " (cutoff:3.500A) Proline residue: B 483 - end of helix Processing helix chain 'B' and resid 496 through 512 Processing helix chain 'B' and resid 518 through 529 removed outlier: 4.198A pdb=" N TRP B 522 " --> pdb=" O LYS B 518 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ASP B 527 " --> pdb=" O LYS B 523 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU B 528 " --> pdb=" O LYS B 524 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLN B 529 " --> pdb=" O PHE B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 873 removed outlier: 3.652A pdb=" N PHE B 869 " --> pdb=" O GLN B 865 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE B 870 " --> pdb=" O LEU B 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 891 removed outlier: 4.172A pdb=" N PHE B 883 " --> pdb=" O ASP B 879 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU B 885 " --> pdb=" O GLU B 881 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N LYS B 888 " --> pdb=" O ILE B 884 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N TRP B 889 " --> pdb=" O LEU B 885 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS B 890 " --> pdb=" O PHE B 886 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N THR B 891 " --> pdb=" O GLU B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 896 through 901 removed outlier: 6.016A pdb=" N LYS B 900 " --> pdb=" O GLU B 896 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU B 901 " --> pdb=" O ILE B 897 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 896 through 901' Processing helix chain 'B' and resid 904 through 911 Processing helix chain 'B' and resid 922 through 934 removed outlier: 3.641A pdb=" N ILE B 930 " --> pdb=" O THR B 926 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ARG B 931 " --> pdb=" O LYS B 927 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASN B 932 " --> pdb=" O SER B 928 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LEU B 933 " --> pdb=" O LYS B 929 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N CYS B 934 " --> pdb=" O ILE B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 936 through 953 Processing helix chain 'B' and resid 961 through 969 removed outlier: 6.031A pdb=" N VAL B 965 " --> pdb=" O MET B 961 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ARG B 966 " --> pdb=" O ASP B 962 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ASN B 967 " --> pdb=" O GLU B 963 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LEU B 968 " --> pdb=" O TYR B 964 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N VAL B 969 " --> pdb=" O VAL B 965 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 961 through 969' Processing helix chain 'B' and resid 1020 through 1025 removed outlier: 4.848A pdb=" N TRP B1024 " --> pdb=" O LEU B1020 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLY B1025 " --> pdb=" O SER B1021 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1020 through 1025' Processing helix chain 'A' and resid 11 through 16 removed outlier: 3.642A pdb=" N LYS A 15 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ILE A 16 " --> pdb=" O GLY A 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 11 through 16' Processing helix chain 'A' and resid 27 through 41 removed outlier: 4.122A pdb=" N GLU A 40 " --> pdb=" O GLN A 36 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N PHE A 41 " --> pdb=" O LYS A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 50 removed outlier: 4.052A pdb=" N VAL A 49 " --> pdb=" O HIS A 45 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N THR A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 45 through 50' Processing helix chain 'A' and resid 78 through 88 removed outlier: 5.804A pdb=" N LEU A 82 " --> pdb=" O ASP A 78 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N PHE A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N LEU A 84 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR A 85 " --> pdb=" O GLU A 81 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ASP A 86 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N PHE A 87 " --> pdb=" O PHE A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 118 removed outlier: 3.658A pdb=" N ASN A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) Proline residue: A 118 - end of helix Processing helix chain 'A' and resid 133 through 144 removed outlier: 3.724A pdb=" N GLN A 138 " --> pdb=" O LYS A 134 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N THR A 139 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET A 143 " --> pdb=" O THR A 139 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N GLU A 144 " --> pdb=" O ILE A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 180 removed outlier: 3.849A pdb=" N ALA A 165 " --> pdb=" O MET A 161 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N THR A 170 " --> pdb=" O ARG A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 192 Processing helix chain 'A' and resid 265 through 287 removed outlier: 5.463A pdb=" N GLN A 269 " --> pdb=" O ASN A 265 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LYS A 270 " --> pdb=" O ARG A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 307 removed outlier: 3.663A pdb=" N ASP A 298 " --> pdb=" O ASN A 294 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS A 305 " --> pdb=" O THR A 301 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL A 306 " --> pdb=" O THR A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 330 removed outlier: 3.515A pdb=" N LEU A 312 " --> pdb=" O ASP A 308 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER A 314 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 343 removed outlier: 3.682A pdb=" N SER A 340 " --> pdb=" O PRO A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 408 removed outlier: 4.458A pdb=" N ILE A 407 " --> pdb=" O ASP A 403 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ASN A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 403 through 408' Processing helix chain 'A' and resid 409 through 429 removed outlier: 3.564A pdb=" N LEU A 428 " --> pdb=" O TYR A 424 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N MET A 429 " --> pdb=" O ASP A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 456 removed outlier: 4.181A pdb=" N LYS A 456 " --> pdb=" O THR A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 471 Processing helix chain 'A' and resid 486 through 500 removed outlier: 3.532A pdb=" N VAL A 490 " --> pdb=" O PRO A 486 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR A 491 " --> pdb=" O ARG A 487 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS A 496 " --> pdb=" O PHE A 492 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEU A 497 " --> pdb=" O TYR A 493 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N PHE A 498 " --> pdb=" O SER A 494 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLU A 499 " --> pdb=" O ASN A 495 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LEU A 500 " --> pdb=" O LYS A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 525 removed outlier: 3.550A pdb=" N LYS A 512 " --> pdb=" O GLU A 508 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR A 514 " --> pdb=" O GLN A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 544 removed outlier: 4.372A pdb=" N THR A 544 " --> pdb=" O ALA A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 566 removed outlier: 4.368A pdb=" N ARG A 555 " --> pdb=" O HIS A 551 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU A 565 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASN A 566 " --> pdb=" O ILE A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 603 removed outlier: 3.534A pdb=" N ILE A 591 " --> pdb=" O LEU A 587 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU A 592 " --> pdb=" O GLN A 588 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ASN A 603 " --> pdb=" O SER A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 618 removed outlier: 3.776A pdb=" N VAL A 608 " --> pdb=" O ASP A 604 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA A 609 " --> pdb=" O PHE A 605 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE A 614 " --> pdb=" O LYS A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 643 removed outlier: 5.425A pdb=" N GLN A 637 " --> pdb=" O LYS A 633 " (cutoff:3.500A) Proline residue: A 638 - end of helix Processing helix chain 'A' and resid 761 through 769 Processing helix chain 'A' and resid 895 through 901 removed outlier: 3.778A pdb=" N LEU A 901 " --> pdb=" O ILE A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 927 removed outlier: 3.733A pdb=" N ILE A 916 " --> pdb=" O ASP A 912 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET A 917 " --> pdb=" O ASP A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1030 Processing helix chain 'A' and resid 1084 through 1089 removed outlier: 4.207A pdb=" N TYR A1088 " --> pdb=" O ASP A1084 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASN A1089 " --> pdb=" O TYR A1085 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1084 through 1089' Processing helix chain 'A' and resid 1110 through 1131 removed outlier: 3.906A pdb=" N GLU A1116 " --> pdb=" O GLU A1112 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE A1127 " --> pdb=" O CYS A1123 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE A1128 " --> pdb=" O ARG A1124 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER A1129 " --> pdb=" O GLU A1125 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LYS A1130 " --> pdb=" O HIS A1126 " (cutoff:3.500A) Processing helix chain 'A' and resid 1148 through 1153 removed outlier: 4.802A pdb=" N PHE A1152 " --> pdb=" O ASP A1148 " (cutoff:3.500A) Processing helix chain 'A' and resid 1157 through 1165 removed outlier: 3.731A pdb=" N TYR A1162 " --> pdb=" O HIS A1158 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR A1163 " --> pdb=" O LYS A1159 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE A1164 " --> pdb=" O MET A1160 " (cutoff:3.500A) Processing helix chain 'A' and resid 1197 through 1203 removed outlier: 3.570A pdb=" N ARG A1202 " --> pdb=" O SER A1198 " (cutoff:3.500A) Processing helix chain 'd' and resid 31 through 50 removed outlier: 3.633A pdb=" N LYS d 35 " --> pdb=" O ASN d 31 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ASP d 45 " --> pdb=" O ASN d 41 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N TYR d 46 " --> pdb=" O ILE d 42 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N PHE d 47 " --> pdb=" O SER d 43 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N GLU d 48 " --> pdb=" O LEU d 44 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N SER d 49 " --> pdb=" O ASP d 45 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N ALA d 50 " --> pdb=" O TYR d 46 " (cutoff:3.500A) Processing helix chain 'd' and resid 98 through 122 Processing helix chain 'd' and resid 129 through 146 removed outlier: 3.565A pdb=" N LYS d 135 " --> pdb=" O LYS d 131 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE d 146 " --> pdb=" O ASP d 142 " (cutoff:3.500A) Processing helix chain 'e' and resid 41 through 64 removed outlier: 4.216A pdb=" N MET e 52 " --> pdb=" O LEU e 48 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL e 53 " --> pdb=" O LEU e 49 " (cutoff:3.500A) Proline residue: e 54 - end of helix removed outlier: 4.056A pdb=" N GLU e 60 " --> pdb=" O ALA e 56 " (cutoff:3.500A) Processing helix chain 'e' and resid 100 through 111 removed outlier: 3.931A pdb=" N LEU e 104 " --> pdb=" O ARG e 100 " (cutoff:3.500A) Processing helix chain 'e' and resid 112 through 142 removed outlier: 4.237A pdb=" N GLU e 136 " --> pdb=" O LEU e 132 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU e 137 " --> pdb=" O LYS e 133 " (cutoff:3.500A) Processing helix chain 'e' and resid 152 through 169 removed outlier: 3.845A pdb=" N ILE e 156 " --> pdb=" O ASP e 152 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL e 164 " --> pdb=" O ILE e 160 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N TRP e 165 " --> pdb=" O CYS e 161 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS e 166 " --> pdb=" O ARG e 162 " (cutoff:3.500A) Processing helix chain 'e' and resid 203 through 230 removed outlier: 3.660A pdb=" N GLU e 207 " --> pdb=" O ALA e 203 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU e 208 " --> pdb=" O LYS e 204 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS e 209 " --> pdb=" O ASN e 205 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU e 212 " --> pdb=" O LEU e 208 " (cutoff:3.500A) Proline residue: e 213 - end of helix removed outlier: 4.532A pdb=" N GLU e 216 " --> pdb=" O GLU e 212 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ILE e 217 " --> pdb=" O PRO e 213 " (cutoff:3.500A) Proline residue: e 218 - end of helix removed outlier: 4.310A pdb=" N SER e 228 " --> pdb=" O GLY e 224 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU e 229 " --> pdb=" O VAL e 225 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY e 230 " --> pdb=" O LEU e 226 " (cutoff:3.500A) Processing helix chain 'e' and resid 232 through 237 removed outlier: 3.882A pdb=" N VAL e 236 " --> pdb=" O SER e 232 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ILE e 237 " --> pdb=" O SER e 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 232 through 237' Processing helix chain 'f' and resid 9 through 20 removed outlier: 3.556A pdb=" N ASN f 20 " --> pdb=" O GLU f 16 " (cutoff:3.500A) Processing helix chain 'f' and resid 26 through 46 removed outlier: 3.638A pdb=" N PHE f 30 " --> pdb=" O ASN f 26 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR f 45 " --> pdb=" O LEU f 41 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLU f 46 " --> pdb=" O CYS f 42 " (cutoff:3.500A) Processing helix chain 'f' and resid 48 through 75 removed outlier: 4.320A pdb=" N ASN f 53 " --> pdb=" O PHE f 49 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N ASP f 54 " --> pdb=" O ASN f 50 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N HIS f 55 " --> pdb=" O LYS f 51 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG f 66 " --> pdb=" O ASN f 62 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N GLU f 69 " --> pdb=" O CYS f 65 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ASP f 70 " --> pdb=" O ARG f 66 " (cutoff:3.500A) Processing helix chain 'f' and resid 82 through 99 removed outlier: 3.998A pdb=" N ALA f 94 " --> pdb=" O LEU f 90 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N PHE f 95 " --> pdb=" O SER f 91 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LYS f 96 " --> pdb=" O LYS f 92 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N PHE f 98 " --> pdb=" O ALA f 94 " (cutoff:3.500A) Processing helix chain 'f' and resid 131 through 138 removed outlier: 3.654A pdb=" N MET f 135 " --> pdb=" O PRO f 131 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N LYS f 136 " --> pdb=" O MET f 132 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N SER f 137 " --> pdb=" O ASP f 133 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU f 138 " --> pdb=" O ALA f 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 131 through 138' Processing helix chain 'f' and resid 141 through 156 removed outlier: 4.042A pdb=" N CYS f 145 " --> pdb=" O SER f 141 " (cutoff:3.500A) Processing helix chain 'g' and resid 38 through 59 removed outlier: 3.736A pdb=" N LYS g 42 " --> pdb=" O GLU g 38 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LEU g 43 " --> pdb=" O GLU g 39 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N LEU g 44 " --> pdb=" O ASP g 40 " (cutoff:3.500A) Processing helix chain 'g' and resid 99 through 115 removed outlier: 4.215A pdb=" N TYR g 111 " --> pdb=" O TYR g 107 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N VAL g 112 " --> pdb=" O SER g 108 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N LYS g 113 " --> pdb=" O HIS g 109 " (cutoff:3.500A) Processing helix chain 'g' and resid 142 through 154 Processing helix chain 'g' and resid 129 through 134 removed outlier: 4.611A pdb=" N MET g 132 " --> pdb=" O GLU g 129 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ARG g 133 " --> pdb=" O ASN g 130 " (cutoff:3.500A) Processing helix chain 'i' and resid 9 through 20 removed outlier: 5.769A pdb=" N MET i 13 " --> pdb=" O SER i 9 " (cutoff:3.500A) Processing helix chain 'i' and resid 26 through 46 removed outlier: 3.805A pdb=" N PHE i 30 " --> pdb=" O ASN i 26 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS i 42 " --> pdb=" O VAL i 38 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN i 43 " --> pdb=" O ALA i 39 " (cutoff:3.500A) Processing helix chain 'i' and resid 48 through 68 removed outlier: 3.824A pdb=" N ARG i 66 " --> pdb=" O ASN i 62 " (cutoff:3.500A) Processing helix chain 'i' and resid 70 through 75 removed outlier: 6.338A pdb=" N THR i 75 " --> pdb=" O PHE i 71 " (cutoff:3.500A) Processing helix chain 'i' and resid 82 through 99 removed outlier: 5.577A pdb=" N THR i 86 " --> pdb=" O ASN i 82 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N SER i 87 " --> pdb=" O LEU i 83 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ALA i 94 " --> pdb=" O LEU i 90 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N PHE i 95 " --> pdb=" O SER i 91 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LYS i 96 " --> pdb=" O LYS i 92 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE i 98 " --> pdb=" O ALA i 94 " (cutoff:3.500A) Processing helix chain 'i' and resid 141 through 156 removed outlier: 4.027A pdb=" N CYS i 145 " --> pdb=" O SER i 141 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN i 156 " --> pdb=" O LEU i 152 " (cutoff:3.500A) Processing helix chain 'b' and resid 296 through 317 removed outlier: 3.616A pdb=" N GLY b 301 " --> pdb=" O THR b 297 " (cutoff:3.500A) Processing helix chain 'b' and resid 322 through 337 removed outlier: 3.717A pdb=" N TYR b 329 " --> pdb=" O GLU b 325 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER b 336 " --> pdb=" O THR b 332 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N TYR b 337 " --> pdb=" O SER b 333 " (cutoff:3.500A) Processing helix chain 'b' and resid 345 through 371 Processing helix chain 'b' and resid 398 through 421 removed outlier: 3.544A pdb=" N PHE b 402 " --> pdb=" O ASP b 398 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN b 403 " --> pdb=" O GLU b 399 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU b 404 " --> pdb=" O THR b 400 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N CYS b 420 " --> pdb=" O LEU b 416 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N GLU b 421 " --> pdb=" O PHE b 417 " (cutoff:3.500A) Processing helix chain 'b' and resid 424 through 443 removed outlier: 4.917A pdb=" N VAL b 428 " --> pdb=" O ARG b 424 " (cutoff:3.500A) Processing helix chain 'b' and resid 444 through 456 removed outlier: 3.571A pdb=" N ALA b 448 " --> pdb=" O LYS b 444 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER b 450 " --> pdb=" O GLU b 446 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER b 454 " --> pdb=" O SER b 450 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N CYS b 455 " --> pdb=" O LEU b 451 " (cutoff:3.500A) Processing helix chain 'b' and resid 457 through 463 removed outlier: 4.629A pdb=" N GLN b 461 " --> pdb=" O GLU b 457 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N THR b 462 " --> pdb=" O TYR b 458 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N ASN b 463 " --> pdb=" O TYR b 459 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 457 through 463' Processing helix chain 'b' and resid 464 through 482 removed outlier: 3.929A pdb=" N CYS b 482 " --> pdb=" O SER b 478 " (cutoff:3.500A) Processing helix chain 'b' and resid 496 through 512 Processing helix chain 'b' and resid 518 through 528 removed outlier: 3.606A pdb=" N LEU b 528 " --> pdb=" O LYS b 524 " (cutoff:3.500A) Processing helix chain 'b' and resid 861 through 873 Processing helix chain 'b' and resid 879 through 891 removed outlier: 4.414A pdb=" N PHE b 883 " --> pdb=" O ASP b 879 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N LYS b 888 " --> pdb=" O ILE b 884 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N TRP b 889 " --> pdb=" O LEU b 885 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS b 890 " --> pdb=" O PHE b 886 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N THR b 891 " --> pdb=" O GLU b 887 " (cutoff:3.500A) Processing helix chain 'b' and resid 896 through 901 removed outlier: 4.414A pdb=" N LYS b 900 " --> pdb=" O GLU b 896 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU b 901 " --> pdb=" O ILE b 897 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 896 through 901' Processing helix chain 'b' and resid 904 through 911 Processing helix chain 'b' and resid 922 through 934 removed outlier: 3.826A pdb=" N SER b 928 " --> pdb=" O ASN b 924 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU b 933 " --> pdb=" O LYS b 929 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N CYS b 934 " --> pdb=" O ILE b 930 " (cutoff:3.500A) Processing helix chain 'b' and resid 936 through 953 Processing helix chain 'b' and resid 964 through 969 removed outlier: 4.414A pdb=" N LEU b 968 " --> pdb=" O TYR b 964 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL b 969 " --> pdb=" O VAL b 965 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 964 through 969' Processing helix chain 'a' and resid 11 through 16 removed outlier: 4.919A pdb=" N ILE a 16 " --> pdb=" O GLY a 12 " (cutoff:3.500A) Processing helix chain 'a' and resid 27 through 41 removed outlier: 4.180A pdb=" N GLU a 40 " --> pdb=" O GLN a 36 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N PHE a 41 " --> pdb=" O LYS a 37 " (cutoff:3.500A) Processing helix chain 'a' and resid 45 through 50 removed outlier: 4.147A pdb=" N VAL a 49 " --> pdb=" O HIS a 45 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N THR a 50 " --> pdb=" O LEU a 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 45 through 50' Processing helix chain 'a' and resid 77 through 89 removed outlier: 3.895A pdb=" N GLU a 81 " --> pdb=" O ASP a 77 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N LEU a 82 " --> pdb=" O ASP a 78 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N PHE a 83 " --> pdb=" O ALA a 79 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N LEU a 84 " --> pdb=" O LEU a 80 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N TYR a 85 " --> pdb=" O GLU a 81 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ASP a 86 " --> pdb=" O LEU a 82 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N PHE a 87 " --> pdb=" O PHE a 83 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU a 88 " --> pdb=" O LEU a 84 " (cutoff:3.500A) Proline residue: a 89 - end of helix No H-bonds generated for 'chain 'a' and resid 77 through 89' Processing helix chain 'a' and resid 105 through 118 Proline residue: a 118 - end of helix Processing helix chain 'a' and resid 133 through 144 removed outlier: 3.590A pdb=" N MET a 143 " --> pdb=" O THR a 139 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLU a 144 " --> pdb=" O ILE a 140 " (cutoff:3.500A) Processing helix chain 'a' and resid 156 through 180 removed outlier: 3.559A pdb=" N THR a 170 " --> pdb=" O ARG a 166 " (cutoff:3.500A) Processing helix chain 'a' and resid 186 through 192 Processing helix chain 'a' and resid 266 through 287 removed outlier: 4.515A pdb=" N LYS a 270 " --> pdb=" O ARG a 266 " (cutoff:3.500A) Processing helix chain 'a' and resid 289 through 307 removed outlier: 3.834A pdb=" N ASP a 298 " --> pdb=" O ASN a 294 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR a 302 " --> pdb=" O ASP a 298 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LYS a 305 " --> pdb=" O THR a 301 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL a 306 " --> pdb=" O THR a 302 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG a 307 " --> pdb=" O LEU a 303 " (cutoff:3.500A) Processing helix chain 'a' and resid 308 through 330 removed outlier: 3.541A pdb=" N SER a 314 " --> pdb=" O LEU a 310 " (cutoff:3.500A) Processing helix chain 'a' and resid 336 through 343 Processing helix chain 'a' and resid 403 through 408 removed outlier: 4.123A pdb=" N ILE a 407 " --> pdb=" O ASP a 403 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ASN a 408 " --> pdb=" O VAL a 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 403 through 408' Processing helix chain 'a' and resid 409 through 428 removed outlier: 4.209A pdb=" N LEU a 428 " --> pdb=" O TYR a 424 " (cutoff:3.500A) Processing helix chain 'a' and resid 436 through 456 removed outlier: 4.241A pdb=" N LYS a 456 " --> pdb=" O THR a 452 " (cutoff:3.500A) Processing helix chain 'a' and resid 461 through 471 removed outlier: 3.512A pdb=" N VAL a 469 " --> pdb=" O LEU a 465 " (cutoff:3.500A) Processing helix chain 'a' and resid 486 through 500 removed outlier: 3.811A pdb=" N VAL a 490 " --> pdb=" O PRO a 486 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N TYR a 491 " --> pdb=" O ARG a 487 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS a 496 " --> pdb=" O PHE a 492 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU a 497 " --> pdb=" O TYR a 493 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N PHE a 498 " --> pdb=" O SER a 494 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU a 499 " --> pdb=" O ASN a 495 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU a 500 " --> pdb=" O LYS a 496 " (cutoff:3.500A) Processing helix chain 'a' and resid 506 through 525 Processing helix chain 'a' and resid 526 through 544 removed outlier: 3.581A pdb=" N THR a 544 " --> pdb=" O ALA a 540 " (cutoff:3.500A) Processing helix chain 'a' and resid 551 through 566 removed outlier: 4.351A pdb=" N ARG a 555 " --> pdb=" O HIS a 551 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR a 556 " --> pdb=" O PRO a 552 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU a 565 " --> pdb=" O ILE a 561 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASN a 566 " --> pdb=" O ILE a 562 " (cutoff:3.500A) Processing helix chain 'a' and resid 584 through 603 removed outlier: 4.623A pdb=" N ASN a 603 " --> pdb=" O SER a 599 " (cutoff:3.500A) Processing helix chain 'a' and resid 604 through 618 removed outlier: 3.919A pdb=" N VAL a 608 " --> pdb=" O ASP a 604 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA a 609 " --> pdb=" O PHE a 605 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE a 614 " --> pdb=" O LYS a 610 " (cutoff:3.500A) Processing helix chain 'a' and resid 624 through 643 removed outlier: 3.768A pdb=" N ILE a 636 " --> pdb=" O PHE a 632 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLN a 637 " --> pdb=" O LYS a 633 " (cutoff:3.500A) Proline residue: a 638 - end of helix removed outlier: 3.877A pdb=" N GLU a 643 " --> pdb=" O SER a 639 " (cutoff:3.500A) Processing helix chain 'a' and resid 666 through 671 removed outlier: 4.543A pdb=" N ASN a 670 " --> pdb=" O ASP a 666 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLU a 671 " --> pdb=" O PRO a 667 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 666 through 671' Processing helix chain 'a' and resid 761 through 769 Processing helix chain 'a' and resid 895 through 901 removed outlier: 3.694A pdb=" N LEU a 901 " --> pdb=" O ILE a 897 " (cutoff:3.500A) Processing helix chain 'a' and resid 910 through 927 removed outlier: 3.698A pdb=" N GLN a 920 " --> pdb=" O ILE a 916 " (cutoff:3.500A) Processing helix chain 'a' and resid 1016 through 1030 Processing helix chain 'a' and resid 1084 through 1089 removed outlier: 4.190A pdb=" N TYR a1088 " --> pdb=" O ASP a1084 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASN a1089 " --> pdb=" O TYR a1085 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 1084 through 1089' Processing helix chain 'a' and resid 1110 through 1131 removed outlier: 3.759A pdb=" N ILE a1127 " --> pdb=" O CYS a1123 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS a1130 " --> pdb=" O HIS a1126 " (cutoff:3.500A) Processing helix chain 'a' and resid 1157 through 1165 Processing helix chain 'a' and resid 1197 through 1203 Processing sheet with id= 1, first strand: chain 'C' and resid 213 through 223 removed outlier: 4.578A pdb=" N SER C 231 " --> pdb=" O ARG C 218 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ASP C 293 " --> pdb=" O THR C 236 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'C' and resid 274 through 277 removed outlier: 4.909A pdb=" N TYR C 266 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ARG C 312 " --> pdb=" O ILE C 269 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ALA C 318 " --> pdb=" O GLN C 262 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N LYS C 258 " --> pdb=" O GLU C 322 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'C' and resid 402 through 405 removed outlier: 5.200A pdb=" N VAL C 410 " --> pdb=" O SER C 405 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ARG C 430 " --> pdb=" O ILE C 415 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ARG C 523 " --> pdb=" O LEU C 502 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'C' and resid 418 through 421 removed outlier: 3.964A pdb=" N ILE C 419 " --> pdb=" O SER C 556 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'C' and resid 312 through 323 removed outlier: 3.708A pdb=" N LEU C 329 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU C 323 " --> pdb=" O LEU C 327 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU C 327 " --> pdb=" O LEU C 323 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'c' and resid 213 through 223 removed outlier: 4.968A pdb=" N SER c 231 " --> pdb=" O ARG c 218 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ASP c 293 " --> pdb=" O THR c 236 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'c' and resid 274 through 277 removed outlier: 4.917A pdb=" N TYR c 266 " --> pdb=" O LEU c 277 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ARG c 312 " --> pdb=" O ILE c 269 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ALA c 318 " --> pdb=" O GLN c 262 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N LYS c 258 " --> pdb=" O GLU c 322 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'c' and resid 402 through 405 removed outlier: 5.465A pdb=" N VAL c 410 " --> pdb=" O SER c 405 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ARG c 430 " --> pdb=" O ILE c 415 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ARG c 523 " --> pdb=" O LEU c 502 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'c' and resid 418 through 421 removed outlier: 4.458A pdb=" N ILE c 419 " --> pdb=" O SER c 556 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'c' and resid 312 through 322 Processing sheet with id= 11, first strand: chain 'D' and resid 7 through 12 removed outlier: 3.749A pdb=" N LEU D 84 " --> pdb=" O ILE D 79 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N LEU D 78 " --> pdb=" O LEU D 62 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LEU D 62 " --> pdb=" O LEU D 78 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'E' and resid 174 through 178 removed outlier: 4.671A pdb=" N ASN E 175 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU E 187 " --> pdb=" O ASN E 175 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N GLY E 182 " --> pdb=" O VAL E 264 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL E 264 " --> pdb=" O GLY E 182 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'F' and resid 114 through 120 removed outlier: 5.340A pdb=" N PHE F 115 " --> pdb=" O VAL F 178 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL F 178 " --> pdb=" O PHE F 115 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLU F 175 " --> pdb=" O VAL F 164 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ASP F 158 " --> pdb=" O ASN F 181 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'G' and resid 16 through 20 removed outlier: 3.701A pdb=" N PHE G 17 " --> pdb=" O ILE G 8 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N TYR G 80 " --> pdb=" O PHE G 88 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'H' and resid 4 through 9 removed outlier: 6.089A pdb=" N ARG H 120 " --> pdb=" O ILE H 131 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'h' and resid 4 through 9 removed outlier: 5.621A pdb=" N ARG h 120 " --> pdb=" O ILE h 131 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'I' and resid 103 through 106 removed outlier: 6.560A pdb=" N ASP I 113 " --> pdb=" O LEU I 180 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N THR I 174 " --> pdb=" O LEU I 119 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'J' and resid 199 through 202 removed outlier: 4.187A pdb=" N GLU J 208 " --> pdb=" O SER J 202 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLN J 269 " --> pdb=" O GLY J 249 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'j' and resid 199 through 202 removed outlier: 3.787A pdb=" N GLU j 208 " --> pdb=" O SER j 202 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N GLN j 269 " --> pdb=" O GLY j 249 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'K' and resid 16 through 21 removed outlier: 5.916A pdb=" N ALA K 102 " --> pdb=" O LEU K 89 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N CYS K 87 " --> pdb=" O ILE K 104 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'k' and resid 16 through 21 removed outlier: 6.092A pdb=" N ALA k 102 " --> pdb=" O LEU k 89 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N CYS k 87 " --> pdb=" O ILE k 104 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'l' and resid 47 through 56 removed outlier: 5.295A pdb=" N GLY l 47 " --> pdb=" O ALA l 70 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU l 49 " --> pdb=" O ASP l 68 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG l 53 " --> pdb=" O ALA l 64 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR l 12 " --> pdb=" O LYS l 61 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N THR l 69 " --> pdb=" O LEU l 18 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N GLY l 20 " --> pdb=" O THR l 69 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ILE l 19 " --> pdb=" O LEU l 90 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA l 120 " --> pdb=" O VAL l 87 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'B' and resid 535 through 540 removed outlier: 3.982A pdb=" N LEU B 536 " --> pdb=" O GLY B 631 " (cutoff:3.500A) removed outlier: 8.829A pdb=" N GLU B 637 " --> pdb=" O LEU B 540 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU B 623 " --> pdb=" O PHE B 638 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR B 579 " --> pdb=" O ILE B 628 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'B' and resid 544 through 549 removed outlier: 4.147A pdb=" N GLU B 563 " --> pdb=" O ASN B 549 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER B 560 " --> pdb=" O CYS B 612 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'B' and resid 574 through 578 removed outlier: 4.389A pdb=" N ILE B 575 " --> pdb=" O LEU B 601 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR B 577 " --> pdb=" O PHE B 599 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE B 599 " --> pdb=" O THR B 577 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'B' and resid 658 through 664 removed outlier: 4.859A pdb=" N TYR B 672 " --> pdb=" O TYR B 729 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR B 729 " --> pdb=" O TYR B 672 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'B' and resid 666 through 669 removed outlier: 4.125A pdb=" N VAL B 857 " --> pdb=" O LEU B 973 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N VAL B 975 " --> pdb=" O LEU B 855 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'B' and resid 715 through 719 removed outlier: 5.088A pdb=" N SER B 686 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLN B 688 " --> pdb=" O SER B 745 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLU B 757 " --> pdb=" O THR B 744 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'B' and resid 769 through 778 removed outlier: 3.528A pdb=" N LEU B 788 " --> pdb=" O PHE B 835 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N PHE B 835 " --> pdb=" O LEU B 788 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'B' and resid 796 through 800 Processing sheet with id= 31, first strand: chain 'B' and resid 1044 through 1047 removed outlier: 3.560A pdb=" N VAL B1015 " --> pdb=" O PHE B1061 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N SER B1012 " --> pdb=" O MET B 993 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N MET B 993 " --> pdb=" O SER B1012 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N PHE B 990 " --> pdb=" O SER B1093 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'B' and resid 1050 through 1054 removed outlier: 6.660A pdb=" N LYS B1050 " --> pdb=" O ILE B1038 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE B1054 " --> pdb=" O TYR B1034 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N TYR B1034 " --> pdb=" O ILE B1054 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N GLY B1033 " --> pdb=" O ILE B1083 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE B1083 " --> pdb=" O GLY B1033 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ILE B1035 " --> pdb=" O THR B1081 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR B1081 " --> pdb=" O ILE B1035 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ARG B1077 " --> pdb=" O LEU B1039 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY B1071 " --> pdb=" O ILE B1101 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ILE B1101 " --> pdb=" O GLY B1071 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'A' and resid 70 through 73 removed outlier: 3.644A pdb=" N VAL A 95 " --> pdb=" O ARG A 17 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ASN A 145 " --> pdb=" O PRO A 123 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'A' and resid 656 through 661 removed outlier: 3.650A pdb=" N GLU A 656 " --> pdb=" O ARG A 734 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA A 729 " --> pdb=" O LEU A 785 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'A' and resid 720 through 724 Processing sheet with id= 36, first strand: chain 'A' and resid 743 through 746 removed outlier: 3.669A pdb=" N PHE A 743 " --> pdb=" O VAL A 773 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'A' and resid 747 through 750 removed outlier: 3.830A pdb=" N ASP A 747 " --> pdb=" O SER A 804 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU A 801 " --> pdb=" O PHE A 813 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'A' and resid 853 through 856 removed outlier: 6.824A pdb=" N HIS A 874 " --> pdb=" O SER A 856 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLU A 942 " --> pdb=" O ASN A 879 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASP A 947 " --> pdb=" O ILE A 932 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE A 932 " --> pdb=" O ASP A 947 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N CYS A 928 " --> pdb=" O ASP A 951 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'A' and resid 861 through 865 removed outlier: 5.940A pdb=" N ASN A 861 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TRP A 863 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'A' and resid 994 through 997 removed outlier: 5.654A pdb=" N THR A 994 " --> pdb=" O SER A1047 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER A1047 " --> pdb=" O THR A 994 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'A' and resid 1065 through 1069 removed outlier: 7.311A pdb=" N GLY A1051 " --> pdb=" O THR A1138 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'A' and resid 1171 through 1175 removed outlier: 4.184A pdb=" N GLU A1195 " --> pdb=" O GLY A1172 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ARG A1230 " --> pdb=" O ILE A1256 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'A' and resid 1237 through 1242 removed outlier: 7.515A pdb=" N LEU A1237 " --> pdb=" O ILE A1213 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ILE A1213 " --> pdb=" O LEU A1237 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL A1214 " --> pdb=" O SER A1264 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N PHE A1216 " --> pdb=" O GLU A1262 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'A' and resid 1036 through 1045 No H-bonds generated for sheet with id= 44 Processing sheet with id= 45, first strand: chain 'd' and resid 19 through 22 removed outlier: 4.230A pdb=" N PHE d 7 " --> pdb=" O GLY d 89 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU d 84 " --> pdb=" O ILE d 79 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'e' and resid 87 through 90 Processing sheet with id= 47, first strand: chain 'e' and resid 183 through 189 Processing sheet with id= 48, first strand: chain 'f' and resid 113 through 119 removed outlier: 6.947A pdb=" N ASP f 113 " --> pdb=" O LEU f 180 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N PHE f 115 " --> pdb=" O VAL f 178 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N THR f 174 " --> pdb=" O LEU f 119 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLU f 175 " --> pdb=" O VAL f 164 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ASP f 158 " --> pdb=" O ASN f 181 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'g' and resid 17 through 21 removed outlier: 7.217A pdb=" N TYR g 4 " --> pdb=" O TRP g 21 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER g 5 " --> pdb=" O LEU g 91 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU g 86 " --> pdb=" O THR g 82 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'i' and resid 103 through 106 removed outlier: 6.638A pdb=" N ASP i 113 " --> pdb=" O LEU i 180 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N THR i 174 " --> pdb=" O LEU i 119 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLU i 175 " --> pdb=" O VAL i 164 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N VAL i 164 " --> pdb=" O GLU i 175 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'b' and resid 536 through 539 removed outlier: 3.740A pdb=" N THR b 579 " --> pdb=" O ILE b 628 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N MET b 580 " --> pdb=" O ALA b 596 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA b 596 " --> pdb=" O MET b 580 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE b 592 " --> pdb=" O LEU b 584 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASP b 590 " --> pdb=" O ASN b 586 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'b' and resid 543 through 548 removed outlier: 6.646A pdb=" N LEU b 543 " --> pdb=" O TYR b 569 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN b 565 " --> pdb=" O THR b 547 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER b 560 " --> pdb=" O CYS b 612 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'b' and resid 574 through 578 removed outlier: 3.723A pdb=" N ILE b 575 " --> pdb=" O LEU b 601 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'b' and resid 658 through 663 removed outlier: 3.616A pdb=" N LYS b 658 " --> pdb=" O VAL b 679 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU b 660 " --> pdb=" O LYS b 677 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N TYR b 672 " --> pdb=" O TYR b 729 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR b 729 " --> pdb=" O TYR b 672 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'b' and resid 665 through 669 removed outlier: 6.449A pdb=" N HIS b 665 " --> pdb=" O PRO b 970 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'b' and resid 686 through 694 removed outlier: 5.017A pdb=" N SER b 686 " --> pdb=" O THR b 747 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLN b 688 " --> pdb=" O SER b 745 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLN b 694 " --> pdb=" O ASP b 739 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ASP b 739 " --> pdb=" O GLN b 694 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU b 757 " --> pdb=" O THR b 744 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE b 746 " --> pdb=" O PHE b 755 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'b' and resid 769 through 778 removed outlier: 4.081A pdb=" N PHE b 835 " --> pdb=" O LEU b 788 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'b' and resid 796 through 800 removed outlier: 3.571A pdb=" N LEU b 799 " --> pdb=" O ALA b 825 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA b 825 " --> pdb=" O LEU b 799 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'b' and resid 1044 through 1047 removed outlier: 5.782A pdb=" N SER b1012 " --> pdb=" O MET b 993 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N MET b 993 " --> pdb=" O SER b1012 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N PHE b 990 " --> pdb=" O SER b1093 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'b' and resid 1050 through 1054 removed outlier: 6.461A pdb=" N LYS b1050 " --> pdb=" O ILE b1038 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE b1054 " --> pdb=" O TYR b1034 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N TYR b1034 " --> pdb=" O ILE b1054 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ARG b1077 " --> pdb=" O LEU b1039 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY b1071 " --> pdb=" O ILE b1101 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N ILE b1101 " --> pdb=" O GLY b1071 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'b' and resid 583 through 586 removed outlier: 6.860A pdb=" N SER b 583 " --> pdb=" O LEU b 623 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'a' and resid 70 through 73 removed outlier: 4.365A pdb=" N VAL a 95 " --> pdb=" O ARG a 17 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU a 19 " --> pdb=" O VAL a 95 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE a 97 " --> pdb=" O LEU a 19 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE a 21 " --> pdb=" O ILE a 97 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ASN a 145 " --> pdb=" O PRO a 123 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'a' and resid 656 through 661 removed outlier: 3.754A pdb=" N GLU a 656 " --> pdb=" O ARG a 734 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA a 729 " --> pdb=" O LEU a 785 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU a 785 " --> pdb=" O ALA a 729 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N SER a 777 " --> pdb=" O ASN a 737 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'a' and resid 720 through 724 Processing sheet with id= 65, first strand: chain 'a' and resid 743 through 746 removed outlier: 3.723A pdb=" N PHE a 743 " --> pdb=" O VAL a 773 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'a' and resid 747 through 751 removed outlier: 4.116A pdb=" N ASP a 747 " --> pdb=" O SER a 804 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ASP a 751 " --> pdb=" O CYS a 800 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N CYS a 800 " --> pdb=" O ASP a 751 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU a 801 " --> pdb=" O PHE a 813 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'a' and resid 853 through 856 removed outlier: 6.787A pdb=" N HIS a 874 " --> pdb=" O SER a 856 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP a 947 " --> pdb=" O ILE a 932 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE a 932 " --> pdb=" O ASP a 947 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'a' and resid 861 through 865 removed outlier: 6.052A pdb=" N ASN a 861 " --> pdb=" O PRO a 986 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N MET a 894 " --> pdb=" O ASP a 963 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU a 965 " --> pdb=" O ILE a 892 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE a 892 " --> pdb=" O LEU a 965 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS a 890 " --> pdb=" O GLU a 967 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'a' and resid 994 through 997 removed outlier: 4.928A pdb=" N THR a 994 " --> pdb=" O SER a1047 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER a1047 " --> pdb=" O THR a 994 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N PHE a1037 " --> pdb=" O LEU a1005 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU a1039 " --> pdb=" O ILE a1003 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ILE a1003 " --> pdb=" O LEU a1039 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N LEU a1041 " --> pdb=" O ASP a1001 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'a' and resid 1065 through 1068 removed outlier: 7.371A pdb=" N GLY a1051 " --> pdb=" O THR a1138 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN a1055 " --> pdb=" O ASN a1134 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'a' and resid 1171 through 1175 removed outlier: 3.524A pdb=" N GLY a1172 " --> pdb=" O GLU a1195 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU a1195 " --> pdb=" O GLY a1172 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU a1190 " --> pdb=" O LEU a1251 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N GLU a1252 " --> pdb=" O ASN a1234 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ASN a1234 " --> pdb=" O GLU a1252 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ARG a1230 " --> pdb=" O ILE a1256 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'a' and resid 1180 through 1183 removed outlier: 3.684A pdb=" N SER a1287 " --> pdb=" O PRO a1180 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL a1182 " --> pdb=" O SER a1287 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N PHE a1216 " --> pdb=" O GLU a1262 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE a1213 " --> pdb=" O LEU a1237 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N LEU a1237 " --> pdb=" O ILE a1213 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'a' and resid 1036 through 1046 No H-bonds generated for sheet with id= 73 2451 hydrogen bonds defined for protein. 7271 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: 44.12 Time building geometry restraints manager: 72.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 60331 1.03 - 1.22: 135 1.22 - 1.42: 26854 1.42 - 1.62: 37749 1.62 - 1.82: 435 Bond restraints: 125504 Sorted by residual: bond pdb=" C ILE a 985 " pdb=" N PRO a 986 " ideal model delta sigma weight residual 1.328 1.361 -0.033 1.25e-02 6.40e+03 7.03e+00 bond pdb=" CG LEU j 101 " pdb=" CD2 LEU j 101 " ideal model delta sigma weight residual 1.521 1.438 0.083 3.30e-02 9.18e+02 6.29e+00 bond pdb=" CB LYS b 470 " pdb=" CG LYS b 470 " ideal model delta sigma weight residual 1.520 1.588 -0.068 3.00e-02 1.11e+03 5.13e+00 bond pdb=" C LYS a 789 " pdb=" N PRO a 790 " ideal model delta sigma weight residual 1.326 1.358 -0.032 1.44e-02 4.82e+03 4.85e+00 bond pdb=" C ILE i 188 " pdb=" N PRO i 189 " ideal model delta sigma weight residual 1.336 1.357 -0.021 1.20e-02 6.94e+03 3.17e+00 ... (remaining 125499 not shown) Histogram of bond angle deviations from ideal: 97.55 - 104.88: 933 104.88 - 112.22: 142456 112.22 - 119.56: 32977 119.56 - 126.90: 48657 126.90 - 134.24: 635 Bond angle restraints: 225658 Sorted by residual: angle pdb=" CA GLN A 628 " pdb=" CB GLN A 628 " pdb=" CG GLN A 628 " ideal model delta sigma weight residual 114.10 122.49 -8.39 2.00e+00 2.50e-01 1.76e+01 angle pdb=" C SER b 681 " pdb=" N ASP b 682 " pdb=" CA ASP b 682 " ideal model delta sigma weight residual 121.54 129.37 -7.83 1.91e+00 2.74e-01 1.68e+01 angle pdb=" N GLN b 304 " pdb=" CA GLN b 304 " pdb=" CB GLN b 304 " ideal model delta sigma weight residual 110.22 116.52 -6.30 1.54e+00 4.22e-01 1.68e+01 angle pdb=" CB MET H 200 " pdb=" CG MET H 200 " pdb=" SD MET H 200 " ideal model delta sigma weight residual 112.70 124.88 -12.18 3.00e+00 1.11e-01 1.65e+01 angle pdb=" N GLU d 110 " pdb=" CA GLU d 110 " pdb=" CB GLU d 110 " ideal model delta sigma weight residual 110.22 116.45 -6.23 1.54e+00 4.22e-01 1.64e+01 ... (remaining 225653 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 53105 17.99 - 35.98: 4991 35.98 - 53.97: 1022 53.97 - 71.97: 188 71.97 - 89.96: 49 Dihedral angle restraints: 59355 sinusoidal: 31084 harmonic: 28271 Sorted by residual: dihedral pdb=" CA TRP A1135 " pdb=" C TRP A1135 " pdb=" N LYS A1136 " pdb=" CA LYS A1136 " ideal model delta harmonic sigma weight residual 180.00 149.83 30.17 0 5.00e+00 4.00e-02 3.64e+01 dihedral pdb=" CA LYS f 51 " pdb=" C LYS f 51 " pdb=" N VAL f 52 " pdb=" CA VAL f 52 " ideal model delta harmonic sigma weight residual 180.00 151.15 28.85 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA ASN i 82 " pdb=" C ASN i 82 " pdb=" N LEU i 83 " pdb=" CA LEU i 83 " ideal model delta harmonic sigma weight residual 180.00 151.81 28.19 0 5.00e+00 4.00e-02 3.18e+01 ... (remaining 59352 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 8241 0.055 - 0.110: 1572 0.110 - 0.166: 343 0.166 - 0.221: 28 0.221 - 0.276: 4 Chirality restraints: 10188 Sorted by residual: chirality pdb=" CB THR i 174 " pdb=" CA THR i 174 " pdb=" OG1 THR i 174 " pdb=" CG2 THR i 174 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CG LEU J 101 " pdb=" CB LEU J 101 " pdb=" CD1 LEU J 101 " pdb=" CD2 LEU J 101 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CB ILE B 776 " pdb=" CA ILE B 776 " pdb=" CG1 ILE B 776 " pdb=" CG2 ILE B 776 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 10185 not shown) Planarity restraints: 18212 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN D 122 " 0.056 5.00e-02 4.00e+02 8.34e-02 1.11e+01 pdb=" N PRO D 123 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO D 123 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO D 123 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLN f 40 " 0.016 2.00e-02 2.50e+03 2.51e-02 9.43e+00 pdb=" CD GLN f 40 " -0.054 2.00e-02 2.50e+03 pdb=" OE1 GLN f 40 " 0.020 2.00e-02 2.50e+03 pdb=" NE2 GLN f 40 " 0.015 2.00e-02 2.50e+03 pdb="HE21 GLN f 40 " 0.000 2.00e-02 2.50e+03 pdb="HE22 GLN f 40 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 151 " 0.015 2.00e-02 2.50e+03 2.99e-02 8.94e+00 pdb=" C PRO A 151 " -0.052 2.00e-02 2.50e+03 pdb=" O PRO A 151 " 0.020 2.00e-02 2.50e+03 pdb=" N ASP A 152 " 0.017 2.00e-02 2.50e+03 ... (remaining 18209 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.23: 10591 2.23 - 2.82: 260531 2.82 - 3.41: 314278 3.41 - 4.01: 416242 4.01 - 4.60: 637800 Nonbonded interactions: 1639442 Sorted by model distance: nonbonded pdb=" H GLU l 49 " pdb=" OD1 ASP l 68 " model vdw 1.631 1.850 nonbonded pdb="HD21 ASN D 37 " pdb=" OG SER B 466 " model vdw 1.650 1.850 nonbonded pdb=" O TYR G 111 " pdb=" H VAL G 115 " model vdw 1.675 1.850 nonbonded pdb="HH22 ARG J 172 " pdb=" O GLN K 52 " model vdw 1.677 1.850 nonbonded pdb=" O MET e 52 " pdb=" H ALA e 56 " model vdw 1.679 1.850 ... (remaining 1639437 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 'A' and (resid 1 through 1138 or (resid 1139 and (name N or name CA or na \ me C or name O or name CB or name OG1 or name CG2 or name H or name HA or name H \ B or name HG21 or name HG22 or name HG23)) or resid 1140 through 1169 or (resid \ 1170 and (name N or name CA or name C or name O or name CB or name CG or name CD \ 1 or name CD2 or name CE1 or name CE2 or name CZ or name HA or name HB2 or name \ HB3 or name HD1 or name HD2 or name HE1 or name HE2 or name HZ )) or resid 1171 \ through 1289)) selection = (chain 'a' and (resid 1 through 676 or resid 718 through 1289)) } ncs_group { reference = (chain 'B' and ((resid 296 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name H \ G or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23) \ ) or resid 297 through 650 or (resid 651 and (name N or name CA or name C or nam \ e O or name CB or name CG1 or name CG2 or name CD1 or name HA or name HB or name \ HG12 or name HG13 or name HG21 or name HG22 or name HG23 or name HD11 or name H \ D12 or name HD13)) or resid 652 through 1104)) selection = (chain 'b' and (resid 296 through 339 or resid 345 through 1104)) } ncs_group { reference = chain 'C' selection = (chain 'c' and (resid 138 through 241 or (resid 242 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name OE1 or name NE2 or name \ H or name HA or name HB2 or name HB3 or name HG2 or name HG3)) or resid 243 thro \ ugh 560)) } ncs_group { reference = (chain 'D' and ((resid 3 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG \ or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23)) \ or resid 4 through 42 or resid 44 through 146)) selection = (chain 'd' and (resid 3 through 42 or resid 44 through 146)) } ncs_group { reference = (chain 'E' and ((resid 37 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG \ or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23)) \ or resid 38 through 265)) selection = (chain 'e' and (resid 37 through 64 or (resid 88 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name HA or name HB2 \ or name HB3 or name HG or name HD11 or name HD12 or name HD13 or name HD21 or n \ ame HD22 or name HD23)) or resid 89 through 140 or (resid 141 through 142 and (n \ ame N or name CA or name C or name O or name CB or name H or name HA or name HB2 \ or name HB3)) or resid 143 through 265)) } ncs_group { reference = (chain 'F' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name NE or name CZ or name NH1 or name NH2 or name HA or \ name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE \ or name HH11 or name HH12 or name HH21 or name HH22)) or resid 9 through 190 or \ resid 201)) selection = chain 'I' selection = (chain 'f' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name NE or name CZ or name NH1 or name NH2 or name HA or \ name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE \ or name HH11 or name HH12 or name HH21 or name HH22)) or resid 9 through 190 or \ resid 201)) selection = (chain 'i' and (resid 8 through 190 or resid 201)) } ncs_group { reference = (chain 'G' and resid 2 through 157) selection = (chain 'g' and (resid 2 through 92 or (resid 93 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 94 through 157)) } ncs_group { reference = chain 'H' selection = (chain 'h' and (resid 2 through 132 or (resid 133 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name OE1 or name NE2 or name H \ or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HE21)) or res \ id 134 through 219)) } ncs_group { reference = chain 'J' selection = chain 'j' } ncs_group { reference = chain 'K' selection = chain 'k' } ncs_group { reference = chain 'M' selection = (chain 'm' and resid 8 through 293) } ncs_group { reference = chain 'N' selection = chain 'n' } 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=0.00 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: 2.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 1.360 Extract box with map and model: 16.470 Check model and map are aligned: 1.320 Set scattering table: 0.840 Process input model: 307.230 Find NCS groups from input model: 4.130 Set up NCS constraints: 0.680 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: 0.020 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 337.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 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 : 0.005 0.083 65054 Z= 0.302 Angle : 0.858 12.184 88071 Z= 0.446 Chirality : 0.047 0.276 10188 Planarity : 0.006 0.093 11161 Dihedral : 14.084 89.957 23687 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.09 % Favored : 88.78 % Rotamer: Outliers : 0.01 % Allowed : 0.31 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.09), residues: 7262 helix: 0.19 (0.10), residues: 2430 sheet: -1.79 (0.13), residues: 1471 loop : -2.62 (0.10), residues: 3361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 522 HIS 0.011 0.001 HIS b 481 PHE 0.031 0.002 PHE B 599 TYR 0.048 0.002 TYR c 492 ARG 0.021 0.001 ARG j 105 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14524 Ramachandran restraints generated. 7262 Oldfield, 0 Emsley, 7262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14524 Ramachandran restraints generated. 7262 Oldfield, 0 Emsley, 7262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 57 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue SER 80 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue THR 1139 is missing expected H atoms. Skipping. Evaluate side-chains 2913 residues out of total 6847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2912 time to evaluate : 7.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 141 LYS cc_start: 0.8185 (tptm) cc_final: 0.7652 (tppt) REVERT: C 142 TYR cc_start: 0.7391 (t80) cc_final: 0.7045 (t80) REVERT: C 425 GLU cc_start: 0.8135 (tt0) cc_final: 0.7897 (tt0) REVERT: C 497 GLU cc_start: 0.7117 (pt0) cc_final: 0.6566 (pt0) REVERT: D 6 CYS cc_start: 0.8540 (t) cc_final: 0.8288 (t) REVERT: D 92 GLN cc_start: 0.8244 (tm-30) cc_final: 0.7829 (tm-30) REVERT: D 107 GLN cc_start: 0.8246 (tp40) cc_final: 0.8025 (tp40) REVERT: D 115 ILE cc_start: 0.8745 (mm) cc_final: 0.8518 (mm) REVERT: D 134 ILE cc_start: 0.8162 (mt) cc_final: 0.7856 (mt) REVERT: D 138 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7378 (mt-10) REVERT: D 139 ARG cc_start: 0.8550 (ttm-80) cc_final: 0.8155 (ttm-80) REVERT: E 205 ASN cc_start: 0.7682 (m-40) cc_final: 0.7313 (m-40) REVERT: F 107 ASN cc_start: 0.8256 (t0) cc_final: 0.7914 (t0) REVERT: F 187 GLU cc_start: 0.7928 (mt-10) cc_final: 0.6512 (mt-10) REVERT: G 56 GLN cc_start: 0.9300 (mm110) cc_final: 0.8972 (tp-100) REVERT: G 118 ASN cc_start: 0.6971 (t0) cc_final: 0.6529 (t0) REVERT: G 132 MET cc_start: 0.7484 (ppp) cc_final: 0.6323 (ppp) REVERT: G 143 ARG cc_start: 0.7949 (tmm-80) cc_final: 0.7686 (ptt90) REVERT: H 18 GLN cc_start: 0.8396 (pp30) cc_final: 0.8050 (pp30) REVERT: H 35 ILE cc_start: 0.8183 (mm) cc_final: 0.7963 (mm) REVERT: H 104 ASP cc_start: 0.7913 (p0) cc_final: 0.7532 (p0) REVERT: H 139 LYS cc_start: 0.8619 (mtmm) cc_final: 0.8372 (mttm) REVERT: H 193 ASP cc_start: 0.9191 (t0) cc_final: 0.8785 (t0) REVERT: I 16 GLU cc_start: 0.8846 (tp30) cc_final: 0.8273 (tp30) REVERT: I 20 ASN cc_start: 0.8727 (p0) cc_final: 0.8467 (p0) REVERT: I 100 ASN cc_start: 0.8636 (t0) cc_final: 0.8356 (t0) REVERT: I 140 TYR cc_start: 0.8956 (t80) cc_final: 0.8364 (t80) REVERT: J 222 ILE cc_start: 0.7826 (mm) cc_final: 0.7305 (mm) REVERT: J 229 CYS cc_start: 0.8335 (m) cc_final: 0.8122 (m) REVERT: J 257 GLN cc_start: 0.7086 (tm-30) cc_final: 0.6563 (tm-30) REVERT: J 277 ARG cc_start: 0.7766 (ppt170) cc_final: 0.7511 (tmm-80) REVERT: K 34 LYS cc_start: 0.7912 (ttmm) cc_final: 0.7402 (ttmm) REVERT: K 104 ILE cc_start: 0.8836 (mt) cc_final: 0.8625 (mt) REVERT: K 162 ASP cc_start: 0.8362 (t0) cc_final: 0.7860 (t0) REVERT: l 107 TRP cc_start: 0.8789 (m100) cc_final: 0.8543 (m100) REVERT: l 150 MET cc_start: 0.8179 (ptm) cc_final: 0.7041 (ptm) REVERT: B 311 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8206 (mt-10) REVERT: B 510 LYS cc_start: 0.8767 (ptmt) cc_final: 0.8472 (ttpt) REVERT: B 625 PHE cc_start: 0.8847 (t80) cc_final: 0.8539 (t80) REVERT: B 640 GLU cc_start: 0.7408 (tm-30) cc_final: 0.7020 (tm-30) REVERT: B 650 GLU cc_start: 0.8393 (pt0) cc_final: 0.8149 (pt0) REVERT: B 662 LYS cc_start: 0.8714 (pttm) cc_final: 0.8465 (ptmt) REVERT: B 672 TYR cc_start: 0.7361 (m-80) cc_final: 0.7156 (m-80) REVERT: B 711 GLU cc_start: 0.7714 (tt0) cc_final: 0.7376 (mm-30) REVERT: B 729 TYR cc_start: 0.7647 (t80) cc_final: 0.7327 (t80) REVERT: B 743 LYS cc_start: 0.7853 (ptmm) cc_final: 0.7289 (ptmm) REVERT: B 780 ASP cc_start: 0.8550 (p0) cc_final: 0.8092 (p0) REVERT: B 795 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7381 (mm-30) REVERT: B 870 ILE cc_start: 0.9094 (mt) cc_final: 0.8886 (mt) REVERT: B 982 PHE cc_start: 0.7204 (p90) cc_final: 0.6864 (p90) REVERT: B 1093 SER cc_start: 0.9010 (p) cc_final: 0.8749 (p) REVERT: A 37 LYS cc_start: 0.8720 (ttmm) cc_final: 0.7827 (ttmm) REVERT: A 152 ASP cc_start: 0.8215 (p0) cc_final: 0.7937 (p0) REVERT: A 172 LEU cc_start: 0.9026 (tt) cc_final: 0.8819 (tt) REVERT: A 319 ILE cc_start: 0.8954 (tt) cc_final: 0.8505 (tt) REVERT: A 322 CYS cc_start: 0.8098 (m) cc_final: 0.7790 (m) REVERT: A 333 TYR cc_start: 0.8489 (p90) cc_final: 0.7793 (p90) REVERT: A 489 GLU cc_start: 0.8169 (tt0) cc_final: 0.7469 (tt0) REVERT: A 492 PHE cc_start: 0.8043 (t80) cc_final: 0.7825 (t80) REVERT: A 503 LYS cc_start: 0.5712 (mmtp) cc_final: 0.5428 (mmtp) REVERT: A 517 MET cc_start: 0.8606 (ttp) cc_final: 0.8403 (ttp) REVERT: A 561 ILE cc_start: 0.9254 (mt) cc_final: 0.8517 (mt) REVERT: A 643 GLU cc_start: 0.8438 (tt0) cc_final: 0.8217 (tt0) REVERT: A 666 ASP cc_start: 0.7947 (p0) cc_final: 0.7681 (p0) REVERT: A 759 GLU cc_start: 0.7809 (pm20) cc_final: 0.7196 (pm20) REVERT: A 815 ILE cc_start: 0.9139 (mm) cc_final: 0.8828 (mm) REVERT: A 879 ASN cc_start: 0.8211 (t0) cc_final: 0.7761 (t0) REVERT: A 984 SER cc_start: 0.8397 (p) cc_final: 0.8188 (p) REVERT: A 996 GLU cc_start: 0.7112 (pt0) cc_final: 0.6728 (pt0) REVERT: A 1002 ILE cc_start: 0.7616 (mm) cc_final: 0.7086 (mm) REVERT: A 1050 ASP cc_start: 0.8422 (m-30) cc_final: 0.8107 (m-30) REVERT: A 1057 GLN cc_start: 0.8191 (mt0) cc_final: 0.7969 (mt0) REVERT: A 1253 ILE cc_start: 0.8683 (mm) cc_final: 0.8432 (mm) REVERT: c 238 LYS cc_start: 0.9066 (mtpt) cc_final: 0.8218 (pptt) REVERT: c 311 HIS cc_start: 0.8110 (m90) cc_final: 0.7853 (m90) REVERT: d 13 GLU cc_start: 0.8181 (pm20) cc_final: 0.7839 (pm20) REVERT: d 32 ASP cc_start: 0.7919 (m-30) cc_final: 0.7714 (m-30) REVERT: d 77 MET cc_start: 0.6868 (mtm) cc_final: 0.6617 (mtm) REVERT: d 135 LYS cc_start: 0.9327 (tptp) cc_final: 0.9110 (tppt) REVERT: e 51 GLU cc_start: 0.8146 (tm-30) cc_final: 0.7910 (tm-30) REVERT: e 191 TYR cc_start: 0.8651 (t80) cc_final: 0.8428 (t80) REVERT: e 262 VAL cc_start: 0.7327 (m) cc_final: 0.7065 (m) REVERT: f 31 THR cc_start: 0.8608 (m) cc_final: 0.8389 (m) REVERT: f 43 GLN cc_start: 0.8744 (tm-30) cc_final: 0.8205 (tm-30) REVERT: f 62 ASN cc_start: 0.9038 (t0) cc_final: 0.8835 (t0) REVERT: f 129 GLU cc_start: 0.7662 (tt0) cc_final: 0.7204 (tt0) REVERT: f 135 MET cc_start: 0.7342 (tpp) cc_final: 0.7122 (tpp) REVERT: g 81 CYS cc_start: 0.7828 (m) cc_final: 0.7535 (m) REVERT: g 87 TRP cc_start: 0.8047 (m-10) cc_final: 0.7481 (m-10) REVERT: g 123 TYR cc_start: 0.7292 (p90) cc_final: 0.6820 (p90) REVERT: g 150 GLU cc_start: 0.8091 (tp30) cc_final: 0.7692 (tp30) REVERT: h 31 ASN cc_start: 0.8854 (t0) cc_final: 0.8618 (t0) REVERT: h 50 LEU cc_start: 0.7559 (mt) cc_final: 0.7323 (mt) REVERT: h 66 THR cc_start: 0.9021 (t) cc_final: 0.8820 (m) REVERT: h 108 LYS cc_start: 0.7902 (mmtp) cc_final: 0.7393 (mmtp) REVERT: h 134 THR cc_start: 0.8391 (m) cc_final: 0.8081 (m) REVERT: i 16 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7644 (tm-30) REVERT: i 34 TYR cc_start: 0.8680 (t80) cc_final: 0.8378 (t80) REVERT: j 23 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7642 (mm-30) REVERT: j 26 VAL cc_start: 0.9177 (p) cc_final: 0.8924 (m) REVERT: j 68 GLU cc_start: 0.8441 (tp30) cc_final: 0.7885 (tp30) REVERT: k 12 ASP cc_start: 0.8242 (t0) cc_final: 0.7855 (t0) REVERT: k 173 LEU cc_start: 0.8439 (tp) cc_final: 0.8185 (tp) REVERT: b 339 GLU cc_start: 0.7820 (mp0) cc_final: 0.6890 (mm-30) REVERT: b 354 GLU cc_start: 0.7348 (tp30) cc_final: 0.7106 (tp30) REVERT: b 363 TRP cc_start: 0.8813 (t60) cc_final: 0.8386 (t60) REVERT: b 377 ASP cc_start: 0.7786 (p0) cc_final: 0.7419 (p0) REVERT: b 434 GLU cc_start: 0.8280 (mm-30) cc_final: 0.8029 (mm-30) REVERT: b 681 SER cc_start: 0.8649 (t) cc_final: 0.8446 (t) REVERT: b 723 GLU cc_start: 0.7672 (mp0) cc_final: 0.7432 (mp0) REVERT: b 733 ASP cc_start: 0.6460 (p0) cc_final: 0.6047 (p0) REVERT: b 846 ASN cc_start: 0.8533 (p0) cc_final: 0.8134 (p0) REVERT: b 867 ASP cc_start: 0.8187 (m-30) cc_final: 0.7944 (m-30) REVERT: b 894 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8186 (mt-10) REVERT: b 973 LEU cc_start: 0.8907 (tt) cc_final: 0.8704 (tt) REVERT: b 982 PHE cc_start: 0.8166 (p90) cc_final: 0.7883 (p90) REVERT: b 986 PHE cc_start: 0.7964 (m-80) cc_final: 0.7747 (m-80) REVERT: b 1069 LYS cc_start: 0.8185 (mtpt) cc_final: 0.7867 (mttp) REVERT: b 1073 LEU cc_start: 0.8971 (mt) cc_final: 0.8755 (mt) REVERT: a 37 LYS cc_start: 0.8616 (mtpp) cc_final: 0.8366 (mtpp) REVERT: a 152 ASP cc_start: 0.8032 (t0) cc_final: 0.7281 (t0) REVERT: a 276 MET cc_start: 0.7555 (tpp) cc_final: 0.6984 (tpp) REVERT: a 308 ASP cc_start: 0.8042 (t0) cc_final: 0.7647 (t0) REVERT: a 403 ASP cc_start: 0.7770 (p0) cc_final: 0.7356 (p0) REVERT: a 553 ASP cc_start: 0.7318 (m-30) cc_final: 0.6608 (m-30) REVERT: a 759 GLU cc_start: 0.7865 (pm20) cc_final: 0.7578 (pm20) REVERT: a 776 GLU cc_start: 0.8653 (mp0) cc_final: 0.8223 (mp0) REVERT: a 815 ILE cc_start: 0.8783 (tp) cc_final: 0.8492 (tp) REVERT: a 816 ILE cc_start: 0.8626 (mt) cc_final: 0.8300 (mt) REVERT: a 865 MET cc_start: 0.8195 (mmp) cc_final: 0.7991 (mmp) REVERT: a 874 HIS cc_start: 0.8458 (m90) cc_final: 0.8210 (m-70) REVERT: a 904 ASP cc_start: 0.7924 (p0) cc_final: 0.7533 (p0) REVERT: a 918 GLU cc_start: 0.8801 (tt0) cc_final: 0.8523 (tt0) REVERT: a 1111 GLU cc_start: 0.7007 (tp30) cc_final: 0.6610 (tp30) REVERT: a 1157 ASP cc_start: 0.8065 (p0) cc_final: 0.7566 (p0) REVERT: a 1195 GLU cc_start: 0.8051 (pt0) cc_final: 0.7821 (pt0) REVERT: a 1285 ILE cc_start: 0.8498 (pt) cc_final: 0.8249 (pt) outliers start: 1 outliers final: 0 residues processed: 2912 average time/residue: 1.3220 time to fit residues: 6523.7102 Evaluate side-chains 2691 residues out of total 6847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2691 time to evaluate : 6.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 803 random chunks: chunk 678 optimal weight: 0.0970 chunk 608 optimal weight: 3.9990 chunk 337 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 410 optimal weight: 0.9990 chunk 325 optimal weight: 0.8980 chunk 629 optimal weight: 1.9990 chunk 243 optimal weight: 0.8980 chunk 382 optimal weight: 2.9990 chunk 468 optimal weight: 1.9990 chunk 729 optimal weight: 50.0000 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 409 ASN ** C 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 143 ASN B 642 GLN A 32 ASN ** A 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 899 GLN A1033 HIS A1089 ASN ** d 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 167 GLN h 177 ASN i 100 ASN j 92 HIS j 243 ASN ** k 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 172 HIS b1082 ASN a 2 ASN a 32 ASN a 471 ASN ** a 847 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a1092 ASN a1158 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 65054 Z= 0.253 Angle : 0.560 7.449 88071 Z= 0.302 Chirality : 0.040 0.162 10188 Planarity : 0.004 0.060 11161 Dihedral : 5.462 59.543 8717 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.49 % Favored : 89.37 % Rotamer: Outliers : 0.03 % Allowed : 3.07 % Favored : 96.90 % 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: -2.02 (0.10), residues: 7262 helix: 0.52 (0.10), residues: 2435 sheet: -1.72 (0.13), residues: 1492 loop : -2.62 (0.10), residues: 3335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 550 HIS 0.009 0.001 HIS e 93 PHE 0.026 0.001 PHE E 214 TYR 0.030 0.001 TYR c 492 ARG 0.005 0.000 ARG a1168 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14524 Ramachandran restraints generated. 7262 Oldfield, 0 Emsley, 7262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14524 Ramachandran restraints generated. 7262 Oldfield, 0 Emsley, 7262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 57 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue SER 80 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue THR 1139 is missing expected H atoms. Skipping. Evaluate side-chains 2829 residues out of total 6847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 2827 time to evaluate : 7.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 141 LYS cc_start: 0.7923 (tptm) cc_final: 0.7436 (tppt) REVERT: C 145 GLU cc_start: 0.8095 (pm20) cc_final: 0.7591 (pm20) REVERT: C 146 GLU cc_start: 0.6930 (mm-30) cc_final: 0.6540 (mm-30) REVERT: C 235 GLN cc_start: 0.7776 (pm20) cc_final: 0.7183 (pm20) REVERT: C 311 HIS cc_start: 0.7624 (m-70) cc_final: 0.7171 (m170) REVERT: C 425 GLU cc_start: 0.8203 (tt0) cc_final: 0.7907 (tt0) REVERT: C 497 GLU cc_start: 0.7119 (pt0) cc_final: 0.6646 (pt0) REVERT: D 32 ASP cc_start: 0.7236 (m-30) cc_final: 0.7015 (m-30) REVERT: D 107 GLN cc_start: 0.8233 (tp40) cc_final: 0.7974 (tp40) REVERT: D 115 ILE cc_start: 0.8754 (mm) cc_final: 0.8468 (mm) REVERT: D 134 ILE cc_start: 0.8140 (mt) cc_final: 0.7925 (mt) REVERT: D 136 SER cc_start: 0.8944 (t) cc_final: 0.8729 (t) REVERT: D 138 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7468 (mt-10) REVERT: D 139 ARG cc_start: 0.8617 (ttm-80) cc_final: 0.8210 (ttm-80) REVERT: E 185 TYR cc_start: 0.8150 (m-80) cc_final: 0.7874 (m-80) REVERT: E 205 ASN cc_start: 0.7704 (m-40) cc_final: 0.7369 (m-40) REVERT: F 28 GLU cc_start: 0.6812 (pp20) cc_final: 0.6326 (pp20) REVERT: F 81 GLU cc_start: 0.8408 (tp30) cc_final: 0.8170 (tp30) REVERT: F 107 ASN cc_start: 0.8439 (t0) cc_final: 0.8176 (t0) REVERT: G 143 ARG cc_start: 0.8091 (tmm-80) cc_final: 0.7846 (ttp80) REVERT: H 35 ILE cc_start: 0.8146 (mm) cc_final: 0.7934 (mm) REVERT: H 104 ASP cc_start: 0.7970 (p0) cc_final: 0.7650 (p0) REVERT: H 193 ASP cc_start: 0.9153 (t0) cc_final: 0.8878 (t0) REVERT: I 16 GLU cc_start: 0.8803 (tp30) cc_final: 0.8507 (tp30) REVERT: I 23 GLU cc_start: 0.7824 (tp30) cc_final: 0.7496 (tp30) REVERT: I 100 ASN cc_start: 0.8652 (t0) cc_final: 0.8208 (t0) REVERT: I 140 TYR cc_start: 0.8918 (t80) cc_final: 0.8468 (t80) REVERT: I 154 MET cc_start: 0.8090 (mmp) cc_final: 0.7759 (mmp) REVERT: J 20 ASP cc_start: 0.7616 (t0) cc_final: 0.7165 (t0) REVERT: J 35 GLU cc_start: 0.7248 (tp30) cc_final: 0.7013 (tm-30) REVERT: J 222 ILE cc_start: 0.7861 (mm) cc_final: 0.7272 (mm) REVERT: J 229 CYS cc_start: 0.8385 (m) cc_final: 0.8154 (m) REVERT: J 257 GLN cc_start: 0.7008 (tm-30) cc_final: 0.6567 (tm-30) REVERT: J 277 ARG cc_start: 0.8106 (ppt170) cc_final: 0.7641 (tmm-80) REVERT: K 49 GLU cc_start: 0.7990 (tt0) cc_final: 0.7788 (mt-10) REVERT: K 104 ILE cc_start: 0.8843 (mt) cc_final: 0.8639 (mt) REVERT: K 162 ASP cc_start: 0.8380 (t0) cc_final: 0.7777 (t0) REVERT: l 150 MET cc_start: 0.8564 (ptm) cc_final: 0.7369 (ptm) REVERT: l 184 ASP cc_start: 0.7980 (t0) cc_final: 0.7744 (t0) REVERT: B 506 LEU cc_start: 0.9119 (tt) cc_final: 0.8857 (tt) REVERT: B 510 LYS cc_start: 0.8822 (ptmt) cc_final: 0.8482 (ttpt) REVERT: B 614 ASP cc_start: 0.6828 (p0) cc_final: 0.5836 (p0) REVERT: B 625 PHE cc_start: 0.8923 (t80) cc_final: 0.8572 (t80) REVERT: B 662 LYS cc_start: 0.8717 (pttm) cc_final: 0.8490 (ptmt) REVERT: B 688 GLN cc_start: 0.8733 (mt0) cc_final: 0.8331 (mt0) REVERT: B 728 GLU cc_start: 0.7795 (mp0) cc_final: 0.7407 (mp0) REVERT: B 729 TYR cc_start: 0.7799 (t80) cc_final: 0.7238 (t80) REVERT: B 743 LYS cc_start: 0.7998 (ptmm) cc_final: 0.7471 (ptmt) REVERT: B 973 LEU cc_start: 0.9506 (tp) cc_final: 0.9163 (tp) REVERT: B 1093 SER cc_start: 0.9033 (p) cc_final: 0.8805 (p) REVERT: A 30 GLU cc_start: 0.7632 (tp30) cc_final: 0.6900 (tp30) REVERT: A 37 LYS cc_start: 0.8664 (ttmm) cc_final: 0.7761 (ttmm) REVERT: A 153 MET cc_start: 0.7786 (mtt) cc_final: 0.7557 (mtt) REVERT: A 172 LEU cc_start: 0.9040 (tt) cc_final: 0.8758 (tt) REVERT: A 319 ILE cc_start: 0.9021 (tt) cc_final: 0.8534 (tt) REVERT: A 322 CYS cc_start: 0.8187 (m) cc_final: 0.7896 (m) REVERT: A 333 TYR cc_start: 0.8606 (p90) cc_final: 0.7869 (p90) REVERT: A 418 ASP cc_start: 0.8145 (m-30) cc_final: 0.7720 (m-30) REVERT: A 433 GLU cc_start: 0.7648 (mp0) cc_final: 0.7235 (mp0) REVERT: A 489 GLU cc_start: 0.8123 (tt0) cc_final: 0.7553 (tt0) REVERT: A 492 PHE cc_start: 0.8080 (t80) cc_final: 0.7848 (t80) REVERT: A 605 PHE cc_start: 0.7921 (m-80) cc_final: 0.7140 (p90) REVERT: A 628 GLN cc_start: 0.7365 (mp10) cc_final: 0.6680 (mp10) REVERT: A 666 ASP cc_start: 0.7821 (p0) cc_final: 0.7526 (p0) REVERT: A 815 ILE cc_start: 0.9177 (mm) cc_final: 0.8762 (mm) REVERT: A 867 ASP cc_start: 0.8181 (t0) cc_final: 0.7972 (t0) REVERT: A 900 MET cc_start: 0.7536 (ttm) cc_final: 0.7123 (tpp) REVERT: A 918 GLU cc_start: 0.8381 (tt0) cc_final: 0.8135 (tt0) REVERT: A 984 SER cc_start: 0.8480 (p) cc_final: 0.8249 (p) REVERT: A 996 GLU cc_start: 0.7459 (pt0) cc_final: 0.7005 (pt0) REVERT: A 1002 ILE cc_start: 0.7648 (mm) cc_final: 0.7155 (mm) REVERT: A 1050 ASP cc_start: 0.8359 (m-30) cc_final: 0.8042 (m-30) REVERT: A 1123 CYS cc_start: 0.8351 (t) cc_final: 0.8051 (t) REVERT: A 1140 ASP cc_start: 0.8157 (t70) cc_final: 0.7882 (t0) REVERT: A 1217 ASP cc_start: 0.7455 (t0) cc_final: 0.7162 (t0) REVERT: A 1253 ILE cc_start: 0.8666 (mm) cc_final: 0.8418 (mm) REVERT: c 238 LYS cc_start: 0.9073 (mtpt) cc_final: 0.8225 (pptt) REVERT: c 311 HIS cc_start: 0.8162 (m90) cc_final: 0.7885 (m90) REVERT: c 425 GLU cc_start: 0.8451 (tt0) cc_final: 0.8191 (tt0) REVERT: d 13 GLU cc_start: 0.8285 (pm20) cc_final: 0.7876 (pm20) REVERT: d 69 LEU cc_start: 0.8577 (mt) cc_final: 0.8287 (mt) REVERT: d 77 MET cc_start: 0.6819 (mtm) cc_final: 0.6503 (mtm) REVERT: d 106 ASN cc_start: 0.8370 (t0) cc_final: 0.8061 (t0) REVERT: d 135 LYS cc_start: 0.9367 (tptp) cc_final: 0.9143 (tppt) REVERT: e 191 TYR cc_start: 0.8649 (t80) cc_final: 0.8265 (t80) REVERT: e 262 VAL cc_start: 0.7068 (m) cc_final: 0.6788 (m) REVERT: f 31 THR cc_start: 0.8699 (m) cc_final: 0.8493 (m) REVERT: f 43 GLN cc_start: 0.8817 (tm-30) cc_final: 0.8153 (tm-30) REVERT: f 62 ASN cc_start: 0.8988 (t0) cc_final: 0.8727 (t0) REVERT: f 74 ARG cc_start: 0.7613 (mtt180) cc_final: 0.6981 (mtt90) REVERT: f 120 ASP cc_start: 0.8844 (t70) cc_final: 0.8596 (t0) REVERT: f 133 ASP cc_start: 0.8375 (p0) cc_final: 0.8080 (p0) REVERT: g 81 CYS cc_start: 0.7851 (m) cc_final: 0.7565 (m) REVERT: g 87 TRP cc_start: 0.8071 (m-10) cc_final: 0.7482 (m-10) REVERT: g 123 TYR cc_start: 0.7170 (p90) cc_final: 0.6744 (p90) REVERT: g 150 GLU cc_start: 0.8123 (tp30) cc_final: 0.7752 (tp30) REVERT: h 108 LYS cc_start: 0.7830 (mmtp) cc_final: 0.7463 (mmtm) REVERT: h 134 THR cc_start: 0.8547 (m) cc_final: 0.8273 (m) REVERT: h 203 ARG cc_start: 0.7710 (ttm-80) cc_final: 0.7109 (mmm-85) REVERT: i 16 GLU cc_start: 0.7931 (tm-30) cc_final: 0.7602 (tm-30) REVERT: i 132 MET cc_start: 0.8176 (tpp) cc_final: 0.7845 (tpp) REVERT: j 23 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7535 (mm-30) REVERT: j 68 GLU cc_start: 0.8648 (tp30) cc_final: 0.8035 (tp30) REVERT: k 12 ASP cc_start: 0.8222 (t0) cc_final: 0.7823 (t0) REVERT: b 363 TRP cc_start: 0.8776 (t60) cc_final: 0.8277 (t60) REVERT: b 377 ASP cc_start: 0.7707 (p0) cc_final: 0.7367 (p0) REVERT: b 391 LEU cc_start: 0.8108 (mt) cc_final: 0.7871 (mt) REVERT: b 409 LEU cc_start: 0.8628 (mt) cc_final: 0.8334 (mt) REVERT: b 434 GLU cc_start: 0.8314 (mm-30) cc_final: 0.7872 (mm-30) REVERT: b 582 LEU cc_start: 0.9117 (tp) cc_final: 0.8817 (tp) REVERT: b 663 GLN cc_start: 0.8820 (tp40) cc_final: 0.8396 (tp40) REVERT: b 816 ARG cc_start: 0.7651 (ptt90) cc_final: 0.7022 (ptt90) REVERT: b 846 ASN cc_start: 0.8381 (p0) cc_final: 0.8124 (p0) REVERT: b 867 ASP cc_start: 0.8482 (m-30) cc_final: 0.8021 (m-30) REVERT: b 882 TRP cc_start: 0.7214 (t-100) cc_final: 0.6768 (t-100) REVERT: b 885 LEU cc_start: 0.8323 (tt) cc_final: 0.8111 (tt) REVERT: b 894 GLU cc_start: 0.8870 (mt-10) cc_final: 0.8393 (mt-10) REVERT: b 895 LEU cc_start: 0.8545 (mp) cc_final: 0.8272 (mp) REVERT: b 963 GLU cc_start: 0.6979 (tp30) cc_final: 0.6702 (tp30) REVERT: b 986 PHE cc_start: 0.7872 (m-80) cc_final: 0.7667 (m-80) REVERT: b 1018 GLU cc_start: 0.7294 (tm-30) cc_final: 0.7094 (tm-30) REVERT: b 1037 GLU cc_start: 0.7852 (pt0) cc_final: 0.7371 (pt0) REVERT: b 1069 LYS cc_start: 0.8314 (mtpt) cc_final: 0.7948 (mttp) REVERT: a 37 LYS cc_start: 0.8666 (mtpp) cc_final: 0.8425 (mtpp) REVERT: a 53 ASP cc_start: 0.6963 (p0) cc_final: 0.6614 (p0) REVERT: a 92 LYS cc_start: 0.7855 (ptmt) cc_final: 0.7582 (ptmm) REVERT: a 276 MET cc_start: 0.7533 (tpp) cc_final: 0.7048 (tpp) REVERT: a 307 ARG cc_start: 0.7777 (ptp90) cc_final: 0.7572 (ptp90) REVERT: a 500 LEU cc_start: 0.8699 (pp) cc_final: 0.8384 (pp) REVERT: a 553 ASP cc_start: 0.7490 (m-30) cc_final: 0.6840 (m-30) REVERT: a 633 LYS cc_start: 0.8535 (ptmm) cc_final: 0.8272 (ptmm) REVERT: a 776 GLU cc_start: 0.8661 (mp0) cc_final: 0.8235 (mp0) REVERT: a 864 MET cc_start: 0.8383 (ttm) cc_final: 0.8022 (ttp) REVERT: a 918 GLU cc_start: 0.8746 (tt0) cc_final: 0.8521 (tt0) REVERT: a 1020 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8051 (tm-30) REVERT: a 1195 GLU cc_start: 0.7974 (pt0) cc_final: 0.7749 (pt0) outliers start: 2 outliers final: 0 residues processed: 2828 average time/residue: 1.3329 time to fit residues: 6353.0869 Evaluate side-chains 2627 residues out of total 6847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2627 time to evaluate : 6.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 803 random chunks: chunk 405 optimal weight: 1.9990 chunk 226 optimal weight: 1.9990 chunk 606 optimal weight: 1.9990 chunk 496 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 730 optimal weight: 30.0000 chunk 789 optimal weight: 50.0000 chunk 650 optimal weight: 0.9990 chunk 724 optimal weight: 1.9990 chunk 249 optimal weight: 1.9990 chunk 586 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 242 GLN ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 ASN ** C 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1082 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1094 ASN A 154 GLN ** A 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 566 ASN A 847 GLN A1209 ASN c 260 ASN c 487 GLN ** d 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 167 GLN e 195 GLN g 37 ASN i 100 ASN ** k 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1082 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 2 ASN a 473 HIS ** a 847 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 920 GLN a1092 ASN a1204 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 65054 Z= 0.414 Angle : 0.640 7.714 88071 Z= 0.347 Chirality : 0.042 0.170 10188 Planarity : 0.004 0.088 11161 Dihedral : 5.653 58.548 8717 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.18 % Allowed : 12.62 % Favored : 87.21 % Rotamer: Outliers : 0.03 % Allowed : 3.39 % Favored : 96.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.09), residues: 7262 helix: 0.27 (0.10), residues: 2448 sheet: -1.84 (0.13), residues: 1496 loop : -2.77 (0.10), residues: 3318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 165 HIS 0.038 0.002 HIS e 106 PHE 0.023 0.002 PHE D 109 TYR 0.031 0.002 TYR f 45 ARG 0.008 0.001 ARG j 75 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14524 Ramachandran restraints generated. 7262 Oldfield, 0 Emsley, 7262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14524 Ramachandran restraints generated. 7262 Oldfield, 0 Emsley, 7262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 57 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue SER 80 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue THR 1139 is missing expected H atoms. Skipping. Evaluate side-chains 2864 residues out of total 6847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 2862 time to evaluate : 6.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 141 LYS cc_start: 0.7990 (tptm) cc_final: 0.7511 (tppt) REVERT: C 145 GLU cc_start: 0.7994 (pm20) cc_final: 0.7587 (pm20) REVERT: C 235 GLN cc_start: 0.8027 (pm20) cc_final: 0.7432 (pm20) REVERT: C 311 HIS cc_start: 0.7435 (m-70) cc_final: 0.7201 (m170) REVERT: C 425 GLU cc_start: 0.8210 (tt0) cc_final: 0.7866 (tt0) REVERT: C 497 GLU cc_start: 0.7361 (pt0) cc_final: 0.6960 (pt0) REVERT: D 19 LEU cc_start: 0.8925 (tt) cc_final: 0.8719 (tt) REVERT: D 107 GLN cc_start: 0.8242 (tp40) cc_final: 0.7794 (tm-30) REVERT: D 115 ILE cc_start: 0.8760 (mm) cc_final: 0.8478 (mm) REVERT: D 136 SER cc_start: 0.8941 (t) cc_final: 0.8710 (t) REVERT: D 139 ARG cc_start: 0.8651 (ttm-80) cc_final: 0.8219 (ttm-80) REVERT: E 45 TYR cc_start: 0.9044 (t80) cc_final: 0.8316 (t80) REVERT: E 151 MET cc_start: 0.4858 (mpp) cc_final: 0.3022 (mpp) REVERT: E 205 ASN cc_start: 0.7952 (m-40) cc_final: 0.7709 (m-40) REVERT: E 235 GLU cc_start: 0.8667 (mp0) cc_final: 0.8459 (mp0) REVERT: F 28 GLU cc_start: 0.7306 (pp20) cc_final: 0.6862 (pp20) REVERT: F 107 ASN cc_start: 0.8488 (t0) cc_final: 0.8177 (t0) REVERT: F 116 SER cc_start: 0.8789 (m) cc_final: 0.8563 (m) REVERT: F 156 GLN cc_start: 0.8585 (mm-40) cc_final: 0.8362 (mm110) REVERT: F 184 LEU cc_start: 0.9182 (pp) cc_final: 0.8633 (pp) REVERT: G 38 GLU cc_start: 0.7922 (tm-30) cc_final: 0.7536 (tm-30) REVERT: G 42 LYS cc_start: 0.9052 (mtmm) cc_final: 0.8565 (mtmm) REVERT: G 143 ARG cc_start: 0.8163 (tmm-80) cc_final: 0.7716 (ttp80) REVERT: H 104 ASP cc_start: 0.8044 (p0) cc_final: 0.7808 (p0) REVERT: H 139 LYS cc_start: 0.8489 (mtmm) cc_final: 0.8186 (mttm) REVERT: I 16 GLU cc_start: 0.8760 (tp30) cc_final: 0.8428 (tp30) REVERT: I 23 GLU cc_start: 0.7879 (tp30) cc_final: 0.7253 (tp30) REVERT: I 140 TYR cc_start: 0.9022 (t80) cc_final: 0.8520 (t80) REVERT: I 154 MET cc_start: 0.8033 (mmp) cc_final: 0.7775 (mmp) REVERT: J 20 ASP cc_start: 0.7826 (t0) cc_final: 0.7455 (t0) REVERT: J 35 GLU cc_start: 0.7417 (tp30) cc_final: 0.6896 (tm-30) REVERT: J 104 PHE cc_start: 0.8728 (t80) cc_final: 0.8298 (t80) REVERT: J 257 GLN cc_start: 0.6957 (tm-30) cc_final: 0.6555 (tm-30) REVERT: K 34 LYS cc_start: 0.7743 (ttmm) cc_final: 0.7422 (ttmm) REVERT: K 162 ASP cc_start: 0.8508 (t0) cc_final: 0.7940 (t0) REVERT: l 150 MET cc_start: 0.8644 (ptm) cc_final: 0.7365 (ptm) REVERT: l 184 ASP cc_start: 0.8076 (t0) cc_final: 0.7789 (t0) REVERT: B 429 ASP cc_start: 0.7741 (m-30) cc_final: 0.7374 (m-30) REVERT: B 506 LEU cc_start: 0.9165 (tt) cc_final: 0.8730 (tt) REVERT: B 510 LYS cc_start: 0.8976 (ptmt) cc_final: 0.8693 (ttpt) REVERT: B 563 GLU cc_start: 0.7361 (pt0) cc_final: 0.7148 (pt0) REVERT: B 617 TYR cc_start: 0.8655 (m-10) cc_final: 0.7427 (m-10) REVERT: B 625 PHE cc_start: 0.8799 (t80) cc_final: 0.8372 (t80) REVERT: B 688 GLN cc_start: 0.8694 (mt0) cc_final: 0.8399 (mt0) REVERT: B 743 LYS cc_start: 0.8119 (ptmm) cc_final: 0.7495 (ptmt) REVERT: B 779 LYS cc_start: 0.8238 (tptm) cc_final: 0.7846 (tptm) REVERT: B 780 ASP cc_start: 0.8638 (p0) cc_final: 0.8205 (p0) REVERT: B 870 ILE cc_start: 0.8907 (mt) cc_final: 0.8705 (mt) REVERT: B 936 GLU cc_start: 0.6651 (tm-30) cc_final: 0.6376 (tt0) REVERT: B 946 CYS cc_start: 0.8794 (t) cc_final: 0.8591 (t) REVERT: B 991 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7486 (mm-30) REVERT: B 1093 SER cc_start: 0.8977 (p) cc_final: 0.8772 (p) REVERT: A 22 PRO cc_start: 0.8593 (Cg_endo) cc_final: 0.8302 (Cg_exo) REVERT: A 29 LYS cc_start: 0.7791 (mppt) cc_final: 0.7264 (mtpp) REVERT: A 30 GLU cc_start: 0.7630 (tp30) cc_final: 0.6847 (tp30) REVERT: A 33 ASN cc_start: 0.8447 (t0) cc_final: 0.8231 (t0) REVERT: A 37 LYS cc_start: 0.8599 (ttmm) cc_final: 0.7778 (ttmm) REVERT: A 172 LEU cc_start: 0.9067 (tt) cc_final: 0.8737 (tt) REVERT: A 333 TYR cc_start: 0.8618 (p90) cc_final: 0.7842 (p90) REVERT: A 417 SER cc_start: 0.9275 (p) cc_final: 0.9042 (p) REVERT: A 418 ASP cc_start: 0.8145 (m-30) cc_final: 0.7626 (m-30) REVERT: A 459 GLU cc_start: 0.7416 (tp30) cc_final: 0.6908 (pm20) REVERT: A 489 GLU cc_start: 0.8268 (tt0) cc_final: 0.7770 (tt0) REVERT: A 492 PHE cc_start: 0.8172 (t80) cc_final: 0.7916 (t80) REVERT: A 605 PHE cc_start: 0.7838 (m-80) cc_final: 0.7348 (p90) REVERT: A 627 GLU cc_start: 0.7281 (tt0) cc_final: 0.7021 (tt0) REVERT: A 628 GLN cc_start: 0.7560 (mp10) cc_final: 0.6671 (mp10) REVERT: A 666 ASP cc_start: 0.7837 (p0) cc_final: 0.7559 (p0) REVERT: A 815 ILE cc_start: 0.9212 (mm) cc_final: 0.8845 (mm) REVERT: A 867 ASP cc_start: 0.8273 (t0) cc_final: 0.8062 (t0) REVERT: A 879 ASN cc_start: 0.8042 (t0) cc_final: 0.7710 (t0) REVERT: A 902 LYS cc_start: 0.8240 (tptm) cc_final: 0.7913 (tppp) REVERT: A 979 TYR cc_start: 0.8078 (m-80) cc_final: 0.7805 (m-80) REVERT: A 984 SER cc_start: 0.8596 (p) cc_final: 0.8337 (p) REVERT: A 996 GLU cc_start: 0.7737 (pt0) cc_final: 0.7484 (pt0) REVERT: A 1002 ILE cc_start: 0.7920 (mm) cc_final: 0.7388 (mm) REVERT: A 1007 GLU cc_start: 0.7149 (pt0) cc_final: 0.6199 (tp30) REVERT: A 1008 LEU cc_start: 0.8646 (pp) cc_final: 0.7816 (pp) REVERT: A 1020 GLU cc_start: 0.8401 (tm-30) cc_final: 0.7971 (tm-30) REVERT: A 1029 GLU cc_start: 0.7566 (tp30) cc_final: 0.7112 (tp30) REVERT: A 1123 CYS cc_start: 0.8404 (t) cc_final: 0.8153 (t) REVERT: A 1140 ASP cc_start: 0.8295 (t70) cc_final: 0.7910 (t70) REVERT: A 1217 ASP cc_start: 0.7358 (t0) cc_final: 0.7068 (t0) REVERT: A 1222 LYS cc_start: 0.8997 (mtmt) cc_final: 0.8646 (mtmt) REVERT: A 1253 ILE cc_start: 0.8721 (mm) cc_final: 0.8494 (mm) REVERT: c 238 LYS cc_start: 0.9103 (mtpt) cc_final: 0.8257 (pptt) REVERT: c 263 GLU cc_start: 0.8024 (pp20) cc_final: 0.7696 (pp20) REVERT: c 425 GLU cc_start: 0.8397 (tt0) cc_final: 0.8093 (tt0) REVERT: d 13 GLU cc_start: 0.8345 (pm20) cc_final: 0.7961 (pm20) REVERT: d 30 MET cc_start: 0.7841 (pmm) cc_final: 0.7569 (pmm) REVERT: d 77 MET cc_start: 0.7319 (mtm) cc_final: 0.7007 (mtm) REVERT: d 106 ASN cc_start: 0.8471 (t0) cc_final: 0.8238 (t0) REVERT: e 51 GLU cc_start: 0.8394 (tm-30) cc_final: 0.8106 (tm-30) REVERT: e 62 GLN cc_start: 0.7925 (tp40) cc_final: 0.7270 (tp40) REVERT: e 262 VAL cc_start: 0.7059 (m) cc_final: 0.6805 (m) REVERT: f 43 GLN cc_start: 0.8811 (tm-30) cc_final: 0.8201 (tm-30) REVERT: f 62 ASN cc_start: 0.8916 (t0) cc_final: 0.8710 (t0) REVERT: g 124 ASP cc_start: 0.6967 (m-30) cc_final: 0.6673 (m-30) REVERT: h 108 LYS cc_start: 0.7856 (mmtp) cc_final: 0.7396 (mmtp) REVERT: h 126 GLN cc_start: 0.7816 (mt0) cc_final: 0.7263 (mt0) REVERT: h 134 THR cc_start: 0.8541 (m) cc_final: 0.8254 (m) REVERT: i 16 GLU cc_start: 0.7992 (tm-30) cc_final: 0.7624 (tm-30) REVERT: i 132 MET cc_start: 0.8272 (tpp) cc_final: 0.7903 (tpp) REVERT: j 23 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7513 (mm-30) REVERT: k 12 ASP cc_start: 0.8481 (t0) cc_final: 0.8085 (t0) REVERT: k 50 ASP cc_start: 0.8293 (t70) cc_final: 0.8081 (t70) REVERT: k 134 TYR cc_start: 0.9006 (m-80) cc_final: 0.8111 (m-80) REVERT: k 163 SER cc_start: 0.8659 (m) cc_final: 0.8396 (m) REVERT: k 170 ARG cc_start: 0.8133 (tmt170) cc_final: 0.7890 (ttt90) REVERT: b 334 MET cc_start: 0.8108 (mmm) cc_final: 0.7583 (mmm) REVERT: b 363 TRP cc_start: 0.8858 (t60) cc_final: 0.8348 (t60) REVERT: b 377 ASP cc_start: 0.7914 (p0) cc_final: 0.7511 (p0) REVERT: b 391 LEU cc_start: 0.8067 (mt) cc_final: 0.7856 (mt) REVERT: b 409 LEU cc_start: 0.8743 (mt) cc_final: 0.8425 (mt) REVERT: b 434 GLU cc_start: 0.8319 (mm-30) cc_final: 0.7900 (mm-30) REVERT: b 663 GLN cc_start: 0.8651 (tp40) cc_final: 0.8311 (tp40) REVERT: b 685 GLU cc_start: 0.7518 (tm-30) cc_final: 0.6992 (tm-30) REVERT: b 703 LEU cc_start: 0.7900 (tp) cc_final: 0.7679 (tt) REVERT: b 728 GLU cc_start: 0.8380 (mm-30) cc_final: 0.7932 (mm-30) REVERT: b 729 TYR cc_start: 0.8418 (t80) cc_final: 0.7277 (t80) REVERT: b 733 ASP cc_start: 0.6714 (p0) cc_final: 0.6096 (p0) REVERT: b 749 LYS cc_start: 0.7135 (mppt) cc_final: 0.6163 (tptp) REVERT: b 816 ARG cc_start: 0.7446 (ptt180) cc_final: 0.6776 (ptt90) REVERT: b 840 GLU cc_start: 0.7497 (pt0) cc_final: 0.7141 (pt0) REVERT: b 846 ASN cc_start: 0.8134 (p0) cc_final: 0.7914 (p0) REVERT: b 882 TRP cc_start: 0.6986 (t-100) cc_final: 0.5362 (t-100) REVERT: b 894 GLU cc_start: 0.8995 (mt-10) cc_final: 0.8584 (mt-10) REVERT: b 895 LEU cc_start: 0.8640 (mp) cc_final: 0.8396 (mp) REVERT: b 963 GLU cc_start: 0.7209 (tp30) cc_final: 0.6857 (tp30) REVERT: b 1007 ILE cc_start: 0.8308 (mm) cc_final: 0.8027 (tp) REVERT: b 1037 GLU cc_start: 0.7790 (pt0) cc_final: 0.7438 (pt0) REVERT: a 276 MET cc_start: 0.7555 (tpp) cc_final: 0.7013 (tpp) REVERT: a 307 ARG cc_start: 0.7818 (ptp90) cc_final: 0.7616 (ptp90) REVERT: a 339 VAL cc_start: 0.7335 (m) cc_final: 0.7086 (m) REVERT: a 500 LEU cc_start: 0.8769 (pp) cc_final: 0.8494 (pp) REVERT: a 553 ASP cc_start: 0.7590 (m-30) cc_final: 0.6939 (m-30) REVERT: a 633 LYS cc_start: 0.8583 (ptmm) cc_final: 0.8345 (ptmm) REVERT: a 735 VAL cc_start: 0.9049 (t) cc_final: 0.8790 (m) REVERT: a 776 GLU cc_start: 0.8705 (mp0) cc_final: 0.8270 (mp0) REVERT: a 864 MET cc_start: 0.8774 (ttm) cc_final: 0.8535 (ttp) REVERT: a 904 ASP cc_start: 0.8092 (p0) cc_final: 0.7707 (p0) REVERT: a 906 TRP cc_start: 0.8708 (p-90) cc_final: 0.8502 (p-90) REVERT: a 918 GLU cc_start: 0.8801 (tt0) cc_final: 0.8438 (tt0) REVERT: a 1020 GLU cc_start: 0.8552 (tm-30) cc_final: 0.8003 (tm-30) REVERT: a 1195 GLU cc_start: 0.8029 (pt0) cc_final: 0.7786 (pt0) REVERT: a 1280 ASP cc_start: 0.7257 (t0) cc_final: 0.6651 (t0) REVERT: a 1282 GLU cc_start: 0.8014 (mp0) cc_final: 0.6811 (mp0) outliers start: 2 outliers final: 0 residues processed: 2862 average time/residue: 1.2836 time to fit residues: 6198.1000 Evaluate side-chains 2579 residues out of total 6847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2579 time to evaluate : 6.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 803 random chunks: chunk 721 optimal weight: 1.9990 chunk 549 optimal weight: 1.9990 chunk 379 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 348 optimal weight: 1.9990 chunk 490 optimal weight: 0.9990 chunk 733 optimal weight: 50.0000 chunk 776 optimal weight: 5.9990 chunk 383 optimal weight: 0.0470 chunk 694 optimal weight: 1.9990 chunk 209 optimal weight: 1.9990 overall best weight: 1.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 ASN ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 92 HIS J 243 ASN B 987 HIS A 32 ASN ** A 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 GLN ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 566 ASN ** d 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 72 GLN ** k 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1082 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1094 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 430 HIS ** a 847 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 874 HIS a1158 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 65054 Z= 0.290 Angle : 0.577 7.037 88071 Z= 0.311 Chirality : 0.041 0.179 10188 Planarity : 0.004 0.056 11161 Dihedral : 5.525 58.482 8717 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.50 % Favored : 88.35 % Rotamer: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.10), residues: 7262 helix: 0.45 (0.10), residues: 2442 sheet: -1.78 (0.13), residues: 1494 loop : -2.76 (0.10), residues: 3326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP a1048 HIS 0.012 0.001 HIS A1158 PHE 0.017 0.001 PHE a 296 TYR 0.021 0.001 TYR c 486 ARG 0.006 0.000 ARG g 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14524 Ramachandran restraints generated. 7262 Oldfield, 0 Emsley, 7262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14524 Ramachandran restraints generated. 7262 Oldfield, 0 Emsley, 7262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 57 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue SER 80 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue THR 1139 is missing expected H atoms. Skipping. Evaluate side-chains 2811 residues out of total 6847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2811 time to evaluate : 6.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 141 LYS cc_start: 0.8037 (tptm) cc_final: 0.7555 (tppt) REVERT: C 145 GLU cc_start: 0.7956 (pm20) cc_final: 0.7648 (pm20) REVERT: C 235 GLN cc_start: 0.7854 (pm20) cc_final: 0.7410 (pm20) REVERT: C 311 HIS cc_start: 0.7578 (m-70) cc_final: 0.7322 (m170) REVERT: C 328 LYS cc_start: 0.8832 (mtpp) cc_final: 0.8484 (mtpp) REVERT: C 425 GLU cc_start: 0.8118 (tt0) cc_final: 0.7852 (tt0) REVERT: C 497 GLU cc_start: 0.7377 (pt0) cc_final: 0.6980 (pt0) REVERT: D 32 ASP cc_start: 0.7413 (m-30) cc_final: 0.6957 (m-30) REVERT: D 35 LYS cc_start: 0.8568 (tmmt) cc_final: 0.8119 (tmmt) REVERT: D 36 TYR cc_start: 0.8325 (m-80) cc_final: 0.7985 (m-80) REVERT: D 107 GLN cc_start: 0.8225 (tp40) cc_final: 0.7793 (tm-30) REVERT: D 108 ILE cc_start: 0.8848 (mt) cc_final: 0.8544 (mt) REVERT: D 115 ILE cc_start: 0.8753 (mm) cc_final: 0.8461 (mm) REVERT: D 134 ILE cc_start: 0.8212 (mt) cc_final: 0.7875 (mt) REVERT: D 136 SER cc_start: 0.8896 (t) cc_final: 0.8668 (t) REVERT: D 138 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7429 (mt-10) REVERT: D 139 ARG cc_start: 0.8681 (ttm-80) cc_final: 0.8238 (ttm-80) REVERT: E 45 TYR cc_start: 0.8961 (t80) cc_final: 0.8245 (t80) REVERT: E 151 MET cc_start: 0.4675 (mpp) cc_final: 0.2929 (mpp) REVERT: E 205 ASN cc_start: 0.7882 (m-40) cc_final: 0.7625 (m-40) REVERT: E 235 GLU cc_start: 0.8613 (mp0) cc_final: 0.8366 (mp0) REVERT: E 262 VAL cc_start: 0.8970 (t) cc_final: 0.8739 (t) REVERT: F 107 ASN cc_start: 0.8477 (t0) cc_final: 0.8161 (t0) REVERT: F 116 SER cc_start: 0.8766 (m) cc_final: 0.8538 (m) REVERT: G 42 LYS cc_start: 0.9059 (mtmm) cc_final: 0.8511 (mtmm) REVERT: G 143 ARG cc_start: 0.8223 (tmm-80) cc_final: 0.7742 (ttp80) REVERT: H 104 ASP cc_start: 0.8017 (p0) cc_final: 0.7747 (p0) REVERT: I 16 GLU cc_start: 0.8761 (tp30) cc_final: 0.8442 (tp30) REVERT: I 23 GLU cc_start: 0.7906 (tp30) cc_final: 0.7200 (tp30) REVERT: I 140 TYR cc_start: 0.9020 (t80) cc_final: 0.8474 (t80) REVERT: I 154 MET cc_start: 0.8030 (mmp) cc_final: 0.7680 (mmp) REVERT: J 20 ASP cc_start: 0.7875 (t0) cc_final: 0.7433 (t0) REVERT: J 35 GLU cc_start: 0.7416 (tp30) cc_final: 0.6905 (tm-30) REVERT: J 229 CYS cc_start: 0.8455 (m) cc_final: 0.8235 (m) REVERT: J 257 GLN cc_start: 0.6950 (tm-30) cc_final: 0.6538 (tm-30) REVERT: K 34 LYS cc_start: 0.7714 (ttmm) cc_final: 0.7275 (ttmm) REVERT: K 104 ILE cc_start: 0.8967 (mt) cc_final: 0.8758 (mt) REVERT: K 139 GLU cc_start: 0.7828 (tp30) cc_final: 0.7513 (tp30) REVERT: K 162 ASP cc_start: 0.8424 (t0) cc_final: 0.7866 (t0) REVERT: l 150 MET cc_start: 0.8744 (ptm) cc_final: 0.8247 (ptm) REVERT: l 184 ASP cc_start: 0.8116 (t0) cc_final: 0.7849 (t0) REVERT: B 311 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8324 (mt-10) REVERT: B 429 ASP cc_start: 0.7943 (m-30) cc_final: 0.7727 (m-30) REVERT: B 506 LEU cc_start: 0.9097 (tt) cc_final: 0.8865 (tt) REVERT: B 510 LYS cc_start: 0.8949 (ptmt) cc_final: 0.8645 (ttpt) REVERT: B 625 PHE cc_start: 0.8782 (t80) cc_final: 0.8364 (t80) REVERT: B 677 LYS cc_start: 0.8432 (ttmt) cc_final: 0.8175 (ttmt) REVERT: B 688 GLN cc_start: 0.8679 (mt0) cc_final: 0.8434 (mt0) REVERT: B 722 PHE cc_start: 0.8718 (p90) cc_final: 0.8460 (p90) REVERT: B 728 GLU cc_start: 0.7919 (mp0) cc_final: 0.7632 (mp0) REVERT: B 743 LYS cc_start: 0.8101 (ptmm) cc_final: 0.7517 (ptmt) REVERT: B 779 LYS cc_start: 0.8221 (tptm) cc_final: 0.7920 (tptm) REVERT: B 780 ASP cc_start: 0.8559 (p0) cc_final: 0.8134 (p0) REVERT: B 795 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7500 (mm-30) REVERT: B 936 GLU cc_start: 0.6719 (tm-30) cc_final: 0.6144 (tt0) REVERT: B 946 CYS cc_start: 0.8769 (t) cc_final: 0.8554 (t) REVERT: A 29 LYS cc_start: 0.7600 (mppt) cc_final: 0.7334 (mtpp) REVERT: A 30 GLU cc_start: 0.7626 (tp30) cc_final: 0.6831 (tp30) REVERT: A 37 LYS cc_start: 0.8575 (ttmm) cc_final: 0.7640 (ttmm) REVERT: A 135 GLU cc_start: 0.8146 (tp30) cc_final: 0.7897 (mm-30) REVERT: A 172 LEU cc_start: 0.9021 (tt) cc_final: 0.8784 (tt) REVERT: A 333 TYR cc_start: 0.8624 (p90) cc_final: 0.7838 (p90) REVERT: A 417 SER cc_start: 0.9281 (p) cc_final: 0.9054 (p) REVERT: A 418 ASP cc_start: 0.8121 (m-30) cc_final: 0.7571 (m-30) REVERT: A 433 GLU cc_start: 0.7618 (mp0) cc_final: 0.7175 (mp0) REVERT: A 489 GLU cc_start: 0.8316 (tt0) cc_final: 0.7759 (tt0) REVERT: A 492 PHE cc_start: 0.8158 (t80) cc_final: 0.7902 (t80) REVERT: A 605 PHE cc_start: 0.7799 (m-80) cc_final: 0.7318 (p90) REVERT: A 643 GLU cc_start: 0.8718 (tt0) cc_final: 0.8510 (tt0) REVERT: A 650 ASP cc_start: 0.9149 (p0) cc_final: 0.8734 (p0) REVERT: A 666 ASP cc_start: 0.7854 (p0) cc_final: 0.7564 (p0) REVERT: A 815 ILE cc_start: 0.9018 (mm) cc_final: 0.8783 (mm) REVERT: A 867 ASP cc_start: 0.8219 (t0) cc_final: 0.7995 (t0) REVERT: A 900 MET cc_start: 0.7649 (ttm) cc_final: 0.7192 (tpp) REVERT: A 902 LYS cc_start: 0.8221 (tptm) cc_final: 0.7872 (tppp) REVERT: A 979 TYR cc_start: 0.8019 (m-80) cc_final: 0.7755 (m-80) REVERT: A 984 SER cc_start: 0.8551 (p) cc_final: 0.8311 (p) REVERT: A 1066 TYR cc_start: 0.8019 (m-80) cc_final: 0.7660 (m-80) REVERT: A 1111 GLU cc_start: 0.7883 (mp0) cc_final: 0.7681 (mp0) REVERT: A 1140 ASP cc_start: 0.8283 (t70) cc_final: 0.7899 (t70) REVERT: A 1217 ASP cc_start: 0.7311 (t0) cc_final: 0.6991 (t0) REVERT: A 1218 SER cc_start: 0.8967 (t) cc_final: 0.8670 (t) REVERT: A 1222 LYS cc_start: 0.8974 (mtmt) cc_final: 0.8337 (mtpt) REVERT: A 1253 ILE cc_start: 0.8758 (mm) cc_final: 0.8522 (mm) REVERT: c 238 LYS cc_start: 0.9097 (mtpt) cc_final: 0.8248 (pptt) REVERT: c 263 GLU cc_start: 0.8024 (pp20) cc_final: 0.7567 (pp20) REVERT: c 338 GLU cc_start: 0.7456 (pm20) cc_final: 0.6986 (mp0) REVERT: c 413 LYS cc_start: 0.8622 (ttmm) cc_final: 0.8016 (ttmm) REVERT: c 425 GLU cc_start: 0.8402 (tt0) cc_final: 0.8076 (tt0) REVERT: c 516 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7596 (mt-10) REVERT: d 13 GLU cc_start: 0.8369 (pm20) cc_final: 0.8000 (pm20) REVERT: d 30 MET cc_start: 0.7829 (pmm) cc_final: 0.7503 (pmm) REVERT: d 69 LEU cc_start: 0.8390 (mt) cc_final: 0.8104 (mt) REVERT: d 77 MET cc_start: 0.7186 (mtm) cc_final: 0.6778 (mtm) REVERT: d 106 ASN cc_start: 0.8423 (t0) cc_final: 0.8051 (t0) REVERT: d 114 LYS cc_start: 0.8325 (mmtp) cc_final: 0.8066 (mmtp) REVERT: e 51 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7958 (tm-30) REVERT: e 115 GLU cc_start: 0.7045 (mm-30) cc_final: 0.6710 (mm-30) REVERT: e 262 VAL cc_start: 0.7051 (m) cc_final: 0.6773 (m) REVERT: f 31 THR cc_start: 0.8865 (m) cc_final: 0.8661 (m) REVERT: f 43 GLN cc_start: 0.8738 (tm-30) cc_final: 0.8225 (tm-30) REVERT: f 49 PHE cc_start: 0.8885 (m-10) cc_final: 0.8556 (m-10) REVERT: f 62 ASN cc_start: 0.8873 (t0) cc_final: 0.8629 (t0) REVERT: f 135 MET cc_start: 0.7764 (tpp) cc_final: 0.7553 (tpp) REVERT: f 140 TYR cc_start: 0.9096 (t80) cc_final: 0.8694 (t80) REVERT: g 131 GLU cc_start: 0.7787 (mp0) cc_final: 0.7517 (mp0) REVERT: h 108 LYS cc_start: 0.7815 (mmtp) cc_final: 0.7407 (mmtp) REVERT: h 126 GLN cc_start: 0.7759 (mt0) cc_final: 0.7195 (mt0) REVERT: h 134 THR cc_start: 0.8558 (m) cc_final: 0.8282 (m) REVERT: h 200 MET cc_start: 0.8919 (mmp) cc_final: 0.8609 (mmm) REVERT: i 16 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7560 (tm-30) REVERT: i 21 LYS cc_start: 0.6385 (mttt) cc_final: 0.6176 (ttmt) REVERT: i 132 MET cc_start: 0.8262 (tpp) cc_final: 0.7919 (tpp) REVERT: j 23 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7469 (mm-30) REVERT: k 12 ASP cc_start: 0.8453 (t0) cc_final: 0.8054 (t0) REVERT: k 50 ASP cc_start: 0.8259 (t70) cc_final: 0.7996 (t70) REVERT: b 347 LEU cc_start: 0.8667 (pp) cc_final: 0.8274 (pp) REVERT: b 363 TRP cc_start: 0.8774 (t60) cc_final: 0.8300 (t60) REVERT: b 399 GLU cc_start: 0.6838 (pp20) cc_final: 0.6330 (pm20) REVERT: b 405 ASN cc_start: 0.8537 (m-40) cc_final: 0.8196 (m-40) REVERT: b 412 GLU cc_start: 0.8373 (tt0) cc_final: 0.8130 (tt0) REVERT: b 434 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7884 (mm-30) REVERT: b 507 ASN cc_start: 0.8611 (m-40) cc_final: 0.8336 (m-40) REVERT: b 511 LEU cc_start: 0.9397 (tp) cc_final: 0.9171 (tp) REVERT: b 663 GLN cc_start: 0.8701 (tp40) cc_final: 0.8334 (tp40) REVERT: b 685 GLU cc_start: 0.7529 (tm-30) cc_final: 0.7097 (tm-30) REVERT: b 723 GLU cc_start: 0.7787 (mp0) cc_final: 0.7510 (tm-30) REVERT: b 728 GLU cc_start: 0.8336 (mm-30) cc_final: 0.7593 (mm-30) REVERT: b 729 TYR cc_start: 0.8407 (t80) cc_final: 0.7286 (t80) REVERT: b 744 THR cc_start: 0.9193 (m) cc_final: 0.8988 (m) REVERT: b 749 LYS cc_start: 0.7087 (mppt) cc_final: 0.6161 (tptp) REVERT: b 816 ARG cc_start: 0.7501 (ptt180) cc_final: 0.6766 (ptt90) REVERT: b 840 GLU cc_start: 0.7405 (pt0) cc_final: 0.7058 (pt0) REVERT: b 879 ASP cc_start: 0.7573 (t70) cc_final: 0.6973 (t0) REVERT: b 881 GLU cc_start: 0.7931 (pm20) cc_final: 0.7728 (pm20) REVERT: b 894 GLU cc_start: 0.8925 (mt-10) cc_final: 0.8549 (mt-10) REVERT: b 895 LEU cc_start: 0.8649 (mp) cc_final: 0.8382 (mp) REVERT: b 936 GLU cc_start: 0.6870 (mm-30) cc_final: 0.6469 (mm-30) REVERT: b 963 GLU cc_start: 0.7081 (tp30) cc_final: 0.6784 (tp30) REVERT: b 1026 GLN cc_start: 0.7388 (mp10) cc_final: 0.7161 (mp10) REVERT: b 1037 GLU cc_start: 0.7670 (pt0) cc_final: 0.7109 (tt0) REVERT: b 1056 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8230 (mp0) REVERT: a 152 ASP cc_start: 0.7952 (t0) cc_final: 0.7423 (t0) REVERT: a 276 MET cc_start: 0.7535 (tpp) cc_final: 0.6955 (tpp) REVERT: a 289 TYR cc_start: 0.5866 (m-80) cc_final: 0.5603 (m-80) REVERT: a 307 ARG cc_start: 0.7805 (ptp90) cc_final: 0.7579 (ptp90) REVERT: a 339 VAL cc_start: 0.7282 (m) cc_final: 0.7070 (m) REVERT: a 403 ASP cc_start: 0.7983 (p0) cc_final: 0.7534 (p0) REVERT: a 500 LEU cc_start: 0.8764 (pp) cc_final: 0.8453 (pp) REVERT: a 553 ASP cc_start: 0.7547 (m-30) cc_final: 0.6899 (m-30) REVERT: a 735 VAL cc_start: 0.9048 (t) cc_final: 0.8787 (m) REVERT: a 776 GLU cc_start: 0.8659 (mp0) cc_final: 0.8231 (mp0) REVERT: a 864 MET cc_start: 0.8703 (ttm) cc_final: 0.8456 (ttp) REVERT: a 887 ASN cc_start: 0.7879 (m110) cc_final: 0.7662 (m110) REVERT: a 904 ASP cc_start: 0.8068 (p0) cc_final: 0.7683 (p0) REVERT: a 906 TRP cc_start: 0.8721 (p-90) cc_final: 0.8496 (p-90) REVERT: a 918 GLU cc_start: 0.8809 (tt0) cc_final: 0.8441 (tt0) REVERT: a 1020 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8038 (tm-30) REVERT: a 1150 ASN cc_start: 0.8920 (m-40) cc_final: 0.8637 (m110) REVERT: a 1157 ASP cc_start: 0.8293 (p0) cc_final: 0.7744 (p0) REVERT: a 1195 GLU cc_start: 0.8029 (pt0) cc_final: 0.7786 (pt0) REVERT: a 1218 SER cc_start: 0.8947 (t) cc_final: 0.8615 (t) REVERT: a 1280 ASP cc_start: 0.7094 (t0) cc_final: 0.6123 (t0) REVERT: a 1282 GLU cc_start: 0.7951 (mp0) cc_final: 0.6637 (mp0) REVERT: a 1285 ILE cc_start: 0.8594 (pt) cc_final: 0.8300 (pt) outliers start: 0 outliers final: 0 residues processed: 2811 average time/residue: 1.3349 time to fit residues: 6329.5671 Evaluate side-chains 2618 residues out of total 6847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2618 time to evaluate : 6.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 803 random chunks: chunk 646 optimal weight: 2.9990 chunk 440 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 577 optimal weight: 1.9990 chunk 320 optimal weight: 1.9990 chunk 662 optimal weight: 0.9990 chunk 536 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 396 optimal weight: 0.9980 chunk 696 optimal weight: 0.9990 chunk 195 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 242 GLN ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 ASN ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 ASN ** A 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 566 ASN c 260 ASN ** d 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 93 HIS ** k 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1094 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 430 HIS ** a 847 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1072 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 65054 Z= 0.246 Angle : 0.560 11.811 88071 Z= 0.300 Chirality : 0.040 0.212 10188 Planarity : 0.004 0.055 11161 Dihedral : 5.421 59.944 8717 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.65 % Favored : 88.21 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.10), residues: 7262 helix: 0.57 (0.10), residues: 2453 sheet: -1.69 (0.13), residues: 1492 loop : -2.75 (0.10), residues: 3317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B1024 HIS 0.008 0.001 HIS k 115 PHE 0.027 0.001 PHE b 505 TYR 0.017 0.001 TYR c 486 ARG 0.006 0.000 ARG b 360 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14524 Ramachandran restraints generated. 7262 Oldfield, 0 Emsley, 7262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14524 Ramachandran restraints generated. 7262 Oldfield, 0 Emsley, 7262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 57 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue SER 80 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue THR 1139 is missing expected H atoms. Skipping. Evaluate side-chains 2831 residues out of total 6847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2831 time to evaluate : 7.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 235 GLN cc_start: 0.7948 (pm20) cc_final: 0.7511 (pm20) REVERT: C 256 PHE cc_start: 0.7931 (p90) cc_final: 0.7024 (p90) REVERT: C 328 LYS cc_start: 0.8822 (mtpp) cc_final: 0.8458 (mtpp) REVERT: C 425 GLU cc_start: 0.8111 (tt0) cc_final: 0.7822 (tt0) REVERT: C 497 GLU cc_start: 0.7376 (pt0) cc_final: 0.6988 (pt0) REVERT: D 6 CYS cc_start: 0.8295 (t) cc_final: 0.8039 (t) REVERT: D 92 GLN cc_start: 0.8578 (tm-30) cc_final: 0.8280 (tm-30) REVERT: D 107 GLN cc_start: 0.8234 (tp40) cc_final: 0.7926 (tp40) REVERT: D 115 ILE cc_start: 0.8765 (mm) cc_final: 0.8481 (mm) REVERT: D 134 ILE cc_start: 0.8284 (mt) cc_final: 0.8004 (mt) REVERT: D 136 SER cc_start: 0.8919 (t) cc_final: 0.8689 (t) REVERT: D 138 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7399 (mt-10) REVERT: D 139 ARG cc_start: 0.8668 (ttm-80) cc_final: 0.8239 (ttm-80) REVERT: E 45 TYR cc_start: 0.8958 (t80) cc_final: 0.8212 (t80) REVERT: E 205 ASN cc_start: 0.7847 (m-40) cc_final: 0.7443 (m-40) REVERT: E 262 VAL cc_start: 0.8973 (t) cc_final: 0.8736 (t) REVERT: F 107 ASN cc_start: 0.8484 (t0) cc_final: 0.8174 (t0) REVERT: F 116 SER cc_start: 0.8738 (m) cc_final: 0.8509 (m) REVERT: G 38 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7412 (tm-30) REVERT: G 42 LYS cc_start: 0.8964 (mtmm) cc_final: 0.8626 (mtmm) REVERT: G 143 ARG cc_start: 0.8262 (tmm-80) cc_final: 0.7623 (ttp80) REVERT: H 104 ASP cc_start: 0.7971 (p0) cc_final: 0.7728 (p0) REVERT: I 16 GLU cc_start: 0.8738 (tp30) cc_final: 0.8420 (tp30) REVERT: I 23 GLU cc_start: 0.7895 (tp30) cc_final: 0.7161 (tp30) REVERT: I 140 TYR cc_start: 0.8943 (t80) cc_final: 0.8511 (t80) REVERT: J 20 ASP cc_start: 0.7788 (t0) cc_final: 0.7367 (t0) REVERT: J 35 GLU cc_start: 0.7382 (tp30) cc_final: 0.6913 (tm-30) REVERT: J 48 GLU cc_start: 0.8569 (tt0) cc_final: 0.8368 (tt0) REVERT: J 98 LEU cc_start: 0.8317 (mm) cc_final: 0.7748 (mm) REVERT: J 229 CYS cc_start: 0.8475 (m) cc_final: 0.8236 (m) REVERT: J 257 GLN cc_start: 0.7058 (tm-30) cc_final: 0.6617 (tm-30) REVERT: K 34 LYS cc_start: 0.7689 (ttmm) cc_final: 0.7284 (ttmm) REVERT: K 104 ILE cc_start: 0.9003 (mt) cc_final: 0.8772 (mt) REVERT: K 139 GLU cc_start: 0.7868 (tp30) cc_final: 0.7533 (tp30) REVERT: K 162 ASP cc_start: 0.8402 (t0) cc_final: 0.7827 (t0) REVERT: l 150 MET cc_start: 0.8762 (ptm) cc_final: 0.8189 (ptm) REVERT: l 184 ASP cc_start: 0.8127 (t0) cc_final: 0.7836 (t0) REVERT: B 311 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8319 (mt-10) REVERT: B 425 GLN cc_start: 0.6988 (pm20) cc_final: 0.6598 (pm20) REVERT: B 426 ARG cc_start: 0.6674 (ptt180) cc_final: 0.6271 (ptt180) REVERT: B 429 ASP cc_start: 0.7954 (m-30) cc_final: 0.7718 (m-30) REVERT: B 506 LEU cc_start: 0.9093 (tt) cc_final: 0.8807 (tt) REVERT: B 510 LYS cc_start: 0.8938 (ptmt) cc_final: 0.8628 (ttpt) REVERT: B 617 TYR cc_start: 0.8620 (m-80) cc_final: 0.7364 (m-10) REVERT: B 625 PHE cc_start: 0.8747 (t80) cc_final: 0.8328 (t80) REVERT: B 677 LYS cc_start: 0.8490 (ttmt) cc_final: 0.8240 (ttmt) REVERT: B 688 GLN cc_start: 0.8736 (mt0) cc_final: 0.8464 (mt0) REVERT: B 711 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7069 (mt-10) REVERT: B 722 PHE cc_start: 0.8726 (p90) cc_final: 0.8220 (p90) REVERT: B 728 GLU cc_start: 0.7900 (mp0) cc_final: 0.7577 (mp0) REVERT: B 729 TYR cc_start: 0.7790 (t80) cc_final: 0.7562 (t80) REVERT: B 735 ILE cc_start: 0.8916 (tt) cc_final: 0.8662 (tt) REVERT: B 743 LYS cc_start: 0.8127 (ptmm) cc_final: 0.7501 (ptmt) REVERT: B 779 LYS cc_start: 0.8262 (tptm) cc_final: 0.7878 (tptm) REVERT: B 780 ASP cc_start: 0.8561 (p0) cc_final: 0.8125 (p0) REVERT: B 795 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7531 (mm-30) REVERT: B 927 LYS cc_start: 0.8491 (tttm) cc_final: 0.8255 (tttm) REVERT: B 936 GLU cc_start: 0.6944 (tm-30) cc_final: 0.6635 (tm-30) REVERT: B 946 CYS cc_start: 0.8798 (t) cc_final: 0.8560 (t) REVERT: A 16 ILE cc_start: 0.8028 (mt) cc_final: 0.7803 (mt) REVERT: A 30 GLU cc_start: 0.7693 (tp30) cc_final: 0.6820 (tp30) REVERT: A 37 LYS cc_start: 0.8545 (ttmm) cc_final: 0.7659 (ttmm) REVERT: A 172 LEU cc_start: 0.9052 (tt) cc_final: 0.8814 (tt) REVERT: A 333 TYR cc_start: 0.8641 (p90) cc_final: 0.7834 (p90) REVERT: A 417 SER cc_start: 0.9282 (p) cc_final: 0.9045 (p) REVERT: A 418 ASP cc_start: 0.8109 (m-30) cc_final: 0.7588 (m-30) REVERT: A 489 GLU cc_start: 0.8374 (tt0) cc_final: 0.7754 (tt0) REVERT: A 492 PHE cc_start: 0.8139 (t80) cc_final: 0.7919 (t80) REVERT: A 497 LEU cc_start: 0.8860 (mt) cc_final: 0.8599 (mt) REVERT: A 563 GLU cc_start: 0.7658 (tm-30) cc_final: 0.7351 (tm-30) REVERT: A 605 PHE cc_start: 0.7808 (m-80) cc_final: 0.7327 (p90) REVERT: A 650 ASP cc_start: 0.9196 (p0) cc_final: 0.8755 (p0) REVERT: A 666 ASP cc_start: 0.7856 (p0) cc_final: 0.7557 (p0) REVERT: A 815 ILE cc_start: 0.9190 (mm) cc_final: 0.8723 (mm) REVERT: A 851 GLU cc_start: 0.7114 (tp30) cc_final: 0.6900 (tp30) REVERT: A 867 ASP cc_start: 0.8185 (t0) cc_final: 0.7977 (t0) REVERT: A 879 ASN cc_start: 0.8427 (t0) cc_final: 0.7925 (t0) REVERT: A 894 MET cc_start: 0.8262 (tpp) cc_final: 0.7047 (tpp) REVERT: A 898 GLU cc_start: 0.7934 (tt0) cc_final: 0.7313 (tt0) REVERT: A 900 MET cc_start: 0.7595 (ttm) cc_final: 0.7147 (tpt) REVERT: A 979 TYR cc_start: 0.8013 (m-80) cc_final: 0.7735 (m-80) REVERT: A 984 SER cc_start: 0.8548 (p) cc_final: 0.8254 (p) REVERT: A 1000 MET cc_start: 0.8710 (ptp) cc_final: 0.8499 (ptp) REVERT: A 1002 ILE cc_start: 0.7746 (mm) cc_final: 0.7305 (mm) REVERT: A 1007 GLU cc_start: 0.6994 (pt0) cc_final: 0.6094 (tp30) REVERT: A 1008 LEU cc_start: 0.8618 (pp) cc_final: 0.7768 (pp) REVERT: A 1020 GLU cc_start: 0.8371 (tm-30) cc_final: 0.7832 (tm-30) REVERT: A 1057 GLN cc_start: 0.8540 (mt0) cc_final: 0.8269 (mt0) REVERT: A 1066 TYR cc_start: 0.8060 (m-80) cc_final: 0.7732 (m-80) REVERT: A 1111 GLU cc_start: 0.7919 (mp0) cc_final: 0.7704 (mp0) REVERT: A 1123 CYS cc_start: 0.8338 (t) cc_final: 0.8048 (t) REVERT: A 1179 GLU cc_start: 0.7116 (mp0) cc_final: 0.6739 (mm-30) REVERT: A 1217 ASP cc_start: 0.7160 (t0) cc_final: 0.6609 (t0) REVERT: A 1219 LYS cc_start: 0.8026 (mptt) cc_final: 0.7713 (mmmm) REVERT: A 1220 THR cc_start: 0.8218 (m) cc_final: 0.7468 (m) REVERT: A 1222 LYS cc_start: 0.8949 (mtmt) cc_final: 0.8357 (mtpt) REVERT: A 1253 ILE cc_start: 0.8775 (mm) cc_final: 0.8498 (mm) REVERT: c 238 LYS cc_start: 0.9089 (mtpt) cc_final: 0.8236 (pptt) REVERT: c 263 GLU cc_start: 0.8033 (pp20) cc_final: 0.7614 (pp20) REVERT: c 338 GLU cc_start: 0.7945 (pm20) cc_final: 0.7609 (mp0) REVERT: c 413 LYS cc_start: 0.8580 (ttmm) cc_final: 0.8003 (ttmm) REVERT: c 425 GLU cc_start: 0.8379 (tt0) cc_final: 0.8066 (tt0) REVERT: d 13 GLU cc_start: 0.8376 (pm20) cc_final: 0.7987 (pm20) REVERT: d 69 LEU cc_start: 0.8284 (mt) cc_final: 0.8065 (mt) REVERT: d 77 MET cc_start: 0.7162 (mtm) cc_final: 0.6959 (mtm) REVERT: d 106 ASN cc_start: 0.8576 (t0) cc_final: 0.8169 (t0) REVERT: d 114 LYS cc_start: 0.8333 (mmtp) cc_final: 0.7988 (mmtp) REVERT: d 121 CYS cc_start: 0.8989 (t) cc_final: 0.8343 (t) REVERT: e 115 GLU cc_start: 0.7301 (mm-30) cc_final: 0.6525 (mm-30) REVERT: e 262 VAL cc_start: 0.7008 (m) cc_final: 0.6741 (m) REVERT: f 43 GLN cc_start: 0.8770 (tm-30) cc_final: 0.8277 (tm-30) REVERT: f 62 ASN cc_start: 0.8915 (t0) cc_final: 0.8653 (t0) REVERT: f 135 MET cc_start: 0.7780 (tpp) cc_final: 0.7565 (tpp) REVERT: f 140 TYR cc_start: 0.9126 (t80) cc_final: 0.8734 (t80) REVERT: g 123 TYR cc_start: 0.7315 (p90) cc_final: 0.7107 (p90) REVERT: h 108 LYS cc_start: 0.7844 (mmtp) cc_final: 0.7458 (mmtp) REVERT: h 126 GLN cc_start: 0.7777 (mt0) cc_final: 0.7148 (mt0) REVERT: h 200 MET cc_start: 0.8908 (mmp) cc_final: 0.8581 (mmm) REVERT: i 16 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7570 (tm-30) REVERT: i 132 MET cc_start: 0.8272 (tpp) cc_final: 0.7901 (tpp) REVERT: i 160 ASP cc_start: 0.8006 (m-30) cc_final: 0.7601 (m-30) REVERT: j 20 ASP cc_start: 0.6729 (t70) cc_final: 0.6376 (t70) REVERT: j 23 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7473 (mm-30) REVERT: j 68 GLU cc_start: 0.8381 (tp30) cc_final: 0.7391 (tp30) REVERT: k 12 ASP cc_start: 0.8481 (t0) cc_final: 0.8025 (t0) REVERT: k 163 SER cc_start: 0.8653 (m) cc_final: 0.8364 (m) REVERT: b 347 LEU cc_start: 0.8701 (pp) cc_final: 0.8279 (pp) REVERT: b 363 TRP cc_start: 0.8719 (t60) cc_final: 0.8233 (t60) REVERT: b 399 GLU cc_start: 0.6853 (pp20) cc_final: 0.6329 (pm20) REVERT: b 405 ASN cc_start: 0.8534 (m-40) cc_final: 0.8202 (m-40) REVERT: b 412 GLU cc_start: 0.8216 (tt0) cc_final: 0.7978 (tt0) REVERT: b 434 GLU cc_start: 0.8322 (mm-30) cc_final: 0.8014 (mm-30) REVERT: b 640 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7706 (tm-30) REVERT: b 644 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7631 (mm-30) REVERT: b 663 GLN cc_start: 0.8650 (tp40) cc_final: 0.8281 (tp40) REVERT: b 687 LEU cc_start: 0.8367 (pp) cc_final: 0.8130 (pp) REVERT: b 703 LEU cc_start: 0.7941 (tp) cc_final: 0.7710 (tt) REVERT: b 723 GLU cc_start: 0.7772 (mp0) cc_final: 0.7484 (tm-30) REVERT: b 728 GLU cc_start: 0.8359 (mm-30) cc_final: 0.7582 (mm-30) REVERT: b 729 TYR cc_start: 0.8331 (t80) cc_final: 0.7151 (t80) REVERT: b 816 ARG cc_start: 0.7480 (ptt180) cc_final: 0.6683 (ptt90) REVERT: b 879 ASP cc_start: 0.7717 (t70) cc_final: 0.7320 (t70) REVERT: b 894 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8525 (mt-10) REVERT: b 895 LEU cc_start: 0.8682 (mp) cc_final: 0.8402 (mp) REVERT: b 936 GLU cc_start: 0.6800 (mm-30) cc_final: 0.6061 (mm-30) REVERT: b 963 GLU cc_start: 0.7185 (tp30) cc_final: 0.6769 (tp30) REVERT: b 983 GLU cc_start: 0.8793 (mm-30) cc_final: 0.8340 (mp0) REVERT: b 1023 GLN cc_start: 0.7787 (mt0) cc_final: 0.7434 (mt0) REVERT: b 1037 GLU cc_start: 0.7701 (pt0) cc_final: 0.7119 (tt0) REVERT: b 1056 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8254 (mp0) REVERT: a 19 LEU cc_start: 0.8446 (tt) cc_final: 0.8245 (tt) REVERT: a 152 ASP cc_start: 0.7901 (t0) cc_final: 0.7364 (t0) REVERT: a 197 LYS cc_start: 0.8621 (mtmt) cc_final: 0.8204 (mttt) REVERT: a 276 MET cc_start: 0.7453 (tpp) cc_final: 0.6946 (tpp) REVERT: a 307 ARG cc_start: 0.7714 (ptp90) cc_final: 0.7474 (ptp90) REVERT: a 339 VAL cc_start: 0.7583 (m) cc_final: 0.7354 (m) REVERT: a 403 ASP cc_start: 0.7994 (p0) cc_final: 0.7574 (p0) REVERT: a 553 ASP cc_start: 0.7531 (m-30) cc_final: 0.6836 (m-30) REVERT: a 735 VAL cc_start: 0.9057 (t) cc_final: 0.8780 (m) REVERT: a 776 GLU cc_start: 0.8617 (mp0) cc_final: 0.8241 (mp0) REVERT: a 815 ILE cc_start: 0.8847 (tp) cc_final: 0.8580 (tp) REVERT: a 836 TYR cc_start: 0.8022 (m-80) cc_final: 0.6992 (m-80) REVERT: a 864 MET cc_start: 0.8789 (ttm) cc_final: 0.8552 (ttp) REVERT: a 887 ASN cc_start: 0.7877 (m110) cc_final: 0.7622 (m110) REVERT: a 918 GLU cc_start: 0.8807 (tt0) cc_final: 0.8548 (tt0) REVERT: a 1020 GLU cc_start: 0.8617 (tm-30) cc_final: 0.8028 (tm-30) REVERT: a 1039 LEU cc_start: 0.8665 (mt) cc_final: 0.8419 (mt) REVERT: a 1150 ASN cc_start: 0.8898 (m-40) cc_final: 0.8606 (m110) REVERT: a 1157 ASP cc_start: 0.8294 (p0) cc_final: 0.7753 (p0) REVERT: a 1195 GLU cc_start: 0.8045 (pt0) cc_final: 0.7800 (pt0) REVERT: a 1280 ASP cc_start: 0.6926 (t0) cc_final: 0.6019 (t0) REVERT: a 1282 GLU cc_start: 0.7737 (mp0) cc_final: 0.6392 (mp0) REVERT: a 1285 ILE cc_start: 0.8662 (pt) cc_final: 0.8340 (pt) outliers start: 0 outliers final: 0 residues processed: 2831 average time/residue: 1.3185 time to fit residues: 6288.9160 Evaluate side-chains 2619 residues out of total 6847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2619 time to evaluate : 6.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 803 random chunks: chunk 261 optimal weight: 0.9990 chunk 698 optimal weight: 3.9990 chunk 153 optimal weight: 0.9980 chunk 455 optimal weight: 0.9990 chunk 191 optimal weight: 2.9990 chunk 776 optimal weight: 5.9990 chunk 644 optimal weight: 1.9990 chunk 359 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 257 optimal weight: 0.9990 chunk 407 optimal weight: 0.9980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 HIS C 409 ASN ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1009 ASN A 32 ASN ** A 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 566 ASN A1271 ASN ** d 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 37 ASN ** k 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 135 GLN ** b1094 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 2 ASN ** a 847 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a1092 ASN a1158 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 65054 Z= 0.258 Angle : 0.559 7.159 88071 Z= 0.300 Chirality : 0.040 0.182 10188 Planarity : 0.004 0.052 11161 Dihedral : 5.358 59.962 8717 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.46 % Favored : 88.40 % Rotamer: Outliers : 0.03 % Allowed : 1.81 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.10), residues: 7262 helix: 0.60 (0.10), residues: 2457 sheet: -1.70 (0.13), residues: 1497 loop : -2.74 (0.10), residues: 3308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B1024 HIS 0.007 0.001 HIS c 489 PHE 0.036 0.001 PHE A 112 TYR 0.019 0.001 TYR h 33 ARG 0.009 0.000 ARG a 555 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14524 Ramachandran restraints generated. 7262 Oldfield, 0 Emsley, 7262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14524 Ramachandran restraints generated. 7262 Oldfield, 0 Emsley, 7262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 57 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue SER 80 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue THR 1139 is missing expected H atoms. Skipping. Evaluate side-chains 2822 residues out of total 6847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 2820 time to evaluate : 6.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 141 LYS cc_start: 0.8334 (tptm) cc_final: 0.8006 (tptt) REVERT: C 235 GLN cc_start: 0.7919 (pm20) cc_final: 0.7466 (pm20) REVERT: C 256 PHE cc_start: 0.7974 (p90) cc_final: 0.7069 (p90) REVERT: C 328 LYS cc_start: 0.8823 (mtpp) cc_final: 0.8446 (mtpp) REVERT: C 425 GLU cc_start: 0.8102 (tt0) cc_final: 0.7813 (tt0) REVERT: C 497 GLU cc_start: 0.7411 (pt0) cc_final: 0.7045 (pt0) REVERT: D 32 ASP cc_start: 0.6928 (m-30) cc_final: 0.6622 (m-30) REVERT: D 36 TYR cc_start: 0.8400 (m-80) cc_final: 0.8068 (m-80) REVERT: D 107 GLN cc_start: 0.8233 (tp40) cc_final: 0.7931 (tp40) REVERT: D 115 ILE cc_start: 0.8767 (mm) cc_final: 0.8485 (mm) REVERT: D 134 ILE cc_start: 0.8302 (mt) cc_final: 0.8011 (mt) REVERT: D 136 SER cc_start: 0.8912 (t) cc_final: 0.8673 (t) REVERT: D 138 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7321 (mt-10) REVERT: E 45 TYR cc_start: 0.8955 (t80) cc_final: 0.8235 (t80) REVERT: E 204 LYS cc_start: 0.8245 (ttmm) cc_final: 0.7905 (ttmm) REVERT: E 205 ASN cc_start: 0.7916 (m-40) cc_final: 0.7671 (m-40) REVERT: E 262 VAL cc_start: 0.8993 (t) cc_final: 0.8761 (t) REVERT: F 107 ASN cc_start: 0.8487 (t0) cc_final: 0.8165 (t0) REVERT: F 116 SER cc_start: 0.8720 (m) cc_final: 0.8491 (m) REVERT: G 42 LYS cc_start: 0.8971 (mtmm) cc_final: 0.8571 (mtmm) REVERT: G 56 GLN cc_start: 0.9365 (mm110) cc_final: 0.9083 (tp-100) REVERT: G 143 ARG cc_start: 0.8104 (tmm-80) cc_final: 0.7531 (ttp80) REVERT: H 18 GLN cc_start: 0.8595 (pp30) cc_final: 0.8243 (pp30) REVERT: H 104 ASP cc_start: 0.7998 (p0) cc_final: 0.7716 (p0) REVERT: I 16 GLU cc_start: 0.8704 (tp30) cc_final: 0.8382 (tp30) REVERT: I 23 GLU cc_start: 0.7902 (tp30) cc_final: 0.7125 (tp30) REVERT: I 100 ASN cc_start: 0.8587 (t0) cc_final: 0.8178 (t0) REVERT: I 140 TYR cc_start: 0.8990 (t80) cc_final: 0.8424 (t80) REVERT: J 20 ASP cc_start: 0.7866 (t0) cc_final: 0.7396 (t0) REVERT: J 35 GLU cc_start: 0.7385 (tp30) cc_final: 0.6913 (tm-30) REVERT: J 48 GLU cc_start: 0.8564 (tt0) cc_final: 0.8355 (tt0) REVERT: J 229 CYS cc_start: 0.8460 (m) cc_final: 0.8250 (m) REVERT: J 257 GLN cc_start: 0.7088 (tm-30) cc_final: 0.6644 (tm-30) REVERT: K 34 LYS cc_start: 0.7693 (ttmm) cc_final: 0.7297 (ttmm) REVERT: K 130 MET cc_start: 0.8600 (mmm) cc_final: 0.8355 (mmm) REVERT: K 139 GLU cc_start: 0.7882 (tp30) cc_final: 0.7394 (tp30) REVERT: K 162 ASP cc_start: 0.8383 (t0) cc_final: 0.7830 (t0) REVERT: l 118 ASN cc_start: 0.7603 (p0) cc_final: 0.7358 (p0) REVERT: l 150 MET cc_start: 0.8789 (ptm) cc_final: 0.8287 (ptm) REVERT: l 184 ASP cc_start: 0.8127 (t0) cc_final: 0.7836 (t0) REVERT: B 426 ARG cc_start: 0.6681 (ptt180) cc_final: 0.6205 (ptt180) REVERT: B 429 ASP cc_start: 0.7968 (m-30) cc_final: 0.7701 (m-30) REVERT: B 506 LEU cc_start: 0.9127 (tt) cc_final: 0.8790 (tt) REVERT: B 510 LYS cc_start: 0.8948 (ptmt) cc_final: 0.8609 (ttpt) REVERT: B 617 TYR cc_start: 0.8632 (m-80) cc_final: 0.7406 (m-10) REVERT: B 625 PHE cc_start: 0.8746 (t80) cc_final: 0.8330 (t80) REVERT: B 688 GLN cc_start: 0.8699 (mt0) cc_final: 0.8478 (mt0) REVERT: B 722 PHE cc_start: 0.8731 (p90) cc_final: 0.8230 (p90) REVERT: B 728 GLU cc_start: 0.7923 (mp0) cc_final: 0.7556 (mp0) REVERT: B 729 TYR cc_start: 0.7769 (t80) cc_final: 0.7513 (t80) REVERT: B 743 LYS cc_start: 0.7940 (ptmm) cc_final: 0.7610 (ptmm) REVERT: B 779 LYS cc_start: 0.8204 (tptm) cc_final: 0.7989 (tptm) REVERT: B 780 ASP cc_start: 0.8557 (p0) cc_final: 0.8125 (p0) REVERT: B 795 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7557 (mm-30) REVERT: B 870 ILE cc_start: 0.8863 (mt) cc_final: 0.8662 (mt) REVERT: B 936 GLU cc_start: 0.6976 (tm-30) cc_final: 0.6635 (tm-30) REVERT: B 937 LYS cc_start: 0.8192 (tptm) cc_final: 0.7193 (tppt) REVERT: B 946 CYS cc_start: 0.8793 (t) cc_final: 0.8579 (t) REVERT: B 973 LEU cc_start: 0.9482 (tp) cc_final: 0.9111 (tp) REVERT: A 16 ILE cc_start: 0.8014 (mt) cc_final: 0.7797 (mt) REVERT: A 30 GLU cc_start: 0.7715 (tp30) cc_final: 0.6814 (tp30) REVERT: A 37 LYS cc_start: 0.8519 (ttmm) cc_final: 0.7635 (ttmm) REVERT: A 135 GLU cc_start: 0.8221 (tp30) cc_final: 0.8016 (mm-30) REVERT: A 172 LEU cc_start: 0.9054 (tt) cc_final: 0.8759 (tt) REVERT: A 333 TYR cc_start: 0.8638 (p90) cc_final: 0.8100 (p90) REVERT: A 433 GLU cc_start: 0.7636 (mp0) cc_final: 0.7173 (mp0) REVERT: A 489 GLU cc_start: 0.8360 (tt0) cc_final: 0.8099 (tt0) REVERT: A 492 PHE cc_start: 0.8148 (t80) cc_final: 0.7926 (t80) REVERT: A 605 PHE cc_start: 0.7768 (m-80) cc_final: 0.7340 (p90) REVERT: A 650 ASP cc_start: 0.9201 (p0) cc_final: 0.8732 (p0) REVERT: A 666 ASP cc_start: 0.7876 (p0) cc_final: 0.7570 (p0) REVERT: A 759 GLU cc_start: 0.8771 (pm20) cc_final: 0.8517 (pm20) REVERT: A 815 ILE cc_start: 0.9198 (mm) cc_final: 0.8743 (mm) REVERT: A 867 ASP cc_start: 0.8128 (t0) cc_final: 0.7908 (t0) REVERT: A 879 ASN cc_start: 0.8450 (t0) cc_final: 0.8027 (t0) REVERT: A 894 MET cc_start: 0.8132 (tpp) cc_final: 0.7902 (tpp) REVERT: A 900 MET cc_start: 0.7638 (ttm) cc_final: 0.7180 (tpt) REVERT: A 979 TYR cc_start: 0.8004 (m-80) cc_final: 0.7752 (m-80) REVERT: A 984 SER cc_start: 0.8558 (p) cc_final: 0.8266 (p) REVERT: A 1002 ILE cc_start: 0.7925 (mm) cc_final: 0.7301 (mm) REVERT: A 1066 TYR cc_start: 0.8196 (m-80) cc_final: 0.7928 (m-80) REVERT: A 1123 CYS cc_start: 0.8453 (t) cc_final: 0.8130 (t) REVERT: A 1217 ASP cc_start: 0.7176 (t0) cc_final: 0.6599 (t0) REVERT: A 1218 SER cc_start: 0.8966 (t) cc_final: 0.8745 (t) REVERT: A 1219 LYS cc_start: 0.7935 (mptt) cc_final: 0.7712 (mmmm) REVERT: A 1220 THR cc_start: 0.8124 (m) cc_final: 0.7512 (m) REVERT: A 1222 LYS cc_start: 0.8925 (mtmt) cc_final: 0.8549 (mtmt) REVERT: A 1253 ILE cc_start: 0.8804 (mm) cc_final: 0.8549 (mm) REVERT: c 238 LYS cc_start: 0.9078 (mtpt) cc_final: 0.8224 (pptt) REVERT: c 263 GLU cc_start: 0.7843 (pp20) cc_final: 0.7524 (pp20) REVERT: c 338 GLU cc_start: 0.8061 (pm20) cc_final: 0.7612 (mp0) REVERT: c 425 GLU cc_start: 0.8469 (tt0) cc_final: 0.8169 (tt0) REVERT: c 516 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7873 (mt-10) REVERT: d 13 GLU cc_start: 0.8386 (pm20) cc_final: 0.8033 (pm20) REVERT: d 69 LEU cc_start: 0.8272 (mt) cc_final: 0.8057 (mt) REVERT: d 77 MET cc_start: 0.7163 (mtm) cc_final: 0.6946 (mtm) REVERT: d 114 LYS cc_start: 0.8376 (mmtp) cc_final: 0.7984 (mmtp) REVERT: e 51 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7690 (tm-30) REVERT: e 115 GLU cc_start: 0.7060 (mm-30) cc_final: 0.6837 (mm-30) REVERT: e 262 VAL cc_start: 0.7073 (m) cc_final: 0.6777 (m) REVERT: f 31 THR cc_start: 0.8894 (m) cc_final: 0.8688 (m) REVERT: f 43 GLN cc_start: 0.8754 (tm-30) cc_final: 0.8280 (tm-30) REVERT: f 62 ASN cc_start: 0.8903 (t0) cc_final: 0.8613 (t0) REVERT: f 140 TYR cc_start: 0.9184 (t80) cc_final: 0.8739 (t80) REVERT: g 123 TYR cc_start: 0.7481 (p90) cc_final: 0.7253 (p90) REVERT: h 108 LYS cc_start: 0.7853 (mmtp) cc_final: 0.7412 (mmtp) REVERT: h 126 GLN cc_start: 0.7761 (mt0) cc_final: 0.7485 (mt0) REVERT: h 200 MET cc_start: 0.8897 (mmp) cc_final: 0.8564 (mmm) REVERT: i 16 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7674 (tm-30) REVERT: i 21 LYS cc_start: 0.6026 (mttt) cc_final: 0.5620 (ttmt) REVERT: i 34 TYR cc_start: 0.8908 (t80) cc_final: 0.8453 (t80) REVERT: i 132 MET cc_start: 0.8248 (tpp) cc_final: 0.7880 (tpp) REVERT: j 20 ASP cc_start: 0.7067 (t70) cc_final: 0.6713 (t70) REVERT: j 23 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7508 (mm-30) REVERT: k 12 ASP cc_start: 0.8460 (t0) cc_final: 0.8037 (t0) REVERT: k 50 ASP cc_start: 0.8219 (t70) cc_final: 0.7991 (t70) REVERT: k 163 SER cc_start: 0.8661 (m) cc_final: 0.8427 (m) REVERT: b 347 LEU cc_start: 0.8729 (pp) cc_final: 0.8315 (pp) REVERT: b 363 TRP cc_start: 0.8662 (t60) cc_final: 0.8160 (t60) REVERT: b 399 GLU cc_start: 0.6826 (pp20) cc_final: 0.6303 (pm20) REVERT: b 405 ASN cc_start: 0.8548 (m-40) cc_final: 0.8219 (m-40) REVERT: b 412 GLU cc_start: 0.8330 (tt0) cc_final: 0.8066 (tt0) REVERT: b 434 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7862 (mm-30) REVERT: b 457 GLU cc_start: 0.7385 (tt0) cc_final: 0.6961 (tt0) REVERT: b 477 ASP cc_start: 0.7852 (t70) cc_final: 0.7382 (t70) REVERT: b 511 LEU cc_start: 0.9381 (tp) cc_final: 0.9163 (tp) REVERT: b 663 GLN cc_start: 0.8650 (tp40) cc_final: 0.8220 (tp40) REVERT: b 685 GLU cc_start: 0.7317 (tm-30) cc_final: 0.6940 (tm-30) REVERT: b 703 LEU cc_start: 0.7982 (tp) cc_final: 0.7739 (tt) REVERT: b 723 GLU cc_start: 0.7772 (mp0) cc_final: 0.7526 (tm-30) REVERT: b 728 GLU cc_start: 0.8324 (mm-30) cc_final: 0.7639 (mm-30) REVERT: b 729 TYR cc_start: 0.8322 (t80) cc_final: 0.7178 (t80) REVERT: b 749 LYS cc_start: 0.7013 (mppt) cc_final: 0.6120 (tptp) REVERT: b 879 ASP cc_start: 0.7702 (t70) cc_final: 0.7354 (t70) REVERT: b 894 GLU cc_start: 0.8912 (mt-10) cc_final: 0.8538 (mt-10) REVERT: b 895 LEU cc_start: 0.8694 (mp) cc_final: 0.8411 (mp) REVERT: b 936 GLU cc_start: 0.6968 (mm-30) cc_final: 0.6254 (mm-30) REVERT: b 963 GLU cc_start: 0.7165 (tp30) cc_final: 0.6764 (tp30) REVERT: b 983 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8282 (mp0) REVERT: b 1023 GLN cc_start: 0.7721 (mt0) cc_final: 0.7444 (mt0) REVERT: b 1037 GLU cc_start: 0.7718 (pt0) cc_final: 0.7119 (tt0) REVERT: b 1056 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8261 (mp0) REVERT: b 1069 LYS cc_start: 0.8487 (mtpt) cc_final: 0.8013 (mttp) REVERT: a 197 LYS cc_start: 0.8534 (mttt) cc_final: 0.8162 (mttt) REVERT: a 276 MET cc_start: 0.7534 (tpp) cc_final: 0.6933 (tpp) REVERT: a 289 TYR cc_start: 0.5455 (m-80) cc_final: 0.5016 (m-80) REVERT: a 307 ARG cc_start: 0.7698 (ptp90) cc_final: 0.7447 (ptp90) REVERT: a 339 VAL cc_start: 0.7575 (m) cc_final: 0.7351 (m) REVERT: a 430 HIS cc_start: 0.7751 (t-170) cc_final: 0.7512 (t-90) REVERT: a 553 ASP cc_start: 0.7520 (m-30) cc_final: 0.6763 (m-30) REVERT: a 670 ASN cc_start: 0.7384 (m-40) cc_final: 0.7173 (m-40) REVERT: a 735 VAL cc_start: 0.9055 (t) cc_final: 0.8801 (m) REVERT: a 776 GLU cc_start: 0.8596 (mp0) cc_final: 0.8243 (mp0) REVERT: a 815 ILE cc_start: 0.8889 (tp) cc_final: 0.8675 (tp) REVERT: a 816 ILE cc_start: 0.8756 (mt) cc_final: 0.8485 (mt) REVERT: a 836 TYR cc_start: 0.8071 (m-80) cc_final: 0.6922 (m-80) REVERT: a 864 MET cc_start: 0.8848 (ttm) cc_final: 0.8648 (ttp) REVERT: a 887 ASN cc_start: 0.7912 (m110) cc_final: 0.7612 (m110) REVERT: a 918 GLU cc_start: 0.8763 (tt0) cc_final: 0.8472 (tt0) REVERT: a 1020 GLU cc_start: 0.8630 (tm-30) cc_final: 0.8038 (tm-30) REVERT: a 1039 LEU cc_start: 0.8679 (mt) cc_final: 0.8416 (mt) REVERT: a 1195 GLU cc_start: 0.8057 (pt0) cc_final: 0.7822 (pt0) REVERT: a 1262 GLU cc_start: 0.8401 (tp30) cc_final: 0.8026 (tp30) REVERT: a 1280 ASP cc_start: 0.7033 (t0) cc_final: 0.6122 (t0) REVERT: a 1282 GLU cc_start: 0.7705 (mp0) cc_final: 0.6394 (mp0) outliers start: 2 outliers final: 0 residues processed: 2821 average time/residue: 1.2957 time to fit residues: 6172.7219 Evaluate side-chains 2619 residues out of total 6847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2619 time to evaluate : 6.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 803 random chunks: chunk 749 optimal weight: 20.0000 chunk 87 optimal weight: 0.2980 chunk 442 optimal weight: 1.9990 chunk 567 optimal weight: 0.7980 chunk 439 optimal weight: 1.9990 chunk 654 optimal weight: 1.9990 chunk 433 optimal weight: 1.9990 chunk 773 optimal weight: 10.0000 chunk 484 optimal weight: 2.9990 chunk 471 optimal weight: 0.3980 chunk 357 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 242 GLN ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 HIS C 409 ASN ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1009 ASN A 32 ASN ** A 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 566 ASN ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 260 ASN c 274 GLN ** d 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1094 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 847 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a1092 ASN a1150 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 65054 Z= 0.274 Angle : 0.565 7.805 88071 Z= 0.304 Chirality : 0.041 0.181 10188 Planarity : 0.004 0.052 11161 Dihedral : 5.334 59.467 8717 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.97 % Favored : 87.88 % Rotamer: Outliers : 0.03 % Allowed : 1.33 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.10), residues: 7262 helix: 0.59 (0.10), residues: 2460 sheet: -1.70 (0.13), residues: 1501 loop : -2.75 (0.10), residues: 3301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B1024 HIS 0.007 0.001 HIS c 489 PHE 0.020 0.001 PHE A 485 TYR 0.024 0.001 TYR h 33 ARG 0.007 0.000 ARG B 793 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14524 Ramachandran restraints generated. 7262 Oldfield, 0 Emsley, 7262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14524 Ramachandran restraints generated. 7262 Oldfield, 0 Emsley, 7262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 57 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue SER 80 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue THR 1139 is missing expected H atoms. Skipping. Evaluate side-chains 2840 residues out of total 6847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 2838 time to evaluate : 7.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 235 GLN cc_start: 0.7878 (pm20) cc_final: 0.7531 (pm20) REVERT: C 256 PHE cc_start: 0.7968 (p90) cc_final: 0.7130 (p90) REVERT: C 328 LYS cc_start: 0.8797 (mtpp) cc_final: 0.8403 (mtpp) REVERT: C 425 GLU cc_start: 0.8092 (tt0) cc_final: 0.7802 (tt0) REVERT: C 497 GLU cc_start: 0.7428 (pt0) cc_final: 0.7029 (pt0) REVERT: D 92 GLN cc_start: 0.8538 (tm-30) cc_final: 0.8264 (tm-30) REVERT: D 107 GLN cc_start: 0.8232 (tp40) cc_final: 0.7936 (tp40) REVERT: D 115 ILE cc_start: 0.8840 (mm) cc_final: 0.8571 (mm) REVERT: D 136 SER cc_start: 0.8913 (t) cc_final: 0.8682 (t) REVERT: E 45 TYR cc_start: 0.8956 (t80) cc_final: 0.8233 (t80) REVERT: E 62 GLN cc_start: 0.7158 (tm-30) cc_final: 0.6796 (tm-30) REVERT: E 114 GLU cc_start: 0.7669 (pp20) cc_final: 0.7463 (pp20) REVERT: E 204 LYS cc_start: 0.8305 (ttmm) cc_final: 0.7756 (ttmm) REVERT: E 205 ASN cc_start: 0.7942 (m-40) cc_final: 0.7700 (m-40) REVERT: E 262 VAL cc_start: 0.9013 (t) cc_final: 0.8763 (t) REVERT: F 28 GLU cc_start: 0.7212 (pp20) cc_final: 0.6815 (pp20) REVERT: F 107 ASN cc_start: 0.8499 (t0) cc_final: 0.8176 (t0) REVERT: F 116 SER cc_start: 0.8720 (m) cc_final: 0.8465 (m) REVERT: G 42 LYS cc_start: 0.8958 (mtmm) cc_final: 0.8583 (mtmm) REVERT: G 143 ARG cc_start: 0.8154 (tmm-80) cc_final: 0.7542 (ttp80) REVERT: H 18 GLN cc_start: 0.8611 (pp30) cc_final: 0.8232 (pp30) REVERT: I 16 GLU cc_start: 0.8706 (tp30) cc_final: 0.8376 (tp30) REVERT: I 23 GLU cc_start: 0.7915 (tp30) cc_final: 0.7072 (tp30) REVERT: I 100 ASN cc_start: 0.8597 (t0) cc_final: 0.8193 (t0) REVERT: I 140 TYR cc_start: 0.8951 (t80) cc_final: 0.8537 (t80) REVERT: J 20 ASP cc_start: 0.7756 (t0) cc_final: 0.7481 (t0) REVERT: J 35 GLU cc_start: 0.7386 (tp30) cc_final: 0.6917 (tm-30) REVERT: J 48 GLU cc_start: 0.8581 (tt0) cc_final: 0.8360 (tt0) REVERT: J 229 CYS cc_start: 0.8470 (m) cc_final: 0.8248 (m) REVERT: J 257 GLN cc_start: 0.7076 (tm-30) cc_final: 0.6608 (tm-30) REVERT: K 34 LYS cc_start: 0.7684 (ttmm) cc_final: 0.7309 (ttmm) REVERT: K 104 ILE cc_start: 0.9007 (mt) cc_final: 0.8781 (mt) REVERT: K 130 MET cc_start: 0.8577 (mmm) cc_final: 0.8340 (mmm) REVERT: K 139 GLU cc_start: 0.7865 (tp30) cc_final: 0.7569 (tp30) REVERT: K 162 ASP cc_start: 0.8417 (t0) cc_final: 0.7852 (t0) REVERT: l 118 ASN cc_start: 0.7750 (p0) cc_final: 0.7515 (p0) REVERT: l 143 ASN cc_start: 0.7431 (m110) cc_final: 0.6887 (m110) REVERT: l 150 MET cc_start: 0.8796 (ptm) cc_final: 0.8387 (ptm) REVERT: l 184 ASP cc_start: 0.7671 (t0) cc_final: 0.7347 (t0) REVERT: B 429 ASP cc_start: 0.8009 (m-30) cc_final: 0.7704 (m-30) REVERT: B 506 LEU cc_start: 0.9081 (tt) cc_final: 0.8717 (tt) REVERT: B 510 LYS cc_start: 0.8950 (ptmt) cc_final: 0.8597 (ttpt) REVERT: B 617 TYR cc_start: 0.8666 (m-80) cc_final: 0.7520 (m-10) REVERT: B 625 PHE cc_start: 0.8758 (t80) cc_final: 0.8351 (t80) REVERT: B 668 ASN cc_start: 0.8766 (m110) cc_final: 0.8560 (m110) REVERT: B 688 GLN cc_start: 0.8683 (mt0) cc_final: 0.8443 (mt0) REVERT: B 722 PHE cc_start: 0.8700 (p90) cc_final: 0.8100 (p90) REVERT: B 728 GLU cc_start: 0.7941 (mp0) cc_final: 0.7549 (mp0) REVERT: B 729 TYR cc_start: 0.7684 (t80) cc_final: 0.7478 (t80) REVERT: B 743 LYS cc_start: 0.7948 (ptmm) cc_final: 0.7623 (ptmm) REVERT: B 779 LYS cc_start: 0.8163 (tptm) cc_final: 0.7951 (tptm) REVERT: B 780 ASP cc_start: 0.8566 (p0) cc_final: 0.8125 (p0) REVERT: B 795 GLU cc_start: 0.8349 (mm-30) cc_final: 0.7544 (mm-30) REVERT: B 936 GLU cc_start: 0.6951 (tm-30) cc_final: 0.6298 (tt0) REVERT: B 937 LYS cc_start: 0.8211 (tptm) cc_final: 0.7073 (tppt) REVERT: B 946 CYS cc_start: 0.8795 (t) cc_final: 0.8577 (t) REVERT: B 1100 LEU cc_start: 0.8638 (tp) cc_final: 0.8437 (tp) REVERT: A 16 ILE cc_start: 0.8035 (mt) cc_final: 0.7810 (mt) REVERT: A 30 GLU cc_start: 0.7741 (tp30) cc_final: 0.6820 (tp30) REVERT: A 37 LYS cc_start: 0.8515 (ttmm) cc_final: 0.7648 (ttmm) REVERT: A 135 GLU cc_start: 0.8269 (tp30) cc_final: 0.8046 (mm-30) REVERT: A 172 LEU cc_start: 0.9074 (tt) cc_final: 0.8848 (tt) REVERT: A 319 ILE cc_start: 0.9245 (tt) cc_final: 0.9009 (tt) REVERT: A 322 CYS cc_start: 0.8314 (m) cc_final: 0.8072 (m) REVERT: A 333 TYR cc_start: 0.8640 (p90) cc_final: 0.8098 (p90) REVERT: A 429 MET cc_start: 0.7549 (mmm) cc_final: 0.7323 (mmm) REVERT: A 433 GLU cc_start: 0.7653 (mp0) cc_final: 0.7193 (mp0) REVERT: A 489 GLU cc_start: 0.8373 (tt0) cc_final: 0.8087 (tt0) REVERT: A 492 PHE cc_start: 0.8141 (t80) cc_final: 0.7931 (t80) REVERT: A 666 ASP cc_start: 0.7876 (p0) cc_final: 0.7579 (p0) REVERT: A 815 ILE cc_start: 0.9206 (mm) cc_final: 0.8755 (mm) REVERT: A 867 ASP cc_start: 0.8121 (t0) cc_final: 0.7917 (t0) REVERT: A 900 MET cc_start: 0.7659 (ttm) cc_final: 0.7082 (tpp) REVERT: A 979 TYR cc_start: 0.8029 (m-80) cc_final: 0.7747 (m-80) REVERT: A 984 SER cc_start: 0.8542 (p) cc_final: 0.8260 (p) REVERT: A 1002 ILE cc_start: 0.7757 (mm) cc_final: 0.7328 (mm) REVERT: A 1066 TYR cc_start: 0.8237 (m-80) cc_final: 0.7967 (m-80) REVERT: A 1123 CYS cc_start: 0.8394 (t) cc_final: 0.8083 (t) REVERT: A 1217 ASP cc_start: 0.7130 (t0) cc_final: 0.6668 (t0) REVERT: A 1218 SER cc_start: 0.8980 (t) cc_final: 0.8711 (t) REVERT: A 1219 LYS cc_start: 0.8188 (mptt) cc_final: 0.7610 (mmmm) REVERT: A 1220 THR cc_start: 0.8186 (m) cc_final: 0.7482 (m) REVERT: A 1222 LYS cc_start: 0.8928 (mtmt) cc_final: 0.8338 (mtpt) REVERT: A 1253 ILE cc_start: 0.8788 (mm) cc_final: 0.8500 (mm) REVERT: A 1269 LYS cc_start: 0.6988 (mmtt) cc_final: 0.6758 (mmtt) REVERT: c 238 LYS cc_start: 0.9069 (mtpt) cc_final: 0.8221 (pptt) REVERT: c 263 GLU cc_start: 0.7839 (pp20) cc_final: 0.7521 (pp20) REVERT: c 295 ILE cc_start: 0.8595 (mm) cc_final: 0.8385 (mm) REVERT: c 338 GLU cc_start: 0.8186 (pm20) cc_final: 0.7723 (mp0) REVERT: c 425 GLU cc_start: 0.8444 (tt0) cc_final: 0.8145 (tt0) REVERT: c 516 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7752 (mt-10) REVERT: d 13 GLU cc_start: 0.8410 (pm20) cc_final: 0.8045 (pm20) REVERT: d 69 LEU cc_start: 0.8290 (mt) cc_final: 0.8056 (mt) REVERT: d 77 MET cc_start: 0.7197 (mtm) cc_final: 0.6379 (mtm) REVERT: d 114 LYS cc_start: 0.8503 (mmtp) cc_final: 0.8066 (mmtp) REVERT: e 51 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7590 (tm-30) REVERT: e 115 GLU cc_start: 0.7124 (mm-30) cc_final: 0.6910 (mm-30) REVERT: e 262 VAL cc_start: 0.7057 (m) cc_final: 0.6795 (m) REVERT: f 43 GLN cc_start: 0.8757 (tm-30) cc_final: 0.8272 (tm-30) REVERT: f 49 PHE cc_start: 0.8952 (m-10) cc_final: 0.8625 (m-10) REVERT: f 62 ASN cc_start: 0.8892 (t0) cc_final: 0.8582 (t0) REVERT: f 140 TYR cc_start: 0.9195 (t80) cc_final: 0.8809 (t80) REVERT: g 13 CYS cc_start: 0.8522 (m) cc_final: 0.8235 (m) REVERT: g 123 TYR cc_start: 0.7568 (p90) cc_final: 0.7304 (p90) REVERT: h 108 LYS cc_start: 0.7866 (mmtp) cc_final: 0.7411 (mmtp) REVERT: h 126 GLN cc_start: 0.7785 (mt0) cc_final: 0.7499 (mt0) REVERT: i 16 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7830 (tm-30) REVERT: i 21 LYS cc_start: 0.6336 (mttt) cc_final: 0.6057 (ttmt) REVERT: i 34 TYR cc_start: 0.8856 (t80) cc_final: 0.8386 (t80) REVERT: i 132 MET cc_start: 0.8252 (tpp) cc_final: 0.7892 (tpp) REVERT: i 180 LEU cc_start: 0.7959 (tp) cc_final: 0.7745 (tp) REVERT: j 23 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7528 (mm-30) REVERT: j 234 CYS cc_start: 0.9128 (m) cc_final: 0.8918 (m) REVERT: k 12 ASP cc_start: 0.8727 (t0) cc_final: 0.8209 (t0) REVERT: k 50 ASP cc_start: 0.8208 (t70) cc_final: 0.7967 (t70) REVERT: b 347 LEU cc_start: 0.8709 (pp) cc_final: 0.8317 (pp) REVERT: b 363 TRP cc_start: 0.8670 (t60) cc_final: 0.8164 (t60) REVERT: b 399 GLU cc_start: 0.7015 (pp20) cc_final: 0.6399 (pm20) REVERT: b 405 ASN cc_start: 0.8534 (m-40) cc_final: 0.8193 (m-40) REVERT: b 412 GLU cc_start: 0.8318 (tt0) cc_final: 0.8069 (tt0) REVERT: b 434 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7888 (mm-30) REVERT: b 457 GLU cc_start: 0.7414 (tt0) cc_final: 0.6834 (tt0) REVERT: b 477 ASP cc_start: 0.7902 (t70) cc_final: 0.7423 (t70) REVERT: b 498 SER cc_start: 0.7682 (m) cc_final: 0.7379 (p) REVERT: b 511 LEU cc_start: 0.9374 (tp) cc_final: 0.9152 (tp) REVERT: b 567 LYS cc_start: 0.7193 (mtmm) cc_final: 0.6952 (mtmm) REVERT: b 663 GLN cc_start: 0.8655 (tp40) cc_final: 0.8215 (tp40) REVERT: b 685 GLU cc_start: 0.7381 (tm-30) cc_final: 0.7017 (tm-30) REVERT: b 703 LEU cc_start: 0.8007 (tp) cc_final: 0.7721 (tt) REVERT: b 723 GLU cc_start: 0.7786 (mp0) cc_final: 0.7547 (tm-30) REVERT: b 728 GLU cc_start: 0.8352 (mm-30) cc_final: 0.7868 (mm-30) REVERT: b 729 TYR cc_start: 0.8378 (t80) cc_final: 0.7194 (t80) REVERT: b 749 LYS cc_start: 0.7039 (mppt) cc_final: 0.6151 (tptp) REVERT: b 879 ASP cc_start: 0.7788 (t70) cc_final: 0.7443 (t70) REVERT: b 894 GLU cc_start: 0.8915 (mt-10) cc_final: 0.8545 (mt-10) REVERT: b 895 LEU cc_start: 0.8699 (mp) cc_final: 0.8406 (mp) REVERT: b 936 GLU cc_start: 0.6984 (mm-30) cc_final: 0.6229 (mm-30) REVERT: b 963 GLU cc_start: 0.7212 (tp30) cc_final: 0.6806 (tp30) REVERT: b 1037 GLU cc_start: 0.7704 (pt0) cc_final: 0.7098 (tt0) REVERT: b 1069 LYS cc_start: 0.8486 (mtpt) cc_final: 0.8017 (mttp) REVERT: a 58 THR cc_start: 0.8170 (m) cc_final: 0.7792 (m) REVERT: a 92 LYS cc_start: 0.7913 (ptmt) cc_final: 0.7700 (ptmm) REVERT: a 197 LYS cc_start: 0.8510 (mttt) cc_final: 0.8097 (mttt) REVERT: a 276 MET cc_start: 0.7536 (tpp) cc_final: 0.6931 (tpp) REVERT: a 283 GLN cc_start: 0.8458 (mt0) cc_final: 0.8212 (mt0) REVERT: a 289 TYR cc_start: 0.5732 (m-80) cc_final: 0.5344 (m-80) REVERT: a 307 ARG cc_start: 0.7684 (ptp90) cc_final: 0.7433 (ptp90) REVERT: a 339 VAL cc_start: 0.7572 (m) cc_final: 0.7359 (m) REVERT: a 500 LEU cc_start: 0.8752 (pp) cc_final: 0.8456 (pp) REVERT: a 553 ASP cc_start: 0.7537 (m-30) cc_final: 0.6778 (m-30) REVERT: a 670 ASN cc_start: 0.7417 (m-40) cc_final: 0.7211 (m-40) REVERT: a 735 VAL cc_start: 0.9058 (t) cc_final: 0.8813 (m) REVERT: a 776 GLU cc_start: 0.8498 (mp0) cc_final: 0.8158 (mp0) REVERT: a 836 TYR cc_start: 0.8110 (m-80) cc_final: 0.7011 (m-80) REVERT: a 864 MET cc_start: 0.8693 (ttm) cc_final: 0.8483 (ttp) REVERT: a 887 ASN cc_start: 0.7932 (m110) cc_final: 0.7661 (m110) REVERT: a 904 ASP cc_start: 0.7979 (p0) cc_final: 0.7610 (p0) REVERT: a 1020 GLU cc_start: 0.8663 (tm-30) cc_final: 0.8080 (tm-30) REVERT: a 1039 LEU cc_start: 0.8529 (mt) cc_final: 0.8234 (mt) REVERT: a 1195 GLU cc_start: 0.8070 (pt0) cc_final: 0.7830 (pt0) REVERT: a 1262 GLU cc_start: 0.8416 (tp30) cc_final: 0.8078 (tp30) REVERT: a 1280 ASP cc_start: 0.7034 (t0) cc_final: 0.6093 (t0) REVERT: a 1282 GLU cc_start: 0.7584 (mp0) cc_final: 0.6373 (mp0) outliers start: 2 outliers final: 0 residues processed: 2839 average time/residue: 1.3658 time to fit residues: 6559.4366 Evaluate side-chains 2617 residues out of total 6847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2617 time to evaluate : 6.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 803 random chunks: chunk 478 optimal weight: 2.9990 chunk 309 optimal weight: 1.9990 chunk 462 optimal weight: 0.0970 chunk 233 optimal weight: 0.9980 chunk 152 optimal weight: 0.2980 chunk 149 optimal weight: 0.8980 chunk 492 optimal weight: 1.9990 chunk 527 optimal weight: 0.0050 chunk 382 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 608 optimal weight: 2.9990 overall best weight: 0.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 HIS C 409 ASN ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 987 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 32 ASN ** A 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 566 ASN ** A1089 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 274 GLN ** k 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 135 GLN ** b1094 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 847 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a1092 ASN a1150 ASN a1158 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 65054 Z= 0.168 Angle : 0.535 7.729 88071 Z= 0.283 Chirality : 0.040 0.195 10188 Planarity : 0.004 0.055 11161 Dihedral : 5.167 59.529 8717 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.37 % Favored : 89.48 % Rotamer: Outliers : 0.03 % Allowed : 0.94 % Favored : 99.03 % 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: -1.81 (0.10), residues: 7262 helix: 0.81 (0.11), residues: 2444 sheet: -1.57 (0.13), residues: 1503 loop : -2.63 (0.10), residues: 3315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 53 HIS 0.012 0.001 HIS e 93 PHE 0.022 0.001 PHE B 330 TYR 0.020 0.001 TYR f 45 ARG 0.007 0.000 ARG B 793 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14524 Ramachandran restraints generated. 7262 Oldfield, 0 Emsley, 7262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14524 Ramachandran restraints generated. 7262 Oldfield, 0 Emsley, 7262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 57 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue SER 80 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue THR 1139 is missing expected H atoms. Skipping. Evaluate side-chains 2840 residues out of total 6847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 2838 time to evaluate : 6.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 141 LYS cc_start: 0.8210 (tptm) cc_final: 0.7969 (tptt) REVERT: C 256 PHE cc_start: 0.7957 (p90) cc_final: 0.7112 (p90) REVERT: C 328 LYS cc_start: 0.8792 (mtpp) cc_final: 0.8370 (mtpp) REVERT: C 425 GLU cc_start: 0.8082 (tt0) cc_final: 0.7788 (tt0) REVERT: D 19 LEU cc_start: 0.8915 (tt) cc_final: 0.8696 (tt) REVERT: D 41 ASN cc_start: 0.9374 (t0) cc_final: 0.8992 (t0) REVERT: D 54 TRP cc_start: 0.5923 (m100) cc_final: 0.5399 (m100) REVERT: D 92 GLN cc_start: 0.8479 (tm-30) cc_final: 0.8202 (tm-30) REVERT: D 107 GLN cc_start: 0.8200 (tp40) cc_final: 0.7964 (tp40) REVERT: D 115 ILE cc_start: 0.8826 (mm) cc_final: 0.8557 (mm) REVERT: D 136 SER cc_start: 0.8854 (t) cc_final: 0.8647 (t) REVERT: D 147 SER cc_start: 0.7754 (t) cc_final: 0.7552 (t) REVERT: E 45 TYR cc_start: 0.8951 (t80) cc_final: 0.8201 (t80) REVERT: E 62 GLN cc_start: 0.7294 (tm-30) cc_final: 0.6869 (tm-30) REVERT: E 205 ASN cc_start: 0.7799 (m-40) cc_final: 0.7522 (m-40) REVERT: E 209 LYS cc_start: 0.9155 (mmmm) cc_final: 0.8949 (mmmm) REVERT: E 262 VAL cc_start: 0.8992 (t) cc_final: 0.8753 (t) REVERT: F 107 ASN cc_start: 0.8511 (t0) cc_final: 0.8211 (t0) REVERT: F 116 SER cc_start: 0.8680 (m) cc_final: 0.8443 (m) REVERT: G 15 CYS cc_start: 0.9065 (p) cc_final: 0.8844 (p) REVERT: H 18 GLN cc_start: 0.8617 (pp30) cc_final: 0.8178 (pp30) REVERT: H 104 ASP cc_start: 0.7925 (p0) cc_final: 0.7615 (p0) REVERT: I 16 GLU cc_start: 0.8690 (tp30) cc_final: 0.8360 (tp30) REVERT: I 23 GLU cc_start: 0.7894 (tp30) cc_final: 0.7041 (tp30) REVERT: I 100 ASN cc_start: 0.8503 (t0) cc_final: 0.8073 (t0) REVERT: I 140 TYR cc_start: 0.8954 (t80) cc_final: 0.8416 (t80) REVERT: J 20 ASP cc_start: 0.7857 (t0) cc_final: 0.7438 (t0) REVERT: J 35 GLU cc_start: 0.7335 (tp30) cc_final: 0.6895 (tm-30) REVERT: J 48 GLU cc_start: 0.8543 (tt0) cc_final: 0.8316 (tt0) REVERT: J 229 CYS cc_start: 0.8417 (m) cc_final: 0.8194 (m) REVERT: K 34 LYS cc_start: 0.7643 (ttmm) cc_final: 0.7242 (ttmm) REVERT: K 130 MET cc_start: 0.8556 (mmm) cc_final: 0.8317 (mmm) REVERT: K 139 GLU cc_start: 0.7839 (tp30) cc_final: 0.7606 (tp30) REVERT: K 162 ASP cc_start: 0.8382 (t0) cc_final: 0.7827 (t0) REVERT: l 118 ASN cc_start: 0.7798 (p0) cc_final: 0.7570 (p0) REVERT: l 143 ASN cc_start: 0.7408 (m110) cc_final: 0.6869 (m110) REVERT: l 150 MET cc_start: 0.8783 (ptm) cc_final: 0.8429 (ptm) REVERT: l 184 ASP cc_start: 0.7652 (t0) cc_final: 0.7321 (t0) REVERT: B 429 ASP cc_start: 0.7725 (m-30) cc_final: 0.7298 (m-30) REVERT: B 506 LEU cc_start: 0.9023 (tt) cc_final: 0.8615 (tt) REVERT: B 510 LYS cc_start: 0.8894 (ptmt) cc_final: 0.8529 (ttpt) REVERT: B 617 TYR cc_start: 0.8539 (m-80) cc_final: 0.7256 (m-10) REVERT: B 625 PHE cc_start: 0.8719 (t80) cc_final: 0.8282 (t80) REVERT: B 712 ILE cc_start: 0.8893 (tt) cc_final: 0.8603 (pt) REVERT: B 722 PHE cc_start: 0.8679 (p90) cc_final: 0.8093 (p90) REVERT: B 728 GLU cc_start: 0.7854 (mp0) cc_final: 0.7456 (mp0) REVERT: B 729 TYR cc_start: 0.7566 (t80) cc_final: 0.7187 (t80) REVERT: B 743 LYS cc_start: 0.7893 (ptmm) cc_final: 0.7592 (ptmm) REVERT: B 779 LYS cc_start: 0.8211 (tptm) cc_final: 0.7943 (tptm) REVERT: B 795 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7520 (mm-30) REVERT: B 936 GLU cc_start: 0.6987 (tm-30) cc_final: 0.6360 (tt0) REVERT: B 937 LYS cc_start: 0.8170 (tptm) cc_final: 0.7056 (tppt) REVERT: B 946 CYS cc_start: 0.8803 (t) cc_final: 0.8575 (t) REVERT: B 973 LEU cc_start: 0.9443 (tp) cc_final: 0.9081 (tp) REVERT: B 991 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7573 (mm-30) REVERT: A 30 GLU cc_start: 0.7715 (tp30) cc_final: 0.6797 (tp30) REVERT: A 37 LYS cc_start: 0.8528 (ttmm) cc_final: 0.7615 (ttmm) REVERT: A 107 LEU cc_start: 0.7990 (tp) cc_final: 0.7750 (tp) REVERT: A 172 LEU cc_start: 0.9070 (tt) cc_final: 0.8858 (tt) REVERT: A 319 ILE cc_start: 0.9231 (tt) cc_final: 0.9001 (tt) REVERT: A 322 CYS cc_start: 0.8466 (m) cc_final: 0.8264 (m) REVERT: A 333 TYR cc_start: 0.8659 (p90) cc_final: 0.8126 (p90) REVERT: A 489 GLU cc_start: 0.8347 (tt0) cc_final: 0.8044 (tt0) REVERT: A 492 PHE cc_start: 0.8110 (t80) cc_final: 0.7896 (t80) REVERT: A 605 PHE cc_start: 0.7743 (m-80) cc_final: 0.7374 (p90) REVERT: A 666 ASP cc_start: 0.8075 (p0) cc_final: 0.7763 (p0) REVERT: A 815 ILE cc_start: 0.9204 (mm) cc_final: 0.8793 (mm) REVERT: A 867 ASP cc_start: 0.8014 (t0) cc_final: 0.7785 (t0) REVERT: A 979 TYR cc_start: 0.8012 (m-80) cc_final: 0.7705 (m-80) REVERT: A 984 SER cc_start: 0.8514 (p) cc_final: 0.8253 (p) REVERT: A 1002 ILE cc_start: 0.7840 (mm) cc_final: 0.7227 (mm) REVERT: A 1007 GLU cc_start: 0.7006 (pt0) cc_final: 0.6205 (tp30) REVERT: A 1008 LEU cc_start: 0.8574 (pp) cc_final: 0.7772 (pp) REVERT: A 1026 ILE cc_start: 0.8224 (pt) cc_final: 0.8016 (pt) REVERT: A 1033 HIS cc_start: 0.8131 (t70) cc_final: 0.7913 (t70) REVERT: A 1066 TYR cc_start: 0.8158 (m-80) cc_final: 0.7866 (m-80) REVERT: A 1111 GLU cc_start: 0.7926 (mp0) cc_final: 0.7726 (mp0) REVERT: A 1123 CYS cc_start: 0.8297 (t) cc_final: 0.7980 (t) REVERT: A 1158 HIS cc_start: 0.7829 (t70) cc_final: 0.7589 (m90) REVERT: A 1217 ASP cc_start: 0.7176 (t0) cc_final: 0.6646 (t0) REVERT: A 1218 SER cc_start: 0.8975 (t) cc_final: 0.8735 (t) REVERT: A 1219 LYS cc_start: 0.8136 (mptt) cc_final: 0.7476 (mmmm) REVERT: A 1222 LYS cc_start: 0.8910 (mtmt) cc_final: 0.8466 (mtmt) REVERT: A 1253 ILE cc_start: 0.8774 (mm) cc_final: 0.8558 (mm) REVERT: A 1269 LYS cc_start: 0.6865 (mmtt) cc_final: 0.6622 (mmtt) REVERT: c 238 LYS cc_start: 0.9176 (mtpt) cc_final: 0.8339 (pptt) REVERT: c 263 GLU cc_start: 0.7905 (pp20) cc_final: 0.7615 (pp20) REVERT: c 295 ILE cc_start: 0.8566 (mm) cc_final: 0.8339 (mm) REVERT: c 338 GLU cc_start: 0.8089 (pm20) cc_final: 0.7631 (mp0) REVERT: c 425 GLU cc_start: 0.8452 (tt0) cc_final: 0.8137 (tt0) REVERT: c 516 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7694 (mt-10) REVERT: d 13 GLU cc_start: 0.8382 (pm20) cc_final: 0.8055 (pm20) REVERT: d 77 MET cc_start: 0.7090 (mtm) cc_final: 0.6415 (mtm) REVERT: d 114 LYS cc_start: 0.8403 (mmtp) cc_final: 0.8013 (mmtp) REVERT: e 51 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7622 (tm-30) REVERT: e 248 ASP cc_start: 0.7487 (m-30) cc_final: 0.7286 (m-30) REVERT: e 262 VAL cc_start: 0.7021 (m) cc_final: 0.6773 (m) REVERT: f 43 GLN cc_start: 0.8711 (tm-30) cc_final: 0.8261 (tm-30) REVERT: f 140 TYR cc_start: 0.9157 (t80) cc_final: 0.8793 (t80) REVERT: h 108 LYS cc_start: 0.7910 (mmtp) cc_final: 0.7544 (mmtp) REVERT: h 126 GLN cc_start: 0.7758 (mt0) cc_final: 0.7058 (mt0) REVERT: i 21 LYS cc_start: 0.6344 (mttt) cc_final: 0.6078 (ttmt) REVERT: i 34 TYR cc_start: 0.8885 (t80) cc_final: 0.8421 (t80) REVERT: i 132 MET cc_start: 0.8218 (tpp) cc_final: 0.7851 (tpp) REVERT: i 175 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7449 (mm-30) REVERT: j 23 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7503 (mm-30) REVERT: k 12 ASP cc_start: 0.8367 (t0) cc_final: 0.7859 (t0) REVERT: k 163 SER cc_start: 0.8635 (m) cc_final: 0.8339 (m) REVERT: b 363 TRP cc_start: 0.8603 (t60) cc_final: 0.8073 (t60) REVERT: b 399 GLU cc_start: 0.6958 (pp20) cc_final: 0.6344 (pm20) REVERT: b 405 ASN cc_start: 0.8538 (m-40) cc_final: 0.8228 (m-40) REVERT: b 412 GLU cc_start: 0.8281 (tt0) cc_final: 0.8014 (tt0) REVERT: b 434 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7820 (mm-30) REVERT: b 477 ASP cc_start: 0.7834 (t70) cc_final: 0.7364 (t70) REVERT: b 498 SER cc_start: 0.7691 (m) cc_final: 0.7403 (p) REVERT: b 511 LEU cc_start: 0.9362 (tp) cc_final: 0.9137 (tp) REVERT: b 567 LYS cc_start: 0.7150 (mtmm) cc_final: 0.6896 (mtmm) REVERT: b 640 GLU cc_start: 0.7965 (tm-30) cc_final: 0.7728 (tm-30) REVERT: b 644 GLU cc_start: 0.8076 (mp0) cc_final: 0.7647 (mp0) REVERT: b 663 GLN cc_start: 0.8850 (tp40) cc_final: 0.8318 (tp40) REVERT: b 703 LEU cc_start: 0.7949 (tp) cc_final: 0.7551 (tt) REVERT: b 729 TYR cc_start: 0.8202 (t80) cc_final: 0.7200 (t80) REVERT: b 879 ASP cc_start: 0.7499 (t70) cc_final: 0.7146 (t70) REVERT: b 894 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8480 (mt-10) REVERT: b 895 LEU cc_start: 0.8683 (mp) cc_final: 0.8390 (mp) REVERT: b 936 GLU cc_start: 0.6821 (mm-30) cc_final: 0.5948 (mm-30) REVERT: b 963 GLU cc_start: 0.7102 (tp30) cc_final: 0.6882 (tp30) REVERT: b 1037 GLU cc_start: 0.7685 (pt0) cc_final: 0.7448 (pt0) REVERT: b 1073 LEU cc_start: 0.8988 (mt) cc_final: 0.8748 (mt) REVERT: a 197 LYS cc_start: 0.8568 (mttt) cc_final: 0.8153 (mttt) REVERT: a 276 MET cc_start: 0.7530 (tpp) cc_final: 0.6976 (tpp) REVERT: a 289 TYR cc_start: 0.5428 (m-80) cc_final: 0.5011 (m-80) REVERT: a 307 ARG cc_start: 0.7671 (ptp90) cc_final: 0.7401 (ptp90) REVERT: a 430 HIS cc_start: 0.7672 (t-170) cc_final: 0.7408 (t-90) REVERT: a 507 VAL cc_start: 0.8137 (t) cc_final: 0.7931 (t) REVERT: a 553 ASP cc_start: 0.7459 (m-30) cc_final: 0.6716 (m-30) REVERT: a 670 ASN cc_start: 0.7445 (m-40) cc_final: 0.7220 (m-40) REVERT: a 735 VAL cc_start: 0.9039 (t) cc_final: 0.8795 (m) REVERT: a 815 ILE cc_start: 0.8880 (tp) cc_final: 0.8577 (tp) REVERT: a 816 ILE cc_start: 0.8735 (mt) cc_final: 0.8462 (mt) REVERT: a 836 TYR cc_start: 0.8070 (m-80) cc_final: 0.6925 (m-80) REVERT: a 864 MET cc_start: 0.8801 (ttm) cc_final: 0.8523 (ttp) REVERT: a 887 ASN cc_start: 0.7923 (m110) cc_final: 0.7637 (m110) REVERT: a 918 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8187 (mt-10) REVERT: a 1020 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8143 (tm-30) REVERT: a 1039 LEU cc_start: 0.8459 (mt) cc_final: 0.8167 (mt) REVERT: a 1262 GLU cc_start: 0.8355 (tp30) cc_final: 0.7904 (tp30) REVERT: a 1280 ASP cc_start: 0.6901 (t0) cc_final: 0.6058 (t0) REVERT: a 1282 GLU cc_start: 0.7662 (mp0) cc_final: 0.6440 (mp0) outliers start: 2 outliers final: 0 residues processed: 2839 average time/residue: 1.2889 time to fit residues: 6155.7053 Evaluate side-chains 2666 residues out of total 6847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2666 time to evaluate : 6.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 803 random chunks: chunk 704 optimal weight: 1.9990 chunk 741 optimal weight: 20.0000 chunk 676 optimal weight: 0.3980 chunk 721 optimal weight: 1.9990 chunk 434 optimal weight: 2.9990 chunk 314 optimal weight: 0.9990 chunk 566 optimal weight: 1.9990 chunk 221 optimal weight: 1.9990 chunk 651 optimal weight: 1.9990 chunk 682 optimal weight: 0.8980 chunk 718 optimal weight: 0.0570 overall best weight: 0.8702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 242 GLN ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 HIS C 409 ASN C 418 ASN ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 987 HIS B1009 ASN A 32 ASN ** A 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 566 ASN ** A1089 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 260 ASN c 274 GLN ** d 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 50 ASN e 129 GLN k 13 ASN ** k 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 503 ASN ** b1094 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 2 ASN a 437 GLN ** a 847 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a1092 ASN a1150 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 65054 Z= 0.237 Angle : 0.551 7.761 88071 Z= 0.294 Chirality : 0.040 0.174 10188 Planarity : 0.004 0.054 11161 Dihedral : 5.164 57.131 8717 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.33 % Favored : 88.51 % Rotamer: Outliers : 0.04 % Allowed : 0.60 % Favored : 99.36 % 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: -1.85 (0.10), residues: 7262 helix: 0.75 (0.11), residues: 2455 sheet: -1.56 (0.13), residues: 1504 loop : -2.66 (0.10), residues: 3303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 53 HIS 0.010 0.001 HIS e 93 PHE 0.026 0.001 PHE A 168 TYR 0.021 0.001 TYR j 90 ARG 0.007 0.000 ARG a1168 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14524 Ramachandran restraints generated. 7262 Oldfield, 0 Emsley, 7262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14524 Ramachandran restraints generated. 7262 Oldfield, 0 Emsley, 7262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 57 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue SER 80 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue THR 1139 is missing expected H atoms. Skipping. Evaluate side-chains 2841 residues out of total 6847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 2838 time to evaluate : 6.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 256 PHE cc_start: 0.7948 (p90) cc_final: 0.7100 (p90) REVERT: C 328 LYS cc_start: 0.8796 (mtpp) cc_final: 0.8383 (mtpp) REVERT: C 425 GLU cc_start: 0.8078 (tt0) cc_final: 0.7779 (tt0) REVERT: D 54 TRP cc_start: 0.5910 (m100) cc_final: 0.5395 (m100) REVERT: D 92 GLN cc_start: 0.8512 (tm-30) cc_final: 0.8227 (tm-30) REVERT: D 107 GLN cc_start: 0.8212 (tp40) cc_final: 0.7926 (tp40) REVERT: D 115 ILE cc_start: 0.8837 (mm) cc_final: 0.8571 (mm) REVERT: D 136 SER cc_start: 0.8848 (t) cc_final: 0.8645 (t) REVERT: E 45 TYR cc_start: 0.8948 (t80) cc_final: 0.8228 (t80) REVERT: E 204 LYS cc_start: 0.8081 (ttmm) cc_final: 0.7862 (ttmt) REVERT: E 205 ASN cc_start: 0.7868 (m-40) cc_final: 0.7609 (m-40) REVERT: E 227 SER cc_start: 0.8657 (t) cc_final: 0.8442 (t) REVERT: E 262 VAL cc_start: 0.8997 (t) cc_final: 0.8770 (t) REVERT: F 107 ASN cc_start: 0.8547 (t0) cc_final: 0.8210 (t0) REVERT: F 116 SER cc_start: 0.8689 (m) cc_final: 0.8430 (m) REVERT: H 18 GLN cc_start: 0.8594 (pp30) cc_final: 0.8167 (pp30) REVERT: I 16 GLU cc_start: 0.8690 (tp30) cc_final: 0.8353 (tp30) REVERT: I 23 GLU cc_start: 0.7866 (tp30) cc_final: 0.7055 (tp30) REVERT: I 100 ASN cc_start: 0.8542 (t0) cc_final: 0.8131 (t0) REVERT: I 140 TYR cc_start: 0.8909 (t80) cc_final: 0.8492 (t80) REVERT: J 20 ASP cc_start: 0.7783 (t0) cc_final: 0.7485 (t0) REVERT: J 35 GLU cc_start: 0.7296 (tp30) cc_final: 0.6881 (tm-30) REVERT: J 48 GLU cc_start: 0.8484 (tt0) cc_final: 0.8252 (tt0) REVERT: J 229 CYS cc_start: 0.8428 (m) cc_final: 0.8217 (m) REVERT: J 257 GLN cc_start: 0.7070 (tm-30) cc_final: 0.6591 (tm-30) REVERT: K 34 LYS cc_start: 0.7669 (ttmm) cc_final: 0.7291 (ttmm) REVERT: K 130 MET cc_start: 0.8560 (mmm) cc_final: 0.8316 (mmm) REVERT: K 139 GLU cc_start: 0.7825 (tp30) cc_final: 0.7570 (tp30) REVERT: K 162 ASP cc_start: 0.8394 (t0) cc_final: 0.7817 (t0) REVERT: l 118 ASN cc_start: 0.7861 (p0) cc_final: 0.7627 (p0) REVERT: l 150 MET cc_start: 0.8788 (ptm) cc_final: 0.8450 (ptm) REVERT: l 184 ASP cc_start: 0.7669 (t0) cc_final: 0.7331 (t0) REVERT: B 425 GLN cc_start: 0.6998 (pm20) cc_final: 0.6571 (pm20) REVERT: B 426 ARG cc_start: 0.6727 (ptt180) cc_final: 0.6288 (ptt180) REVERT: B 429 ASP cc_start: 0.7810 (m-30) cc_final: 0.7382 (m-30) REVERT: B 506 LEU cc_start: 0.9046 (tt) cc_final: 0.8641 (tt) REVERT: B 510 LYS cc_start: 0.8917 (ptmt) cc_final: 0.8549 (ttpt) REVERT: B 617 TYR cc_start: 0.8647 (m-80) cc_final: 0.7506 (m-10) REVERT: B 625 PHE cc_start: 0.8750 (t80) cc_final: 0.8325 (t80) REVERT: B 722 PHE cc_start: 0.8708 (p90) cc_final: 0.8083 (p90) REVERT: B 728 GLU cc_start: 0.7906 (mp0) cc_final: 0.7486 (mp0) REVERT: B 729 TYR cc_start: 0.7549 (t80) cc_final: 0.7248 (t80) REVERT: B 743 LYS cc_start: 0.7924 (ptmm) cc_final: 0.7589 (ptmm) REVERT: B 795 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7525 (mm-30) REVERT: B 936 GLU cc_start: 0.6888 (tm-30) cc_final: 0.6258 (tt0) REVERT: B 937 LYS cc_start: 0.8207 (tptm) cc_final: 0.7035 (tppt) REVERT: B 946 CYS cc_start: 0.8819 (t) cc_final: 0.8605 (t) REVERT: B 973 LEU cc_start: 0.9465 (tp) cc_final: 0.9114 (tp) REVERT: B 991 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7609 (mm-30) REVERT: A 30 GLU cc_start: 0.7713 (tp30) cc_final: 0.6776 (tp30) REVERT: A 37 LYS cc_start: 0.8504 (ttmm) cc_final: 0.7614 (ttmm) REVERT: A 107 LEU cc_start: 0.7969 (tp) cc_final: 0.7739 (tp) REVERT: A 319 ILE cc_start: 0.9245 (tt) cc_final: 0.9018 (tt) REVERT: A 322 CYS cc_start: 0.8449 (m) cc_final: 0.8203 (m) REVERT: A 333 TYR cc_start: 0.8656 (p90) cc_final: 0.8106 (p90) REVERT: A 489 GLU cc_start: 0.8353 (tt0) cc_final: 0.8053 (tt0) REVERT: A 492 PHE cc_start: 0.8128 (t80) cc_final: 0.7897 (t80) REVERT: A 666 ASP cc_start: 0.8083 (p0) cc_final: 0.7774 (p0) REVERT: A 815 ILE cc_start: 0.9209 (mm) cc_final: 0.8755 (mm) REVERT: A 867 ASP cc_start: 0.8162 (t0) cc_final: 0.7945 (t0) REVERT: A 900 MET cc_start: 0.7687 (ttm) cc_final: 0.7095 (tpp) REVERT: A 979 TYR cc_start: 0.8066 (m-80) cc_final: 0.7742 (m-80) REVERT: A 984 SER cc_start: 0.8580 (p) cc_final: 0.8331 (p) REVERT: A 1000 MET cc_start: 0.8736 (ptt) cc_final: 0.8534 (ptm) REVERT: A 1002 ILE cc_start: 0.7668 (mm) cc_final: 0.7184 (mm) REVERT: A 1007 GLU cc_start: 0.7101 (pt0) cc_final: 0.6240 (tp30) REVERT: A 1008 LEU cc_start: 0.8607 (pp) cc_final: 0.7814 (pp) REVERT: A 1026 ILE cc_start: 0.8221 (pt) cc_final: 0.8015 (pt) REVERT: A 1057 GLN cc_start: 0.8234 (mt0) cc_final: 0.8016 (mt0) REVERT: A 1111 GLU cc_start: 0.7922 (mp0) cc_final: 0.7716 (mp0) REVERT: A 1123 CYS cc_start: 0.8359 (t) cc_final: 0.8013 (t) REVERT: A 1179 GLU cc_start: 0.7081 (mp0) cc_final: 0.6683 (mm-30) REVERT: A 1217 ASP cc_start: 0.7227 (t0) cc_final: 0.6723 (t0) REVERT: A 1218 SER cc_start: 0.9006 (t) cc_final: 0.8761 (t) REVERT: A 1219 LYS cc_start: 0.8176 (mptt) cc_final: 0.7532 (mmmm) REVERT: A 1220 THR cc_start: 0.8408 (m) cc_final: 0.7847 (m) REVERT: A 1222 LYS cc_start: 0.8870 (mtmt) cc_final: 0.8442 (mtmt) REVERT: A 1253 ILE cc_start: 0.8728 (mm) cc_final: 0.8474 (mm) REVERT: c 238 LYS cc_start: 0.9184 (mtpt) cc_final: 0.8368 (pptt) REVERT: c 263 GLU cc_start: 0.7845 (pp20) cc_final: 0.7601 (pp20) REVERT: c 295 ILE cc_start: 0.8596 (mm) cc_final: 0.8388 (mm) REVERT: c 338 GLU cc_start: 0.8134 (pm20) cc_final: 0.7661 (mp0) REVERT: c 425 GLU cc_start: 0.8437 (tt0) cc_final: 0.8133 (tt0) REVERT: c 516 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7711 (mt-10) REVERT: d 13 GLU cc_start: 0.8412 (pm20) cc_final: 0.8050 (pm20) REVERT: d 77 MET cc_start: 0.7122 (mtm) cc_final: 0.6884 (mtm) REVERT: d 114 LYS cc_start: 0.8481 (mmtp) cc_final: 0.8086 (mmtp) REVERT: e 51 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7692 (tm-30) REVERT: e 115 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6846 (mm-30) REVERT: e 262 VAL cc_start: 0.7095 (m) cc_final: 0.6801 (m) REVERT: f 43 GLN cc_start: 0.8724 (tm-30) cc_final: 0.8289 (tm-30) REVERT: f 47 ARG cc_start: 0.7541 (mtp85) cc_final: 0.7147 (mtp85) REVERT: f 49 PHE cc_start: 0.8968 (m-10) cc_final: 0.8629 (m-10) REVERT: f 140 TYR cc_start: 0.9158 (t80) cc_final: 0.8832 (t80) REVERT: g 13 CYS cc_start: 0.8547 (m) cc_final: 0.8217 (m) REVERT: g 150 GLU cc_start: 0.8053 (tp30) cc_final: 0.7813 (tp30) REVERT: h 108 LYS cc_start: 0.7908 (mmtp) cc_final: 0.7460 (mmtp) REVERT: h 126 GLN cc_start: 0.7769 (mt0) cc_final: 0.7041 (mt0) REVERT: i 16 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7656 (tm-30) REVERT: i 21 LYS cc_start: 0.6358 (mttt) cc_final: 0.6087 (ttmt) REVERT: i 53 ASN cc_start: 0.8991 (m-40) cc_final: 0.8764 (m-40) REVERT: i 132 MET cc_start: 0.8159 (tpp) cc_final: 0.7784 (tpp) REVERT: i 175 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7476 (mm-30) REVERT: i 180 LEU cc_start: 0.7830 (tp) cc_final: 0.7579 (tp) REVERT: j 23 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7497 (mm-30) REVERT: j 234 CYS cc_start: 0.9138 (m) cc_final: 0.8933 (m) REVERT: k 12 ASP cc_start: 0.8421 (t0) cc_final: 0.7887 (t0) REVERT: k 163 SER cc_start: 0.8671 (m) cc_final: 0.8423 (m) REVERT: b 363 TRP cc_start: 0.8633 (t60) cc_final: 0.8110 (t60) REVERT: b 405 ASN cc_start: 0.8533 (m-40) cc_final: 0.8220 (m-40) REVERT: b 412 GLU cc_start: 0.8206 (tt0) cc_final: 0.7989 (tt0) REVERT: b 434 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7840 (mm-30) REVERT: b 477 ASP cc_start: 0.7793 (t70) cc_final: 0.7299 (t70) REVERT: b 498 SER cc_start: 0.7716 (m) cc_final: 0.7408 (p) REVERT: b 545 GLU cc_start: 0.6610 (mp0) cc_final: 0.6204 (mp0) REVERT: b 567 LYS cc_start: 0.7079 (mtmm) cc_final: 0.6714 (mtmm) REVERT: b 640 GLU cc_start: 0.7991 (tm-30) cc_final: 0.7784 (tm-30) REVERT: b 663 GLN cc_start: 0.8786 (tp40) cc_final: 0.8238 (tp40) REVERT: b 685 GLU cc_start: 0.7456 (tm-30) cc_final: 0.7069 (tm-30) REVERT: b 703 LEU cc_start: 0.7971 (tp) cc_final: 0.7681 (tt) REVERT: b 723 GLU cc_start: 0.7735 (mp0) cc_final: 0.7479 (tm-30) REVERT: b 728 GLU cc_start: 0.8349 (mm-30) cc_final: 0.8108 (mm-30) REVERT: b 729 TYR cc_start: 0.8145 (t80) cc_final: 0.6809 (t80) REVERT: b 744 THR cc_start: 0.9239 (m) cc_final: 0.9029 (m) REVERT: b 879 ASP cc_start: 0.7684 (t70) cc_final: 0.7343 (t70) REVERT: b 894 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8513 (mt-10) REVERT: b 895 LEU cc_start: 0.8767 (mp) cc_final: 0.8434 (mp) REVERT: b 936 GLU cc_start: 0.6911 (mm-30) cc_final: 0.6384 (mm-30) REVERT: b 963 GLU cc_start: 0.7154 (tp30) cc_final: 0.6912 (tp30) REVERT: b 1037 GLU cc_start: 0.7712 (pt0) cc_final: 0.7132 (tt0) REVERT: b 1073 LEU cc_start: 0.9013 (mt) cc_final: 0.8785 (mt) REVERT: a 92 LYS cc_start: 0.7986 (ptmt) cc_final: 0.7759 (ptmm) REVERT: a 143 MET cc_start: 0.2613 (tpt) cc_final: 0.1730 (tpt) REVERT: a 197 LYS cc_start: 0.8450 (mttt) cc_final: 0.8046 (mttt) REVERT: a 276 MET cc_start: 0.7554 (tpp) cc_final: 0.6958 (tpp) REVERT: a 289 TYR cc_start: 0.5642 (m-80) cc_final: 0.5278 (m-80) REVERT: a 307 ARG cc_start: 0.7663 (ptp90) cc_final: 0.7398 (ptp90) REVERT: a 430 HIS cc_start: 0.7685 (t-170) cc_final: 0.7477 (t-170) REVERT: a 553 ASP cc_start: 0.7509 (m-30) cc_final: 0.6853 (m-30) REVERT: a 735 VAL cc_start: 0.9039 (t) cc_final: 0.8807 (m) REVERT: a 786 ILE cc_start: 0.8920 (tt) cc_final: 0.8555 (tt) REVERT: a 836 TYR cc_start: 0.8239 (m-80) cc_final: 0.7287 (m-80) REVERT: a 864 MET cc_start: 0.8774 (ttm) cc_final: 0.8510 (ttp) REVERT: a 887 ASN cc_start: 0.7978 (m110) cc_final: 0.7677 (m110) REVERT: a 904 ASP cc_start: 0.8060 (p0) cc_final: 0.7723 (p0) REVERT: a 1020 GLU cc_start: 0.8727 (tm-30) cc_final: 0.8163 (tm-30) REVERT: a 1039 LEU cc_start: 0.8526 (mt) cc_final: 0.8236 (mt) REVERT: a 1262 GLU cc_start: 0.8348 (tp30) cc_final: 0.7868 (tp30) REVERT: a 1280 ASP cc_start: 0.6956 (t0) cc_final: 0.6069 (t0) REVERT: a 1282 GLU cc_start: 0.7676 (mp0) cc_final: 0.6455 (mp0) outliers start: 3 outliers final: 0 residues processed: 2839 average time/residue: 1.3674 time to fit residues: 6565.5903 Evaluate side-chains 2642 residues out of total 6847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2642 time to evaluate : 7.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 803 random chunks: chunk 473 optimal weight: 1.9990 chunk 762 optimal weight: 20.0000 chunk 465 optimal weight: 0.9980 chunk 361 optimal weight: 0.9980 chunk 530 optimal weight: 1.9990 chunk 799 optimal weight: 10.0000 chunk 736 optimal weight: 50.0000 chunk 637 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 492 optimal weight: 1.9990 chunk 390 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 HIS C 409 ASN C 418 ASN ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 243 ASN B 668 ASN B1009 ASN A 32 ASN ** A 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 473 HIS A 566 ASN c 274 GLN ** d 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 13 ASN ** k 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1094 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 847 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a1092 ASN a1158 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 65054 Z= 0.302 Angle : 0.585 8.651 88071 Z= 0.314 Chirality : 0.041 0.241 10188 Planarity : 0.004 0.065 11161 Dihedral : 5.258 56.227 8717 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.84 % Favored : 88.00 % Rotamer: Outliers : 0.04 % Allowed : 0.37 % Favored : 99.59 % 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: -1.96 (0.10), residues: 7262 helix: 0.62 (0.11), residues: 2463 sheet: -1.60 (0.13), residues: 1492 loop : -2.72 (0.10), residues: 3307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP K 53 HIS 0.008 0.001 HIS e 93 PHE 0.024 0.002 PHE b 303 TYR 0.031 0.002 TYR G 99 ARG 0.008 0.001 ARG a1168 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14524 Ramachandran restraints generated. 7262 Oldfield, 0 Emsley, 7262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14524 Ramachandran restraints generated. 7262 Oldfield, 0 Emsley, 7262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 57 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue SER 80 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue THR 1139 is missing expected H atoms. Skipping. Evaluate side-chains 2823 residues out of total 6847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 2820 time to evaluate : 7.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 256 PHE cc_start: 0.7949 (p90) cc_final: 0.7102 (p90) REVERT: C 328 LYS cc_start: 0.8796 (mtpp) cc_final: 0.8384 (mtpp) REVERT: C 425 GLU cc_start: 0.8060 (tt0) cc_final: 0.7776 (tt0) REVERT: C 497 GLU cc_start: 0.7175 (pt0) cc_final: 0.6838 (pt0) REVERT: D 54 TRP cc_start: 0.5912 (m100) cc_final: 0.5417 (m100) REVERT: D 92 GLN cc_start: 0.8507 (tm-30) cc_final: 0.8178 (tm-30) REVERT: D 94 SER cc_start: 0.9092 (t) cc_final: 0.8890 (p) REVERT: D 107 GLN cc_start: 0.8221 (tp40) cc_final: 0.7931 (tp40) REVERT: D 115 ILE cc_start: 0.8846 (mm) cc_final: 0.8581 (mm) REVERT: D 136 SER cc_start: 0.8840 (t) cc_final: 0.8607 (t) REVERT: D 139 ARG cc_start: 0.8664 (ttm-80) cc_final: 0.8254 (ttm-80) REVERT: E 45 TYR cc_start: 0.8957 (t80) cc_final: 0.8220 (t80) REVERT: E 114 GLU cc_start: 0.7645 (pp20) cc_final: 0.7414 (pp20) REVERT: E 205 ASN cc_start: 0.7919 (m-40) cc_final: 0.7645 (m-40) REVERT: E 262 VAL cc_start: 0.9030 (t) cc_final: 0.8791 (t) REVERT: F 107 ASN cc_start: 0.8508 (t0) cc_final: 0.8131 (t0) REVERT: F 116 SER cc_start: 0.8648 (m) cc_final: 0.8345 (m) REVERT: H 18 GLN cc_start: 0.8518 (pp30) cc_final: 0.8187 (pp30) REVERT: I 16 GLU cc_start: 0.8691 (tp30) cc_final: 0.8352 (tp30) REVERT: I 23 GLU cc_start: 0.7886 (tp30) cc_final: 0.7039 (tp30) REVERT: I 100 ASN cc_start: 0.8627 (t0) cc_final: 0.8180 (t0) REVERT: I 120 ASP cc_start: 0.8133 (t0) cc_final: 0.7895 (t0) REVERT: I 140 TYR cc_start: 0.8965 (t80) cc_final: 0.8414 (t80) REVERT: J 20 ASP cc_start: 0.7928 (t0) cc_final: 0.7472 (t0) REVERT: J 35 GLU cc_start: 0.7250 (tp30) cc_final: 0.6876 (tm-30) REVERT: J 48 GLU cc_start: 0.8482 (tt0) cc_final: 0.8263 (tt0) REVERT: J 229 CYS cc_start: 0.8478 (m) cc_final: 0.8238 (m) REVERT: J 257 GLN cc_start: 0.7071 (tm-30) cc_final: 0.6566 (tm-30) REVERT: K 130 MET cc_start: 0.8515 (mmm) cc_final: 0.8255 (mmm) REVERT: K 139 GLU cc_start: 0.7820 (tp30) cc_final: 0.7496 (tp30) REVERT: K 162 ASP cc_start: 0.8458 (t0) cc_final: 0.7894 (t0) REVERT: l 118 ASN cc_start: 0.7937 (p0) cc_final: 0.7717 (p0) REVERT: l 143 ASN cc_start: 0.7338 (m110) cc_final: 0.6826 (m110) REVERT: l 150 MET cc_start: 0.8832 (ptm) cc_final: 0.8474 (ptm) REVERT: l 184 ASP cc_start: 0.7694 (t0) cc_final: 0.7352 (t0) REVERT: B 426 ARG cc_start: 0.6694 (ptt180) cc_final: 0.6490 (ptt180) REVERT: B 506 LEU cc_start: 0.9020 (tt) cc_final: 0.8573 (tt) REVERT: B 510 LYS cc_start: 0.8936 (ptmt) cc_final: 0.8568 (ttpt) REVERT: B 617 TYR cc_start: 0.8662 (m-80) cc_final: 0.7526 (m-10) REVERT: B 625 PHE cc_start: 0.8746 (t80) cc_final: 0.8302 (t80) REVERT: B 688 GLN cc_start: 0.8718 (mt0) cc_final: 0.8456 (mt0) REVERT: B 728 GLU cc_start: 0.7971 (mp0) cc_final: 0.7559 (mp0) REVERT: B 743 LYS cc_start: 0.7972 (ptmm) cc_final: 0.7635 (ptmm) REVERT: B 760 LYS cc_start: 0.8256 (tttt) cc_final: 0.8026 (tttt) REVERT: B 795 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7538 (mm-30) REVERT: B 936 GLU cc_start: 0.6953 (tm-30) cc_final: 0.6436 (tt0) REVERT: B 937 LYS cc_start: 0.7907 (tptm) cc_final: 0.7063 (tppt) REVERT: B 946 CYS cc_start: 0.8824 (t) cc_final: 0.8593 (t) REVERT: B 991 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7618 (mm-30) REVERT: A 16 ILE cc_start: 0.7918 (mt) cc_final: 0.7704 (mt) REVERT: A 30 GLU cc_start: 0.7736 (tp30) cc_final: 0.6784 (tp30) REVERT: A 37 LYS cc_start: 0.8521 (ttmm) cc_final: 0.7703 (ttmm) REVERT: A 319 ILE cc_start: 0.9250 (tt) cc_final: 0.9022 (tt) REVERT: A 322 CYS cc_start: 0.8485 (m) cc_final: 0.8247 (m) REVERT: A 333 TYR cc_start: 0.8628 (p90) cc_final: 0.8052 (p90) REVERT: A 489 GLU cc_start: 0.8385 (tt0) cc_final: 0.7708 (tt0) REVERT: A 492 PHE cc_start: 0.8156 (t80) cc_final: 0.7929 (t80) REVERT: A 666 ASP cc_start: 0.8124 (p0) cc_final: 0.7803 (p0) REVERT: A 815 ILE cc_start: 0.9240 (mm) cc_final: 0.8778 (mm) REVERT: A 867 ASP cc_start: 0.8154 (t0) cc_final: 0.7929 (t0) REVERT: A 900 MET cc_start: 0.7637 (ttm) cc_final: 0.7152 (tpp) REVERT: A 979 TYR cc_start: 0.8094 (m-80) cc_final: 0.7791 (m-80) REVERT: A 984 SER cc_start: 0.8505 (p) cc_final: 0.8251 (p) REVERT: A 1026 ILE cc_start: 0.8229 (pt) cc_final: 0.8010 (pt) REVERT: A 1057 GLN cc_start: 0.8393 (mt0) cc_final: 0.8130 (mt0) REVERT: A 1111 GLU cc_start: 0.7929 (mp0) cc_final: 0.7700 (mp0) REVERT: A 1123 CYS cc_start: 0.8329 (t) cc_final: 0.8001 (t) REVERT: A 1179 GLU cc_start: 0.7088 (mp0) cc_final: 0.6701 (mm-30) REVERT: A 1217 ASP cc_start: 0.7252 (t0) cc_final: 0.6729 (t0) REVERT: A 1218 SER cc_start: 0.9003 (t) cc_final: 0.8744 (t) REVERT: A 1219 LYS cc_start: 0.8158 (mptt) cc_final: 0.7505 (mmmm) REVERT: A 1220 THR cc_start: 0.8412 (m) cc_final: 0.7853 (m) REVERT: A 1222 LYS cc_start: 0.8875 (mtmt) cc_final: 0.8447 (mtmt) REVERT: A 1253 ILE cc_start: 0.8777 (mm) cc_final: 0.8544 (mm) REVERT: A 1269 LYS cc_start: 0.7100 (mmtt) cc_final: 0.6856 (mmtt) REVERT: c 238 LYS cc_start: 0.9068 (mtpt) cc_final: 0.8240 (pptt) REVERT: c 295 ILE cc_start: 0.8609 (mm) cc_final: 0.8394 (mm) REVERT: c 338 GLU cc_start: 0.8144 (pm20) cc_final: 0.7695 (mp0) REVERT: c 425 GLU cc_start: 0.8438 (tt0) cc_final: 0.8118 (tt0) REVERT: c 516 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7682 (mt-10) REVERT: d 13 GLU cc_start: 0.8440 (pm20) cc_final: 0.8089 (pm20) REVERT: d 77 MET cc_start: 0.7170 (mtm) cc_final: 0.6933 (mtm) REVERT: d 107 GLN cc_start: 0.8489 (tp40) cc_final: 0.8206 (tt0) REVERT: d 114 LYS cc_start: 0.8519 (mmtp) cc_final: 0.8090 (mmtp) REVERT: e 51 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7593 (tm-30) REVERT: e 115 GLU cc_start: 0.7193 (mm-30) cc_final: 0.6959 (mm-30) REVERT: e 262 VAL cc_start: 0.7159 (m) cc_final: 0.6880 (m) REVERT: f 43 GLN cc_start: 0.8756 (tm-30) cc_final: 0.8282 (tm-30) REVERT: f 140 TYR cc_start: 0.9188 (t80) cc_final: 0.8869 (t80) REVERT: g 13 CYS cc_start: 0.8619 (m) cc_final: 0.8322 (m) REVERT: g 150 GLU cc_start: 0.8087 (tp30) cc_final: 0.7830 (tp30) REVERT: h 108 LYS cc_start: 0.7811 (mmtp) cc_final: 0.7476 (mmtp) REVERT: h 126 GLN cc_start: 0.7782 (mt0) cc_final: 0.7463 (mt0) REVERT: i 16 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7675 (tm-30) REVERT: i 34 TYR cc_start: 0.8852 (t80) cc_final: 0.8398 (t80) REVERT: i 53 ASN cc_start: 0.9060 (m-40) cc_final: 0.8844 (m-40) REVERT: i 87 SER cc_start: 0.8508 (p) cc_final: 0.8306 (p) REVERT: i 132 MET cc_start: 0.8178 (tpp) cc_final: 0.7812 (tpp) REVERT: i 175 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7504 (mm-30) REVERT: i 180 LEU cc_start: 0.7906 (tp) cc_final: 0.7640 (tp) REVERT: j 23 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7532 (mm-30) REVERT: j 68 GLU cc_start: 0.8624 (tp30) cc_final: 0.7751 (tp30) REVERT: j 234 CYS cc_start: 0.9126 (m) cc_final: 0.8916 (m) REVERT: k 12 ASP cc_start: 0.8732 (t0) cc_final: 0.8206 (t0) REVERT: k 50 ASP cc_start: 0.8194 (t70) cc_final: 0.7973 (t70) REVERT: b 334 MET cc_start: 0.8177 (mmm) cc_final: 0.7472 (mmm) REVERT: b 363 TRP cc_start: 0.8718 (t60) cc_final: 0.8198 (t60) REVERT: b 405 ASN cc_start: 0.8531 (m-40) cc_final: 0.8231 (m-40) REVERT: b 412 GLU cc_start: 0.8327 (tt0) cc_final: 0.8073 (tt0) REVERT: b 434 GLU cc_start: 0.8316 (mm-30) cc_final: 0.7842 (mm-30) REVERT: b 477 ASP cc_start: 0.7852 (t70) cc_final: 0.7294 (t70) REVERT: b 498 SER cc_start: 0.7639 (m) cc_final: 0.7426 (p) REVERT: b 505 PHE cc_start: 0.8454 (m-80) cc_final: 0.8254 (m-80) REVERT: b 615 ILE cc_start: 0.8012 (pt) cc_final: 0.7800 (pt) REVERT: b 640 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7782 (tm-30) REVERT: b 685 GLU cc_start: 0.7456 (tm-30) cc_final: 0.6919 (tm-30) REVERT: b 703 LEU cc_start: 0.8047 (tp) cc_final: 0.7727 (tt) REVERT: b 729 TYR cc_start: 0.8215 (t80) cc_final: 0.6964 (t80) REVERT: b 744 THR cc_start: 0.9163 (m) cc_final: 0.8933 (m) REVERT: b 749 LYS cc_start: 0.7068 (mppt) cc_final: 0.6177 (tptp) REVERT: b 833 GLU cc_start: 0.8722 (pm20) cc_final: 0.8477 (pm20) REVERT: b 879 ASP cc_start: 0.7765 (t70) cc_final: 0.7465 (t70) REVERT: b 894 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8547 (mt-10) REVERT: b 895 LEU cc_start: 0.8767 (mp) cc_final: 0.8456 (mp) REVERT: b 936 GLU cc_start: 0.7046 (mm-30) cc_final: 0.6537 (mm-30) REVERT: b 963 GLU cc_start: 0.7206 (tp30) cc_final: 0.6989 (tp30) REVERT: b 1073 LEU cc_start: 0.9074 (mt) cc_final: 0.8839 (mt) REVERT: a 92 LYS cc_start: 0.8042 (ptmt) cc_final: 0.7809 (ptmm) REVERT: a 197 LYS cc_start: 0.8505 (mttt) cc_final: 0.8110 (mttt) REVERT: a 276 MET cc_start: 0.7577 (tpp) cc_final: 0.7026 (tpp) REVERT: a 289 TYR cc_start: 0.5936 (m-80) cc_final: 0.5631 (m-80) REVERT: a 307 ARG cc_start: 0.7678 (ptp90) cc_final: 0.7427 (ptp90) REVERT: a 430 HIS cc_start: 0.7686 (t-170) cc_final: 0.7420 (t-90) REVERT: a 553 ASP cc_start: 0.7461 (m-30) cc_final: 0.6798 (m-30) REVERT: a 668 THR cc_start: 0.8289 (m) cc_final: 0.8085 (t) REVERT: a 670 ASN cc_start: 0.7189 (m-40) cc_final: 0.6964 (m-40) REVERT: a 735 VAL cc_start: 0.9044 (t) cc_final: 0.8839 (m) REVERT: a 786 ILE cc_start: 0.8935 (tt) cc_final: 0.8563 (tt) REVERT: a 815 ILE cc_start: 0.8901 (tp) cc_final: 0.8698 (tp) REVERT: a 816 ILE cc_start: 0.8773 (mt) cc_final: 0.8569 (mt) REVERT: a 836 TYR cc_start: 0.8214 (m-80) cc_final: 0.6928 (m-80) REVERT: a 887 ASN cc_start: 0.7969 (m110) cc_final: 0.7682 (m110) REVERT: a 1020 GLU cc_start: 0.8677 (tm-30) cc_final: 0.8130 (tm-30) REVERT: a 1039 LEU cc_start: 0.8572 (mt) cc_final: 0.8262 (mt) REVERT: a 1262 GLU cc_start: 0.8236 (tp30) cc_final: 0.7646 (tp30) REVERT: a 1276 ILE cc_start: 0.9015 (mm) cc_final: 0.8734 (mm) REVERT: a 1280 ASP cc_start: 0.7409 (t0) cc_final: 0.6383 (t0) REVERT: a 1282 GLU cc_start: 0.7660 (mp0) cc_final: 0.6470 (mp0) REVERT: a 1285 ILE cc_start: 0.8664 (pt) cc_final: 0.7859 (pt) outliers start: 3 outliers final: 0 residues processed: 2821 average time/residue: 1.3275 time to fit residues: 6326.3317 Evaluate side-chains 2618 residues out of total 6847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2618 time to evaluate : 6.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 803 random chunks: chunk 506 optimal weight: 0.4980 chunk 678 optimal weight: 0.5980 chunk 195 optimal weight: 3.9990 chunk 587 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 177 optimal weight: 5.9990 chunk 638 optimal weight: 0.9980 chunk 267 optimal weight: 0.6980 chunk 655 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 242 GLN ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 HIS C 409 ASN C 418 ASN ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 40 GLN K 37 ASN ** K 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 ASN B1009 ASN A 32 ASN ** A 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 566 ASN A1158 HIS ** c 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 260 ASN c 274 GLN e 50 ASN ** e 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 13 ASN ** k 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 503 ASN ** a 847 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a1092 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.150364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.116614 restraints weight = 296074.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.123563 restraints weight = 142177.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.125756 restraints weight = 74726.289| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3148 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 319 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 319 | |-----------------------------------------------------------------------------| r_final: 0.3148 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 65054 Z= 0.212 Angle : 0.553 7.109 88071 Z= 0.294 Chirality : 0.041 0.183 10188 Planarity : 0.004 0.067 11161 Dihedral : 5.167 55.357 8717 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.14 % Favored : 88.71 % Rotamer: Outliers : 0.04 % Allowed : 0.25 % Favored : 99.71 % 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: -1.86 (0.10), residues: 7262 helix: 0.71 (0.11), residues: 2465 sheet: -1.58 (0.13), residues: 1506 loop : -2.65 (0.10), residues: 3291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP K 53 HIS 0.009 0.001 HIS e 93 PHE 0.024 0.001 PHE a 296 TYR 0.018 0.001 TYR e 45 ARG 0.010 0.000 ARG b 931 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 71723.97 seconds wall clock time: 1218 minutes 36.85 seconds (73116.85 seconds total)