Starting phenix.real_space_refine on Mon Feb 19 11:16:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oql_3847/02_2024/5oql_3847_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oql_3847/02_2024/5oql_3847.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oql_3847/02_2024/5oql_3847.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oql_3847/02_2024/5oql_3847.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oql_3847/02_2024/5oql_3847_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oql_3847/02_2024/5oql_3847_neut.pdb" } resolution = 3.2 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= 0.000 sd= 0.011 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 1578 5.49 5 S 357 5.16 5 C 79468 2.51 5 N 25059 2.21 5 O 28657 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 87": "NH1" <-> "NH2" Residue "A ARG 109": "NH1" <-> "NH2" Residue "A ARG 155": "NH1" <-> "NH2" Residue "A ARG 164": "NH1" <-> "NH2" Residue "A PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 354": "NH1" <-> "NH2" Residue "A ARG 418": "NH1" <-> "NH2" Residue "A ARG 551": "NH1" <-> "NH2" Residue "A ARG 552": "NH1" <-> "NH2" Residue "A ARG 558": "NH1" <-> "NH2" Residue "A ARG 559": "NH1" <-> "NH2" Residue "A ARG 579": "NH1" <-> "NH2" Residue "A ARG 674": "NH1" <-> "NH2" Residue "A ARG 832": "NH1" <-> "NH2" Residue "B ARG 843": "NH1" <-> "NH2" Residue "B ARG 845": "NH1" <-> "NH2" Residue "B ARG 860": "NH1" <-> "NH2" Residue "B ARG 898": "NH1" <-> "NH2" Residue "B ARG 903": "NH1" <-> "NH2" Residue "C ARG 598": "NH1" <-> "NH2" Residue "C ARG 601": "NH1" <-> "NH2" Residue "C ARG 605": "NH1" <-> "NH2" Residue "D ARG 120": "NH1" <-> "NH2" Residue "D ARG 152": "NH1" <-> "NH2" Residue "D ARG 181": "NH1" <-> "NH2" Residue "D ARG 215": "NH1" <-> "NH2" Residue "D ARG 312": "NH1" <-> "NH2" Residue "D ARG 319": "NH1" <-> "NH2" Residue "E ARG 34": "NH1" <-> "NH2" Residue "E ARG 65": "NH1" <-> "NH2" Residue "E ARG 74": "NH1" <-> "NH2" Residue "F ARG 41": "NH1" <-> "NH2" Residue "F ARG 54": "NH1" <-> "NH2" Residue "F ARG 70": "NH1" <-> "NH2" Residue "F ARG 149": "NH1" <-> "NH2" Residue "F ARG 300": "NH1" <-> "NH2" Residue "F ARG 304": "NH1" <-> "NH2" Residue "F ARG 330": "NH1" <-> "NH2" Residue "F TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 397": "NH1" <-> "NH2" Residue "F ARG 442": "NH1" <-> "NH2" Residue "G ARG 126": "NH1" <-> "NH2" Residue "G ARG 165": "NH1" <-> "NH2" Residue "G ARG 179": "NH1" <-> "NH2" Residue "G ARG 198": "NH1" <-> "NH2" Residue "G ARG 236": "NH1" <-> "NH2" Residue "G ARG 306": "NH1" <-> "NH2" Residue "G ARG 365": "NH1" <-> "NH2" Residue "H ARG 24": "NH1" <-> "NH2" Residue "H ARG 70": "NH1" <-> "NH2" Residue "H ARG 79": "NH1" <-> "NH2" Residue "H ARG 116": "NH1" <-> "NH2" Residue "H ARG 261": "NH1" <-> "NH2" Residue "H ARG 268": "NH1" <-> "NH2" Residue "I ARG 896": "NH1" <-> "NH2" Residue "J ARG 755": "NH1" <-> "NH2" Residue "J ARG 781": "NH1" <-> "NH2" Residue "J ARG 812": "NH1" <-> "NH2" Residue "K ARG 325": "NH1" <-> "NH2" Residue "K ARG 350": "NH1" <-> "NH2" Residue "K ARG 902": "NH1" <-> "NH2" Residue "L ARG 89": "NH1" <-> "NH2" Residue "L ARG 97": "NH1" <-> "NH2" Residue "L ARG 181": "NH1" <-> "NH2" Residue "L ARG 191": "NH1" <-> "NH2" Residue "L ARG 286": "NH1" <-> "NH2" Residue "L ARG 287": "NH1" <-> "NH2" Residue "L ARG 332": "NH1" <-> "NH2" Residue "M ARG 251": "NH1" <-> "NH2" Residue "M ARG 349": "NH1" <-> "NH2" Residue "M ARG 355": "NH1" <-> "NH2" Residue "N ARG 155": "NH1" <-> "NH2" Residue "N ARG 158": "NH1" <-> "NH2" Residue "N ARG 173": "NH1" <-> "NH2" Residue "N ARG 181": "NH1" <-> "NH2" Residue "N ARG 235": "NH1" <-> "NH2" Residue "N ARG 257": "NH1" <-> "NH2" Residue "N ARG 267": "NH1" <-> "NH2" Residue "N ARG 285": "NH1" <-> "NH2" Residue "N ARG 371": "NH1" <-> "NH2" Residue "N ARG 377": "NH1" <-> "NH2" Residue "O PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 78": "NH1" <-> "NH2" Residue "O ARG 87": "NH1" <-> "NH2" Residue "O ARG 112": "NH1" <-> "NH2" Residue "O ARG 324": "NH1" <-> "NH2" Residue "O ARG 389": "NH1" <-> "NH2" Residue "O ARG 415": "NH1" <-> "NH2" Residue "O ARG 424": "NH1" <-> "NH2" Residue "O ARG 528": "NH1" <-> "NH2" Residue "O ARG 529": "NH1" <-> "NH2" Residue "O ARG 635": "NH1" <-> "NH2" Residue "O ARG 672": "NH1" <-> "NH2" Residue "O ARG 690": "NH1" <-> "NH2" Residue "O ARG 732": "NH1" <-> "NH2" Residue "O ARG 746": "NH1" <-> "NH2" Residue "O ARG 783": "NH1" <-> "NH2" Residue "O ARG 985": "NH1" <-> "NH2" Residue "P ARG 151": "NH1" <-> "NH2" Residue "P ARG 155": "NH1" <-> "NH2" Residue "P ARG 156": "NH1" <-> "NH2" Residue "P ARG 177": "NH1" <-> "NH2" Residue "R TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 134": "NH1" <-> "NH2" Residue "R ARG 188": "NH1" <-> "NH2" Residue "R ARG 191": "NH1" <-> "NH2" Residue "R ARG 199": "NH1" <-> "NH2" Residue "R ARG 211": "NH1" <-> "NH2" Residue "R TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 280": "NH1" <-> "NH2" Residue "R ARG 297": "NH1" <-> "NH2" Residue "S TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 134": "NH1" <-> "NH2" Residue "S ARG 188": "NH1" <-> "NH2" Residue "S ARG 191": "NH1" <-> "NH2" Residue "S ARG 199": "NH1" <-> "NH2" Residue "S ARG 211": "NH1" <-> "NH2" Residue "S TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 280": "NH1" <-> "NH2" Residue "S ARG 297": "NH1" <-> "NH2" Residue "T ARG 163": "NH1" <-> "NH2" Residue "U ARG 438": "NH1" <-> "NH2" Residue "V ARG 32": "NH1" <-> "NH2" Residue "V ARG 47": "NH1" <-> "NH2" Residue "V ARG 119": "NH1" <-> "NH2" Residue "W ARG 32": "NH1" <-> "NH2" Residue "W ARG 47": "NH1" <-> "NH2" Residue "W ARG 119": "NH1" <-> "NH2" Residue "X PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 590": "NH1" <-> "NH2" Residue "Y TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 113": "NH1" <-> "NH2" Residue "Z ARG 192": "NH1" <-> "NH2" Residue "Z ARG 285": "NH1" <-> "NH2" Residue "Z ARG 816": "NH1" <-> "NH2" Residue "Z ARG 819": "NH1" <-> "NH2" Residue "Z ARG 854": "NH1" <-> "NH2" Residue "Z ARG 856": "NH1" <-> "NH2" Residue "Z ARG 858": "NH1" <-> "NH2" Residue "Z ARG 959": "NH1" <-> "NH2" Residue "Z ARG 964": "NH1" <-> "NH2" Residue "Z ARG 974": "NH1" <-> "NH2" Residue "Z ARG 1049": "NH1" <-> "NH2" Residue "a ARG 3": "NH1" <-> "NH2" Residue "a ARG 28": "NH1" <-> "NH2" Residue "a ARG 108": "NH1" <-> "NH2" Residue "a ARG 119": "NH1" <-> "NH2" Residue "a ARG 174": "NH1" <-> "NH2" Residue "b ARG 7": "NH1" <-> "NH2" Residue "b ARG 15": "NH1" <-> "NH2" Residue "b ARG 16": "NH1" <-> "NH2" Residue "b ARG 29": "NH1" <-> "NH2" Residue "b ARG 62": "NH1" <-> "NH2" Residue "b ARG 108": "NH1" <-> "NH2" Residue "b ARG 119": "NH1" <-> "NH2" Residue "b ARG 135": "NH1" <-> "NH2" Residue "b ARG 146": "NH1" <-> "NH2" Residue "c ARG 488": "NH1" <-> "NH2" Residue "c ARG 613": "NH1" <-> "NH2" Residue "c ARG 716": "NH1" <-> "NH2" Residue "c ARG 717": "NH1" <-> "NH2" Residue "c ARG 719": "NH1" <-> "NH2" Residue "c ARG 725": "NH1" <-> "NH2" Residue "d ARG 22": "NH1" <-> "NH2" Residue "d ARG 105": "NH1" <-> "NH2" Residue "d ARG 178": "NH1" <-> "NH2" Residue "d ARG 228": "NH1" <-> "NH2" Residue "d ARG 325": "NH1" <-> "NH2" Residue "d ARG 354": "NH1" <-> "NH2" Residue "d ARG 367": "NH1" <-> "NH2" Residue "d ARG 369": "NH1" <-> "NH2" Residue "d ARG 381": "NH1" <-> "NH2" Residue "d ARG 389": "NH1" <-> "NH2" Residue "d ARG 390": "NH1" <-> "NH2" Residue "d ARG 423": "NH1" <-> "NH2" Residue "d ARG 433": "NH1" <-> "NH2" Residue "g PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 127": "NH1" <-> "NH2" Residue "k ARG 154": "NH1" <-> "NH2" Residue "k ARG 176": "NH1" <-> "NH2" Residue "k ARG 189": "NH1" <-> "NH2" Residue "n ARG 41": "NH1" <-> "NH2" Residue "n ARG 52": "NH1" <-> "NH2" Residue "n ARG 68": "NH1" <-> "NH2" Residue "n ARG 70": "NH1" <-> "NH2" Residue "n ARG 99": "NH1" <-> "NH2" Residue "n ARG 130": "NH1" <-> "NH2" Residue "n ARG 206": "NH1" <-> "NH2" Residue "n ARG 212": "NH1" <-> "NH2" Residue "o ARG 87": "NH1" <-> "NH2" Residue "p ARG 16": "NH1" <-> "NH2" Residue "r ARG 52": "NH1" <-> "NH2" Residue "r ARG 55": "NH1" <-> "NH2" Residue "r ARG 76": "NH1" <-> "NH2" Residue "r ARG 105": "NH1" <-> "NH2" Residue "r ARG 128": "NH1" <-> "NH2" Residue "r ARG 130": "NH1" <-> "NH2" Residue "r ARG 133": "NH1" <-> "NH2" Residue "r ARG 171": "NH1" <-> "NH2" Residue "t ARG 31": "NH1" <-> "NH2" Residue "t ARG 49": "NH1" <-> "NH2" Residue "u ARG 21": "NH1" <-> "NH2" Residue "u ARG 114": "NH1" <-> "NH2" Residue "u ARG 123": "NH1" <-> "NH2" Residue "v ARG 31": "NH1" <-> "NH2" Residue "v ARG 37": "NH1" <-> "NH2" Residue "v ARG 74": "NH1" <-> "NH2" Residue "v ARG 79": "NH1" <-> "NH2" Residue "v ARG 121": "NH1" <-> "NH2" Residue "v ARG 146": "NH1" <-> "NH2" Residue "v ARG 150": "NH1" <-> "NH2" Residue "x ARG 69": "NH1" <-> "NH2" Residue "z ARG 15": "NH1" <-> "NH2" Residue "z ARG 19": "NH1" <-> "NH2" Residue "z ARG 23": "NH1" <-> "NH2" Residue "z ARG 43": "NH1" <-> "NH2" Residue "z ARG 50": "NH1" <-> "NH2" Residue "0 ARG 194": "NH1" <-> "NH2" Time to flip residues: 0.20s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 135120 Number of models: 1 Model: "" Number of chains: 56 Chain: "A" Number of atoms: 6242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 827, 6242 Classifications: {'peptide': 827} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 31, 'TRANS': 795} Chain breaks: 1 Unresolved non-hydrogen bonds: 268 Unresolved non-hydrogen angles: 342 Unresolved non-hydrogen dihedrals: 194 Planarities with less than four sites: {'GLU:plan': 28, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 43} Unresolved non-hydrogen planarities: 254 Chain: "B" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 537 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'TRANS': 68} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 11, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "C" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 588 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 70} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 2170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2170 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 7, 'TRANS': 284} Chain breaks: 5 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 52 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 16} Unresolved non-hydrogen planarities: 75 Chain: "E" Number of atoms: 2591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2591 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 15, 'TRANS': 315} Chain breaks: 2 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 70 Planarities with less than four sites: {'GLU:plan': 16, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 97 Chain: "F" Number of atoms: 3282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3282 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 17, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 145 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 24, 'ASP:plan': 14} Unresolved non-hydrogen planarities: 138 Chain: "G" Number of atoms: 2772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2772 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 17, 'TRANS': 345} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 56 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 12} Unresolved non-hydrogen planarities: 68 Chain: "H" Number of atoms: 1456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1456 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 2, 'TRANS': 187} Chain breaks: 1 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 54 Planarities with less than four sites: {'GLU:plan': 14, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 74 Chain: "I" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1230 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 9, 'TRANS': 145} Chain: "J" Number of atoms: 1201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1201 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 145} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "K" Number of atoms: 1139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1139 Classifications: {'peptide': 147} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 137} Chain breaks: 1 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 63 Chain: "L" Number of atoms: 2070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2070 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 16, 'TRANS': 263} Chain breaks: 3 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 53 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 68 Chain: "M" Number of atoms: 2134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2134 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 14, 'TRANS': 269} Chain breaks: 8 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 50 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 12} Unresolved non-hydrogen planarities: 64 Chain: "N" Number of atoms: 3435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3435 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 421} Chain breaks: 4 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 52 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 14} Unresolved non-hydrogen planarities: 74 Chain: "O" Number of atoms: 6446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 864, 6446 Classifications: {'peptide': 864} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 818} Chain breaks: 6 Unresolved non-hydrogen bonds: 263 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 187 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 27, 'ARG:plan': 2, 'ASP:plan': 45} Unresolved non-hydrogen planarities: 261 Chain: "P" Number of atoms: 1460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1460 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 180} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 53 Planarities with less than four sites: {'GLU:plan': 10, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 60 Chain: "Q" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 905 Classifications: {'peptide': 182} Incomplete info: {'truncation_to_alanine': 161} Link IDs: {'PTRANS': 12, 'TRANS': 169} Chain breaks: 4 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 602 Unresolved non-hydrogen angles: 771 Unresolved non-hydrogen dihedrals: 509 Unresolved non-hydrogen chiralities: 60 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 7, 'TYR:plan': 5, 'ASN:plan1': 7, 'TRP:plan': 3, 'HIS:plan': 7, 'PHE:plan': 7, 'GLU:plan': 9, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 291 Chain: "R" Number of atoms: 1778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1778 Classifications: {'peptide': 242} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 14, 'TRANS': 227} Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 62 Planarities with less than four sites: {'GLU:plan': 14, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 86 Chain: "S" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1816 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 15, 'TRANS': 221} Chain: "T" Number of atoms: 2866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2866 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 11, 'TRANS': 375} Chain breaks: 1 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 85 Planarities with less than four sites: {'GLU:plan': 17, 'ASP:plan': 17} Unresolved non-hydrogen planarities: 119 Chain: "U" Number of atoms: 3035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3035 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 18, 'TRANS': 386} Chain breaks: 3 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 60 Planarities with less than four sites: {'GLU:plan': 14, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 83 Chain: "V" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 879 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 6, 'TRANS': 114} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 40 Chain: "W" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 864 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 6, 'TRANS': 113} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 48 Chain: "X" Number of atoms: 2686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2686 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 334} Chain breaks: 4 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 46 Chain: "Y" Number of atoms: 2594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2594 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 326} Chain breaks: 5 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Z" Number of atoms: 4848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 4848 Classifications: {'peptide': 639} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 102} Link IDs: {'PTRANS': 42, 'TRANS': 596} Chain breaks: 5 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 395 Unresolved non-hydrogen angles: 498 Unresolved non-hydrogen dihedrals: 313 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 23, 'GLU:plan': 36, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 304 Chain: "a" Number of atoms: 1434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1434 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 5, 'TRANS': 173} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 62 Chain: "b" Number of atoms: 2279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2279 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 274} Chain breaks: 1 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 9, 'ASN:plan1': 1, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 79 Chain: "c" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1387 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 7, 'TRANS': 167} Chain breaks: 2 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 43 Chain: "d" Number of atoms: 3436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3436 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 15, 'TRANS': 423} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 54 Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 12} Unresolved non-hydrogen planarities: 76 Chain: "e" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1683 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 201} Chain breaks: 1 Chain: "f" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1683 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 201} Chain breaks: 1 Chain: "g" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1393 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 6, 'TRANS': 167} Chain: "h" Number of atoms: 1288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1288 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 160} Chain breaks: 1 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: "i" Number of atoms: 3254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 3254 Classifications: {'peptide': 659} Incomplete info: {'truncation_to_alanine': 564} Link IDs: {'PTRANS': 32, 'TRANS': 626} Chain breaks: 7 Unresolved chain link angles: 32 Unresolved non-hydrogen bonds: 2007 Unresolved non-hydrogen angles: 2582 Unresolved non-hydrogen dihedrals: 1655 Unresolved non-hydrogen chiralities: 214 Planarities with less than four sites: {'GLN:plan1': 31, 'ASP:plan': 36, 'TYR:plan': 24, 'ASN:plan1': 19, 'TRP:plan': 5, 'HIS:plan': 15, 'PHE:plan': 27, 'GLU:plan': 32, 'ARG:plan': 30} Unresolved non-hydrogen planarities: 1017 Chain: "j" Number of atoms: 3342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 677, 3342 Classifications: {'peptide': 677} Incomplete info: {'truncation_to_alanine': 579} Link IDs: {'PTRANS': 33, 'TRANS': 643} Chain breaks: 6 Unresolved chain link angles: 33 Unresolved non-hydrogen bonds: 2052 Unresolved non-hydrogen angles: 2636 Unresolved non-hydrogen dihedrals: 1692 Unresolved non-hydrogen chiralities: 218 Planarities with less than four sites: {'GLN:plan1': 34, 'ASP:plan': 36, 'TYR:plan': 24, 'ASN:plan1': 19, 'TRP:plan': 5, 'HIS:plan': 15, 'PHE:plan': 27, 'GLU:plan': 32, 'ARG:plan': 31} Unresolved non-hydrogen planarities: 1034 Chain: "k" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 930 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 3, 'TRANS': 113} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 29 Chain: "l" Number of atoms: 1735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1735 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 7, 'TRANS': 206} Chain: "m" Number of atoms: 2057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2057 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 12, 'TRANS': 245} Chain: "n" Number of atoms: 1447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1447 Classifications: {'peptide': 192} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain breaks: 1 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 52 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 64 Chain: "o" Number of atoms: 1911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1911 Classifications: {'peptide': 237} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 221} Chain: "p" Number of atoms: 1279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1279 Classifications: {'peptide': 159} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 151} Chain breaks: 1 Chain: "q" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1622 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 193} Chain: "r" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1242 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 4, 'TRANS': 154} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 1, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 58 Chain: "s" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 416 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 48} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "t" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 791 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 5, 'TRANS': 109} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 40 Chain: "u" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 943 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 120} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 35 Chain: "v" Number of atoms: 1286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1286 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 148} Chain: "w" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 985 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "x" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 684 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 32 Chain: "y" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 752 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 5, 'TRANS': 87} Chain: "z" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 455 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 58} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "0" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 694 Classifications: {'peptide': 92} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 89} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 7} Unresolved non-hydrogen planarities: 28 Chain: "1" Number of atoms: 28796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1350, 28796 Inner-chain residues flagged as termini: ['pdbres=" U 11729 "'] Classifications: {'RNA': 1350} Modifications used: {'5*END': 2, 'rna2p_pur': 103, 'rna2p_pyr': 100, 'rna3p_pur': 598, 'rna3p_pyr': 549} Link IDs: {'rna2p': 203, 'rna3p': 1146} Chain breaks: 29 Chain: "2" Number of atoms: 4891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 4891 Classifications: {'RNA': 230} Modifications used: {'rna2p_pur': 27, 'rna2p_pyr': 21, 'rna3p_pur': 85, 'rna3p_pyr': 97} Link IDs: {'rna2p': 48, 'rna3p': 181} Chain breaks: 3 Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 38070 SG CYS P 94 163.749 137.683 198.657 1.00 47.94 S ATOM 38300 SG CYS P 123 166.997 136.231 198.775 1.00 55.12 S ATOM 38374 SG CYS P 133 163.174 133.801 198.206 1.00 46.20 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N HIS f 243 " occ=0.56 ... (8 atoms not shown) pdb=" NE2 HIS f 243 " occ=0.56 Time building chain proxies: 52.18, per 1000 atoms: 0.39 Number of scatterers: 135120 At special positions: 0 Unit cell: (272.084, 259.076, 355.552, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 357 16.00 P 1578 15.00 O 28657 8.00 N 25059 7.00 C 79468 6.00 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=0, symmetry=0 Time building additional restraints: 45.25 Conformation dependent library (CDL) restraints added in 14.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN P 200 " pdb="ZN ZN P 200 " - pdb=" NE2 HIS P 125 " pdb="ZN ZN P 200 " - pdb=" SG CYS P 133 " pdb="ZN ZN P 200 " - pdb=" SG CYS P 123 " pdb="ZN ZN P 200 " - pdb=" SG CYS P 94 " Number of angles added : 3 26978 Ramachandran restraints generated. 13489 Oldfield, 0 Emsley, 13489 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 25736 Finding SS restraints... Secondary structure from input PDB file: 416 helices and 152 sheets defined 36.2% alpha, 17.7% beta 497 base pairs and 818 stacking pairs defined. Time for finding SS restraints: 38.31 Creating SS restraints... Processing helix chain 'A' and resid 647 through 652 Processing helix chain 'A' and resid 716 through 726 Processing helix chain 'A' and resid 729 through 741 Processing helix chain 'A' and resid 742 through 751 Processing helix chain 'A' and resid 757 through 764 Processing helix chain 'A' and resid 769 through 784 Processing helix chain 'A' and resid 786 through 801 Processing helix chain 'A' and resid 801 through 809 Processing helix chain 'A' and resid 814 through 823 Processing helix chain 'A' and resid 830 through 847 Processing helix chain 'B' and resid 837 through 903 Processing helix chain 'C' and resid 580 through 585 Processing helix chain 'C' and resid 594 through 599 removed outlier: 4.002A pdb=" N ASN C 599 " --> pdb=" O LYS C 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 619 removed outlier: 3.667A pdb=" N GLU C 610 " --> pdb=" O LYS C 606 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU C 615 " --> pdb=" O LYS C 611 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG C 616 " --> pdb=" O GLN C 612 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER C 617 " --> pdb=" O LYS C 613 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 25 Proline residue: E 17 - end of helix Processing helix chain 'E' and resid 29 through 49 Processing helix chain 'E' and resid 53 through 78 Processing helix chain 'E' and resid 85 through 103 Processing helix chain 'E' and resid 106 through 120 Processing helix chain 'E' and resid 122 through 137 Processing helix chain 'E' and resid 140 through 155 Processing helix chain 'E' and resid 156 through 171 Processing helix chain 'E' and resid 175 through 196 Processing helix chain 'E' and resid 277 through 287 Processing helix chain 'E' and resid 293 through 305 Processing helix chain 'E' and resid 312 through 328 Processing helix chain 'E' and resid 331 through 341 Processing helix chain 'E' and resid 342 through 344 No H-bonds generated for 'chain 'E' and resid 342 through 344' Processing helix chain 'E' and resid 351 through 369 removed outlier: 3.961A pdb=" N GLN E 369 " --> pdb=" O LYS E 365 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 386 Processing helix chain 'E' and resid 395 through 409 Processing helix chain 'F' and resid 37 through 52 Processing helix chain 'F' and resid 67 through 89 Processing helix chain 'F' and resid 113 through 121 Processing helix chain 'F' and resid 122 through 127 Processing helix chain 'F' and resid 438 through 452 Processing helix chain 'F' and resid 455 through 459 removed outlier: 3.962A pdb=" N ILE F 459 " --> pdb=" O PRO F 456 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 16 Processing helix chain 'G' and resid 21 through 30 Processing helix chain 'G' and resid 36 through 42 removed outlier: 4.488A pdb=" N SER G 42 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 63 Processing helix chain 'G' and resid 66 through 72 Processing helix chain 'G' and resid 75 through 80 removed outlier: 4.024A pdb=" N GLN G 79 " --> pdb=" O ALA G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 106 Processing helix chain 'G' and resid 111 through 124 Processing helix chain 'G' and resid 126 through 131 Processing helix chain 'G' and resid 131 through 140 Processing helix chain 'G' and resid 141 through 143 No H-bonds generated for 'chain 'G' and resid 141 through 143' Processing helix chain 'G' and resid 146 through 155 Processing helix chain 'G' and resid 163 through 166 removed outlier: 4.248A pdb=" N PHE G 166 " --> pdb=" O GLU G 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 163 through 166' Processing helix chain 'G' and resid 167 through 173 Processing helix chain 'G' and resid 178 through 189 Processing helix chain 'G' and resid 189 through 205 removed outlier: 3.531A pdb=" N LEU G 193 " --> pdb=" O ARG G 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 233 Processing helix chain 'G' and resid 236 through 259 Proline residue: G 253 - end of helix Processing helix chain 'G' and resid 264 through 282 Processing helix chain 'G' and resid 285 through 299 Processing helix chain 'G' and resid 304 through 319 removed outlier: 3.763A pdb=" N VAL G 310 " --> pdb=" O ARG G 306 " (cutoff:3.500A) Processing helix chain 'G' and resid 326 through 334 Processing helix chain 'G' and resid 337 through 347 Processing helix chain 'G' and resid 351 through 364 Processing helix chain 'H' and resid 21 through 25 removed outlier: 3.520A pdb=" N ARG H 24 " --> pdb=" O GLU H 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 57 Processing helix chain 'H' and resid 64 through 69 Processing helix chain 'H' and resid 79 through 83 removed outlier: 3.514A pdb=" N GLY H 82 " --> pdb=" O ARG H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 134 Processing helix chain 'H' and resid 216 through 247 Processing helix chain 'I' and resid 778 through 806 Processing helix chain 'I' and resid 825 through 836 Processing helix chain 'I' and resid 841 through 848 Processing helix chain 'I' and resid 853 through 868 removed outlier: 3.672A pdb=" N LEU I 857 " --> pdb=" O THR I 853 " (cutoff:3.500A) Processing helix chain 'I' and resid 870 through 885 Processing helix chain 'I' and resid 885 through 892 Processing helix chain 'I' and resid 893 through 931 Processing helix chain 'J' and resid 732 through 751 removed outlier: 4.139A pdb=" N ASN J 747 " --> pdb=" O GLN J 743 " (cutoff:3.500A) Processing helix chain 'J' and resid 754 through 765 Processing helix chain 'J' and resid 767 through 779 Processing helix chain 'J' and resid 791 through 800 removed outlier: 4.242A pdb=" N ASP J 795 " --> pdb=" O LEU J 791 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ASP J 796 " --> pdb=" O LYS J 792 " (cutoff:3.500A) Processing helix chain 'J' and resid 802 through 817 Processing helix chain 'J' and resid 826 through 837 Processing helix chain 'J' and resid 856 through 889 removed outlier: 4.717A pdb=" N LEU J 883 " --> pdb=" O ASP J 879 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N VAL J 884 " --> pdb=" O GLU J 880 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ARG J 889 " --> pdb=" O GLU J 885 " (cutoff:3.500A) Processing helix chain 'K' and resid 306 through 322 Processing helix chain 'K' and resid 323 through 331 removed outlier: 4.714A pdb=" N THR K 329 " --> pdb=" O ARG K 325 " (cutoff:3.500A) Processing helix chain 'K' and resid 331 through 336 removed outlier: 3.740A pdb=" N ARG K 335 " --> pdb=" O LYS K 331 " (cutoff:3.500A) Processing helix chain 'K' and resid 367 through 379 Processing helix chain 'K' and resid 893 through 900 Processing helix chain 'K' and resid 911 through 920 Processing helix chain 'M' and resid 922 through 930 removed outlier: 4.249A pdb=" N LEU M 926 " --> pdb=" O ALA M 922 " (cutoff:3.500A) Processing helix chain 'M' and resid 940 through 952 Processing helix chain 'N' and resid 49 through 59 Processing helix chain 'N' and resid 62 through 71 Processing helix chain 'N' and resid 139 through 143 removed outlier: 3.757A pdb=" N GLU N 142 " --> pdb=" O SER N 139 " (cutoff:3.500A) Processing helix chain 'N' and resid 151 through 155 Processing helix chain 'N' and resid 167 through 183 Processing helix chain 'N' and resid 228 through 235 Processing helix chain 'N' and resid 474 through 478 removed outlier: 3.629A pdb=" N GLY N 478 " --> pdb=" O ALA N 475 " (cutoff:3.500A) Processing helix chain 'N' and resid 498 through 501 removed outlier: 3.937A pdb=" N ILE N 501 " --> pdb=" O ASN N 498 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 498 through 501' Processing helix chain 'O' and resid 110 through 114 removed outlier: 3.826A pdb=" N GLY O 114 " --> pdb=" O PRO O 111 " (cutoff:3.500A) Processing helix chain 'O' and resid 424 through 428 removed outlier: 3.534A pdb=" N GLN O 427 " --> pdb=" O ARG O 424 " (cutoff:3.500A) Processing helix chain 'O' and resid 435 through 443 Processing helix chain 'O' and resid 444 through 447 Processing helix chain 'O' and resid 456 through 461 Processing helix chain 'O' and resid 500 through 506 Processing helix chain 'O' and resid 779 through 783 Processing helix chain 'O' and resid 847 through 856 removed outlier: 5.237A pdb=" N THR O 853 " --> pdb=" O SER O 849 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU O 854 " --> pdb=" O ARG O 850 " (cutoff:3.500A) Processing helix chain 'O' and resid 859 through 864 Processing helix chain 'O' and resid 926 through 934 Processing helix chain 'O' and resid 937 through 945 Processing helix chain 'O' and resid 948 through 957 Processing helix chain 'O' and resid 970 through 985 Processing helix chain 'O' and resid 987 through 1002 Processing helix chain 'O' and resid 1002 through 1009 removed outlier: 3.638A pdb=" N ILE O1006 " --> pdb=" O HIS O1002 " (cutoff:3.500A) Processing helix chain 'O' and resid 1012 through 1045 Processing helix chain 'P' and resid 16 through 32 Processing helix chain 'P' and resid 61 through 71 Processing helix chain 'P' and resid 74 through 84 Processing helix chain 'P' and resid 93 through 102 Processing helix chain 'P' and resid 103 through 105 No H-bonds generated for 'chain 'P' and resid 103 through 105' Processing helix chain 'P' and resid 106 through 114 Processing helix chain 'P' and resid 129 through 142 Processing helix chain 'P' and resid 150 through 157 Processing helix chain 'Q' and resid 19 through 34 Processing helix chain 'Q' and resid 132 through 139 removed outlier: 3.974A pdb=" N LYS Q 136 " --> pdb=" O HIS Q 132 " (cutoff:3.500A) Processing helix chain 'Q' and resid 139 through 144 Processing helix chain 'Q' and resid 145 through 150 Processing helix chain 'Q' and resid 156 through 163 Processing helix chain 'Q' and resid 251 through 270 Processing helix chain 'R' and resid 135 through 142 Processing helix chain 'R' and resid 164 through 175 Processing helix chain 'R' and resid 186 through 200 Processing helix chain 'R' and resid 212 through 216 Processing helix chain 'R' and resid 234 through 246 Processing helix chain 'R' and resid 259 through 263 Processing helix chain 'R' and resid 267 through 281 Processing helix chain 'S' and resid 135 through 142 Processing helix chain 'S' and resid 164 through 175 Processing helix chain 'S' and resid 186 through 200 Processing helix chain 'S' and resid 212 through 216 Processing helix chain 'S' and resid 234 through 246 Processing helix chain 'S' and resid 259 through 263 Processing helix chain 'S' and resid 267 through 281 Processing helix chain 'T' and resid 31 through 38 Processing helix chain 'T' and resid 40 through 45 Processing helix chain 'T' and resid 58 through 70 Processing helix chain 'T' and resid 75 through 86 Processing helix chain 'T' and resid 102 through 113 Processing helix chain 'T' and resid 124 through 132 Processing helix chain 'T' and resid 133 through 143 removed outlier: 5.676A pdb=" N ASN T 139 " --> pdb=" O ARG T 135 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LYS T 140 " --> pdb=" O THR T 136 " (cutoff:3.500A) Processing helix chain 'T' and resid 150 through 167 Processing helix chain 'T' and resid 174 through 206 removed outlier: 4.022A pdb=" N ILE T 178 " --> pdb=" O ASP T 174 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN T 179 " --> pdb=" O ASN T 175 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLY T 180 " --> pdb=" O HIS T 176 " (cutoff:3.500A) Processing helix chain 'T' and resid 208 through 213 Processing helix chain 'T' and resid 215 through 226 Processing helix chain 'T' and resid 239 through 244 Processing helix chain 'T' and resid 250 through 260 Processing helix chain 'T' and resid 267 through 303 Processing helix chain 'T' and resid 303 through 311 removed outlier: 4.062A pdb=" N GLN T 307 " --> pdb=" O ALA T 303 " (cutoff:3.500A) Processing helix chain 'T' and resid 311 through 323 Processing helix chain 'T' and resid 324 through 331 Processing helix chain 'T' and resid 332 through 339 Processing helix chain 'T' and resid 373 through 395 Processing helix chain 'T' and resid 401 through 420 Processing helix chain 'U' and resid 58 through 64 Processing helix chain 'U' and resid 70 through 77 Processing helix chain 'U' and resid 92 through 99 Processing helix chain 'U' and resid 115 through 124 removed outlier: 4.732A pdb=" N PHE U 119 " --> pdb=" O THR U 115 " (cutoff:3.500A) Processing helix chain 'U' and resid 138 through 157 removed outlier: 4.308A pdb=" N HIS U 152 " --> pdb=" O SER U 148 " (cutoff:3.500A) Processing helix chain 'U' and resid 162 through 192 Processing helix chain 'U' and resid 195 through 201 removed outlier: 4.176A pdb=" N LYS U 199 " --> pdb=" O PRO U 195 " (cutoff:3.500A) Processing helix chain 'U' and resid 203 through 213 Processing helix chain 'U' and resid 233 through 244 Processing helix chain 'U' and resid 250 through 286 Processing helix chain 'U' and resid 286 through 291 Processing helix chain 'U' and resid 294 through 306 Processing helix chain 'U' and resid 307 through 313 Processing helix chain 'U' and resid 315 through 321 Processing helix chain 'U' and resid 324 through 335 Processing helix chain 'U' and resid 342 through 347 removed outlier: 3.785A pdb=" N TYR U 345 " --> pdb=" O GLY U 342 " (cutoff:3.500A) Processing helix chain 'U' and resid 355 through 379 removed outlier: 4.376A pdb=" N GLY U 359 " --> pdb=" O GLY U 355 " (cutoff:3.500A) Processing helix chain 'U' and resid 393 through 410 Processing helix chain 'V' and resid 16 through 31 Processing helix chain 'V' and resid 37 through 47 Processing helix chain 'V' and resid 61 through 65 Processing helix chain 'V' and resid 67 through 76 removed outlier: 3.907A pdb=" N ILE V 71 " --> pdb=" O HIS V 67 " (cutoff:3.500A) Processing helix chain 'V' and resid 84 through 93 Processing helix chain 'V' and resid 109 through 126 Processing helix chain 'W' and resid 16 through 31 Processing helix chain 'W' and resid 37 through 47 Processing helix chain 'W' and resid 61 through 65 Processing helix chain 'W' and resid 67 through 76 removed outlier: 3.907A pdb=" N ILE W 71 " --> pdb=" O HIS W 67 " (cutoff:3.500A) Processing helix chain 'W' and resid 84 through 93 Processing helix chain 'W' and resid 109 through 126 Processing helix chain 'X' and resid 157 through 161 removed outlier: 3.673A pdb=" N LYS X 160 " --> pdb=" O ALA X 157 " (cutoff:3.500A) Processing helix chain 'Y' and resid 16 through 28 Processing helix chain 'Y' and resid 47 through 60 Processing helix chain 'Y' and resid 110 through 115 Processing helix chain 'Y' and resid 120 through 124 removed outlier: 3.912A pdb=" N SER Y 124 " --> pdb=" O ALA Y 121 " (cutoff:3.500A) Processing helix chain 'Y' and resid 149 through 157 Processing helix chain 'Y' and resid 157 through 162 removed outlier: 4.370A pdb=" N TYR Y 161 " --> pdb=" O VAL Y 157 " (cutoff:3.500A) Processing helix chain 'Y' and resid 167 through 169 No H-bonds generated for 'chain 'Y' and resid 167 through 169' Processing helix chain 'Y' and resid 228 through 244 removed outlier: 4.256A pdb=" N ASN Y 232 " --> pdb=" O ALA Y 228 " (cutoff:3.500A) Processing helix chain 'Y' and resid 306 through 324 Processing helix chain 'Y' and resid 331 through 340 removed outlier: 4.023A pdb=" N VAL Y 335 " --> pdb=" O SER Y 331 " (cutoff:3.500A) Processing helix chain 'Y' and resid 357 through 372 Processing helix chain 'Z' and resid 78 through 93 Processing helix chain 'Z' and resid 122 through 133 Processing helix chain 'Z' and resid 147 through 161 removed outlier: 3.985A pdb=" N MET Z 151 " --> pdb=" O GLU Z 147 " (cutoff:3.500A) Processing helix chain 'Z' and resid 178 through 197 Processing helix chain 'Z' and resid 216 through 224 Processing helix chain 'Z' and resid 236 through 241 Processing helix chain 'Z' and resid 254 through 261 Processing helix chain 'Z' and resid 544 through 548 removed outlier: 3.585A pdb=" N TYR Z 547 " --> pdb=" O ARG Z 544 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP Z 548 " --> pdb=" O LEU Z 545 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 544 through 548' Processing helix chain 'Z' and resid 552 through 561 Processing helix chain 'Z' and resid 603 through 610 Processing helix chain 'Z' and resid 615 through 620 Processing helix chain 'Z' and resid 785 through 791 Processing helix chain 'Z' and resid 805 through 808 Processing helix chain 'Z' and resid 851 through 855 removed outlier: 3.950A pdb=" N THR Z 855 " --> pdb=" O ASP Z 852 " (cutoff:3.500A) Processing helix chain 'Z' and resid 940 through 947 Processing helix chain 'Z' and resid 1051 through 1058 Processing helix chain 'Z' and resid 1059 through 1063 Processing helix chain 'Z' and resid 1074 through 1079 Processing helix chain 'Z' and resid 1084 through 1149 Processing helix chain 'a' and resid 6 through 12 Processing helix chain 'a' and resid 24 through 26 No H-bonds generated for 'chain 'a' and resid 24 through 26' Processing helix chain 'a' and resid 27 through 36 Processing helix chain 'a' and resid 40 through 62 Processing helix chain 'a' and resid 68 through 86 removed outlier: 4.486A pdb=" N THR a 76 " --> pdb=" O ARG a 72 " (cutoff:3.500A) Processing helix chain 'a' and resid 94 through 101 removed outlier: 4.054A pdb=" N VAL a 101 " --> pdb=" O VAL a 97 " (cutoff:3.500A) Processing helix chain 'a' and resid 102 through 110 Processing helix chain 'a' and resid 110 through 118 Processing helix chain 'a' and resid 123 through 134 Processing helix chain 'a' and resid 164 through 174 Processing helix chain 'b' and resid 2 through 22 Processing helix chain 'b' and resid 22 through 38 Processing helix chain 'b' and resid 43 through 49 Processing helix chain 'b' and resid 49 through 59 removed outlier: 3.623A pdb=" N ARG b 53 " --> pdb=" O ASP b 49 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS b 54 " --> pdb=" O LYS b 50 " (cutoff:3.500A) Processing helix chain 'b' and resid 60 through 69 Processing helix chain 'b' and resid 97 through 109 Processing helix chain 'b' and resid 123 through 134 Processing helix chain 'b' and resid 198 through 210 Processing helix chain 'c' and resid 477 through 496 Processing helix chain 'c' and resid 534 through 551 Processing helix chain 'c' and resid 609 through 634 Processing helix chain 'c' and resid 678 through 683 Processing helix chain 'c' and resid 709 through 727 Processing helix chain 'd' and resid 9 through 13 removed outlier: 3.697A pdb=" N ALA d 12 " --> pdb=" O SER d 9 " (cutoff:3.500A) Processing helix chain 'd' and resid 34 through 53 Processing helix chain 'd' and resid 365 through 383 Processing helix chain 'd' and resid 385 through 394 Processing helix chain 'd' and resid 398 through 425 Processing helix chain 'e' and resid 73 through 80 Processing helix chain 'e' and resid 89 through 101 Processing helix chain 'e' and resid 102 through 108 Processing helix chain 'e' and resid 133 through 148 Processing helix chain 'e' and resid 166 through 170 removed outlier: 3.846A pdb=" N ASP e 169 " --> pdb=" O PRO e 166 " (cutoff:3.500A) Processing helix chain 'e' and resid 188 through 195 Processing helix chain 'e' and resid 213 through 217 removed outlier: 3.970A pdb=" N PHE e 216 " --> pdb=" O PRO e 213 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA e 217 " --> pdb=" O ASP e 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 213 through 217' Processing helix chain 'e' and resid 233 through 250 Processing helix chain 'f' and resid 73 through 80 Processing helix chain 'f' and resid 89 through 101 Processing helix chain 'f' and resid 102 through 108 Processing helix chain 'f' and resid 133 through 148 Processing helix chain 'f' and resid 166 through 170 removed outlier: 3.847A pdb=" N ASP f 169 " --> pdb=" O PRO f 166 " (cutoff:3.500A) Processing helix chain 'f' and resid 188 through 195 Processing helix chain 'f' and resid 213 through 217 removed outlier: 3.970A pdb=" N PHE f 216 " --> pdb=" O PRO f 213 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA f 217 " --> pdb=" O ASP f 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 213 through 217' Processing helix chain 'f' and resid 233 through 250 Processing helix chain 'g' and resid 47 through 53 Processing helix chain 'g' and resid 54 through 64 Processing helix chain 'g' and resid 90 through 104 Processing helix chain 'g' and resid 107 through 112 Processing helix chain 'g' and resid 113 through 116 removed outlier: 3.939A pdb=" N GLU g 116 " --> pdb=" O LYS g 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 113 through 116' Processing helix chain 'g' and resid 132 through 145 Processing helix chain 'g' and resid 148 through 159 Processing helix chain 'g' and resid 174 through 190 Processing helix chain 'g' and resid 193 through 207 Processing helix chain 'h' and resid 91 through 97 Processing helix chain 'h' and resid 105 through 109 Processing helix chain 'h' and resid 132 through 148 Processing helix chain 'h' and resid 155 through 161 Processing helix chain 'h' and resid 182 through 192 Processing helix chain 'h' and resid 195 through 205 Processing helix chain 'h' and resid 221 through 237 Processing helix chain 'h' and resid 240 through 250 Processing helix chain 'i' and resid 11 through 18 Processing helix chain 'i' and resid 38 through 47 Processing helix chain 'i' and resid 132 through 141 Processing helix chain 'i' and resid 155 through 161 Processing helix chain 'i' and resid 168 through 174 removed outlier: 3.887A pdb=" N TYR i 173 " --> pdb=" O HIS i 170 " (cutoff:3.500A) Processing helix chain 'i' and resid 182 through 194 Processing helix chain 'i' and resid 264 through 270 Processing helix chain 'i' and resid 290 through 302 Processing helix chain 'i' and resid 320 through 325 Processing helix chain 'i' and resid 395 through 403 Processing helix chain 'i' and resid 421 through 431 Processing helix chain 'i' and resid 484 through 495 Processing helix chain 'i' and resid 523 through 527 removed outlier: 3.945A pdb=" N PHE i 527 " --> pdb=" O ASP i 524 " (cutoff:3.500A) Processing helix chain 'i' and resid 533 through 545 Processing helix chain 'i' and resid 552 through 561 Processing helix chain 'i' and resid 614 through 620 Processing helix chain 'i' and resid 625 through 630 Processing helix chain 'i' and resid 648 through 660 Processing helix chain 'i' and resid 730 through 740 Processing helix chain 'i' and resid 770 through 785 Processing helix chain 'i' and resid 785 through 792 Processing helix chain 'i' and resid 835 through 846 Processing helix chain 'i' and resid 850 through 855 Processing helix chain 'i' and resid 859 through 867 Processing helix chain 'i' and resid 893 through 901 Processing helix chain 'i' and resid 906 through 924 Processing helix chain 'i' and resid 924 through 933 Processing helix chain 'j' and resid 11 through 18 Processing helix chain 'j' and resid 38 through 47 Processing helix chain 'j' and resid 132 through 141 Processing helix chain 'j' and resid 155 through 161 Processing helix chain 'j' and resid 168 through 174 removed outlier: 3.887A pdb=" N TYR j 173 " --> pdb=" O HIS j 170 " (cutoff:3.500A) Processing helix chain 'j' and resid 182 through 194 Processing helix chain 'j' and resid 264 through 270 Processing helix chain 'j' and resid 290 through 302 Processing helix chain 'j' and resid 320 through 325 Processing helix chain 'j' and resid 395 through 403 Processing helix chain 'j' and resid 421 through 431 Processing helix chain 'j' and resid 484 through 495 Processing helix chain 'j' and resid 523 through 527 removed outlier: 3.945A pdb=" N PHE j 527 " --> pdb=" O ASP j 524 " (cutoff:3.500A) Processing helix chain 'j' and resid 533 through 545 Processing helix chain 'j' and resid 552 through 561 Processing helix chain 'j' and resid 595 through 601 Processing helix chain 'j' and resid 614 through 620 Processing helix chain 'j' and resid 625 through 630 Processing helix chain 'j' and resid 648 through 660 Processing helix chain 'j' and resid 730 through 740 Processing helix chain 'j' and resid 770 through 785 Processing helix chain 'j' and resid 785 through 792 Processing helix chain 'j' and resid 835 through 846 Processing helix chain 'j' and resid 850 through 855 Processing helix chain 'j' and resid 859 through 867 Processing helix chain 'j' and resid 893 through 901 Processing helix chain 'j' and resid 906 through 924 Processing helix chain 'j' and resid 924 through 933 Processing helix chain 'k' and resid 99 through 111 Processing helix chain 'k' and resid 111 through 116 removed outlier: 3.565A pdb=" N VAL k 115 " --> pdb=" O MET k 111 " (cutoff:3.500A) Processing helix chain 'k' and resid 160 through 168 Processing helix chain 'k' and resid 170 through 186 Processing helix chain 'k' and resid 190 through 202 Processing helix chain 'l' and resid 106 through 113 Processing helix chain 'l' and resid 158 through 175 Processing helix chain 'l' and resid 180 through 189 Processing helix chain 'l' and resid 191 through 202 Processing helix chain 'l' and resid 224 through 232 removed outlier: 4.037A pdb=" N LEU l 228 " --> pdb=" O ASP l 224 " (cutoff:3.500A) Processing helix chain 'm' and resid 43 through 50 Processing helix chain 'm' and resid 57 through 66 Processing helix chain 'm' and resid 93 through 96 Processing helix chain 'm' and resid 115 through 121 Processing helix chain 'm' and resid 133 through 135 No H-bonds generated for 'chain 'm' and resid 133 through 135' Processing helix chain 'm' and resid 238 through 243 removed outlier: 3.563A pdb=" N LYS m 241 " --> pdb=" O PRO m 238 " (cutoff:3.500A) Processing helix chain 'm' and resid 246 through 258 Processing helix chain 'n' and resid 17 through 23 Processing helix chain 'n' and resid 30 through 32 No H-bonds generated for 'chain 'n' and resid 30 through 32' Processing helix chain 'n' and resid 42 through 47 removed outlier: 4.677A pdb=" N ASP n 47 " --> pdb=" O ILE n 43 " (cutoff:3.500A) Processing helix chain 'n' and resid 75 through 84 Processing helix chain 'n' and resid 94 through 113 Processing helix chain 'n' and resid 115 through 128 Processing helix chain 'n' and resid 150 through 170 Processing helix chain 'n' and resid 176 through 191 Processing helix chain 'n' and resid 195 through 212 Processing helix chain 'o' and resid 20 through 26 removed outlier: 4.444A pdb=" N HIS o 26 " --> pdb=" O ARG o 22 " (cutoff:3.500A) Processing helix chain 'o' and resid 137 through 146 Processing helix chain 'o' and resid 152 through 156 removed outlier: 3.825A pdb=" N LYS o 155 " --> pdb=" O ASP o 152 " (cutoff:3.500A) Processing helix chain 'o' and resid 183 through 226 Processing helix chain 'o' and resid 227 through 231 removed outlier: 3.662A pdb=" N ARG o 230 " --> pdb=" O ALA o 227 " (cutoff:3.500A) Processing helix chain 'o' and resid 232 through 236 removed outlier: 4.184A pdb=" N SER o 235 " --> pdb=" O ARG o 232 " (cutoff:3.500A) Processing helix chain 'p' and resid 22 through 32 Processing helix chain 'p' and resid 69 through 74 removed outlier: 3.749A pdb=" N LEU p 73 " --> pdb=" O VAL p 70 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLN p 74 " --> pdb=" O PRO p 71 " (cutoff:3.500A) Processing helix chain 'p' and resid 82 through 91 Processing helix chain 'p' and resid 129 through 140 Processing helix chain 'p' and resid 171 through 187 removed outlier: 4.988A pdb=" N ASP p 177 " --> pdb=" O ASP p 173 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N THR p 178 " --> pdb=" O TYR p 174 " (cutoff:3.500A) Processing helix chain 'q' and resid 87 through 93 Processing helix chain 'q' and resid 106 through 117 Processing helix chain 'q' and resid 139 through 152 removed outlier: 4.442A pdb=" N ALA q 152 " --> pdb=" O ALA q 148 " (cutoff:3.500A) Processing helix chain 'q' and resid 157 through 166 Processing helix chain 'q' and resid 176 through 181 Processing helix chain 'q' and resid 190 through 202 Processing helix chain 'r' and resid 19 through 32 Processing helix chain 'r' and resid 37 through 59 Processing helix chain 'r' and resid 64 through 81 Processing helix chain 'r' and resid 90 through 96 Processing helix chain 'r' and resid 98 through 106 removed outlier: 4.035A pdb=" N PHE r 102 " --> pdb=" O LYS r 98 " (cutoff:3.500A) Processing helix chain 'r' and resid 106 through 114 Processing helix chain 'r' and resid 119 through 129 Processing helix chain 'r' and resid 167 through 176 removed outlier: 4.297A pdb=" N ARG r 171 " --> pdb=" O PRO r 167 " (cutoff:3.500A) Processing helix chain 's' and resid 87 through 105 Processing helix chain 's' and resid 108 through 132 Processing helix chain 't' and resid 69 through 87 Processing helix chain 't' and resid 110 through 121 Processing helix chain 'u' and resid 41 through 43 No H-bonds generated for 'chain 'u' and resid 41 through 43' Processing helix chain 'u' and resid 44 through 56 Proline residue: u 51 - end of helix Processing helix chain 'u' and resid 57 through 60 Processing helix chain 'u' and resid 73 through 96 Processing helix chain 'u' and resid 98 through 113 removed outlier: 3.816A pdb=" N LYS u 102 " --> pdb=" O ASP u 98 " (cutoff:3.500A) Processing helix chain 'u' and resid 114 through 117 Processing helix chain 'v' and resid 22 through 27 removed outlier: 3.607A pdb=" N VAL v 25 " --> pdb=" O ASN v 22 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS v 26 " --> pdb=" O SER v 23 " (cutoff:3.500A) Processing helix chain 'v' and resid 51 through 56 Processing helix chain 'w' and resid 5 through 20 Processing helix chain 'w' and resid 32 through 44 Processing helix chain 'w' and resid 85 through 94 Processing helix chain 'w' and resid 112 through 119 Processing helix chain 'x' and resid 66 through 70 Processing helix chain 'x' and resid 89 through 94 Processing helix chain 'x' and resid 132 through 137 Processing helix chain 'y' and resid 367 through 373 Processing helix chain 'y' and resid 409 through 417 Processing helix chain 'y' and resid 418 through 425 Processing helix chain '0' and resid 160 through 167 Processing helix chain '0' and resid 167 through 175 removed outlier: 4.279A pdb=" N GLY 0 175 " --> pdb=" O LEU 0 171 " (cutoff:3.500A) Processing helix chain '0' and resid 180 through 187 Processing helix chain '0' and resid 197 through 213 Processing helix chain '0' and resid 227 through 247 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 11 removed outlier: 5.118A pdb=" N VAL A 697 " --> pdb=" O SER A 8 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N LEU A 10 " --> pdb=" O LEU A 695 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU A 695 " --> pdb=" O LEU A 10 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N SER A 686 " --> pdb=" O PHE A 680 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N PHE A 680 " --> pdb=" O SER A 686 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N CYS A 688 " --> pdb=" O VAL A 678 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL A 678 " --> pdb=" O CYS A 688 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ALA A 690 " --> pdb=" O SER A 676 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 21 through 22 Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 63 removed outlier: 6.442A pdb=" N ILE A 73 " --> pdb=" O SER A 59 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ILE A 61 " --> pdb=" O LEU A 71 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU A 71 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LEU A 63 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU A 69 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ALA A 79 " --> pdb=" O HIS A 92 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N HIS A 92 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU A 81 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 101 through 104 removed outlier: 5.862A pdb=" N HIS A 123 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ARG A 143 " --> pdb=" O HIS A 123 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 154 through 159 Processing sheet with id=AA6, first strand: chain 'A' and resid 210 through 213 Processing sheet with id=AA7, first strand: chain 'A' and resid 260 through 264 removed outlier: 5.948A pdb=" N GLU A 283 " --> pdb=" O LEU A 289 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N LEU A 289 " --> pdb=" O GLU A 283 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 302 through 305 removed outlier: 6.778A pdb=" N GLU A 326 " --> pdb=" O TYR A 332 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N TYR A 332 " --> pdb=" O GLU A 326 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 343 through 348 removed outlier: 6.693A pdb=" N ALA A 358 " --> pdb=" O ASN A 344 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU A 346 " --> pdb=" O VAL A 356 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL A 356 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N TYR A 348 " --> pdb=" O ARG A 354 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ARG A 354 " --> pdb=" O TYR A 348 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE A 364 " --> pdb=" O THR A 377 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N THR A 377 " --> pdb=" O ILE A 364 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL A 366 " --> pdb=" O ILE A 375 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 385 through 390 removed outlier: 3.757A pdb=" N ARG A 418 " --> pdb=" O ALA A 408 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ASP A 410 " --> pdb=" O ASN A 416 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ASN A 416 " --> pdb=" O ASP A 410 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 428 through 433 removed outlier: 6.147A pdb=" N SER A 454 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N LEU A 460 " --> pdb=" O SER A 454 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 471 through 476 removed outlier: 6.499A pdb=" N GLY A 486 " --> pdb=" O SER A 472 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU A 474 " --> pdb=" O VAL A 484 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL A 484 " --> pdb=" O LEU A 474 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 513 through 518 removed outlier: 6.654A pdb=" N LEU A 534 " --> pdb=" O GLY A 547 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLY A 547 " --> pdb=" O LEU A 534 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N PHE A 536 " --> pdb=" O VAL A 545 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN A 543 " --> pdb=" O SER A 538 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 575 through 580 removed outlier: 4.950A pdb=" N GLY A 591 " --> pdb=" O TYR A 595 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N TYR A 595 " --> pdb=" O GLY A 591 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N SER A 600 " --> pdb=" O LEU A 606 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU A 606 " --> pdb=" O SER A 600 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 630 through 631 Processing sheet with id=AB7, first strand: chain 'C' and resid 642 through 643 Processing sheet with id=AB8, first strand: chain 'C' and resid 646 through 647 removed outlier: 6.498A pdb=" N VAL R 305 " --> pdb=" O PRO R 286 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ASP R 224 " --> pdb=" O GLY R 252 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N LEU R 254 " --> pdb=" O ASP R 224 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE R 226 " --> pdb=" O LEU R 254 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N SER R 256 " --> pdb=" O ILE R 226 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA R 228 " --> pdb=" O SER R 256 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N LYS R 258 " --> pdb=" O ALA R 228 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LYS R 155 " --> pdb=" O VAL R 225 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N PHE R 227 " --> pdb=" O LYS R 155 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N LEU R 157 " --> pdb=" O PHE R 227 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL R 156 " --> pdb=" O TYR R 181 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N VAL R 183 " --> pdb=" O VAL R 156 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N TYR R 158 " --> pdb=" O VAL R 183 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL R 180 " --> pdb=" O ILE R 204 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ILE R 206 " --> pdb=" O VAL R 180 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ALA R 182 " --> pdb=" O ILE R 206 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 16 through 21 removed outlier: 3.864A pdb=" N ALA D 18 " --> pdb=" O GLY D 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 77 through 83 removed outlier: 6.508A pdb=" N ILE D 105 " --> pdb=" O ASP D 78 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU D 80 " --> pdb=" O PHE D 103 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N PHE D 103 " --> pdb=" O LEU D 80 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N TRP D 82 " --> pdb=" O ARG D 101 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ARG D 101 " --> pdb=" O TRP D 82 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU D 102 " --> pdb=" O TRP D 114 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 136 through 137 removed outlier: 7.574A pdb=" N LEU D 163 " --> pdb=" O LEU D 179 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU D 179 " --> pdb=" O LEU D 163 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N SER D 167 " --> pdb=" O PHE D 175 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N PHE D 175 " --> pdb=" O SER D 167 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 189 through 193 removed outlier: 4.525A pdb=" N SER D 191 " --> pdb=" O GLY D 203 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N THR D 208 " --> pdb=" O CYS D 204 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA D 211 " --> pdb=" O ARG D 221 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ARG D 221 " --> pdb=" O ALA D 211 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASP D 213 " --> pdb=" O MET D 219 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N MET D 219 " --> pdb=" O ASP D 213 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 240 through 243 removed outlier: 6.850A pdb=" N ILE D 260 " --> pdb=" O ALA D 269 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 279 through 284 Processing sheet with id=AC6, first strand: chain 'D' and resid 326 through 334 removed outlier: 3.873A pdb=" N GLY D 334 " --> pdb=" O MET D 337 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 131 through 133 Processing sheet with id=AC8, first strand: chain 'F' and resid 140 through 144 removed outlier: 6.597A pdb=" N VAL F 160 " --> pdb=" O GLU F 173 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLU F 173 " --> pdb=" O VAL F 160 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N THR F 162 " --> pdb=" O GLY F 171 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 182 through 185 removed outlier: 6.433A pdb=" N ASP F 204 " --> pdb=" O GLU F 209 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLU F 209 " --> pdb=" O ASP F 204 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 219 through 225 removed outlier: 6.819A pdb=" N LEU F 234 " --> pdb=" O SER F 220 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N MET F 222 " --> pdb=" O ALA F 232 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA F 232 " --> pdb=" O MET F 222 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N PHE F 224 " --> pdb=" O LEU F 230 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU F 230 " --> pdb=" O PHE F 224 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLN F 239 " --> pdb=" O SER F 235 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LEU F 240 " --> pdb=" O GLU F 253 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLU F 253 " --> pdb=" O LEU F 240 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N TYR F 242 " --> pdb=" O VAL F 251 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 261 through 266 removed outlier: 6.134A pdb=" N GLY F 276 " --> pdb=" O VAL F 262 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU F 264 " --> pdb=" O HIS F 274 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N HIS F 274 " --> pdb=" O LEU F 264 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 303 through 308 removed outlier: 3.692A pdb=" N GLY F 319 " --> pdb=" O LYS F 323 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N LYS F 323 " --> pdb=" O GLY F 319 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 347 through 350 removed outlier: 3.608A pdb=" N TRP F 360 " --> pdb=" O HIS F 363 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N MET F 386 " --> pdb=" O ILE F 366 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 339 through 341 Processing sheet with id=AD6, first strand: chain 'L' and resid 44 through 48 removed outlier: 6.083A pdb=" N SER L 85 " --> pdb=" O PRO L 91 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 106 through 107 removed outlier: 3.691A pdb=" N VAL L 115 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ASP L 127 " --> pdb=" O ILE L 136 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ILE L 136 " --> pdb=" O ASP L 127 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 149 through 152 Processing sheet with id=AD9, first strand: chain 'L' and resid 192 through 196 Processing sheet with id=AE1, first strand: chain 'L' and resid 235 through 240 Processing sheet with id=AE2, first strand: chain 'L' and resid 276 through 281 removed outlier: 6.910A pdb=" N GLY L 291 " --> pdb=" O THR L 277 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N LEU L 279 " --> pdb=" O VAL L 289 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N VAL L 289 " --> pdb=" O LEU L 279 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 319 through 326 removed outlier: 6.943A pdb=" N SER L 319 " --> pdb=" O MET L 338 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N MET L 338 " --> pdb=" O SER L 319 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N SER L 321 " --> pdb=" O VAL L 336 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N VAL L 336 " --> pdb=" O SER L 321 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE L 323 " --> pdb=" O LEU L 334 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N LEU L 334 " --> pdb=" O ILE L 323 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ALA L 325 " --> pdb=" O ARG L 332 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 102 through 106 removed outlier: 3.680A pdb=" N ILE M 111 " --> pdb=" O ILE M 125 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL M 113 " --> pdb=" O ARG M 123 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG M 123 " --> pdb=" O VAL M 113 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 145 through 147 Processing sheet with id=AE6, first strand: chain 'M' and resid 189 through 192 Processing sheet with id=AE7, first strand: chain 'M' and resid 241 through 247 removed outlier: 6.998A pdb=" N ALA M 256 " --> pdb=" O GLN M 242 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LEU M 244 " --> pdb=" O VAL M 254 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL M 254 " --> pdb=" O LEU M 244 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N SER M 246 " --> pdb=" O ALA M 252 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ALA M 252 " --> pdb=" O SER M 246 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 293 through 296 Processing sheet with id=AE9, first strand: chain 'M' and resid 361 through 363 Processing sheet with id=AF1, first strand: chain 'M' and resid 399 through 404 removed outlier: 4.983A pdb=" N ASN M 401 " --> pdb=" O HIS M 414 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ALA M 420 " --> pdb=" O TYR M 433 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N TYR M 433 " --> pdb=" O ALA M 420 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL M 422 " --> pdb=" O SER M 431 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'N' and resid 146 through 147 Processing sheet with id=AF3, first strand: chain 'N' and resid 262 through 266 removed outlier: 4.354A pdb=" N ASP N 262 " --> pdb=" O ARG N 617 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU N 613 " --> pdb=" O THR N 266 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'N' and resid 277 through 282 removed outlier: 3.959A pdb=" N ILE N 297 " --> pdb=" O SER N 293 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR N 316 " --> pdb=" O LEU N 300 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N LYS N 302 " --> pdb=" O LEU N 314 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N LEU N 314 " --> pdb=" O LYS N 302 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'N' and resid 327 through 331 removed outlier: 4.185A pdb=" N GLU N 337 " --> pdb=" O VAL N 331 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'N' and resid 376 through 378 removed outlier: 3.719A pdb=" N ALA N 410 " --> pdb=" O ILE N 400 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ASN N 402 " --> pdb=" O TRP N 408 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N TRP N 408 " --> pdb=" O ASN N 402 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'N' and resid 420 through 425 removed outlier: 6.830A pdb=" N ALA N 435 " --> pdb=" O ALA N 421 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N PHE N 423 " --> pdb=" O THR N 433 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR N 433 " --> pdb=" O PHE N 423 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N TRP N 425 " --> pdb=" O GLY N 431 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N GLY N 431 " --> pdb=" O TRP N 425 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N GLN N 440 " --> pdb=" O GLY N 436 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N SER N 445 " --> pdb=" O THR N 451 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N THR N 451 " --> pdb=" O SER N 445 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'N' and resid 465 through 469 Processing sheet with id=AF9, first strand: chain 'N' and resid 543 through 548 Processing sheet with id=AG1, first strand: chain 'O' and resid 35 through 41 removed outlier: 5.799A pdb=" N THR O 777 " --> pdb=" O PRO O 37 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG O 39 " --> pdb=" O ILE O 775 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N TYR O 762 " --> pdb=" O PHE O 756 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N PHE O 756 " --> pdb=" O TYR O 762 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ALA O 764 " --> pdb=" O LEU O 754 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU O 754 " --> pdb=" O ALA O 764 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ALA O 766 " --> pdb=" O THR O 752 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'O' and resid 53 through 56 removed outlier: 6.404A pdb=" N LEU O 71 " --> pdb=" O VAL O 85 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N VAL O 85 " --> pdb=" O LEU O 71 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N THR O 73 " --> pdb=" O VAL O 83 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'O' and resid 94 through 99 removed outlier: 6.863A pdb=" N VAL O 121 " --> pdb=" O VAL O 128 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'O' and resid 143 through 147 removed outlier: 5.646A pdb=" N LYS O 163 " --> pdb=" O HIS O 169 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N HIS O 169 " --> pdb=" O LYS O 163 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'O' and resid 188 through 190 removed outlier: 3.944A pdb=" N GLY O 188 " --> pdb=" O GLY O 202 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ASN O 212 " --> pdb=" O LEU O 218 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LEU O 218 " --> pdb=" O ASN O 212 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'O' and resid 232 through 237 removed outlier: 5.764A pdb=" N ASN O 257 " --> pdb=" O THR O 263 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N THR O 263 " --> pdb=" O ASN O 257 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'O' and resid 276 through 281 removed outlier: 6.550A pdb=" N ALA O 301 " --> pdb=" O THR O 277 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ILE O 279 " --> pdb=" O ALA O 299 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA O 299 " --> pdb=" O ILE O 279 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N PHE O 281 " --> pdb=" O VAL O 297 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N VAL O 297 " --> pdb=" O PHE O 281 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY O 321 " --> pdb=" O PHE O 310 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ASP O 312 " --> pdb=" O ILE O 319 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ILE O 319 " --> pdb=" O ASP O 312 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'O' and resid 340 through 345 removed outlier: 6.652A pdb=" N SER O 355 " --> pdb=" O SER O 341 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ILE O 343 " --> pdb=" O VAL O 353 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL O 353 " --> pdb=" O ILE O 343 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N PHE O 345 " --> pdb=" O VAL O 351 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL O 351 " --> pdb=" O PHE O 345 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N SER O 360 " --> pdb=" O GLY O 356 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N LEU O 361 " --> pdb=" O GLN O 380 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N GLN O 380 " --> pdb=" O LEU O 361 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR O 363 " --> pdb=" O LEU O 378 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG O 376 " --> pdb=" O ILE O 365 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'O' and resid 388 through 393 Processing sheet with id=AH1, first strand: chain 'O' and resid 465 through 470 removed outlier: 6.930A pdb=" N ALA O 521 " --> pdb=" O TRP O 534 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N TRP O 534 " --> pdb=" O ALA O 521 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N THR O 523 " --> pdb=" O GLY O 532 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'O' and resid 544 through 549 removed outlier: 6.751A pdb=" N GLY O 559 " --> pdb=" O SER O 545 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL O 547 " --> pdb=" O LEU O 557 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU O 557 " --> pdb=" O VAL O 547 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILE O 549 " --> pdb=" O PHE O 555 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N PHE O 555 " --> pdb=" O ILE O 549 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ILE O 565 " --> pdb=" O ARG O 578 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ARG O 578 " --> pdb=" O ILE O 565 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N MET O 567 " --> pdb=" O ARG O 576 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'O' and resid 625 through 630 removed outlier: 6.796A pdb=" N VAL O 646 " --> pdb=" O GLU O 659 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N GLU O 659 " --> pdb=" O VAL O 646 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N PHE O 648 " --> pdb=" O VAL O 657 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'O' and resid 668 through 674 removed outlier: 6.636A pdb=" N ALA O 683 " --> pdb=" O ILE O 669 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N CYS O 671 " --> pdb=" O ALA O 681 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ALA O 681 " --> pdb=" O CYS O 671 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N TYR O 673 " --> pdb=" O LEU O 679 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU O 679 " --> pdb=" O TYR O 673 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ASP O 693 " --> pdb=" O THR O 699 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N THR O 699 " --> pdb=" O ASP O 693 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'O' and resid 710 through 715 removed outlier: 4.283A pdb=" N ILE O 730 " --> pdb=" O SER O 726 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ASP O 735 " --> pdb=" O LEU O 741 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N LEU O 741 " --> pdb=" O ASP O 735 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'P' and resid 119 through 121 removed outlier: 6.039A pdb=" N TYR P 56 " --> pdb=" O ASN P 88 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ILE P 90 " --> pdb=" O TYR P 56 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N VAL P 58 " --> pdb=" O ILE P 90 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N THR P 92 " --> pdb=" O VAL P 58 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N VAL P 60 " --> pdb=" O THR P 92 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ASN P 57 " --> pdb=" O ILE P 145 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ALA P 147 " --> pdb=" O ASN P 57 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LEU P 59 " --> pdb=" O ALA P 147 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL P 146 " --> pdb=" O MET P 166 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N VAL P 168 " --> pdb=" O VAL P 146 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'Q' and resid 240 through 244 Processing sheet with id=AH8, first strand: chain 'Q' and resid 128 through 129 removed outlier: 4.161A pdb=" N LEU Q 154 " --> pdb=" O CYS Q 98 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'R' and resid 70 through 75 removed outlier: 3.672A pdb=" N THR k 139 " --> pdb=" O SER R 110 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'S' and resid 73 through 75 Processing sheet with id=AI2, first strand: chain 'S' and resid 203 through 207 removed outlier: 6.608A pdb=" N VAL S 180 " --> pdb=" O ILE S 204 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ILE S 206 " --> pdb=" O VAL S 180 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ALA S 182 " --> pdb=" O ILE S 206 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL S 156 " --> pdb=" O TYR S 181 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N VAL S 183 " --> pdb=" O VAL S 156 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N TYR S 158 " --> pdb=" O VAL S 183 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LYS S 155 " --> pdb=" O VAL S 225 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N PHE S 227 " --> pdb=" O LYS S 155 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LEU S 157 " --> pdb=" O PHE S 227 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ASP S 224 " --> pdb=" O GLY S 252 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N LEU S 254 " --> pdb=" O ASP S 224 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE S 226 " --> pdb=" O LEU S 254 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N SER S 256 " --> pdb=" O ILE S 226 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA S 228 " --> pdb=" O SER S 256 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N LYS S 258 " --> pdb=" O ALA S 228 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL S 305 " --> pdb=" O PRO S 286 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'T' and resid 52 through 55 removed outlier: 5.915A pdb=" N VAL T 96 " --> pdb=" O GLN T 117 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N GLU T 119 " --> pdb=" O VAL T 96 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU T 98 " --> pdb=" O GLU T 119 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'U' and resid 4 through 5 removed outlier: 7.933A pdb=" N PHE U 4 " --> pdb=" O ALA U 89 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LEU U 88 " --> pdb=" O ILE U 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI4 Processing sheet with id=AI5, first strand: chain 'U' and resid 7 through 8 removed outlier: 4.180A pdb=" N THR U 7 " --> pdb=" O ALA U 14 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA U 14 " --> pdb=" O THR U 7 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'V' and resid 34 through 36 removed outlier: 9.435A pdb=" N VAL V 80 " --> pdb=" O GLU V 51 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL V 53 " --> pdb=" O VAL V 80 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N VAL V 82 " --> pdb=" O VAL V 53 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU V 55 " --> pdb=" O VAL V 82 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'W' and resid 34 through 36 removed outlier: 9.435A pdb=" N VAL W 80 " --> pdb=" O GLU W 51 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL W 53 " --> pdb=" O VAL W 80 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N VAL W 82 " --> pdb=" O VAL W 53 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N LEU W 55 " --> pdb=" O VAL W 82 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'X' and resid 165 through 168 removed outlier: 4.528A pdb=" N CYS X 599 " --> pdb=" O TRP X 168 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'X' and resid 175 through 178 removed outlier: 3.728A pdb=" N SER X 175 " --> pdb=" O THR X 186 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR X 186 " --> pdb=" O SER X 175 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'X' and resid 251 through 254 removed outlier: 3.835A pdb=" N VAL X 251 " --> pdb=" O GLY X 264 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY X 264 " --> pdb=" O VAL X 251 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS X 253 " --> pdb=" O VAL X 262 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL X 262 " --> pdb=" O LYS X 253 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'X' and resid 291 through 297 removed outlier: 5.269A pdb=" N GLN X 302 " --> pdb=" O ARG X 297 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL X 312 " --> pdb=" O THR X 325 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N THR X 325 " --> pdb=" O VAL X 312 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL X 314 " --> pdb=" O VAL X 323 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'X' and resid 333 through 337 removed outlier: 6.733A pdb=" N VAL X 347 " --> pdb=" O LEU X 334 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ILE X 336 " --> pdb=" O VAL X 345 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL X 345 " --> pdb=" O ILE X 336 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N THR X 353 " --> pdb=" O GLY X 348 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'X' and resid 398 through 403 removed outlier: 6.257A pdb=" N SER X 422 " --> pdb=" O PRO X 428 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'X' and resid 468 through 471 removed outlier: 6.427A pdb=" N ARG X 491 " --> pdb=" O ALA X 501 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ALA X 501 " --> pdb=" O ARG X 491 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'Y' and resid 11 through 12 removed outlier: 6.115A pdb=" N PHE Y 11 " --> pdb=" O SER Y 34 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'Y' and resid 61 through 62 Processing sheet with id=AJ8, first strand: chain 'Y' and resid 98 through 101 removed outlier: 6.895A pdb=" N ILE Y 98 " --> pdb=" O ARG Y 131 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N THR Y 133 " --> pdb=" O ILE Y 98 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N HIS Y 100 " --> pdb=" O THR Y 133 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE Y 191 " --> pdb=" O LEU Y 176 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'Y' and resid 253 through 256 removed outlier: 7.808A pdb=" N ALA Y 253 " --> pdb=" O ILE Y 218 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLY Y 220 " --> pdb=" O ALA Y 253 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N GLN Y 255 " --> pdb=" O GLY Y 220 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ALA Y 222 " --> pdb=" O GLN Y 255 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'Y' and resid 346 through 351 Processing sheet with id=AK2, first strand: chain 'Z' and resid 103 through 106 removed outlier: 3.792A pdb=" N ILE Z 117 " --> pdb=" O VAL Z 71 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE Z 73 " --> pdb=" O ILE Z 117 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'Z' and resid 251 through 252 removed outlier: 7.568A pdb=" N TYR Z 273 " --> pdb=" O ILE Z 246 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ILE Z 246 " --> pdb=" O TYR Z 273 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'Z' and resid 251 through 252 removed outlier: 6.124A pdb=" N ARG Z 266 " --> pdb=" O GLY Z 783 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLY Z 783 " --> pdb=" O ARG Z 266 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'Z' and resid 840 through 844 removed outlier: 5.233A pdb=" N GLY Z 903 " --> pdb=" O LYS Z 818 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N LYS Z 818 " --> pdb=" O GLY Z 903 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N VAL Z 905 " --> pdb=" O ARG Z 816 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ARG Z 816 " --> pdb=" O VAL Z 905 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'Z' and resid 849 through 850 Processing sheet with id=AK7, first strand: chain 'Z' and resid 914 through 927 removed outlier: 6.609A pdb=" N PHE Z 933 " --> pdb=" O TRP Z 925 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ILE Z 927 " --> pdb=" O THR Z 931 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N THR Z 931 " --> pdb=" O ILE Z 927 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ARG Z 974 " --> pdb=" O LYS Z 963 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N ALA Z 951 " --> pdb=" O LYS Z 990 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N LYS Z 990 " --> pdb=" O ALA Z 951 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE Z 914 " --> pdb=" O VAL Z 995 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'a' and resid 136 through 138 Processing sheet with id=AK9, first strand: chain 'b' and resid 114 through 116 removed outlier: 6.971A pdb=" N ILE b 139 " --> pdb=" O ILE b 154 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ILE b 154 " --> pdb=" O ILE b 139 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU b 141 " --> pdb=" O ILE b 152 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ILE b 152 " --> pdb=" O LEU b 141 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N HIS b 143 " --> pdb=" O THR b 150 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N THR b 150 " --> pdb=" O LEU b 167 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR b 162 " --> pdb=" O ILE b 268 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ILE b 268 " --> pdb=" O THR b 162 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N MET b 164 " --> pdb=" O PHE b 266 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR b 262 " --> pdb=" O HIS b 168 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL b 170 " --> pdb=" O ARG b 260 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ARG b 260 " --> pdb=" O VAL b 170 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'b' and resid 190 through 194 removed outlier: 5.734A pdb=" N HIS b 190 " --> pdb=" O ILE b 228 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N PHE b 230 " --> pdb=" O HIS b 190 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ILE b 192 " --> pdb=" O PHE b 230 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ASN b 232 " --> pdb=" O ILE b 192 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N GLU b 194 " --> pdb=" O ASN b 232 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N PHE b 266 " --> pdb=" O HIS b 283 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N HIS b 283 " --> pdb=" O PHE b 266 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE b 268 " --> pdb=" O GLU b 281 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'c' and resid 694 through 696 Processing sheet with id=AL3, first strand: chain 'd' and resid 57 through 60 removed outlier: 6.017A pdb=" N PHE d 57 " --> pdb=" O ARG d 354 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ARG d 354 " --> pdb=" O PHE d 57 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'd' and resid 71 through 74 Processing sheet with id=AL5, first strand: chain 'd' and resid 115 through 118 Processing sheet with id=AL6, first strand: chain 'd' and resid 158 through 161 Processing sheet with id=AL7, first strand: chain 'd' and resid 202 through 205 removed outlier: 3.560A pdb=" N ASP d 202 " --> pdb=" O VAL d 216 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ASP d 226 " --> pdb=" O PRO d 232 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LYS d 235 " --> pdb=" O GLN d 445 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'd' and resid 242 through 247 Processing sheet with id=AL9, first strand: chain 'd' and resid 286 through 291 Processing sheet with id=AM1, first strand: chain 'e' and resid 149 through 151 removed outlier: 6.561A pdb=" N ILE e 150 " --> pdb=" O LEU e 159 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU e 121 " --> pdb=" O ILE e 163 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE e 112 " --> pdb=" O VAL e 124 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N GLN e 111 " --> pdb=" O ILE e 38 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N VAL e 40 " --> pdb=" O GLN e 111 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TYR e 113 " --> pdb=" O VAL e 40 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N SER e 42 " --> pdb=" O TYR e 113 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N GLN e 115 " --> pdb=" O SER e 42 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'e' and resid 48 through 49 Processing sheet with id=AM3, first strand: chain 'e' and resid 178 through 180 removed outlier: 6.046A pdb=" N THR e 179 " --> pdb=" O ILE e 225 " (cutoff:3.500A) No H-bonds generated for sheet with id=AM3 Processing sheet with id=AM4, first strand: chain 'f' and resid 149 through 151 removed outlier: 6.561A pdb=" N ILE f 150 " --> pdb=" O LEU f 159 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU f 121 " --> pdb=" O ILE f 163 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE f 112 " --> pdb=" O VAL f 124 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLN f 111 " --> pdb=" O ILE f 38 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N VAL f 40 " --> pdb=" O GLN f 111 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N TYR f 113 " --> pdb=" O VAL f 40 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N SER f 42 " --> pdb=" O TYR f 113 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N GLN f 115 " --> pdb=" O SER f 42 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'f' and resid 48 through 49 Processing sheet with id=AM6, first strand: chain 'f' and resid 178 through 180 removed outlier: 6.046A pdb=" N THR f 179 " --> pdb=" O ILE f 225 " (cutoff:3.500A) No H-bonds generated for sheet with id=AM6 Processing sheet with id=AM7, first strand: chain 'g' and resid 37 through 42 Processing sheet with id=AM8, first strand: chain 'g' and resid 123 through 125 Processing sheet with id=AM9, first strand: chain 'h' and resid 82 through 86 Processing sheet with id=AN1, first strand: chain 'h' and resid 165 through 170 removed outlier: 3.776A pdb=" N LYS h 215 " --> pdb=" O ALA h 212 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA h 212 " --> pdb=" O LYS h 215 " (cutoff:3.500A) Processing sheet with id=AN2, first strand: chain 'i' and resid 123 through 126 removed outlier: 6.374A pdb=" N PHE i 27 " --> pdb=" O LEU i 151 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N LEU i 153 " --> pdb=" O PHE i 27 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL i 29 " --> pdb=" O LEU i 153 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain 'i' and resid 310 through 313 removed outlier: 6.766A pdb=" N PHE i 311 " --> pdb=" O VAL i 387 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N ASP i 389 " --> pdb=" O PHE i 311 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N THR i 313 " --> pdb=" O ASP i 389 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL i 386 " --> pdb=" O PHE i 409 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N ALA i 411 " --> pdb=" O VAL i 386 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ILE i 388 " --> pdb=" O ALA i 411 " (cutoff:3.500A) removed outlier: 8.892A pdb=" N THR i 413 " --> pdb=" O ILE i 388 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N THR i 280 " --> pdb=" O LYS i 470 " (cutoff:3.500A) Processing sheet with id=AN4, first strand: chain 'i' and resid 565 through 566 Processing sheet with id=AN5, first strand: chain 'i' and resid 565 through 566 Processing sheet with id=AN6, first strand: chain 'i' and resid 722 through 728 removed outlier: 5.356A pdb=" N ILE i 763 " --> pdb=" O PRO i 744 " (cutoff:3.500A) Processing sheet with id=AN7, first strand: chain 'j' and resid 123 through 126 removed outlier: 6.375A pdb=" N PHE j 27 " --> pdb=" O LEU j 151 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N LEU j 153 " --> pdb=" O PHE j 27 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL j 29 " --> pdb=" O LEU j 153 " (cutoff:3.500A) Processing sheet with id=AN8, first strand: chain 'j' and resid 310 through 313 removed outlier: 6.765A pdb=" N PHE j 311 " --> pdb=" O VAL j 387 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ASP j 389 " --> pdb=" O PHE j 311 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR j 313 " --> pdb=" O ASP j 389 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL j 386 " --> pdb=" O PHE j 409 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N ALA j 411 " --> pdb=" O VAL j 386 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ILE j 388 " --> pdb=" O ALA j 411 " (cutoff:3.500A) removed outlier: 8.893A pdb=" N THR j 413 " --> pdb=" O ILE j 388 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N THR j 280 " --> pdb=" O LYS j 470 " (cutoff:3.500A) Processing sheet with id=AN9, first strand: chain 'j' and resid 565 through 566 Processing sheet with id=AO1, first strand: chain 'j' and resid 565 through 566 Processing sheet with id=AO2, first strand: chain 'j' and resid 722 through 728 removed outlier: 5.355A pdb=" N ILE j 763 " --> pdb=" O PRO j 744 " (cutoff:3.500A) Processing sheet with id=AO3, first strand: chain 'l' and resid 29 through 33 Processing sheet with id=AO4, first strand: chain 'l' and resid 83 through 85 removed outlier: 3.759A pdb=" N LEU l 103 " --> pdb=" O VAL l 215 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ASN l 209 " --> pdb=" O PHE l 142 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE l 142 " --> pdb=" O ASN l 209 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N PHE l 138 " --> pdb=" O ARG l 213 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL l 215 " --> pdb=" O ARG l 136 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ARG l 136 " --> pdb=" O VAL l 215 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU l 217 " --> pdb=" O LEU l 134 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N LEU l 134 " --> pdb=" O LEU l 217 " (cutoff:3.500A) Processing sheet with id=AO5, first strand: chain 'l' and resid 91 through 92 removed outlier: 3.720A pdb=" N GLN l 92 " --> pdb=" O ASN l 95 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN l 95 " --> pdb=" O GLN l 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AO5 Processing sheet with id=AO6, first strand: chain 'm' and resid 89 through 92 Processing sheet with id=AO7, first strand: chain 'm' and resid 102 through 103 Processing sheet with id=AO8, first strand: chain 'm' and resid 146 through 147 removed outlier: 6.106A pdb=" N PHE m 138 " --> pdb=" O VAL m 129 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL m 129 " --> pdb=" O PHE m 138 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL m 140 " --> pdb=" O LYS m 127 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N THR m 159 " --> pdb=" O PHE m 172 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N PHE m 172 " --> pdb=" O THR m 159 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LYS m 161 " --> pdb=" O THR m 170 " (cutoff:3.500A) Processing sheet with id=AO9, first strand: chain 'm' and resid 217 through 221 removed outlier: 6.655A pdb=" N ILE m 207 " --> pdb=" O ARG m 198 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ARG m 198 " --> pdb=" O ILE m 207 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N HIS m 209 " --> pdb=" O THR m 196 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N VAL m 194 " --> pdb=" O LYS m 211 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N LEU m 180 " --> pdb=" O ILE m 228 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE m 228 " --> pdb=" O LEU m 180 " (cutoff:3.500A) Processing sheet with id=AP1, first strand: chain 'n' and resid 28 through 29 Processing sheet with id=AP2, first strand: chain 'n' and resid 131 through 134 removed outlier: 7.679A pdb=" N ALA n 146 " --> pdb=" O ASN z 44 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N LYS z 46 " --> pdb=" O ALA n 146 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ASP n 148 " --> pdb=" O LYS z 46 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS z 9 " --> pdb=" O LEU z 57 " (cutoff:3.500A) Processing sheet with id=AP3, first strand: chain 'o' and resid 12 through 17 removed outlier: 6.575A pdb=" N LYS o 2 " --> pdb=" O LEU o 109 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N LEU o 111 " --> pdb=" O LYS o 2 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ASN o 4 " --> pdb=" O LEU o 111 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ILE o 113 " --> pdb=" O ASN o 4 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N SER o 6 " --> pdb=" O ILE o 113 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N LYS o 115 " --> pdb=" O SER o 6 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU o 106 " --> pdb=" O ASP o 57 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ASP o 57 " --> pdb=" O LEU o 106 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL o 108 " --> pdb=" O GLY o 55 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLY o 55 " --> pdb=" O VAL o 108 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ALA o 110 " --> pdb=" O THR o 53 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ILE o 49 " --> pdb=" O VAL o 114 " (cutoff:3.500A) Processing sheet with id=AP4, first strand: chain 'o' and resid 72 through 73 removed outlier: 3.551A pdb=" N VAL o 73 " --> pdb=" O VAL o 97 " (cutoff:3.500A) Processing sheet with id=AP5, first strand: chain 'o' and resid 160 through 162 Processing sheet with id=AP6, first strand: chain 'p' and resid 52 through 56 removed outlier: 4.416A pdb=" N HIS p 95 " --> pdb=" O LYS p 62 " (cutoff:3.500A) Processing sheet with id=AP7, first strand: chain 'p' and resid 191 through 194 removed outlier: 9.236A pdb=" N THR p 192 " --> pdb=" O LYS p 158 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU p 160 " --> pdb=" O THR p 192 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N GLU p 194 " --> pdb=" O LEU p 160 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N VAL p 162 " --> pdb=" O GLU p 194 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N VAL p 159 " --> pdb=" O LEU p 150 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LEU p 150 " --> pdb=" O VAL p 159 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LYS p 161 " --> pdb=" O LYS p 148 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N LYS p 148 " --> pdb=" O LYS p 161 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE p 163 " --> pdb=" O VAL p 146 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N PHE w 50 " --> pdb=" O THR p 152 " (cutoff:3.500A) Processing sheet with id=AP8, first strand: chain 'q' and resid 37 through 38 removed outlier: 6.455A pdb=" N ARG q 37 " --> pdb=" O LEU q 60 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ARG q 42 " --> pdb=" O LEU q 58 " (cutoff:3.500A) Processing sheet with id=AP9, first strand: chain 'q' and resid 62 through 66 removed outlier: 7.656A pdb=" N ILE q 78 " --> pdb=" O ASP q 105 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ASP q 105 " --> pdb=" O ILE q 78 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL q 101 " --> pdb=" O VAL q 82 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N GLY q 185 " --> pdb=" O SER q 62 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ASN q 64 " --> pdb=" O GLY q 185 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N ILE q 187 " --> pdb=" O ASN q 64 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ALA q 66 " --> pdb=" O ILE q 187 " (cutoff:3.500A) Processing sheet with id=AQ1, first strand: chain 'r' and resid 137 through 138 Processing sheet with id=AQ2, first strand: chain 't' and resid 53 through 55 removed outlier: 3.745A pdb=" N CYS t 53 " --> pdb=" O VAL t 43 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL t 55 " --> pdb=" O VAL t 41 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL t 41 " --> pdb=" O VAL t 55 " (cutoff:3.500A) Processing sheet with id=AQ3, first strand: chain 'u' and resid 6 through 12 removed outlier: 6.650A pdb=" N LYS u 30 " --> pdb=" O ILE u 67 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N VAL u 69 " --> pdb=" O LYS u 30 " (cutoff:3.500A) Processing sheet with id=AQ4, first strand: chain 'v' and resid 75 through 79 removed outlier: 6.528A pdb=" N GLY v 131 " --> pdb=" O VAL v 144 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N VAL v 144 " --> pdb=" O GLY v 131 " (cutoff:3.500A) removed outlier: 15.791A pdb=" N VAL v 140 " --> pdb=" O HIS v 109 " (cutoff:3.500A) removed outlier: 13.622A pdb=" N ASN v 111 " --> pdb=" O VAL v 140 " (cutoff:3.500A) removed outlier: 10.181A pdb=" N PHE v 142 " --> pdb=" O ASN v 111 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ALA v 113 " --> pdb=" O PHE v 142 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N VAL v 144 " --> pdb=" O ALA v 113 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N HIS v 115 " --> pdb=" O VAL v 144 " (cutoff:3.500A) removed outlier: 9.056A pdb=" N ARG v 146 " --> pdb=" O HIS v 115 " (cutoff:3.500A) Processing sheet with id=AQ5, first strand: chain 'w' and resid 109 through 111 removed outlier: 6.740A pdb=" N TYR w 101 " --> pdb=" O PHE w 128 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N PHE w 128 " --> pdb=" O TYR w 101 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE w 103 " --> pdb=" O ILE w 126 " (cutoff:3.500A) Processing sheet with id=AQ6, first strand: chain 'x' and resid 49 through 55 removed outlier: 6.900A pdb=" N ARG x 73 " --> pdb=" O LEU x 54 " (cutoff:3.500A) removed outlier: 10.071A pdb=" N PHE x 122 " --> pdb=" O LYS x 82 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N THR x 84 " --> pdb=" O PHE x 122 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N VAL x 124 " --> pdb=" O THR x 84 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N PHE x 86 " --> pdb=" O VAL x 124 " (cutoff:3.500A) Processing sheet with id=AQ7, first strand: chain 'x' and resid 126 through 127 Processing sheet with id=AQ8, first strand: chain 'y' and resid 337 through 341 removed outlier: 7.263A pdb=" N LYS y 399 " --> pdb=" O THR y 393 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N THR y 393 " --> pdb=" O LYS y 399 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N THR y 401 " --> pdb=" O LEU y 391 " (cutoff:3.500A) 4709 hydrogen bonds defined for protein. 13389 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1269 hydrogen bonds 2160 hydrogen bond angles 0 basepair planarities 497 basepair parallelities 818 stacking parallelities Total time for adding SS restraints: 121.57 Time building geometry restraints manager: 49.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 20489 1.32 - 1.45: 45666 1.45 - 1.58: 70965 1.58 - 1.70: 3123 1.70 - 1.83: 585 Bond restraints: 140828 Sorted by residual: bond pdb=" C LEU g 42 " pdb=" N PHE g 43 " ideal model delta sigma weight residual 1.327 1.436 -0.109 1.71e-02 3.42e+03 4.05e+01 bond pdb=" C ARG p 45 " pdb=" N PRO p 46 " ideal model delta sigma weight residual 1.336 1.386 -0.050 9.80e-03 1.04e+04 2.62e+01 bond pdb=" C VAL X 359 " pdb=" N PRO X 360 " ideal model delta sigma weight residual 1.336 1.393 -0.057 1.20e-02 6.94e+03 2.22e+01 bond pdb=" CA ALA o 227 " pdb=" C ALA o 227 " ideal model delta sigma weight residual 1.523 1.579 -0.056 1.34e-02 5.57e+03 1.76e+01 bond pdb=" C LEU Y 158 " pdb=" N PRO Y 159 " ideal model delta sigma weight residual 1.337 1.376 -0.040 9.80e-03 1.04e+04 1.65e+01 ... (remaining 140823 not shown) Histogram of bond angle deviations from ideal: 71.28 - 86.10: 3 86.10 - 100.92: 366 100.92 - 115.74: 102757 115.74 - 130.56: 94054 130.56 - 145.38: 1159 Bond angle restraints: 198339 Sorted by residual: angle pdb=" C LEU O 222 " pdb=" N LEU O 223 " pdb=" CA LEU O 223 " ideal model delta sigma weight residual 120.49 145.38 -24.89 1.42e+00 4.96e-01 3.07e+02 angle pdb=" OP1 G 2 2 " pdb=" P G 2 2 " pdb=" OP2 G 2 2 " ideal model delta sigma weight residual 119.60 79.59 40.01 3.00e+00 1.11e-01 1.78e+02 angle pdb=" OP1 G 2 2 " pdb=" P G 2 2 " pdb=" O5' G 2 2 " ideal model delta sigma weight residual 108.00 71.28 36.72 3.00e+00 1.11e-01 1.50e+02 angle pdb=" O3' A 2 1 " pdb=" P G 2 2 " pdb=" OP2 G 2 2 " ideal model delta sigma weight residual 108.00 79.73 28.27 3.00e+00 1.11e-01 8.88e+01 angle pdb=" O3' A 2 1 " pdb=" P G 2 2 " pdb=" OP1 G 2 2 " ideal model delta sigma weight residual 108.00 135.41 -27.41 3.00e+00 1.11e-01 8.35e+01 ... (remaining 198334 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 82237 35.86 - 71.72: 4372 71.72 - 107.58: 554 107.58 - 143.45: 26 143.45 - 179.31: 27 Dihedral angle restraints: 87216 sinusoidal: 47543 harmonic: 39673 Sorted by residual: dihedral pdb=" CA ILE f 84 " pdb=" C ILE f 84 " pdb=" N SER f 85 " pdb=" CA SER f 85 " ideal model delta harmonic sigma weight residual 180.00 127.86 52.14 0 5.00e+00 4.00e-02 1.09e+02 dihedral pdb=" CA ILE e 84 " pdb=" C ILE e 84 " pdb=" N SER e 85 " pdb=" CA SER e 85 " ideal model delta harmonic sigma weight residual 180.00 127.88 52.12 0 5.00e+00 4.00e-02 1.09e+02 dihedral pdb=" CA PRO j 531 " pdb=" C PRO j 531 " pdb=" N VAL j 532 " pdb=" CA VAL j 532 " ideal model delta harmonic sigma weight residual -180.00 -130.35 -49.65 0 5.00e+00 4.00e-02 9.86e+01 ... (remaining 87213 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 22591 0.109 - 0.217: 1540 0.217 - 0.326: 117 0.326 - 0.435: 25 0.435 - 0.543: 6 Chirality restraints: 24279 Sorted by residual: chirality pdb=" CB ILE O 255 " pdb=" CA ILE O 255 " pdb=" CG1 ILE O 255 " pdb=" CG2 ILE O 255 " both_signs ideal model delta sigma weight residual False 2.64 2.10 0.54 2.00e-01 2.50e+01 7.38e+00 chirality pdb=" CB VAL z 11 " pdb=" CA VAL z 11 " pdb=" CG1 VAL z 11 " pdb=" CG2 VAL z 11 " both_signs ideal model delta sigma weight residual False -2.63 -2.12 -0.51 2.00e-01 2.50e+01 6.54e+00 chirality pdb=" CB ILE b 123 " pdb=" CA ILE b 123 " pdb=" CG1 ILE b 123 " pdb=" CG2 ILE b 123 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.47 2.00e-01 2.50e+01 5.54e+00 ... (remaining 24276 not shown) Planarity restraints: 19356 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G 1 152 " -0.076 2.00e-02 2.50e+03 4.99e-02 7.46e+01 pdb=" N9 G 1 152 " 0.083 2.00e-02 2.50e+03 pdb=" C8 G 1 152 " -0.002 2.00e-02 2.50e+03 pdb=" N7 G 1 152 " -0.077 2.00e-02 2.50e+03 pdb=" C5 G 1 152 " 0.008 2.00e-02 2.50e+03 pdb=" C6 G 1 152 " 0.003 2.00e-02 2.50e+03 pdb=" O6 G 1 152 " -0.000 2.00e-02 2.50e+03 pdb=" N1 G 1 152 " -0.000 2.00e-02 2.50e+03 pdb=" C2 G 1 152 " -0.000 2.00e-02 2.50e+03 pdb=" N2 G 1 152 " -0.042 2.00e-02 2.50e+03 pdb=" N3 G 1 152 " 0.008 2.00e-02 2.50e+03 pdb=" C4 G 1 152 " 0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 1 190 " -0.020 2.00e-02 2.50e+03 2.60e-02 2.03e+01 pdb=" N9 G 1 190 " 0.011 2.00e-02 2.50e+03 pdb=" C8 G 1 190 " 0.003 2.00e-02 2.50e+03 pdb=" N7 G 1 190 " -0.004 2.00e-02 2.50e+03 pdb=" C5 G 1 190 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G 1 190 " 0.024 2.00e-02 2.50e+03 pdb=" O6 G 1 190 " -0.029 2.00e-02 2.50e+03 pdb=" N1 G 1 190 " -0.009 2.00e-02 2.50e+03 pdb=" C2 G 1 190 " 0.067 2.00e-02 2.50e+03 pdb=" N2 G 1 190 " -0.037 2.00e-02 2.50e+03 pdb=" N3 G 1 190 " -0.010 2.00e-02 2.50e+03 pdb=" C4 G 1 190 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU R 293 " -0.072 5.00e-02 4.00e+02 1.10e-01 1.93e+01 pdb=" N PRO R 294 " 0.190 5.00e-02 4.00e+02 pdb=" CA PRO R 294 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO R 294 " -0.061 5.00e-02 4.00e+02 ... (remaining 19353 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 2787 2.64 - 3.21: 112149 3.21 - 3.77: 227929 3.77 - 4.34: 298780 4.34 - 4.90: 456845 Nonbonded interactions: 1098490 Sorted by model distance: nonbonded pdb=" O2' G 1 152 " pdb=" O5' C 1 153 " model vdw 2.080 2.440 nonbonded pdb=" O2' G 1 152 " pdb=" C6 C 1 153 " model vdw 2.102 3.340 nonbonded pdb=" O4 U 11759 " pdb=" O6 G 12047 " model vdw 2.110 3.040 nonbonded pdb=" OH TYR A 202 " pdb=" O ALA A 261 " model vdw 2.196 2.440 nonbonded pdb=" OG1 THR g 160 " pdb=" O MET g 172 " model vdw 2.214 2.440 ... (remaining 1098485 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 'R' and resid 72 through 308) selection = (chain 'S' and (resid 72 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 88 or (resid 89 through 90 and (na \ me N or name CA or name C or name O or name CB )) or resid 91 through 100 or (re \ sid 101 and (name N or name CA or name C or name O or name CB )) or resid 102 th \ rough 111 or (resid 112 and (name N or name CA or name C or name O or name CB )) \ or resid 113 through 114 or resid 123 through 125 or (resid 126 and (name N or \ name CA or name C or name O or name CB )) or resid 127 through 145 or (resid 146 \ and (name N or name CA or name C or name O or name CB )) or resid 147 through 1 \ 71 or (resid 172 and (name N or name CA or name C or name O or name CB )) or res \ id 173 through 183 or (resid 184 and (name N or name CA or name C or name O or n \ ame CB )) or resid 185 through 191 or (resid 192 and (name N or name CA or name \ C or name O or name CB )) or resid 193 through 207 or (resid 208 through 210 and \ (name N or name CA or name C or name O or name CB )) or resid 211 through 223 o \ r (resid 224 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 25 through 228 or (resid 229 and (name N or name CA or name C or name O or name \ CB )) or resid 230 through 233 or (resid 234 and (name N or name CA or name C or \ name O or name CB )) or resid 235 through 262 or (resid 263 and (name N or name \ CA or name C or name O or name CB )) or resid 264 through 268 or (resid 269 and \ (name N or name CA or name C or name O or name CB )) or resid 270 through 274 o \ r (resid 275 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 76 through 280 or (resid 281 through 282 and (name N or name CA or name C or nam \ e O or name CB )) or resid 283 through 287 or (resid 288 and (name N or name CA \ or name C or name O or name CB )) or resid 289 through 295 or (resid 296 and (na \ me N or name CA or name C or name O or name CB )) or resid 297 or (resid 298 and \ (name N or name CA or name C or name O or name CB )) or resid 299 through 308)) \ } ncs_group { reference = (chain 'V' and (resid 7 through 109 or (resid 110 and (name N or name CA or name \ C or name O or name CB )) or resid 111 through 115 or (resid 116 through 117 an \ d (name N or name CA or name C or name O or name CB )) or resid 118 through 126) \ ) selection = chain 'W' } ncs_group { reference = chain 'e' selection = chain 'f' } ncs_group { reference = chain 'i' selection = (chain 'j' and (resid 10 through 593 or resid 612 through 934)) } 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=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.100 Extract box with map and model: 24.350 Check model and map are aligned: 1.370 Set scattering table: 0.850 Process input model: 385.020 Find NCS groups from input model: 4.790 Set up NCS constraints: 0.650 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: 0.040 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 425.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6051 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 : 0.007 0.123 140828 Z= 0.472 Angle : 1.165 40.008 198339 Z= 0.610 Chirality : 0.059 0.543 24279 Planarity : 0.008 0.110 19356 Dihedral : 19.118 179.308 61480 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.96 % Favored : 90.84 % Rotamer: Outliers : 0.81 % Allowed : 3.66 % Favored : 95.52 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.01 % Twisted Proline : 1.98 % Twisted General : 0.40 % 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: -4.63 (0.06), residues: 13489 helix: -3.27 (0.05), residues: 4610 sheet: -2.29 (0.09), residues: 2675 loop : -3.20 (0.06), residues: 6204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.004 TRP S 130 HIS 0.031 0.003 HIS A 194 PHE 0.043 0.004 PHE A 448 TYR 0.073 0.004 TYR E 113 ARG 0.028 0.001 ARG d 308 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26978 Ramachandran restraints generated. 13489 Oldfield, 0 Emsley, 13489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26978 Ramachandran restraints generated. 13489 Oldfield, 0 Emsley, 13489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3097 residues out of total 11710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 3019 time to evaluate : 9.408 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: A 6 LYS cc_start: 0.8091 (mmmt) cc_final: 0.7889 (tppt) REVERT: A 21 LEU cc_start: 0.7738 (mt) cc_final: 0.7470 (mt) REVERT: A 323 LEU cc_start: 0.5812 (pp) cc_final: 0.5574 (pp) REVERT: A 605 VAL cc_start: 0.8819 (t) cc_final: 0.8599 (m) REVERT: A 624 PHE cc_start: 0.8591 (m-80) cc_final: 0.8242 (m-80) REVERT: A 741 ASN cc_start: 0.8213 (t0) cc_final: 0.7917 (t0) REVERT: A 748 ARG cc_start: 0.6685 (tpt90) cc_final: 0.6440 (mtt90) REVERT: A 817 ARG cc_start: 0.7651 (ttp80) cc_final: 0.6986 (ttm170) REVERT: A 826 MET cc_start: 0.6762 (tpp) cc_final: 0.6544 (tpp) REVERT: A 827 ARG cc_start: 0.7165 (ttp80) cc_final: 0.6668 (ttm170) REVERT: A 847 GLN cc_start: 0.5838 (mt0) cc_final: 0.5621 (mm-40) REVERT: B 894 ASN cc_start: 0.7969 (t0) cc_final: 0.7731 (t0) REVERT: B 900 LYS cc_start: 0.7713 (tptp) cc_final: 0.7276 (ttpp) REVERT: D 41 GLN cc_start: 0.6947 (tt0) cc_final: 0.6686 (tm-30) REVERT: D 187 THR cc_start: 0.7992 (p) cc_final: 0.7729 (p) REVERT: D 314 SER cc_start: 0.7573 (t) cc_final: 0.7262 (m) REVERT: D 327 LYS cc_start: 0.8837 (mttm) cc_final: 0.8476 (mttp) REVERT: E 320 VAL cc_start: 0.8503 (t) cc_final: 0.8249 (t) REVERT: F 44 ARG cc_start: 0.6558 (mtm-85) cc_final: 0.5864 (mmp-170) REVERT: F 92 LEU cc_start: 0.9001 (mt) cc_final: 0.8798 (mt) REVERT: F 153 LEU cc_start: 0.8524 (pp) cc_final: 0.8264 (mt) REVERT: F 214 ARG cc_start: 0.7866 (mmm-85) cc_final: 0.7639 (ttm-80) REVERT: G 53 TYR cc_start: 0.8120 (t80) cc_final: 0.7842 (t80) REVERT: J 794 VAL cc_start: 0.8352 (t) cc_final: 0.8148 (p) REVERT: K 311 MET cc_start: 0.7740 (mmm) cc_final: 0.7438 (mmp) REVERT: K 364 THR cc_start: 0.5668 (p) cc_final: 0.3530 (p) REVERT: K 369 LEU cc_start: 0.7929 (mt) cc_final: 0.7711 (mp) REVERT: L 73 PHE cc_start: 0.4340 (t80) cc_final: 0.3771 (t80) REVERT: L 331 ASP cc_start: 0.7997 (p0) cc_final: 0.7770 (p0) REVERT: N 56 GLU cc_start: 0.7076 (mt-10) cc_final: 0.6867 (tt0) REVERT: N 63 LYS cc_start: 0.7319 (mtpt) cc_final: 0.6976 (ptpt) REVERT: N 397 MET cc_start: 0.6793 (pmm) cc_final: 0.6179 (pmm) REVERT: N 454 ILE cc_start: 0.8924 (mt) cc_final: 0.8652 (tt) REVERT: O 185 LEU cc_start: 0.8120 (tt) cc_final: 0.7767 (tp) REVERT: O 861 LYS cc_start: 0.6747 (mttt) cc_final: 0.6541 (mttt) REVERT: P 21 LYS cc_start: 0.7990 (mttt) cc_final: 0.7066 (tptp) REVERT: P 65 LEU cc_start: 0.8389 (mt) cc_final: 0.8000 (mp) REVERT: P 155 ARG cc_start: 0.7977 (ttm170) cc_final: 0.6521 (ttp80) REVERT: R 205 PRO cc_start: 0.7447 (Cg_endo) cc_final: 0.7197 (Cg_exo) REVERT: S 198 THR cc_start: 0.6365 (m) cc_final: 0.5896 (t) REVERT: T 335 THR cc_start: 0.8348 (m) cc_final: 0.8130 (p) REVERT: T 392 ILE cc_start: 0.8398 (tp) cc_final: 0.8022 (pt) REVERT: U 184 MET cc_start: 0.7679 (mmm) cc_final: 0.7435 (mmm) REVERT: U 204 ASN cc_start: 0.7025 (p0) cc_final: 0.6464 (p0) REVERT: V 68 ILE cc_start: 0.8021 (pt) cc_final: 0.7788 (mt) REVERT: W 35 LYS cc_start: 0.7153 (mmtm) cc_final: 0.6952 (mmtt) REVERT: X 185 THR cc_start: 0.6935 (p) cc_final: 0.6663 (p) REVERT: X 326 LEU cc_start: 0.8390 (mt) cc_final: 0.8077 (mp) REVERT: X 604 PHE cc_start: 0.6371 (p90) cc_final: 0.6130 (p90) REVERT: Y 196 PHE cc_start: 0.6470 (m-10) cc_final: 0.6105 (m-80) REVERT: Y 355 VAL cc_start: 0.8245 (p) cc_final: 0.7936 (m) REVERT: Z 139 MET cc_start: 0.7306 (ttp) cc_final: 0.6806 (tmm) REVERT: Z 152 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7587 (mt-10) REVERT: Z 156 ILE cc_start: 0.7276 (OUTLIER) cc_final: 0.6719 (tt) REVERT: Z 162 MET cc_start: 0.7662 (tpt) cc_final: 0.7403 (tpt) REVERT: Z 220 HIS cc_start: 0.6754 (t70) cc_final: 0.6474 (t70) REVERT: Z 223 SER cc_start: 0.8521 (m) cc_final: 0.7975 (p) REVERT: Z 229 MET cc_start: 0.5730 (mmm) cc_final: 0.5483 (mtm) REVERT: Z 972 TYR cc_start: 0.7867 (OUTLIER) cc_final: 0.7522 (m-10) REVERT: Z 1129 ARG cc_start: 0.7150 (mtt180) cc_final: 0.6915 (ptt90) REVERT: Z 1130 ARG cc_start: 0.6335 (tpp80) cc_final: 0.6016 (tpt170) REVERT: a 104 SER cc_start: 0.9025 (t) cc_final: 0.8666 (m) REVERT: c 480 GLN cc_start: 0.7083 (mt0) cc_final: 0.6734 (tm-30) REVERT: d 159 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7411 (tp) REVERT: d 177 ILE cc_start: 0.7781 (pp) cc_final: 0.7459 (pt) REVERT: e 113 TYR cc_start: 0.6836 (m-80) cc_final: 0.6450 (m-80) REVERT: g 135 ARG cc_start: 0.5807 (ttm110) cc_final: 0.5533 (tpt170) REVERT: r 77 ARG cc_start: 0.7273 (mtt180) cc_final: 0.6881 (ttt180) REVERT: u 24 GLN cc_start: 0.7120 (tp40) cc_final: 0.6758 (tp40) REVERT: u 106 LYS cc_start: 0.8093 (mttt) cc_final: 0.7893 (mtpp) REVERT: v 85 MET cc_start: 0.2340 (mtp) cc_final: 0.1900 (ttp) REVERT: z 9 LYS cc_start: 0.8301 (mmtt) cc_final: 0.8030 (mmmt) outliers start: 78 outliers final: 22 residues processed: 3072 average time/residue: 1.2685 time to fit residues: 6546.2588 Evaluate side-chains 1823 residues out of total 11710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 1798 time to evaluate : 9.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 420 VAL Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain N residue 158 ARG Chi-restraints excluded: chain O residue 161 VAL Chi-restraints excluded: chain O residue 733 VAL Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 168 VAL Chi-restraints excluded: chain S residue 262 ILE Chi-restraints excluded: chain V residue 53 VAL Chi-restraints excluded: chain Z residue 156 ILE Chi-restraints excluded: chain Z residue 972 TYR Chi-restraints excluded: chain a residue 158 VAL Chi-restraints excluded: chain b residue 231 VAL Chi-restraints excluded: chain d residue 90 VAL Chi-restraints excluded: chain d residue 159 LEU Chi-restraints excluded: chain o residue 162 VAL Chi-restraints excluded: chain r residue 94 VAL Chi-restraints excluded: chain u residue 9 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1508 random chunks: chunk 1273 optimal weight: 5.9990 chunk 1142 optimal weight: 7.9990 chunk 634 optimal weight: 0.7980 chunk 390 optimal weight: 2.9990 chunk 771 optimal weight: 0.7980 chunk 610 optimal weight: 30.0000 chunk 1181 optimal weight: 0.8980 chunk 457 optimal weight: 3.9990 chunk 718 optimal weight: 0.9990 chunk 879 optimal weight: 0.6980 chunk 1369 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 ASN A 78 GLN A 145 HIS A 147 HIS A 253 GLN A 337 GLN A 702 ASN C 578 GLN D 275 HIS E 140 ASN E 158 GLN ** E 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 95 ASN F 96 GLN F 175 GLN F 190 GLN ** F 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 HIS F 221 HIS F 239 GLN ** F 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 299 HIS F 322 ASN F 378 GLN ** F 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 77 GLN G 103 HIS G 240 GLN G 245 HIS G 268 GLN G 318 HIS H 6 HIS H 13 HIS H 53 GLN H 117 ASN ** I 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 827 GLN K 332 HIS K 333 ASN K 338 HIS K 345 GLN K 371 GLN K 916 GLN L 70 ASN L 103 HIS L 124 GLN M 108 ASN M 167 HIS ** N 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 348 HIS ** N 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 411 GLN N 440 GLN O 117 GLN O 197 ASN O 334 ASN ** O 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 575 HIS O 577 GLN O 621 HIS O 636 HIS O 784 HIS O 992 GLN O1023 GLN ** P 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 63 ASN R 96 ASN R 131 ASN R 235 GLN R 249 GLN S 96 ASN S 131 ASN S 299 HIS ** T 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 54 ASN T 176 HIS T 305 ASN U 147 HIS U 167 HIS U 280 ASN U 288 ASN ** U 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 33 GLN W 67 HIS X 301 ASN ** X 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 316 GLN ** Z 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 239 ASN Z 866 HIS a 135 HIS ** a 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 68 GLN b 210 HIS b 275 ASN d 21 GLN d 111 ASN d 166 ASN d 206 ASN d 262 HIS d 327 GLN ** e 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 93 HIS e 94 GLN e 105 ASN e 111 GLN e 174 ASN f 93 HIS f 94 GLN f 111 GLN f 115 GLN f 143 GLN g 167 ASN h 137 GLN k 120 GLN k 179 HIS l 21 GLN l 74 GLN ** l 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 160 GLN ** l 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 17 HIS m 36 HIS m 98 ASN ** n 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 194 ASN o 13 GLN ** o 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 185 GLN o 189 HIS o 200 GLN p 95 HIS q 84 HIS q 153 HIS q 163 GLN q 179 GLN u 15 ASN u 77 GLN v 16 GLN v 86 HIS ** v 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 113 HIS x 65 ASN ** x 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 192 ASN ** 0 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6091 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 140828 Z= 0.216 Angle : 0.746 40.101 198339 Z= 0.379 Chirality : 0.044 0.390 24279 Planarity : 0.006 0.078 19356 Dihedral : 21.736 179.069 39643 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.39 % Favored : 92.52 % Rotamer: Outliers : 3.55 % Allowed : 11.25 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.02 % Twisted Proline : 1.16 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.12 (0.06), residues: 13489 helix: -1.31 (0.07), residues: 4700 sheet: -1.83 (0.09), residues: 2660 loop : -2.77 (0.07), residues: 6129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP R 130 HIS 0.011 0.001 HIS h 108 PHE 0.039 0.002 PHE A 687 TYR 0.025 0.002 TYR p 179 ARG 0.011 0.001 ARG g 142 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26978 Ramachandran restraints generated. 13489 Oldfield, 0 Emsley, 13489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26978 Ramachandran restraints generated. 13489 Oldfield, 0 Emsley, 13489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2348 residues out of total 11710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 341 poor density : 2007 time to evaluate : 9.613 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: A 21 LEU cc_start: 0.7535 (mt) cc_final: 0.7302 (mt) REVERT: A 448 PHE cc_start: 0.7216 (p90) cc_final: 0.6687 (p90) REVERT: A 741 ASN cc_start: 0.8235 (t0) cc_final: 0.7799 (t0) REVERT: A 827 ARG cc_start: 0.6963 (ttp80) cc_final: 0.6547 (ttp-110) REVERT: A 847 GLN cc_start: 0.6078 (mt0) cc_final: 0.5731 (mm-40) REVERT: B 900 LYS cc_start: 0.7914 (tptp) cc_final: 0.7269 (mtpp) REVERT: D 41 GLN cc_start: 0.6929 (tt0) cc_final: 0.6680 (tm-30) REVERT: E 20 ARG cc_start: 0.7106 (tmt170) cc_final: 0.6752 (ttp80) REVERT: E 381 MET cc_start: 0.6796 (mmm) cc_final: 0.6580 (mmm) REVERT: F 45 TYR cc_start: 0.6369 (t80) cc_final: 0.6066 (t80) REVERT: G 53 TYR cc_start: 0.8084 (t80) cc_final: 0.7873 (t80) REVERT: K 369 LEU cc_start: 0.7947 (mt) cc_final: 0.7676 (mp) REVERT: L 137 LEU cc_start: 0.6855 (OUTLIER) cc_final: 0.6344 (mp) REVERT: L 274 LYS cc_start: 0.6293 (mtmp) cc_final: 0.6076 (mttt) REVERT: N 63 LYS cc_start: 0.7369 (mtpt) cc_final: 0.7147 (pttt) REVERT: N 137 GLU cc_start: 0.7469 (pm20) cc_final: 0.7233 (pm20) REVERT: N 324 ASP cc_start: 0.7624 (p0) cc_final: 0.7394 (p0) REVERT: N 397 MET cc_start: 0.6888 (pmm) cc_final: 0.6283 (pmm) REVERT: N 454 ILE cc_start: 0.8849 (mt) cc_final: 0.8483 (tt) REVERT: O 235 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.8005 (pp) REVERT: O 298 MET cc_start: 0.7472 (ttm) cc_final: 0.7256 (mtp) REVERT: O 633 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8758 (mp) REVERT: O 861 LYS cc_start: 0.6508 (mttt) cc_final: 0.5735 (mmtt) REVERT: O 981 ARG cc_start: 0.7489 (tpp-160) cc_final: 0.7172 (tpp-160) REVERT: O 1006 ILE cc_start: 0.8095 (OUTLIER) cc_final: 0.7542 (pp) REVERT: P 65 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7508 (mp) REVERT: P 122 THR cc_start: 0.8697 (t) cc_final: 0.8276 (p) REVERT: P 155 ARG cc_start: 0.7981 (ttm170) cc_final: 0.6718 (ttt-90) REVERT: R 205 PRO cc_start: 0.7281 (Cg_endo) cc_final: 0.6984 (Cg_exo) REVERT: S 254 LEU cc_start: 0.1601 (OUTLIER) cc_final: 0.1304 (pp) REVERT: T 154 GLN cc_start: 0.7646 (mt0) cc_final: 0.7429 (mt0) REVERT: T 309 ILE cc_start: 0.8209 (pt) cc_final: 0.7969 (mt) REVERT: T 336 LEU cc_start: 0.7936 (tt) cc_final: 0.7708 (tt) REVERT: T 392 ILE cc_start: 0.8480 (tp) cc_final: 0.8128 (pt) REVERT: U 179 LEU cc_start: 0.8319 (tt) cc_final: 0.7892 (mp) REVERT: W 35 LYS cc_start: 0.7308 (mmtm) cc_final: 0.7098 (mmtt) REVERT: X 182 TYR cc_start: 0.5811 (OUTLIER) cc_final: 0.4092 (t80) REVERT: X 326 LEU cc_start: 0.8474 (mt) cc_final: 0.8137 (mp) REVERT: X 415 ASN cc_start: 0.6576 (p0) cc_final: 0.6376 (p0) REVERT: X 604 PHE cc_start: 0.6378 (p90) cc_final: 0.6130 (p90) REVERT: X 606 VAL cc_start: 0.5924 (t) cc_final: 0.5391 (t) REVERT: Z 139 MET cc_start: 0.6873 (ttp) cc_final: 0.6309 (tmm) REVERT: Z 223 SER cc_start: 0.8617 (m) cc_final: 0.8256 (p) REVERT: Z 229 MET cc_start: 0.5869 (mmm) cc_final: 0.5520 (mtm) REVERT: Z 931 THR cc_start: 0.8475 (p) cc_final: 0.8266 (t) REVERT: Z 972 TYR cc_start: 0.7903 (OUTLIER) cc_final: 0.7425 (m-10) REVERT: Z 1129 ARG cc_start: 0.6930 (mtt180) cc_final: 0.6548 (ptt90) REVERT: Z 1130 ARG cc_start: 0.6315 (tpp80) cc_final: 0.5859 (tpt170) REVERT: a 104 SER cc_start: 0.9112 (t) cc_final: 0.8705 (m) REVERT: a 120 MET cc_start: 0.7639 (mmt) cc_final: 0.7435 (mmm) REVERT: a 159 THR cc_start: 0.8436 (t) cc_final: 0.8230 (t) REVERT: b 66 LYS cc_start: 0.7897 (mmtt) cc_final: 0.7616 (mtpp) REVERT: c 480 GLN cc_start: 0.6892 (mt0) cc_final: 0.6612 (tm-30) REVERT: c 485 GLU cc_start: 0.8118 (tp30) cc_final: 0.7894 (tp30) REVERT: c 676 MET cc_start: 0.6844 (ptp) cc_final: 0.4329 (mmt) REVERT: c 683 TYR cc_start: 0.7425 (t80) cc_final: 0.7158 (t80) REVERT: d 177 ILE cc_start: 0.7937 (pp) cc_final: 0.7550 (pt) REVERT: e 113 TYR cc_start: 0.6944 (m-80) cc_final: 0.6368 (m-80) REVERT: e 151 LYS cc_start: 0.6096 (OUTLIER) cc_final: 0.5619 (tttp) REVERT: g 204 LYS cc_start: 0.8075 (mttt) cc_final: 0.7627 (mmtt) REVERT: h 206 LYS cc_start: 0.6081 (tptt) cc_final: 0.5624 (tptt) REVERT: l 22 ASP cc_start: 0.4082 (p0) cc_final: 0.3778 (p0) REVERT: l 168 MET cc_start: 0.6114 (tpp) cc_final: 0.5646 (tpp) REVERT: n 209 LYS cc_start: 0.8269 (mmmm) cc_final: 0.8046 (mmtt) REVERT: q 45 ILE cc_start: 0.4840 (mm) cc_final: 0.4575 (mm) REVERT: r 136 LYS cc_start: 0.5183 (pttm) cc_final: 0.4886 (pttt) REVERT: u 24 GLN cc_start: 0.6891 (tp40) cc_final: 0.6664 (tp40) REVERT: u 93 TYR cc_start: 0.7868 (m-10) cc_final: 0.7657 (m-80) REVERT: y 419 ARG cc_start: 0.5224 (tpt-90) cc_final: 0.4662 (ptt90) outliers start: 341 outliers final: 203 residues processed: 2206 average time/residue: 1.1500 time to fit residues: 4368.6913 Evaluate side-chains 1875 residues out of total 11710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 1663 time to evaluate : 8.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 147 HIS Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 243 TRP Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 533 GLN Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 249 ILE Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 172 CYS Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 189 ASN Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 233 THR Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 338 SER Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 401 CYS Chi-restraints excluded: chain F residue 420 VAL Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain G residue 283 SER Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain I residue 777 MET Chi-restraints excluded: chain I residue 862 ASN Chi-restraints excluded: chain I residue 921 ILE Chi-restraints excluded: chain J residue 888 LEU Chi-restraints excluded: chain K residue 329 THR Chi-restraints excluded: chain L residue 86 ILE Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 150 THR Chi-restraints excluded: chain L residue 158 THR Chi-restraints excluded: chain L residue 190 VAL Chi-restraints excluded: chain L residue 329 HIS Chi-restraints excluded: chain M residue 111 ILE Chi-restraints excluded: chain M residue 162 ASP Chi-restraints excluded: chain M residue 170 TRP Chi-restraints excluded: chain M residue 219 ILE Chi-restraints excluded: chain M residue 432 MET Chi-restraints excluded: chain N residue 51 GLU Chi-restraints excluded: chain N residue 279 SER Chi-restraints excluded: chain N residue 293 SER Chi-restraints excluded: chain N residue 448 THR Chi-restraints excluded: chain N residue 575 THR Chi-restraints excluded: chain O residue 151 ILE Chi-restraints excluded: chain O residue 161 VAL Chi-restraints excluded: chain O residue 235 LEU Chi-restraints excluded: chain O residue 286 LEU Chi-restraints excluded: chain O residue 369 SER Chi-restraints excluded: chain O residue 546 THR Chi-restraints excluded: chain O residue 626 THR Chi-restraints excluded: chain O residue 633 LEU Chi-restraints excluded: chain O residue 733 VAL Chi-restraints excluded: chain O residue 771 LEU Chi-restraints excluded: chain O residue 773 VAL Chi-restraints excluded: chain O residue 1006 ILE Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 112 ILE Chi-restraints excluded: chain P residue 128 THR Chi-restraints excluded: chain P residue 168 VAL Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 203 VAL Chi-restraints excluded: chain R residue 256 SER Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain S residue 203 VAL Chi-restraints excluded: chain S residue 204 ILE Chi-restraints excluded: chain S residue 254 LEU Chi-restraints excluded: chain S residue 264 SER Chi-restraints excluded: chain T residue 8 LEU Chi-restraints excluded: chain T residue 19 GLU Chi-restraints excluded: chain T residue 52 SER Chi-restraints excluded: chain T residue 88 GLN Chi-restraints excluded: chain T residue 98 LEU Chi-restraints excluded: chain T residue 184 LEU Chi-restraints excluded: chain T residue 217 ILE Chi-restraints excluded: chain T residue 274 VAL Chi-restraints excluded: chain T residue 321 HIS Chi-restraints excluded: chain T residue 334 SER Chi-restraints excluded: chain U residue 166 VAL Chi-restraints excluded: chain U residue 169 VAL Chi-restraints excluded: chain U residue 212 LEU Chi-restraints excluded: chain U residue 237 VAL Chi-restraints excluded: chain U residue 251 THR Chi-restraints excluded: chain U residue 262 VAL Chi-restraints excluded: chain V residue 53 VAL Chi-restraints excluded: chain V residue 62 LEU Chi-restraints excluded: chain W residue 86 VAL Chi-restraints excluded: chain W residue 94 VAL Chi-restraints excluded: chain X residue 182 TYR Chi-restraints excluded: chain X residue 312 VAL Chi-restraints excluded: chain X residue 320 LEU Chi-restraints excluded: chain X residue 432 ILE Chi-restraints excluded: chain X residue 582 THR Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Y residue 60 VAL Chi-restraints excluded: chain Y residue 98 ILE Chi-restraints excluded: chain Y residue 102 ILE Chi-restraints excluded: chain Y residue 164 PHE Chi-restraints excluded: chain Y residue 305 VAL Chi-restraints excluded: chain Y residue 334 THR Chi-restraints excluded: chain Z residue 166 VAL Chi-restraints excluded: chain Z residue 170 LEU Chi-restraints excluded: chain Z residue 219 ILE Chi-restraints excluded: chain Z residue 271 SER Chi-restraints excluded: chain Z residue 799 LEU Chi-restraints excluded: chain Z residue 836 SER Chi-restraints excluded: chain Z residue 845 LEU Chi-restraints excluded: chain Z residue 886 CYS Chi-restraints excluded: chain Z residue 902 THR Chi-restraints excluded: chain Z residue 912 THR Chi-restraints excluded: chain Z residue 937 MET Chi-restraints excluded: chain Z residue 952 ILE Chi-restraints excluded: chain Z residue 972 TYR Chi-restraints excluded: chain Z residue 1081 VAL Chi-restraints excluded: chain a residue 51 CYS Chi-restraints excluded: chain a residue 95 SER Chi-restraints excluded: chain a residue 103 VAL Chi-restraints excluded: chain a residue 123 THR Chi-restraints excluded: chain a residue 136 VAL Chi-restraints excluded: chain a residue 149 LEU Chi-restraints excluded: chain a residue 158 VAL Chi-restraints excluded: chain b residue 104 SER Chi-restraints excluded: chain b residue 107 ILE Chi-restraints excluded: chain b residue 130 SER Chi-restraints excluded: chain b residue 154 ILE Chi-restraints excluded: chain b residue 184 VAL Chi-restraints excluded: chain b residue 205 VAL Chi-restraints excluded: chain b residue 229 THR Chi-restraints excluded: chain b residue 231 VAL Chi-restraints excluded: chain b residue 239 VAL Chi-restraints excluded: chain b residue 262 THR Chi-restraints excluded: chain c residue 494 LEU Chi-restraints excluded: chain c residue 521 MET Chi-restraints excluded: chain c residue 619 ILE Chi-restraints excluded: chain c residue 696 VAL Chi-restraints excluded: chain d residue 88 ASP Chi-restraints excluded: chain d residue 90 VAL Chi-restraints excluded: chain d residue 132 ILE Chi-restraints excluded: chain d residue 201 THR Chi-restraints excluded: chain d residue 233 VAL Chi-restraints excluded: chain d residue 292 SER Chi-restraints excluded: chain d residue 358 SER Chi-restraints excluded: chain d residue 441 VAL Chi-restraints excluded: chain e residue 151 LYS Chi-restraints excluded: chain e residue 183 ASP Chi-restraints excluded: chain e residue 250 ASP Chi-restraints excluded: chain f residue 120 VAL Chi-restraints excluded: chain f residue 236 VAL Chi-restraints excluded: chain g residue 73 ILE Chi-restraints excluded: chain g residue 201 LEU Chi-restraints excluded: chain k residue 86 THR Chi-restraints excluded: chain k residue 96 THR Chi-restraints excluded: chain l residue 209 ASN Chi-restraints excluded: chain m residue 17 HIS Chi-restraints excluded: chain m residue 48 VAL Chi-restraints excluded: chain m residue 114 ILE Chi-restraints excluded: chain m residue 176 ASP Chi-restraints excluded: chain m residue 202 ASP Chi-restraints excluded: chain n residue 34 SER Chi-restraints excluded: chain n residue 193 SER Chi-restraints excluded: chain n residue 194 ASN Chi-restraints excluded: chain o residue 52 ILE Chi-restraints excluded: chain o residue 162 VAL Chi-restraints excluded: chain p residue 182 VAL Chi-restraints excluded: chain q residue 60 LEU Chi-restraints excluded: chain r residue 94 VAL Chi-restraints excluded: chain r residue 125 VAL Chi-restraints excluded: chain t residue 53 CYS Chi-restraints excluded: chain u residue 9 VAL Chi-restraints excluded: chain u residue 23 VAL Chi-restraints excluded: chain u residue 53 LEU Chi-restraints excluded: chain u residue 66 ARG Chi-restraints excluded: chain u residue 69 VAL Chi-restraints excluded: chain u residue 95 LYS Chi-restraints excluded: chain u residue 97 VAL Chi-restraints excluded: chain v residue 66 THR Chi-restraints excluded: chain x residue 52 ILE Chi-restraints excluded: chain y residue 358 ILE Chi-restraints excluded: chain y residue 391 LEU Chi-restraints excluded: chain z residue 37 THR Chi-restraints excluded: chain 0 residue 184 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1508 random chunks: chunk 761 optimal weight: 8.9990 chunk 425 optimal weight: 2.9990 chunk 1139 optimal weight: 3.9990 chunk 932 optimal weight: 50.0000 chunk 377 optimal weight: 4.9990 chunk 1371 optimal weight: 3.9990 chunk 1482 optimal weight: 9.9990 chunk 1221 optimal weight: 0.3980 chunk 1360 optimal weight: 7.9990 chunk 467 optimal weight: 7.9990 chunk 1100 optimal weight: 7.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 HIS A 147 HIS ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 HIS ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 273 GLN E 154 ASN E 158 GLN ** E 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 49 GLN F 127 GLN F 190 GLN F 196 GLN F 228 HIS F 299 HIS ** F 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 HIS H 244 GLN ** I 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 776 ASN ** J 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 837 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 333 ASN ** K 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 112 GLN M 352 HIS M 394 HIS ** N 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 370 GLN N 440 GLN N 561 HIS O 117 GLN ** O 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 427 GLN O 515 HIS O 636 HIS O 992 GLN O1023 GLN P 39 GLN R 78 HIS R 235 GLN R 249 GLN R 299 HIS S 78 HIS ** T 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 61 GLN U 336 HIS ** U 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 422 ASN ** V 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 143 HIS Y 207 HIS ** Z 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z1030 ASN a 25 ASN ** a 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 111 ASN d 207 GLN e 111 GLN f 94 GLN f 143 GLN k 126 ASN k 179 HIS ** k 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 124 ASN l 160 GLN m 50 ASN ** n 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 73 ASN ** o 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 74 HIS ** v 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 39 GLN ** w 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 44 HIS ** x 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 382 GLN ** y 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6262 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.099 140828 Z= 0.449 Angle : 0.838 39.776 198339 Z= 0.426 Chirality : 0.048 0.377 24279 Planarity : 0.007 0.089 19356 Dihedral : 21.653 179.743 39629 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.07 % Favored : 90.83 % Rotamer: Outliers : 5.78 % Allowed : 13.35 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.02 % Twisted Proline : 1.16 % Twisted General : 0.12 % 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: -2.61 (0.07), residues: 13489 helix: -0.61 (0.07), residues: 4717 sheet: -1.74 (0.09), residues: 2691 loop : -2.63 (0.07), residues: 6081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP N 426 HIS 0.022 0.002 HIS F 363 PHE 0.058 0.003 PHE A 687 TYR 0.028 0.003 TYR F 385 ARG 0.018 0.001 ARG q 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26978 Ramachandran restraints generated. 13489 Oldfield, 0 Emsley, 13489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26978 Ramachandran restraints generated. 13489 Oldfield, 0 Emsley, 13489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2280 residues out of total 11710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 555 poor density : 1725 time to evaluate : 9.669 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: A 81 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7385 (tt) REVERT: A 90 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8498 (tp) REVERT: A 459 GLN cc_start: 0.7843 (pt0) cc_final: 0.7155 (mm110) REVERT: A 827 ARG cc_start: 0.7353 (ttp80) cc_final: 0.6874 (ttm170) REVERT: B 861 ARG cc_start: 0.8316 (mtm-85) cc_final: 0.7170 (mtm-85) REVERT: B 900 LYS cc_start: 0.8007 (tptp) cc_final: 0.7409 (mtpp) REVERT: D 80 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8277 (pp) REVERT: D 292 ILE cc_start: 0.8382 (mm) cc_final: 0.8170 (mm) REVERT: F 93 LEU cc_start: 0.8328 (mt) cc_final: 0.8012 (mt) REVERT: F 100 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.8002 (pt) REVERT: F 152 ILE cc_start: 0.8715 (OUTLIER) cc_final: 0.8310 (mp) REVERT: F 362 THR cc_start: 0.8738 (t) cc_final: 0.8464 (m) REVERT: H 69 SER cc_start: 0.8863 (p) cc_final: 0.8490 (m) REVERT: I 846 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8477 (mp) REVERT: I 877 ILE cc_start: 0.7631 (OUTLIER) cc_final: 0.7211 (pt) REVERT: I 895 MET cc_start: 0.5622 (mmp) cc_final: 0.5363 (tpt) REVERT: J 865 VAL cc_start: 0.8444 (t) cc_final: 0.8224 (m) REVERT: K 369 LEU cc_start: 0.8005 (mt) cc_final: 0.7599 (mp) REVERT: L 137 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.7024 (mp) REVERT: L 166 ASP cc_start: 0.5867 (m-30) cc_final: 0.5642 (m-30) REVERT: L 274 LYS cc_start: 0.6402 (mtmt) cc_final: 0.6097 (mttt) REVERT: M 384 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.8022 (mp) REVERT: N 52 GLU cc_start: 0.7537 (tm-30) cc_final: 0.7305 (tm-30) REVERT: N 63 LYS cc_start: 0.7610 (mtpt) cc_final: 0.7359 (pttt) REVERT: N 144 LEU cc_start: 0.6062 (OUTLIER) cc_final: 0.5658 (tm) REVERT: N 157 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8427 (pp) REVERT: N 397 MET cc_start: 0.7039 (pmm) cc_final: 0.6479 (pmm) REVERT: O 105 TYR cc_start: 0.8547 (OUTLIER) cc_final: 0.8150 (m-80) REVERT: O 222 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.7707 (pp) REVERT: O 861 LYS cc_start: 0.6575 (mttt) cc_final: 0.5929 (mmtt) REVERT: O 1006 ILE cc_start: 0.8313 (OUTLIER) cc_final: 0.7617 (pp) REVERT: O 1007 MET cc_start: 0.7983 (ttm) cc_final: 0.7783 (ttm) REVERT: P 28 LYS cc_start: 0.7830 (mttt) cc_final: 0.7604 (mmmt) REVERT: P 65 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7883 (mt) REVERT: P 155 ARG cc_start: 0.8051 (ttm170) cc_final: 0.6684 (ttt-90) REVERT: R 205 PRO cc_start: 0.8094 (Cg_endo) cc_final: 0.7833 (Cg_exo) REVERT: T 38 MET cc_start: 0.7793 (mmp) cc_final: 0.7244 (mmp) REVERT: T 83 GLU cc_start: 0.7058 (OUTLIER) cc_final: 0.6845 (tt0) REVERT: T 154 GLN cc_start: 0.7823 (mt0) cc_final: 0.7588 (mt0) REVERT: T 262 MET cc_start: 0.5188 (mpp) cc_final: 0.4941 (mpp) REVERT: T 309 ILE cc_start: 0.8202 (pt) cc_final: 0.7934 (mt) REVERT: T 392 ILE cc_start: 0.8429 (tp) cc_final: 0.8111 (pt) REVERT: V 125 LEU cc_start: 0.6968 (OUTLIER) cc_final: 0.6638 (tt) REVERT: W 35 LYS cc_start: 0.7971 (mmtm) cc_final: 0.7682 (mmtt) REVERT: W 121 LYS cc_start: 0.7751 (tppt) cc_final: 0.7034 (mtpp) REVERT: X 182 TYR cc_start: 0.5894 (OUTLIER) cc_final: 0.4277 (t80) REVERT: X 326 LEU cc_start: 0.8597 (mt) cc_final: 0.8355 (mp) REVERT: X 415 ASN cc_start: 0.6965 (p0) cc_final: 0.6737 (p0) REVERT: X 604 PHE cc_start: 0.6500 (p90) cc_final: 0.6299 (p90) REVERT: Y 57 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7329 (mp) REVERT: Y 131 ARG cc_start: 0.7228 (tpp80) cc_final: 0.6588 (tpp80) REVERT: Z 223 SER cc_start: 0.8601 (m) cc_final: 0.8318 (p) REVERT: Z 972 TYR cc_start: 0.8228 (OUTLIER) cc_final: 0.7839 (m-10) REVERT: Z 1129 ARG cc_start: 0.7297 (mtt180) cc_final: 0.6741 (ptt90) REVERT: Z 1130 ARG cc_start: 0.6406 (tpp80) cc_final: 0.5931 (tpt170) REVERT: a 20 ASN cc_start: 0.7703 (OUTLIER) cc_final: 0.7271 (p0) REVERT: b 66 LYS cc_start: 0.7951 (mmtt) cc_final: 0.7674 (mtpp) REVERT: b 162 THR cc_start: 0.8668 (p) cc_final: 0.8452 (m) REVERT: c 480 GLN cc_start: 0.7087 (mt0) cc_final: 0.6706 (tm-30) REVERT: c 676 MET cc_start: 0.7270 (ptp) cc_final: 0.4705 (mmt) REVERT: d 177 ILE cc_start: 0.7871 (OUTLIER) cc_final: 0.7540 (pt) REVERT: d 397 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8203 (pp) REVERT: e 113 TYR cc_start: 0.7169 (m-80) cc_final: 0.6255 (m-80) REVERT: e 118 LYS cc_start: 0.6693 (OUTLIER) cc_final: 0.5995 (tppt) REVERT: g 204 LYS cc_start: 0.7965 (mttt) cc_final: 0.7483 (mmtt) REVERT: h 227 MET cc_start: 0.6023 (ptm) cc_final: 0.5797 (ptp) REVERT: l 168 MET cc_start: 0.6147 (tpp) cc_final: 0.5789 (mmt) REVERT: n 111 MET cc_start: 0.6073 (ttt) cc_final: 0.5866 (ttt) REVERT: n 209 LYS cc_start: 0.8440 (mmmm) cc_final: 0.8199 (tptp) REVERT: o 177 ARG cc_start: -0.1334 (OUTLIER) cc_final: -0.1634 (mtt180) REVERT: p 151 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.7418 (ttm-80) REVERT: q 45 ILE cc_start: 0.4896 (mm) cc_final: 0.4677 (mm) REVERT: u 24 GLN cc_start: 0.7171 (tp40) cc_final: 0.6843 (tp40) outliers start: 555 outliers final: 380 residues processed: 2079 average time/residue: 1.2023 time to fit residues: 4323.7783 Evaluate side-chains 1968 residues out of total 11710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 406 poor density : 1562 time to evaluate : 11.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 147 HIS Chi-restraints excluded: chain A residue 150 HIS Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 243 TRP Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 250 PHE Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 533 GLN Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 687 PHE Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 738 PHE Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 772 ARG Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 103 PHE Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 249 ILE Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 172 CYS Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 233 THR Chi-restraints excluded: chain F residue 245 THR Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 281 THR Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 318 THR Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 338 SER Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 401 CYS Chi-restraints excluded: chain F residue 406 ILE Chi-restraints excluded: chain F residue 420 VAL Chi-restraints excluded: chain F residue 438 THR Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain G residue 191 ASP Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 129 ARG Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 223 VAL Chi-restraints excluded: chain H residue 257 THR Chi-restraints excluded: chain I residue 846 LEU Chi-restraints excluded: chain I residue 862 ASN Chi-restraints excluded: chain I residue 877 ILE Chi-restraints excluded: chain I residue 906 LEU Chi-restraints excluded: chain I residue 921 ILE Chi-restraints excluded: chain J residue 797 VAL Chi-restraints excluded: chain J residue 829 VAL Chi-restraints excluded: chain J residue 856 LEU Chi-restraints excluded: chain J residue 860 LEU Chi-restraints excluded: chain J residue 863 ILE Chi-restraints excluded: chain J residue 881 SER Chi-restraints excluded: chain J residue 888 LEU Chi-restraints excluded: chain K residue 327 ILE Chi-restraints excluded: chain K residue 329 THR Chi-restraints excluded: chain K residue 340 VAL Chi-restraints excluded: chain K residue 343 LEU Chi-restraints excluded: chain K residue 905 VAL Chi-restraints excluded: chain L residue 86 ILE Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 150 THR Chi-restraints excluded: chain L residue 158 THR Chi-restraints excluded: chain L residue 190 VAL Chi-restraints excluded: chain L residue 317 ILE Chi-restraints excluded: chain L residue 347 THR Chi-restraints excluded: chain M residue 111 ILE Chi-restraints excluded: chain M residue 148 LEU Chi-restraints excluded: chain M residue 162 ASP Chi-restraints excluded: chain M residue 170 TRP Chi-restraints excluded: chain M residue 219 ILE Chi-restraints excluded: chain M residue 312 ILE Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 402 ILE Chi-restraints excluded: chain M residue 920 VAL Chi-restraints excluded: chain N residue 51 GLU Chi-restraints excluded: chain N residue 144 LEU Chi-restraints excluded: chain N residue 157 LEU Chi-restraints excluded: chain N residue 158 ARG Chi-restraints excluded: chain N residue 260 THR Chi-restraints excluded: chain N residue 279 SER Chi-restraints excluded: chain N residue 293 SER Chi-restraints excluded: chain N residue 323 THR Chi-restraints excluded: chain N residue 381 CYS Chi-restraints excluded: chain N residue 448 THR Chi-restraints excluded: chain N residue 528 LYS Chi-restraints excluded: chain N residue 541 THR Chi-restraints excluded: chain N residue 575 THR Chi-restraints excluded: chain O residue 40 THR Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 85 VAL Chi-restraints excluded: chain O residue 97 THR Chi-restraints excluded: chain O residue 105 TYR Chi-restraints excluded: chain O residue 145 LEU Chi-restraints excluded: chain O residue 151 ILE Chi-restraints excluded: chain O residue 161 VAL Chi-restraints excluded: chain O residue 222 LEU Chi-restraints excluded: chain O residue 254 VAL Chi-restraints excluded: chain O residue 286 LEU Chi-restraints excluded: chain O residue 369 SER Chi-restraints excluded: chain O residue 432 SER Chi-restraints excluded: chain O residue 443 MET Chi-restraints excluded: chain O residue 506 THR Chi-restraints excluded: chain O residue 546 THR Chi-restraints excluded: chain O residue 547 VAL Chi-restraints excluded: chain O residue 550 SER Chi-restraints excluded: chain O residue 554 THR Chi-restraints excluded: chain O residue 557 LEU Chi-restraints excluded: chain O residue 560 SER Chi-restraints excluded: chain O residue 564 SER Chi-restraints excluded: chain O residue 630 VAL Chi-restraints excluded: chain O residue 640 CYS Chi-restraints excluded: chain O residue 660 ILE Chi-restraints excluded: chain O residue 702 GLU Chi-restraints excluded: chain O residue 733 VAL Chi-restraints excluded: chain O residue 771 LEU Chi-restraints excluded: chain O residue 773 VAL Chi-restraints excluded: chain O residue 840 MET Chi-restraints excluded: chain O residue 844 SER Chi-restraints excluded: chain O residue 854 LEU Chi-restraints excluded: chain O residue 859 ILE Chi-restraints excluded: chain O residue 1006 ILE Chi-restraints excluded: chain O residue 1041 VAL Chi-restraints excluded: chain P residue 6 ILE Chi-restraints excluded: chain P residue 15 LYS Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 112 ILE Chi-restraints excluded: chain P residue 128 THR Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 168 VAL Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 203 VAL Chi-restraints excluded: chain R residue 249 GLN Chi-restraints excluded: chain R residue 256 SER Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain S residue 203 VAL Chi-restraints excluded: chain S residue 292 LEU Chi-restraints excluded: chain T residue 8 LEU Chi-restraints excluded: chain T residue 19 GLU Chi-restraints excluded: chain T residue 52 SER Chi-restraints excluded: chain T residue 83 GLU Chi-restraints excluded: chain T residue 173 ASN Chi-restraints excluded: chain T residue 184 LEU Chi-restraints excluded: chain T residue 274 VAL Chi-restraints excluded: chain T residue 321 HIS Chi-restraints excluded: chain U residue 166 VAL Chi-restraints excluded: chain U residue 169 VAL Chi-restraints excluded: chain U residue 212 LEU Chi-restraints excluded: chain U residue 237 VAL Chi-restraints excluded: chain U residue 251 THR Chi-restraints excluded: chain U residue 341 TYR Chi-restraints excluded: chain U residue 348 SER Chi-restraints excluded: chain U residue 369 ILE Chi-restraints excluded: chain V residue 17 LEU Chi-restraints excluded: chain V residue 101 VAL Chi-restraints excluded: chain V residue 105 SER Chi-restraints excluded: chain V residue 125 LEU Chi-restraints excluded: chain W residue 18 VAL Chi-restraints excluded: chain W residue 77 VAL Chi-restraints excluded: chain W residue 94 VAL Chi-restraints excluded: chain W residue 102 SER Chi-restraints excluded: chain W residue 103 LEU Chi-restraints excluded: chain X residue 182 TYR Chi-restraints excluded: chain X residue 312 VAL Chi-restraints excluded: chain X residue 329 HIS Chi-restraints excluded: chain X residue 432 ILE Chi-restraints excluded: chain X residue 502 VAL Chi-restraints excluded: chain X residue 580 VAL Chi-restraints excluded: chain X residue 582 THR Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Y residue 58 GLU Chi-restraints excluded: chain Y residue 60 VAL Chi-restraints excluded: chain Y residue 75 ILE Chi-restraints excluded: chain Y residue 82 ILE Chi-restraints excluded: chain Y residue 98 ILE Chi-restraints excluded: chain Y residue 102 ILE Chi-restraints excluded: chain Y residue 152 THR Chi-restraints excluded: chain Y residue 164 PHE Chi-restraints excluded: chain Y residue 221 VAL Chi-restraints excluded: chain Y residue 280 SER Chi-restraints excluded: chain Y residue 305 VAL Chi-restraints excluded: chain Y residue 318 LEU Chi-restraints excluded: chain Y residue 334 THR Chi-restraints excluded: chain Y residue 356 VAL Chi-restraints excluded: chain Y residue 396 VAL Chi-restraints excluded: chain Y residue 398 VAL Chi-restraints excluded: chain Z residue 84 LEU Chi-restraints excluded: chain Z residue 89 VAL Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain Z residue 106 VAL Chi-restraints excluded: chain Z residue 166 VAL Chi-restraints excluded: chain Z residue 170 LEU Chi-restraints excluded: chain Z residue 175 LEU Chi-restraints excluded: chain Z residue 219 ILE Chi-restraints excluded: chain Z residue 236 VAL Chi-restraints excluded: chain Z residue 271 SER Chi-restraints excluded: chain Z residue 799 LEU Chi-restraints excluded: chain Z residue 845 LEU Chi-restraints excluded: chain Z residue 867 MET Chi-restraints excluded: chain Z residue 878 ILE Chi-restraints excluded: chain Z residue 886 CYS Chi-restraints excluded: chain Z residue 902 THR Chi-restraints excluded: chain Z residue 904 THR Chi-restraints excluded: chain Z residue 906 LEU Chi-restraints excluded: chain Z residue 915 VAL Chi-restraints excluded: chain Z residue 923 THR Chi-restraints excluded: chain Z residue 931 THR Chi-restraints excluded: chain Z residue 952 ILE Chi-restraints excluded: chain Z residue 972 TYR Chi-restraints excluded: chain Z residue 988 ILE Chi-restraints excluded: chain Z residue 1058 LEU Chi-restraints excluded: chain Z residue 1081 VAL Chi-restraints excluded: chain a residue 20 ASN Chi-restraints excluded: chain a residue 51 CYS Chi-restraints excluded: chain a residue 95 SER Chi-restraints excluded: chain a residue 103 VAL Chi-restraints excluded: chain a residue 113 VAL Chi-restraints excluded: chain a residue 114 VAL Chi-restraints excluded: chain a residue 131 ILE Chi-restraints excluded: chain a residue 136 VAL Chi-restraints excluded: chain a residue 149 LEU Chi-restraints excluded: chain a residue 158 VAL Chi-restraints excluded: chain b residue 38 SER Chi-restraints excluded: chain b residue 83 ILE Chi-restraints excluded: chain b residue 107 ILE Chi-restraints excluded: chain b residue 127 LEU Chi-restraints excluded: chain b residue 130 SER Chi-restraints excluded: chain b residue 139 ILE Chi-restraints excluded: chain b residue 140 ILE Chi-restraints excluded: chain b residue 141 LEU Chi-restraints excluded: chain b residue 154 ILE Chi-restraints excluded: chain b residue 167 LEU Chi-restraints excluded: chain b residue 184 VAL Chi-restraints excluded: chain b residue 192 ILE Chi-restraints excluded: chain b residue 198 THR Chi-restraints excluded: chain b residue 205 VAL Chi-restraints excluded: chain b residue 231 VAL Chi-restraints excluded: chain b residue 239 VAL Chi-restraints excluded: chain b residue 243 VAL Chi-restraints excluded: chain b residue 262 THR Chi-restraints excluded: chain b residue 270 MET Chi-restraints excluded: chain b residue 290 THR Chi-restraints excluded: chain c residue 494 LEU Chi-restraints excluded: chain c residue 501 THR Chi-restraints excluded: chain c residue 502 LEU Chi-restraints excluded: chain c residue 526 VAL Chi-restraints excluded: chain c residue 538 SER Chi-restraints excluded: chain c residue 555 ASP Chi-restraints excluded: chain c residue 619 ILE Chi-restraints excluded: chain c residue 634 SER Chi-restraints excluded: chain c residue 696 VAL Chi-restraints excluded: chain d residue 6 LEU Chi-restraints excluded: chain d residue 88 ASP Chi-restraints excluded: chain d residue 90 VAL Chi-restraints excluded: chain d residue 98 THR Chi-restraints excluded: chain d residue 105 ARG Chi-restraints excluded: chain d residue 116 LEU Chi-restraints excluded: chain d residue 132 ILE Chi-restraints excluded: chain d residue 147 ILE Chi-restraints excluded: chain d residue 160 SER Chi-restraints excluded: chain d residue 177 ILE Chi-restraints excluded: chain d residue 201 THR Chi-restraints excluded: chain d residue 215 SER Chi-restraints excluded: chain d residue 233 VAL Chi-restraints excluded: chain d residue 236 THR Chi-restraints excluded: chain d residue 253 MET Chi-restraints excluded: chain d residue 292 SER Chi-restraints excluded: chain d residue 300 SER Chi-restraints excluded: chain d residue 343 THR Chi-restraints excluded: chain d residue 397 LEU Chi-restraints excluded: chain d residue 441 VAL Chi-restraints excluded: chain e residue 118 LYS Chi-restraints excluded: chain e residue 183 ASP Chi-restraints excluded: chain f residue 181 SER Chi-restraints excluded: chain f residue 236 VAL Chi-restraints excluded: chain g residue 73 ILE Chi-restraints excluded: chain g residue 130 VAL Chi-restraints excluded: chain g residue 156 LEU Chi-restraints excluded: chain g residue 188 THR Chi-restraints excluded: chain g residue 201 LEU Chi-restraints excluded: chain h residue 87 ILE Chi-restraints excluded: chain h residue 210 VAL Chi-restraints excluded: chain h residue 246 ASN Chi-restraints excluded: chain k residue 86 THR Chi-restraints excluded: chain k residue 96 THR Chi-restraints excluded: chain k residue 110 ARG Chi-restraints excluded: chain k residue 160 THR Chi-restraints excluded: chain k residue 165 VAL Chi-restraints excluded: chain l residue 67 GLU Chi-restraints excluded: chain l residue 98 THR Chi-restraints excluded: chain l residue 209 ASN Chi-restraints excluded: chain m residue 40 ASP Chi-restraints excluded: chain m residue 79 ASP Chi-restraints excluded: chain m residue 114 ILE Chi-restraints excluded: chain m residue 176 ASP Chi-restraints excluded: chain m residue 189 MET Chi-restraints excluded: chain m residue 202 ASP Chi-restraints excluded: chain n residue 34 SER Chi-restraints excluded: chain n residue 38 ILE Chi-restraints excluded: chain n residue 86 MET Chi-restraints excluded: chain n residue 112 THR Chi-restraints excluded: chain n residue 194 ASN Chi-restraints excluded: chain o residue 52 ILE Chi-restraints excluded: chain o residue 63 MET Chi-restraints excluded: chain o residue 133 LEU Chi-restraints excluded: chain o residue 162 VAL Chi-restraints excluded: chain o residue 177 ARG Chi-restraints excluded: chain p residue 73 LEU Chi-restraints excluded: chain p residue 143 VAL Chi-restraints excluded: chain p residue 151 ARG Chi-restraints excluded: chain p residue 178 THR Chi-restraints excluded: chain q residue 36 THR Chi-restraints excluded: chain q residue 37 ARG Chi-restraints excluded: chain q residue 60 LEU Chi-restraints excluded: chain q residue 136 VAL Chi-restraints excluded: chain r residue 46 THR Chi-restraints excluded: chain r residue 94 VAL Chi-restraints excluded: chain r residue 125 VAL Chi-restraints excluded: chain r residue 141 VAL Chi-restraints excluded: chain r residue 160 SER Chi-restraints excluded: chain s residue 134 VAL Chi-restraints excluded: chain t residue 53 CYS Chi-restraints excluded: chain t residue 61 VAL Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain t residue 136 SER Chi-restraints excluded: chain u residue 9 VAL Chi-restraints excluded: chain u residue 17 THR Chi-restraints excluded: chain u residue 23 VAL Chi-restraints excluded: chain u residue 48 LEU Chi-restraints excluded: chain u residue 66 ARG Chi-restraints excluded: chain u residue 69 VAL Chi-restraints excluded: chain u residue 95 LYS Chi-restraints excluded: chain u residue 97 VAL Chi-restraints excluded: chain v residue 66 THR Chi-restraints excluded: chain w residue 51 GLU Chi-restraints excluded: chain x residue 83 VAL Chi-restraints excluded: chain y residue 391 LEU Chi-restraints excluded: chain z residue 31 VAL Chi-restraints excluded: chain z residue 37 THR Chi-restraints excluded: chain z residue 57 LEU Chi-restraints excluded: chain z residue 66 ARG Chi-restraints excluded: chain 0 residue 164 LEU Chi-restraints excluded: chain 0 residue 184 SER Chi-restraints excluded: chain 0 residue 192 ASN Chi-restraints excluded: chain 0 residue 219 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1508 random chunks: chunk 1355 optimal weight: 8.9990 chunk 1031 optimal weight: 40.0000 chunk 711 optimal weight: 7.9990 chunk 151 optimal weight: 6.9990 chunk 654 optimal weight: 0.9990 chunk 921 optimal weight: 20.0000 chunk 1376 optimal weight: 4.9990 chunk 1457 optimal weight: 30.0000 chunk 719 optimal weight: 7.9990 chunk 1304 optimal weight: 8.9990 chunk 392 optimal weight: 0.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN A 291 HIS A 321 GLN ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 502 GLN ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 GLN ** E 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 GLN ** F 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 GLN G 15 ASN H 93 ASN ** I 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 886 HIS ** I 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 766 HIS ** J 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 837 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 333 ASN ** K 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 296 HIS ** M 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 383 GLN ** N 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 440 GLN N 560 GLN O 117 GLN O 334 ASN ** O 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 636 HIS O 677 ASN ** O 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 195 ASN ** T 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 193 GLN T 394 ASN U 256 ASN ** U 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 336 HIS U 352 GLN ** U 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 441 ASN ** V 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 165 GLN X 286 GLN X 302 GLN ** X 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 561 ASN ** Z 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 239 ASN Z 823 HIS Z1030 ASN a 30 HIS b 121 ASN b 169 ASN d 77 ASN e 73 HIS k 179 HIS ** k 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 124 ASN ** m 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 194 ASN o 81 HIS ** o 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 8 GLN ** v 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 39 GLN ** w 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 44 HIS ** y 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 169 HIS 0 180 HIS 0 192 ASN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6349 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.118 140828 Z= 0.559 Angle : 0.915 39.545 198339 Z= 0.464 Chirality : 0.052 0.416 24279 Planarity : 0.007 0.121 19356 Dihedral : 21.702 179.992 39628 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.11 % Favored : 89.79 % Rotamer: Outliers : 7.52 % Allowed : 14.80 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.02 % Twisted Proline : 0.99 % Twisted General : 0.16 % 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: -2.55 (0.07), residues: 13489 helix: -0.48 (0.07), residues: 4695 sheet: -1.76 (0.09), residues: 2662 loop : -2.63 (0.07), residues: 6132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP N 426 HIS 0.025 0.002 HIS F 363 PHE 0.063 0.003 PHE A 687 TYR 0.031 0.003 TYR p 183 ARG 0.027 0.001 ARG a 34 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26978 Ramachandran restraints generated. 13489 Oldfield, 0 Emsley, 13489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26978 Ramachandran restraints generated. 13489 Oldfield, 0 Emsley, 13489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2360 residues out of total 11710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 722 poor density : 1638 time to evaluate : 9.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7697 (tp) REVERT: A 459 GLN cc_start: 0.8145 (pt0) cc_final: 0.7063 (mm110) REVERT: A 826 MET cc_start: 0.6656 (ttp) cc_final: 0.5943 (ptp) REVERT: A 827 ARG cc_start: 0.7542 (ttp80) cc_final: 0.7341 (ttp80) REVERT: B 861 ARG cc_start: 0.8284 (mtm-85) cc_final: 0.7216 (mtm-85) REVERT: B 900 LYS cc_start: 0.7992 (tptp) cc_final: 0.7327 (ttmm) REVERT: D 80 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8354 (pp) REVERT: D 198 ASN cc_start: 0.7271 (OUTLIER) cc_final: 0.7063 (p0) REVERT: D 292 ILE cc_start: 0.8536 (mm) cc_final: 0.8218 (mm) REVERT: E 191 ARG cc_start: 0.6856 (mtp180) cc_final: 0.6321 (mtt-85) REVERT: F 106 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7516 (tt) REVERT: F 152 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8340 (mp) REVERT: F 214 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7050 (mmm-85) REVERT: F 363 HIS cc_start: 0.7904 (OUTLIER) cc_final: 0.7063 (p-80) REVERT: G 298 HIS cc_start: 0.6168 (t-90) cc_final: 0.5816 (t-90) REVERT: H 34 TYR cc_start: 0.8045 (t80) cc_final: 0.7737 (t80) REVERT: H 69 SER cc_start: 0.8859 (p) cc_final: 0.8611 (m) REVERT: I 846 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8394 (mp) REVERT: I 877 ILE cc_start: 0.7590 (OUTLIER) cc_final: 0.7244 (pp) REVERT: J 867 THR cc_start: 0.7304 (OUTLIER) cc_final: 0.7078 (t) REVERT: K 370 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7240 (mt-10) REVERT: L 137 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7178 (mp) REVERT: L 274 LYS cc_start: 0.6420 (mtmt) cc_final: 0.6046 (mttt) REVERT: L 298 LYS cc_start: 0.4135 (tptt) cc_final: 0.3162 (tmtt) REVERT: N 52 GLU cc_start: 0.7778 (tm-30) cc_final: 0.7437 (tm-30) REVERT: N 63 LYS cc_start: 0.7911 (mtpt) cc_final: 0.7542 (pttm) REVERT: N 144 LEU cc_start: 0.6201 (OUTLIER) cc_final: 0.5812 (tm) REVERT: N 157 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8403 (pp) REVERT: N 393 LYS cc_start: 0.7826 (tptt) cc_final: 0.7540 (tttt) REVERT: N 397 MET cc_start: 0.7058 (pmm) cc_final: 0.6490 (pmm) REVERT: N 449 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7611 (ttp-110) REVERT: O 222 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.7894 (pp) REVERT: O 300 THR cc_start: 0.9014 (OUTLIER) cc_final: 0.8678 (p) REVERT: O 340 ILE cc_start: 0.7678 (OUTLIER) cc_final: 0.7316 (tt) REVERT: O 486 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.7104 (ptp) REVERT: O 861 LYS cc_start: 0.6552 (mttt) cc_final: 0.5877 (mmtt) REVERT: O 954 LEU cc_start: 0.7108 (OUTLIER) cc_final: 0.6900 (tt) REVERT: O 1006 ILE cc_start: 0.8309 (OUTLIER) cc_final: 0.7599 (pp) REVERT: O 1007 MET cc_start: 0.8034 (ttm) cc_final: 0.7607 (ttm) REVERT: P 28 LYS cc_start: 0.7807 (mttt) cc_final: 0.7508 (tptm) REVERT: P 65 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7877 (mp) REVERT: P 126 LYS cc_start: 0.8330 (ttmm) cc_final: 0.7906 (mttt) REVERT: P 150 ASP cc_start: 0.8329 (p0) cc_final: 0.8061 (p0) REVERT: P 155 ARG cc_start: 0.8107 (ttm170) cc_final: 0.6690 (ttt-90) REVERT: T 84 MET cc_start: 0.8027 (tpp) cc_final: 0.7264 (ttp) REVERT: T 154 GLN cc_start: 0.7924 (mt0) cc_final: 0.7696 (mt0) REVERT: T 262 MET cc_start: 0.4879 (mpp) cc_final: 0.4538 (mpp) REVERT: T 309 ILE cc_start: 0.8245 (pt) cc_final: 0.7959 (mt) REVERT: T 392 ILE cc_start: 0.8495 (tp) cc_final: 0.8231 (pt) REVERT: U 133 MET cc_start: 0.0644 (ttt) cc_final: -0.0577 (mmt) REVERT: U 226 SER cc_start: 0.7857 (m) cc_final: 0.7638 (p) REVERT: V 27 GLN cc_start: 0.7917 (tt0) cc_final: 0.7587 (mt0) REVERT: V 125 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.7052 (tt) REVERT: W 35 LYS cc_start: 0.8307 (mmtm) cc_final: 0.7965 (mmtt) REVERT: W 121 LYS cc_start: 0.7869 (tppt) cc_final: 0.7353 (mtpp) REVERT: X 182 TYR cc_start: 0.5949 (OUTLIER) cc_final: 0.4285 (t80) REVERT: X 326 LEU cc_start: 0.8624 (mt) cc_final: 0.8397 (mp) REVERT: Y 57 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7582 (mp) REVERT: Y 111 THR cc_start: 0.7614 (OUTLIER) cc_final: 0.7099 (m) REVERT: Y 359 GLU cc_start: 0.4750 (mm-30) cc_final: 0.4531 (mm-30) REVERT: Z 176 PHE cc_start: 0.7542 (OUTLIER) cc_final: 0.6557 (m-10) REVERT: Z 972 TYR cc_start: 0.8445 (OUTLIER) cc_final: 0.7988 (m-10) REVERT: Z 1038 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.7912 (mp) REVERT: Z 1126 ILE cc_start: 0.7638 (OUTLIER) cc_final: 0.7271 (tt) REVERT: Z 1129 ARG cc_start: 0.7355 (mtt180) cc_final: 0.6741 (ptt90) REVERT: Z 1130 ARG cc_start: 0.6502 (tpp80) cc_final: 0.5996 (tpt170) REVERT: a 20 ASN cc_start: 0.7733 (OUTLIER) cc_final: 0.7081 (p0) REVERT: b 66 LYS cc_start: 0.8065 (mmtt) cc_final: 0.7723 (mtpp) REVERT: b 109 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8319 (mp) REVERT: b 117 LEU cc_start: 0.7227 (OUTLIER) cc_final: 0.6971 (mp) REVERT: c 480 GLN cc_start: 0.7118 (mt0) cc_final: 0.6739 (tm-30) REVERT: d 47 VAL cc_start: 0.8276 (OUTLIER) cc_final: 0.8074 (t) REVERT: d 177 ILE cc_start: 0.7760 (OUTLIER) cc_final: 0.7556 (pt) REVERT: d 298 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7950 (mp) REVERT: d 333 MET cc_start: 0.8095 (ptt) cc_final: 0.7894 (ptt) REVERT: d 392 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7114 (ttp-170) REVERT: d 397 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8234 (pp) REVERT: e 113 TYR cc_start: 0.7233 (m-80) cc_final: 0.6374 (m-80) REVERT: e 118 LYS cc_start: 0.6430 (OUTLIER) cc_final: 0.5930 (tppt) REVERT: g 179 LYS cc_start: 0.7095 (ttmt) cc_final: 0.6850 (ttmm) REVERT: g 204 LYS cc_start: 0.8143 (mttt) cc_final: 0.7634 (mmtt) REVERT: h 206 LYS cc_start: 0.6767 (tptt) cc_final: 0.6063 (ttpt) REVERT: k 117 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.7415 (mtp) REVERT: l 168 MET cc_start: 0.6321 (tpp) cc_final: 0.5998 (mmt) REVERT: m 42 MET cc_start: 0.5382 (mmm) cc_final: 0.4925 (mtt) REVERT: n 209 LYS cc_start: 0.8525 (mmmm) cc_final: 0.8272 (tptp) REVERT: o 177 ARG cc_start: -0.1138 (OUTLIER) cc_final: -0.1360 (mtp180) REVERT: p 94 ARG cc_start: 0.6939 (ptp-170) cc_final: 0.6481 (ptp-170) REVERT: p 151 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7537 (ttm-80) REVERT: q 141 SER cc_start: 0.0150 (OUTLIER) cc_final: -0.0255 (m) REVERT: r 133 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7065 (ptt-90) REVERT: u 5 GLN cc_start: 0.7726 (mt0) cc_final: 0.7393 (mt0) REVERT: w 53 VAL cc_start: 0.8282 (OUTLIER) cc_final: 0.8077 (p) REVERT: w 121 VAL cc_start: 0.8497 (t) cc_final: 0.8214 (p) REVERT: z 23 ARG cc_start: 0.7107 (OUTLIER) cc_final: 0.6610 (ttt90) outliers start: 722 outliers final: 487 residues processed: 2126 average time/residue: 1.2038 time to fit residues: 4491.3907 Evaluate side-chains 2072 residues out of total 11710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 532 poor density : 1540 time to evaluate : 8.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 147 HIS Chi-restraints excluded: chain A residue 150 HIS Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 243 TRP Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 250 PHE Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 417 PHE Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 502 GLN Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 533 GLN Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 687 PHE Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 738 PHE Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 772 ARG Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain B residue 859 ILE Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 103 PHE Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 186 LYS Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 198 ASN Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 249 ILE Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 172 CYS Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 211 HIS Chi-restraints excluded: chain F residue 214 ARG Chi-restraints excluded: chain F residue 216 HIS Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 233 THR Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 245 THR Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 263 SER Chi-restraints excluded: chain F residue 281 THR Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 318 THR Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 338 SER Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 363 HIS Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 398 VAL Chi-restraints excluded: chain F residue 401 CYS Chi-restraints excluded: chain F residue 406 ILE Chi-restraints excluded: chain F residue 420 VAL Chi-restraints excluded: chain F residue 438 THR Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 70 ASP Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 153 SER Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain G residue 191 ASP Chi-restraints excluded: chain G residue 194 SER Chi-restraints excluded: chain G residue 267 ILE Chi-restraints excluded: chain G residue 274 VAL Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 304 THR Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 129 ARG Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 223 VAL Chi-restraints excluded: chain H residue 247 MET Chi-restraints excluded: chain H residue 257 THR Chi-restraints excluded: chain I residue 846 LEU Chi-restraints excluded: chain I residue 862 ASN Chi-restraints excluded: chain I residue 877 ILE Chi-restraints excluded: chain I residue 890 VAL Chi-restraints excluded: chain I residue 906 LEU Chi-restraints excluded: chain I residue 921 ILE Chi-restraints excluded: chain J residue 777 VAL Chi-restraints excluded: chain J residue 797 VAL Chi-restraints excluded: chain J residue 818 THR Chi-restraints excluded: chain J residue 829 VAL Chi-restraints excluded: chain J residue 863 ILE Chi-restraints excluded: chain J residue 867 THR Chi-restraints excluded: chain J residue 881 SER Chi-restraints excluded: chain J residue 888 LEU Chi-restraints excluded: chain K residue 327 ILE Chi-restraints excluded: chain K residue 329 THR Chi-restraints excluded: chain K residue 340 VAL Chi-restraints excluded: chain K residue 343 LEU Chi-restraints excluded: chain K residue 905 VAL Chi-restraints excluded: chain L residue 86 ILE Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 150 THR Chi-restraints excluded: chain L residue 158 THR Chi-restraints excluded: chain L residue 190 VAL Chi-restraints excluded: chain L residue 317 ILE Chi-restraints excluded: chain L residue 334 LEU Chi-restraints excluded: chain L residue 336 VAL Chi-restraints excluded: chain L residue 347 THR Chi-restraints excluded: chain M residue 111 ILE Chi-restraints excluded: chain M residue 148 LEU Chi-restraints excluded: chain M residue 162 ASP Chi-restraints excluded: chain M residue 165 ILE Chi-restraints excluded: chain M residue 170 TRP Chi-restraints excluded: chain M residue 219 ILE Chi-restraints excluded: chain M residue 289 ILE Chi-restraints excluded: chain M residue 312 ILE Chi-restraints excluded: chain M residue 377 THR Chi-restraints excluded: chain M residue 389 VAL Chi-restraints excluded: chain M residue 399 ILE Chi-restraints excluded: chain M residue 402 ILE Chi-restraints excluded: chain M residue 425 THR Chi-restraints excluded: chain M residue 920 VAL Chi-restraints excluded: chain N residue 51 GLU Chi-restraints excluded: chain N residue 144 LEU Chi-restraints excluded: chain N residue 157 LEU Chi-restraints excluded: chain N residue 158 ARG Chi-restraints excluded: chain N residue 260 THR Chi-restraints excluded: chain N residue 279 SER Chi-restraints excluded: chain N residue 293 SER Chi-restraints excluded: chain N residue 323 THR Chi-restraints excluded: chain N residue 448 THR Chi-restraints excluded: chain N residue 449 ARG Chi-restraints excluded: chain N residue 528 LYS Chi-restraints excluded: chain N residue 541 THR Chi-restraints excluded: chain N residue 575 THR Chi-restraints excluded: chain N residue 591 THR Chi-restraints excluded: chain O residue 40 THR Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 85 VAL Chi-restraints excluded: chain O residue 97 THR Chi-restraints excluded: chain O residue 151 ILE Chi-restraints excluded: chain O residue 161 VAL Chi-restraints excluded: chain O residue 185 LEU Chi-restraints excluded: chain O residue 201 VAL Chi-restraints excluded: chain O residue 222 LEU Chi-restraints excluded: chain O residue 254 VAL Chi-restraints excluded: chain O residue 276 VAL Chi-restraints excluded: chain O residue 279 ILE Chi-restraints excluded: chain O residue 286 LEU Chi-restraints excluded: chain O residue 300 THR Chi-restraints excluded: chain O residue 340 ILE Chi-restraints excluded: chain O residue 351 VAL Chi-restraints excluded: chain O residue 369 SER Chi-restraints excluded: chain O residue 378 LEU Chi-restraints excluded: chain O residue 446 LEU Chi-restraints excluded: chain O residue 472 LEU Chi-restraints excluded: chain O residue 486 MET Chi-restraints excluded: chain O residue 506 THR Chi-restraints excluded: chain O residue 546 THR Chi-restraints excluded: chain O residue 547 VAL Chi-restraints excluded: chain O residue 550 SER Chi-restraints excluded: chain O residue 554 THR Chi-restraints excluded: chain O residue 557 LEU Chi-restraints excluded: chain O residue 560 SER Chi-restraints excluded: chain O residue 564 SER Chi-restraints excluded: chain O residue 629 VAL Chi-restraints excluded: chain O residue 630 VAL Chi-restraints excluded: chain O residue 640 CYS Chi-restraints excluded: chain O residue 660 ILE Chi-restraints excluded: chain O residue 702 GLU Chi-restraints excluded: chain O residue 733 VAL Chi-restraints excluded: chain O residue 771 LEU Chi-restraints excluded: chain O residue 773 VAL Chi-restraints excluded: chain O residue 785 VAL Chi-restraints excluded: chain O residue 840 MET Chi-restraints excluded: chain O residue 843 LEU Chi-restraints excluded: chain O residue 854 LEU Chi-restraints excluded: chain O residue 859 ILE Chi-restraints excluded: chain O residue 943 HIS Chi-restraints excluded: chain O residue 954 LEU Chi-restraints excluded: chain O residue 1006 ILE Chi-restraints excluded: chain O residue 1012 LEU Chi-restraints excluded: chain P residue 6 ILE Chi-restraints excluded: chain P residue 15 LYS Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 63 ASN Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 128 THR Chi-restraints excluded: chain P residue 168 VAL Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 203 VAL Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 256 SER Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain S residue 183 VAL Chi-restraints excluded: chain S residue 203 VAL Chi-restraints excluded: chain S residue 292 LEU Chi-restraints excluded: chain T residue 8 LEU Chi-restraints excluded: chain T residue 19 GLU Chi-restraints excluded: chain T residue 26 THR Chi-restraints excluded: chain T residue 52 SER Chi-restraints excluded: chain T residue 66 ILE Chi-restraints excluded: chain T residue 88 GLN Chi-restraints excluded: chain T residue 173 ASN Chi-restraints excluded: chain T residue 184 LEU Chi-restraints excluded: chain T residue 274 VAL Chi-restraints excluded: chain T residue 312 THR Chi-restraints excluded: chain T residue 321 HIS Chi-restraints excluded: chain T residue 334 SER Chi-restraints excluded: chain U residue 166 VAL Chi-restraints excluded: chain U residue 169 VAL Chi-restraints excluded: chain U residue 212 LEU Chi-restraints excluded: chain U residue 237 VAL Chi-restraints excluded: chain U residue 251 THR Chi-restraints excluded: chain U residue 341 TYR Chi-restraints excluded: chain U residue 348 SER Chi-restraints excluded: chain U residue 369 ILE Chi-restraints excluded: chain V residue 17 LEU Chi-restraints excluded: chain V residue 52 LEU Chi-restraints excluded: chain V residue 95 SER Chi-restraints excluded: chain V residue 104 THR Chi-restraints excluded: chain V residue 105 SER Chi-restraints excluded: chain V residue 125 LEU Chi-restraints excluded: chain W residue 18 VAL Chi-restraints excluded: chain W residue 62 LEU Chi-restraints excluded: chain W residue 77 VAL Chi-restraints excluded: chain W residue 86 VAL Chi-restraints excluded: chain W residue 94 VAL Chi-restraints excluded: chain W residue 102 SER Chi-restraints excluded: chain W residue 103 LEU Chi-restraints excluded: chain X residue 182 TYR Chi-restraints excluded: chain X residue 273 TYR Chi-restraints excluded: chain X residue 312 VAL Chi-restraints excluded: chain X residue 432 ILE Chi-restraints excluded: chain X residue 471 THR Chi-restraints excluded: chain X residue 478 ILE Chi-restraints excluded: chain X residue 502 VAL Chi-restraints excluded: chain X residue 580 VAL Chi-restraints excluded: chain X residue 582 THR Chi-restraints excluded: chain X residue 606 VAL Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Y residue 58 GLU Chi-restraints excluded: chain Y residue 60 VAL Chi-restraints excluded: chain Y residue 75 ILE Chi-restraints excluded: chain Y residue 82 ILE Chi-restraints excluded: chain Y residue 98 ILE Chi-restraints excluded: chain Y residue 102 ILE Chi-restraints excluded: chain Y residue 111 THR Chi-restraints excluded: chain Y residue 142 THR Chi-restraints excluded: chain Y residue 152 THR Chi-restraints excluded: chain Y residue 164 PHE Chi-restraints excluded: chain Y residue 221 VAL Chi-restraints excluded: chain Y residue 305 VAL Chi-restraints excluded: chain Y residue 318 LEU Chi-restraints excluded: chain Y residue 334 THR Chi-restraints excluded: chain Y residue 356 VAL Chi-restraints excluded: chain Y residue 396 VAL Chi-restraints excluded: chain Y residue 398 VAL Chi-restraints excluded: chain Z residue 84 LEU Chi-restraints excluded: chain Z residue 89 VAL Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain Z residue 106 VAL Chi-restraints excluded: chain Z residue 140 ILE Chi-restraints excluded: chain Z residue 156 ILE Chi-restraints excluded: chain Z residue 166 VAL Chi-restraints excluded: chain Z residue 170 LEU Chi-restraints excluded: chain Z residue 175 LEU Chi-restraints excluded: chain Z residue 176 PHE Chi-restraints excluded: chain Z residue 195 THR Chi-restraints excluded: chain Z residue 205 TYR Chi-restraints excluded: chain Z residue 271 SER Chi-restraints excluded: chain Z residue 789 CYS Chi-restraints excluded: chain Z residue 799 LEU Chi-restraints excluded: chain Z residue 834 ILE Chi-restraints excluded: chain Z residue 842 PHE Chi-restraints excluded: chain Z residue 845 LEU Chi-restraints excluded: chain Z residue 850 ILE Chi-restraints excluded: chain Z residue 866 HIS Chi-restraints excluded: chain Z residue 867 MET Chi-restraints excluded: chain Z residue 878 ILE Chi-restraints excluded: chain Z residue 886 CYS Chi-restraints excluded: chain Z residue 902 THR Chi-restraints excluded: chain Z residue 904 THR Chi-restraints excluded: chain Z residue 914 ILE Chi-restraints excluded: chain Z residue 915 VAL Chi-restraints excluded: chain Z residue 923 THR Chi-restraints excluded: chain Z residue 931 THR Chi-restraints excluded: chain Z residue 934 ILE Chi-restraints excluded: chain Z residue 952 ILE Chi-restraints excluded: chain Z residue 972 TYR Chi-restraints excluded: chain Z residue 988 ILE Chi-restraints excluded: chain Z residue 1038 ILE Chi-restraints excluded: chain Z residue 1058 LEU Chi-restraints excluded: chain Z residue 1081 VAL Chi-restraints excluded: chain Z residue 1083 VAL Chi-restraints excluded: chain Z residue 1093 LEU Chi-restraints excluded: chain Z residue 1126 ILE Chi-restraints excluded: chain a residue 20 ASN Chi-restraints excluded: chain a residue 30 HIS Chi-restraints excluded: chain a residue 51 CYS Chi-restraints excluded: chain a residue 62 SER Chi-restraints excluded: chain a residue 95 SER Chi-restraints excluded: chain a residue 102 THR Chi-restraints excluded: chain a residue 103 VAL Chi-restraints excluded: chain a residue 113 VAL Chi-restraints excluded: chain a residue 131 ILE Chi-restraints excluded: chain a residue 136 VAL Chi-restraints excluded: chain a residue 149 LEU Chi-restraints excluded: chain a residue 158 VAL Chi-restraints excluded: chain b residue 107 ILE Chi-restraints excluded: chain b residue 109 LEU Chi-restraints excluded: chain b residue 115 ILE Chi-restraints excluded: chain b residue 117 LEU Chi-restraints excluded: chain b residue 127 LEU Chi-restraints excluded: chain b residue 130 SER Chi-restraints excluded: chain b residue 139 ILE Chi-restraints excluded: chain b residue 140 ILE Chi-restraints excluded: chain b residue 156 HIS Chi-restraints excluded: chain b residue 167 LEU Chi-restraints excluded: chain b residue 184 VAL Chi-restraints excluded: chain b residue 198 THR Chi-restraints excluded: chain b residue 205 VAL Chi-restraints excluded: chain b residue 229 THR Chi-restraints excluded: chain b residue 231 VAL Chi-restraints excluded: chain b residue 239 VAL Chi-restraints excluded: chain b residue 243 VAL Chi-restraints excluded: chain b residue 262 THR Chi-restraints excluded: chain b residue 263 MET Chi-restraints excluded: chain b residue 290 THR Chi-restraints excluded: chain c residue 494 LEU Chi-restraints excluded: chain c residue 501 THR Chi-restraints excluded: chain c residue 502 LEU Chi-restraints excluded: chain c residue 526 VAL Chi-restraints excluded: chain c residue 538 SER Chi-restraints excluded: chain c residue 555 ASP Chi-restraints excluded: chain c residue 619 ILE Chi-restraints excluded: chain c residue 633 LEU Chi-restraints excluded: chain c residue 634 SER Chi-restraints excluded: chain c residue 696 VAL Chi-restraints excluded: chain d residue 6 LEU Chi-restraints excluded: chain d residue 47 VAL Chi-restraints excluded: chain d residue 88 ASP Chi-restraints excluded: chain d residue 90 VAL Chi-restraints excluded: chain d residue 91 VAL Chi-restraints excluded: chain d residue 98 THR Chi-restraints excluded: chain d residue 116 LEU Chi-restraints excluded: chain d residue 132 ILE Chi-restraints excluded: chain d residue 147 ILE Chi-restraints excluded: chain d residue 159 LEU Chi-restraints excluded: chain d residue 177 ILE Chi-restraints excluded: chain d residue 200 ILE Chi-restraints excluded: chain d residue 201 THR Chi-restraints excluded: chain d residue 215 SER Chi-restraints excluded: chain d residue 233 VAL Chi-restraints excluded: chain d residue 236 THR Chi-restraints excluded: chain d residue 253 MET Chi-restraints excluded: chain d residue 283 VAL Chi-restraints excluded: chain d residue 292 SER Chi-restraints excluded: chain d residue 298 LEU Chi-restraints excluded: chain d residue 300 SER Chi-restraints excluded: chain d residue 343 THR Chi-restraints excluded: chain d residue 392 ARG Chi-restraints excluded: chain d residue 397 LEU Chi-restraints excluded: chain d residue 441 VAL Chi-restraints excluded: chain e residue 118 LYS Chi-restraints excluded: chain e residue 133 THR Chi-restraints excluded: chain e residue 202 ILE Chi-restraints excluded: chain e residue 204 VAL Chi-restraints excluded: chain f residue 181 SER Chi-restraints excluded: chain g residue 73 ILE Chi-restraints excluded: chain g residue 130 VAL Chi-restraints excluded: chain g residue 156 LEU Chi-restraints excluded: chain g residue 188 THR Chi-restraints excluded: chain g residue 201 LEU Chi-restraints excluded: chain g residue 203 ILE Chi-restraints excluded: chain h residue 87 ILE Chi-restraints excluded: chain h residue 161 LEU Chi-restraints excluded: chain h residue 210 VAL Chi-restraints excluded: chain h residue 246 ASN Chi-restraints excluded: chain k residue 86 THR Chi-restraints excluded: chain k residue 110 ARG Chi-restraints excluded: chain k residue 115 VAL Chi-restraints excluded: chain k residue 117 MET Chi-restraints excluded: chain k residue 165 VAL Chi-restraints excluded: chain l residue 67 GLU Chi-restraints excluded: chain l residue 68 VAL Chi-restraints excluded: chain l residue 181 LEU Chi-restraints excluded: chain l residue 185 VAL Chi-restraints excluded: chain m residue 40 ASP Chi-restraints excluded: chain m residue 78 THR Chi-restraints excluded: chain m residue 79 ASP Chi-restraints excluded: chain m residue 90 ILE Chi-restraints excluded: chain m residue 114 ILE Chi-restraints excluded: chain m residue 172 PHE Chi-restraints excluded: chain m residue 176 ASP Chi-restraints excluded: chain m residue 189 MET Chi-restraints excluded: chain m residue 202 ASP Chi-restraints excluded: chain m residue 227 VAL Chi-restraints excluded: chain n residue 34 SER Chi-restraints excluded: chain n residue 38 ILE Chi-restraints excluded: chain n residue 60 SER Chi-restraints excluded: chain n residue 86 MET Chi-restraints excluded: chain n residue 174 VAL Chi-restraints excluded: chain n residue 193 SER Chi-restraints excluded: chain n residue 194 ASN Chi-restraints excluded: chain n residue 195 SER Chi-restraints excluded: chain o residue 52 ILE Chi-restraints excluded: chain o residue 63 MET Chi-restraints excluded: chain o residue 162 VAL Chi-restraints excluded: chain o residue 177 ARG Chi-restraints excluded: chain o residue 187 LEU Chi-restraints excluded: chain p residue 73 LEU Chi-restraints excluded: chain p residue 143 VAL Chi-restraints excluded: chain p residue 151 ARG Chi-restraints excluded: chain p residue 162 VAL Chi-restraints excluded: chain p residue 178 THR Chi-restraints excluded: chain q residue 36 THR Chi-restraints excluded: chain q residue 44 HIS Chi-restraints excluded: chain q residue 60 LEU Chi-restraints excluded: chain q residue 136 VAL Chi-restraints excluded: chain q residue 141 SER Chi-restraints excluded: chain q residue 193 LEU Chi-restraints excluded: chain r residue 46 THR Chi-restraints excluded: chain r residue 94 VAL Chi-restraints excluded: chain r residue 109 THR Chi-restraints excluded: chain r residue 120 ILE Chi-restraints excluded: chain r residue 125 VAL Chi-restraints excluded: chain r residue 132 ILE Chi-restraints excluded: chain r residue 133 ARG Chi-restraints excluded: chain r residue 141 VAL Chi-restraints excluded: chain r residue 143 SER Chi-restraints excluded: chain r residue 160 SER Chi-restraints excluded: chain s residue 125 LEU Chi-restraints excluded: chain t residue 53 CYS Chi-restraints excluded: chain t residue 61 VAL Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain u residue 7 VAL Chi-restraints excluded: chain u residue 9 VAL Chi-restraints excluded: chain u residue 17 THR Chi-restraints excluded: chain u residue 23 VAL Chi-restraints excluded: chain u residue 44 LEU Chi-restraints excluded: chain u residue 48 LEU Chi-restraints excluded: chain u residue 66 ARG Chi-restraints excluded: chain u residue 69 VAL Chi-restraints excluded: chain u residue 95 LYS Chi-restraints excluded: chain u residue 97 VAL Chi-restraints excluded: chain v residue 66 THR Chi-restraints excluded: chain w residue 13 SER Chi-restraints excluded: chain w residue 51 GLU Chi-restraints excluded: chain w residue 53 VAL Chi-restraints excluded: chain x residue 52 ILE Chi-restraints excluded: chain x residue 83 VAL Chi-restraints excluded: chain y residue 337 THR Chi-restraints excluded: chain y residue 391 LEU Chi-restraints excluded: chain z residue 23 ARG Chi-restraints excluded: chain z residue 31 VAL Chi-restraints excluded: chain z residue 37 THR Chi-restraints excluded: chain z residue 40 SER Chi-restraints excluded: chain z residue 55 LEU Chi-restraints excluded: chain z residue 57 LEU Chi-restraints excluded: chain z residue 66 ARG Chi-restraints excluded: chain 0 residue 164 LEU Chi-restraints excluded: chain 0 residue 184 SER Chi-restraints excluded: chain 0 residue 192 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1508 random chunks: chunk 1213 optimal weight: 9.9990 chunk 827 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 1085 optimal weight: 8.9990 chunk 601 optimal weight: 6.9990 chunk 1243 optimal weight: 0.0030 chunk 1007 optimal weight: 50.0000 chunk 1 optimal weight: 0.5980 chunk 744 optimal weight: 0.7980 chunk 1308 optimal weight: 2.9990 chunk 367 optimal weight: 0.9980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 35 ASN ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 273 GLN E 140 ASN E 158 GLN F 49 GLN F 190 GLN ** F 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 299 HIS G 103 HIS G 131 ASN G 349 HIS H 117 ASN ** J 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 333 ASN ** K 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 370 GLN N 399 ASN N 440 GLN O 117 GLN ** O 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 636 HIS ** O 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 39 GLN ** P 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 336 HIS ** U 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 165 GLN X 302 GLN X 436 HIS ** Z 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 239 ASN Z1030 ASN a 16 HIS a 30 HIS ** b 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 242 HIS e 170 HIS k 179 HIS ** l 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 118 GLN n 31 ASN n 91 ASN n 194 ASN ** o 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 179 GLN ** r 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 44 HIS ** y 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6172 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 140828 Z= 0.186 Angle : 0.684 40.699 198339 Z= 0.345 Chirality : 0.042 0.308 24279 Planarity : 0.005 0.079 19356 Dihedral : 21.448 179.806 39627 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.18 % Favored : 92.73 % Rotamer: Outliers : 4.66 % Allowed : 18.42 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.02 % Twisted Proline : 0.83 % Twisted General : 0.08 % 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: -1.80 (0.07), residues: 13489 helix: 0.35 (0.07), residues: 4734 sheet: -1.44 (0.09), residues: 2645 loop : -2.35 (0.08), residues: 6110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP N 426 HIS 0.022 0.001 HIS a 30 PHE 0.039 0.002 PHE A 687 TYR 0.023 0.002 TYR F 314 ARG 0.012 0.001 ARG M 296 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26978 Ramachandran restraints generated. 13489 Oldfield, 0 Emsley, 13489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26978 Ramachandran restraints generated. 13489 Oldfield, 0 Emsley, 13489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2192 residues out of total 11710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 448 poor density : 1744 time to evaluate : 9.541 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: A 81 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7126 (tt) REVERT: A 90 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8313 (tp) REVERT: A 452 ILE cc_start: 0.7951 (OUTLIER) cc_final: 0.7651 (mt) REVERT: A 459 GLN cc_start: 0.7974 (pt0) cc_final: 0.7073 (mm110) REVERT: A 698 TYR cc_start: 0.8000 (m-80) cc_final: 0.7697 (m-80) REVERT: A 826 MET cc_start: 0.6386 (ttp) cc_final: 0.6089 (ptp) REVERT: B 861 ARG cc_start: 0.8107 (mtm-85) cc_final: 0.7074 (mtm-85) REVERT: B 900 LYS cc_start: 0.7823 (tptp) cc_final: 0.7338 (mtmt) REVERT: D 80 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8174 (pp) REVERT: D 195 GLN cc_start: 0.6733 (OUTLIER) cc_final: 0.6403 (tp40) REVERT: D 292 ILE cc_start: 0.8345 (mm) cc_final: 0.8090 (mm) REVERT: D 323 GLN cc_start: 0.7823 (tp40) cc_final: 0.7567 (mm-40) REVERT: E 20 ARG cc_start: 0.7057 (tmt170) cc_final: 0.6806 (ttp80) REVERT: E 102 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8595 (tppt) REVERT: E 191 ARG cc_start: 0.6757 (mtp180) cc_final: 0.6322 (mtt-85) REVERT: F 106 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7260 (tt) REVERT: F 326 ILE cc_start: 0.7894 (pt) cc_final: 0.7685 (pt) REVERT: F 425 GLU cc_start: 0.7858 (tp30) cc_final: 0.7647 (tp30) REVERT: G 25 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7704 (tp) REVERT: H 34 TYR cc_start: 0.7561 (t80) cc_final: 0.7135 (t80) REVERT: I 790 MET cc_start: 0.4157 (tpp) cc_final: 0.3887 (mtp) REVERT: I 877 ILE cc_start: 0.7408 (OUTLIER) cc_final: 0.7081 (pt) REVERT: I 895 MET cc_start: 0.6147 (mmp) cc_final: 0.5714 (tpt) REVERT: J 815 ASP cc_start: 0.7772 (m-30) cc_final: 0.7381 (m-30) REVERT: J 818 THR cc_start: 0.8520 (m) cc_final: 0.8297 (p) REVERT: L 137 LEU cc_start: 0.7220 (OUTLIER) cc_final: 0.6898 (mp) REVERT: L 274 LYS cc_start: 0.6274 (mtmt) cc_final: 0.6043 (mttt) REVERT: L 298 LYS cc_start: 0.3630 (tptt) cc_final: 0.2900 (tmtt) REVERT: M 262 HIS cc_start: 0.7326 (m-70) cc_final: 0.7114 (m170) REVERT: N 52 GLU cc_start: 0.7689 (tm-30) cc_final: 0.7467 (tm-30) REVERT: N 63 LYS cc_start: 0.7727 (mtpt) cc_final: 0.7303 (pttt) REVERT: N 144 LEU cc_start: 0.5858 (OUTLIER) cc_final: 0.5485 (tm) REVERT: N 157 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8354 (pp) REVERT: N 393 LYS cc_start: 0.7652 (tptt) cc_final: 0.7393 (tttt) REVERT: N 397 MET cc_start: 0.6818 (pmm) cc_final: 0.6267 (pmm) REVERT: N 449 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.7778 (ttp-110) REVERT: O 861 LYS cc_start: 0.6442 (mttt) cc_final: 0.6007 (mmtt) REVERT: O 1006 ILE cc_start: 0.8138 (OUTLIER) cc_final: 0.7586 (pp) REVERT: O 1007 MET cc_start: 0.7955 (ttm) cc_final: 0.7488 (ttm) REVERT: P 28 LYS cc_start: 0.7782 (mttt) cc_final: 0.7451 (tptm) REVERT: P 122 THR cc_start: 0.8555 (t) cc_final: 0.8122 (p) REVERT: P 150 ASP cc_start: 0.8352 (p0) cc_final: 0.7990 (p0) REVERT: P 155 ARG cc_start: 0.8085 (ttm170) cc_final: 0.6605 (ttt-90) REVERT: R 205 PRO cc_start: 0.8125 (Cg_endo) cc_final: 0.7779 (Cg_exo) REVERT: T 392 ILE cc_start: 0.8501 (tp) cc_final: 0.8274 (pt) REVERT: T 398 LYS cc_start: 0.8254 (ttpt) cc_final: 0.7772 (pttp) REVERT: U 133 MET cc_start: 0.0868 (ttt) cc_final: -0.0512 (mmt) REVERT: U 179 LEU cc_start: 0.8310 (tt) cc_final: 0.7928 (mp) REVERT: U 226 SER cc_start: 0.8046 (m) cc_final: 0.7761 (p) REVERT: W 35 LYS cc_start: 0.8155 (mmtm) cc_final: 0.7851 (mmtt) REVERT: W 121 LYS cc_start: 0.7666 (tppt) cc_final: 0.7398 (mtpp) REVERT: X 182 TYR cc_start: 0.5834 (OUTLIER) cc_final: 0.4072 (t80) REVERT: X 462 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7763 (mt0) REVERT: Y 131 ARG cc_start: 0.7079 (tpp80) cc_final: 0.6873 (tpp80) REVERT: Z 176 PHE cc_start: 0.7522 (OUTLIER) cc_final: 0.6505 (m-10) REVERT: Z 931 THR cc_start: 0.8542 (p) cc_final: 0.8298 (m) REVERT: Z 972 TYR cc_start: 0.8002 (OUTLIER) cc_final: 0.7318 (m-10) REVERT: Z 1129 ARG cc_start: 0.7187 (mtt180) cc_final: 0.6650 (ptt90) REVERT: Z 1130 ARG cc_start: 0.6461 (tpp80) cc_final: 0.5851 (tpt170) REVERT: b 66 LYS cc_start: 0.7977 (mmtt) cc_final: 0.7588 (mtpp) REVERT: b 109 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8430 (mp) REVERT: b 126 ASP cc_start: 0.6559 (t0) cc_final: 0.6243 (t0) REVERT: b 138 ASP cc_start: 0.6762 (t0) cc_final: 0.6553 (t0) REVERT: b 230 PHE cc_start: 0.8082 (m-80) cc_final: 0.7600 (m-80) REVERT: c 502 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8421 (mm) REVERT: c 676 MET cc_start: 0.6897 (ptp) cc_final: 0.4601 (mmt) REVERT: d 177 ILE cc_start: 0.7778 (OUTLIER) cc_final: 0.7553 (pt) REVERT: d 184 HIS cc_start: 0.6589 (OUTLIER) cc_final: 0.5925 (p-80) REVERT: d 250 MET cc_start: 0.8479 (mmm) cc_final: 0.7483 (mmm) REVERT: d 397 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7940 (pp) REVERT: e 92 THR cc_start: 0.4736 (p) cc_final: 0.4526 (t) REVERT: e 113 TYR cc_start: 0.7058 (m-80) cc_final: 0.6430 (m-80) REVERT: g 172 MET cc_start: 0.5072 (mtt) cc_final: 0.4836 (mtt) REVERT: g 183 ARG cc_start: 0.6636 (OUTLIER) cc_final: 0.6002 (mtp85) REVERT: g 204 LYS cc_start: 0.7748 (mttt) cc_final: 0.7304 (mmtt) REVERT: h 206 LYS cc_start: 0.6637 (tptt) cc_final: 0.5839 (ttmt) REVERT: h 246 ASN cc_start: 0.6292 (OUTLIER) cc_final: 0.5987 (m-40) REVERT: l 168 MET cc_start: 0.6225 (tpp) cc_final: 0.5946 (mmt) REVERT: n 96 MET cc_start: 0.7907 (ttp) cc_final: 0.7692 (ttp) REVERT: n 111 MET cc_start: 0.5858 (ttt) cc_final: 0.5409 (ttt) REVERT: n 209 LYS cc_start: 0.8465 (mmmm) cc_final: 0.8235 (tptt) REVERT: v 127 MET cc_start: 0.3773 (tmm) cc_final: 0.3510 (tmm) REVERT: x 107 PHE cc_start: 0.6938 (OUTLIER) cc_final: 0.6467 (m-80) REVERT: z 23 ARG cc_start: 0.6685 (OUTLIER) cc_final: 0.6385 (ttt90) outliers start: 448 outliers final: 271 residues processed: 2022 average time/residue: 1.1537 time to fit residues: 4043.9339 Evaluate side-chains 1871 residues out of total 11710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 298 poor density : 1573 time to evaluate : 9.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 147 HIS Chi-restraints excluded: chain A residue 150 HIS Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 250 PHE Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 533 GLN Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 772 ARG Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 103 PHE Chi-restraints excluded: chain D residue 195 GLN Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 249 ILE Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain E residue 102 LYS Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 172 CYS Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 318 THR Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 338 SER Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 401 CYS Chi-restraints excluded: chain F residue 406 ILE Chi-restraints excluded: chain F residue 407 LEU Chi-restraints excluded: chain F residue 420 VAL Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 153 SER Chi-restraints excluded: chain G residue 191 ASP Chi-restraints excluded: chain G residue 267 ILE Chi-restraints excluded: chain H residue 2 SER Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain I residue 871 VAL Chi-restraints excluded: chain I residue 877 ILE Chi-restraints excluded: chain I residue 906 LEU Chi-restraints excluded: chain I residue 921 ILE Chi-restraints excluded: chain J residue 789 THR Chi-restraints excluded: chain J residue 860 LEU Chi-restraints excluded: chain J residue 863 ILE Chi-restraints excluded: chain K residue 369 LEU Chi-restraints excluded: chain K residue 905 VAL Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 150 THR Chi-restraints excluded: chain L residue 158 THR Chi-restraints excluded: chain L residue 190 VAL Chi-restraints excluded: chain L residue 239 LEU Chi-restraints excluded: chain L residue 267 ARG Chi-restraints excluded: chain L residue 334 LEU Chi-restraints excluded: chain L residue 347 THR Chi-restraints excluded: chain M residue 111 ILE Chi-restraints excluded: chain M residue 162 ASP Chi-restraints excluded: chain M residue 170 TRP Chi-restraints excluded: chain M residue 219 ILE Chi-restraints excluded: chain M residue 312 ILE Chi-restraints excluded: chain M residue 432 MET Chi-restraints excluded: chain N residue 144 LEU Chi-restraints excluded: chain N residue 157 LEU Chi-restraints excluded: chain N residue 260 THR Chi-restraints excluded: chain N residue 278 SER Chi-restraints excluded: chain N residue 323 THR Chi-restraints excluded: chain N residue 449 ARG Chi-restraints excluded: chain N residue 575 THR Chi-restraints excluded: chain O residue 151 ILE Chi-restraints excluded: chain O residue 161 VAL Chi-restraints excluded: chain O residue 254 VAL Chi-restraints excluded: chain O residue 286 LEU Chi-restraints excluded: chain O residue 351 VAL Chi-restraints excluded: chain O residue 369 SER Chi-restraints excluded: chain O residue 506 THR Chi-restraints excluded: chain O residue 546 THR Chi-restraints excluded: chain O residue 557 LEU Chi-restraints excluded: chain O residue 560 SER Chi-restraints excluded: chain O residue 629 VAL Chi-restraints excluded: chain O residue 630 VAL Chi-restraints excluded: chain O residue 638 VAL Chi-restraints excluded: chain O residue 660 ILE Chi-restraints excluded: chain O residue 718 ASP Chi-restraints excluded: chain O residue 733 VAL Chi-restraints excluded: chain O residue 756 PHE Chi-restraints excluded: chain O residue 771 LEU Chi-restraints excluded: chain O residue 773 VAL Chi-restraints excluded: chain O residue 785 VAL Chi-restraints excluded: chain O residue 843 LEU Chi-restraints excluded: chain O residue 854 LEU Chi-restraints excluded: chain O residue 943 HIS Chi-restraints excluded: chain O residue 1006 ILE Chi-restraints excluded: chain P residue 6 ILE Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 168 VAL Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 203 VAL Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 256 SER Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain S residue 183 VAL Chi-restraints excluded: chain S residue 203 VAL Chi-restraints excluded: chain S residue 204 ILE Chi-restraints excluded: chain S residue 225 VAL Chi-restraints excluded: chain S residue 292 LEU Chi-restraints excluded: chain T residue 8 LEU Chi-restraints excluded: chain T residue 19 GLU Chi-restraints excluded: chain T residue 52 SER Chi-restraints excluded: chain T residue 108 GLU Chi-restraints excluded: chain T residue 173 ASN Chi-restraints excluded: chain T residue 179 GLN Chi-restraints excluded: chain T residue 184 LEU Chi-restraints excluded: chain T residue 274 VAL Chi-restraints excluded: chain T residue 295 LEU Chi-restraints excluded: chain T residue 312 THR Chi-restraints excluded: chain T residue 321 HIS Chi-restraints excluded: chain T residue 334 SER Chi-restraints excluded: chain U residue 169 VAL Chi-restraints excluded: chain U residue 237 VAL Chi-restraints excluded: chain U residue 341 TYR Chi-restraints excluded: chain V residue 17 LEU Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain W residue 71 ILE Chi-restraints excluded: chain W residue 94 VAL Chi-restraints excluded: chain W residue 102 SER Chi-restraints excluded: chain W residue 103 LEU Chi-restraints excluded: chain X residue 182 TYR Chi-restraints excluded: chain X residue 261 VAL Chi-restraints excluded: chain X residue 270 LEU Chi-restraints excluded: chain X residue 312 VAL Chi-restraints excluded: chain X residue 432 ILE Chi-restraints excluded: chain X residue 462 GLN Chi-restraints excluded: chain X residue 502 VAL Chi-restraints excluded: chain X residue 579 VAL Chi-restraints excluded: chain X residue 580 VAL Chi-restraints excluded: chain X residue 582 THR Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Y residue 65 ILE Chi-restraints excluded: chain Y residue 98 ILE Chi-restraints excluded: chain Y residue 102 ILE Chi-restraints excluded: chain Y residue 114 LEU Chi-restraints excluded: chain Y residue 152 THR Chi-restraints excluded: chain Y residue 164 PHE Chi-restraints excluded: chain Y residue 305 VAL Chi-restraints excluded: chain Y residue 318 LEU Chi-restraints excluded: chain Y residue 396 VAL Chi-restraints excluded: chain Z residue 84 LEU Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain Z residue 136 VAL Chi-restraints excluded: chain Z residue 166 VAL Chi-restraints excluded: chain Z residue 170 LEU Chi-restraints excluded: chain Z residue 176 PHE Chi-restraints excluded: chain Z residue 205 TYR Chi-restraints excluded: chain Z residue 271 SER Chi-restraints excluded: chain Z residue 789 CYS Chi-restraints excluded: chain Z residue 799 LEU Chi-restraints excluded: chain Z residue 842 PHE Chi-restraints excluded: chain Z residue 845 LEU Chi-restraints excluded: chain Z residue 867 MET Chi-restraints excluded: chain Z residue 878 ILE Chi-restraints excluded: chain Z residue 886 CYS Chi-restraints excluded: chain Z residue 914 ILE Chi-restraints excluded: chain Z residue 915 VAL Chi-restraints excluded: chain Z residue 952 ILE Chi-restraints excluded: chain Z residue 972 TYR Chi-restraints excluded: chain Z residue 1058 LEU Chi-restraints excluded: chain Z residue 1093 LEU Chi-restraints excluded: chain a residue 30 HIS Chi-restraints excluded: chain a residue 51 CYS Chi-restraints excluded: chain a residue 62 SER Chi-restraints excluded: chain a residue 103 VAL Chi-restraints excluded: chain a residue 113 VAL Chi-restraints excluded: chain a residue 136 VAL Chi-restraints excluded: chain a residue 158 VAL Chi-restraints excluded: chain a residue 162 VAL Chi-restraints excluded: chain b residue 109 LEU Chi-restraints excluded: chain b residue 130 SER Chi-restraints excluded: chain b residue 141 LEU Chi-restraints excluded: chain b residue 156 HIS Chi-restraints excluded: chain b residue 184 VAL Chi-restraints excluded: chain b residue 205 VAL Chi-restraints excluded: chain b residue 231 VAL Chi-restraints excluded: chain b residue 239 VAL Chi-restraints excluded: chain b residue 290 THR Chi-restraints excluded: chain c residue 494 LEU Chi-restraints excluded: chain c residue 501 THR Chi-restraints excluded: chain c residue 502 LEU Chi-restraints excluded: chain c residue 619 ILE Chi-restraints excluded: chain c residue 696 VAL Chi-restraints excluded: chain d residue 6 LEU Chi-restraints excluded: chain d residue 90 VAL Chi-restraints excluded: chain d residue 147 ILE Chi-restraints excluded: chain d residue 160 SER Chi-restraints excluded: chain d residue 177 ILE Chi-restraints excluded: chain d residue 184 HIS Chi-restraints excluded: chain d residue 185 SER Chi-restraints excluded: chain d residue 215 SER Chi-restraints excluded: chain d residue 302 SER Chi-restraints excluded: chain d residue 397 LEU Chi-restraints excluded: chain d residue 441 VAL Chi-restraints excluded: chain e residue 133 THR Chi-restraints excluded: chain e residue 163 ILE Chi-restraints excluded: chain e residue 183 ASP Chi-restraints excluded: chain e residue 245 CYS Chi-restraints excluded: chain e residue 250 ASP Chi-restraints excluded: chain g residue 73 ILE Chi-restraints excluded: chain g residue 99 ILE Chi-restraints excluded: chain g residue 130 VAL Chi-restraints excluded: chain g residue 183 ARG Chi-restraints excluded: chain g residue 201 LEU Chi-restraints excluded: chain h residue 87 ILE Chi-restraints excluded: chain h residue 219 LEU Chi-restraints excluded: chain h residue 237 LEU Chi-restraints excluded: chain h residue 246 ASN Chi-restraints excluded: chain k residue 108 LEU Chi-restraints excluded: chain k residue 172 SER Chi-restraints excluded: chain l residue 67 GLU Chi-restraints excluded: chain l residue 68 VAL Chi-restraints excluded: chain l residue 127 VAL Chi-restraints excluded: chain l residue 181 LEU Chi-restraints excluded: chain m residue 79 ASP Chi-restraints excluded: chain m residue 114 ILE Chi-restraints excluded: chain m residue 172 PHE Chi-restraints excluded: chain m residue 176 ASP Chi-restraints excluded: chain m residue 189 MET Chi-restraints excluded: chain n residue 31 ASN Chi-restraints excluded: chain n residue 34 SER Chi-restraints excluded: chain n residue 193 SER Chi-restraints excluded: chain n residue 195 SER Chi-restraints excluded: chain o residue 52 ILE Chi-restraints excluded: chain o residue 133 LEU Chi-restraints excluded: chain o residue 162 VAL Chi-restraints excluded: chain p residue 192 THR Chi-restraints excluded: chain q residue 44 HIS Chi-restraints excluded: chain q residue 60 LEU Chi-restraints excluded: chain q residue 136 VAL Chi-restraints excluded: chain r residue 94 VAL Chi-restraints excluded: chain r residue 132 ILE Chi-restraints excluded: chain r residue 160 SER Chi-restraints excluded: chain r residue 171 ARG Chi-restraints excluded: chain t residue 32 ILE Chi-restraints excluded: chain t residue 53 CYS Chi-restraints excluded: chain t residue 61 VAL Chi-restraints excluded: chain u residue 9 VAL Chi-restraints excluded: chain u residue 44 LEU Chi-restraints excluded: chain u residue 66 ARG Chi-restraints excluded: chain u residue 69 VAL Chi-restraints excluded: chain u residue 95 LYS Chi-restraints excluded: chain w residue 126 ILE Chi-restraints excluded: chain x residue 52 ILE Chi-restraints excluded: chain x residue 59 VAL Chi-restraints excluded: chain x residue 107 PHE Chi-restraints excluded: chain y residue 337 THR Chi-restraints excluded: chain y residue 388 VAL Chi-restraints excluded: chain y residue 391 LEU Chi-restraints excluded: chain z residue 23 ARG Chi-restraints excluded: chain z residue 37 THR Chi-restraints excluded: chain z residue 57 LEU Chi-restraints excluded: chain z residue 66 ARG Chi-restraints excluded: chain 0 residue 164 LEU Chi-restraints excluded: chain 0 residue 184 SER Chi-restraints excluded: chain 0 residue 227 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1508 random chunks: chunk 490 optimal weight: 2.9990 chunk 1312 optimal weight: 9.9990 chunk 288 optimal weight: 8.9990 chunk 855 optimal weight: 8.9990 chunk 359 optimal weight: 3.9990 chunk 1459 optimal weight: 20.0000 chunk 1211 optimal weight: 5.9990 chunk 675 optimal weight: 9.9990 chunk 121 optimal weight: 0.9990 chunk 482 optimal weight: 3.9990 chunk 765 optimal weight: 0.0170 overall best weight: 2.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 9 ASN A 147 HIS ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 ASN E 158 GLN ** F 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 21 ASN G 103 HIS I 886 HIS ** J 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 837 HIS K 333 ASN ** K 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 203 ASN M 242 GLN M 347 GLN ** N 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 117 GLN O 334 ASN ** O 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 636 HIS ** O 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 39 GLN R 249 GLN ** T 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 336 HIS ** U 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 27 GLN X 165 GLN X 286 GLN X 302 GLN ** Z 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 239 ASN Z1030 ASN Z1134 GLN a 30 HIS ** b 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 476 HIS ** k 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 91 ASN o 179 GLN ** o 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 179 GLN ** r 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 151 GLN v 16 GLN ** v 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 39 GLN ** w 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 44 HIS ** y 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 192 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6272 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 140828 Z= 0.348 Angle : 0.746 39.892 198339 Z= 0.376 Chirality : 0.045 0.353 24279 Planarity : 0.006 0.081 19356 Dihedral : 21.398 179.532 39626 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.76 % Favored : 91.16 % Rotamer: Outliers : 5.65 % Allowed : 18.59 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.02 % Twisted Proline : 0.66 % Twisted General : 0.08 % 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: -1.74 (0.07), residues: 13489 helix: 0.43 (0.08), residues: 4736 sheet: -1.42 (0.09), residues: 2693 loop : -2.34 (0.08), residues: 6060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.002 TRP N 426 HIS 0.019 0.002 HIS T 176 PHE 0.051 0.002 PHE A 687 TYR 0.025 0.002 TYR k 193 ARG 0.011 0.001 ARG a 34 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26978 Ramachandran restraints generated. 13489 Oldfield, 0 Emsley, 13489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26978 Ramachandran restraints generated. 13489 Oldfield, 0 Emsley, 13489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2136 residues out of total 11710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 543 poor density : 1593 time to evaluate : 11.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7500 (tt) REVERT: A 90 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8404 (tp) REVERT: A 409 TRP cc_start: 0.7397 (m100) cc_final: 0.7179 (m100) REVERT: A 459 GLN cc_start: 0.7880 (pt0) cc_final: 0.7081 (mm110) REVERT: A 518 PHE cc_start: 0.8683 (OUTLIER) cc_final: 0.7660 (m-80) REVERT: A 827 ARG cc_start: 0.7480 (ttp80) cc_final: 0.7006 (ttp-170) REVERT: B 861 ARG cc_start: 0.8175 (mtm-85) cc_final: 0.7088 (mtm-85) REVERT: B 900 LYS cc_start: 0.7896 (tptp) cc_final: 0.7321 (mtmt) REVERT: C 607 LYS cc_start: 0.8007 (tppt) cc_final: 0.7707 (tptp) REVERT: D 80 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8258 (pp) REVERT: D 195 GLN cc_start: 0.6846 (OUTLIER) cc_final: 0.6569 (tp40) REVERT: D 292 ILE cc_start: 0.8467 (OUTLIER) cc_final: 0.8180 (mm) REVERT: D 323 GLN cc_start: 0.7643 (tp40) cc_final: 0.7369 (mm-40) REVERT: E 20 ARG cc_start: 0.7064 (tmt170) cc_final: 0.6783 (ttp80) REVERT: E 23 GLU cc_start: 0.5918 (OUTLIER) cc_final: 0.5656 (tt0) REVERT: E 191 ARG cc_start: 0.6805 (mtp180) cc_final: 0.6346 (mtt-85) REVERT: E 300 PHE cc_start: 0.7635 (OUTLIER) cc_final: 0.7074 (t80) REVERT: F 106 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7350 (tt) REVERT: F 363 HIS cc_start: 0.7979 (OUTLIER) cc_final: 0.6988 (p-80) REVERT: F 425 GLU cc_start: 0.7986 (tp30) cc_final: 0.7771 (tp30) REVERT: F 442 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7011 (ttp-170) REVERT: G 25 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7829 (tp) REVERT: G 51 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.7571 (mt0) REVERT: H 69 SER cc_start: 0.8833 (p) cc_final: 0.8583 (m) REVERT: I 877 ILE cc_start: 0.7586 (OUTLIER) cc_final: 0.7160 (pt) REVERT: I 895 MET cc_start: 0.6270 (mmp) cc_final: 0.5855 (tpt) REVERT: L 137 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.7053 (mp) REVERT: L 274 LYS cc_start: 0.6407 (mtmt) cc_final: 0.6096 (mttt) REVERT: L 298 LYS cc_start: 0.4061 (tptt) cc_final: 0.3154 (tmtt) REVERT: M 98 GLN cc_start: 0.7905 (tp-100) cc_final: 0.7461 (tp40) REVERT: M 262 HIS cc_start: 0.7343 (m-70) cc_final: 0.7120 (m170) REVERT: N 52 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7471 (tm-30) REVERT: N 63 LYS cc_start: 0.7853 (mtpt) cc_final: 0.7484 (pttm) REVERT: N 144 LEU cc_start: 0.5994 (OUTLIER) cc_final: 0.5612 (tm) REVERT: N 157 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8412 (pp) REVERT: N 324 ASP cc_start: 0.7663 (p0) cc_final: 0.7461 (p0) REVERT: N 393 LYS cc_start: 0.7721 (tptt) cc_final: 0.7440 (tttt) REVERT: N 397 MET cc_start: 0.6948 (pmm) cc_final: 0.6359 (pmm) REVERT: N 449 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7785 (ttp-110) REVERT: O 340 ILE cc_start: 0.7713 (OUTLIER) cc_final: 0.7390 (tt) REVERT: O 486 MET cc_start: 0.7628 (OUTLIER) cc_final: 0.6621 (ptp) REVERT: O 858 ASP cc_start: 0.6464 (m-30) cc_final: 0.6258 (m-30) REVERT: O 861 LYS cc_start: 0.6271 (mttt) cc_final: 0.5814 (mmtt) REVERT: O 995 MET cc_start: 0.7370 (tpp) cc_final: 0.7157 (tpp) REVERT: O 1006 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7555 (pp) REVERT: O 1007 MET cc_start: 0.8044 (ttm) cc_final: 0.7714 (ttm) REVERT: P 28 LYS cc_start: 0.7798 (mttt) cc_final: 0.7438 (tptm) REVERT: P 65 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7800 (mt) REVERT: P 122 THR cc_start: 0.8547 (t) cc_final: 0.8107 (p) REVERT: P 155 ARG cc_start: 0.8068 (ttm170) cc_final: 0.6671 (ttt-90) REVERT: T 83 GLU cc_start: 0.7306 (tm-30) cc_final: 0.7080 (tm-30) REVERT: T 84 MET cc_start: 0.8051 (tpp) cc_final: 0.7353 (ttp) REVERT: T 392 ILE cc_start: 0.8501 (tp) cc_final: 0.8282 (pt) REVERT: T 398 LYS cc_start: 0.8330 (ttpt) cc_final: 0.7818 (pttp) REVERT: U 133 MET cc_start: 0.0852 (ttt) cc_final: -0.0536 (mmt) REVERT: W 35 LYS cc_start: 0.8149 (mmtm) cc_final: 0.7799 (mmtt) REVERT: W 90 ARG cc_start: 0.8237 (ptm160) cc_final: 0.7922 (mtp-110) REVERT: X 182 TYR cc_start: 0.5907 (OUTLIER) cc_final: 0.4070 (t80) REVERT: Y 111 THR cc_start: 0.7619 (OUTLIER) cc_final: 0.7257 (m) REVERT: Y 131 ARG cc_start: 0.7117 (tpp80) cc_final: 0.6890 (tpp80) REVERT: Y 359 GLU cc_start: 0.4862 (mm-30) cc_final: 0.4571 (mm-30) REVERT: Z 176 PHE cc_start: 0.7506 (OUTLIER) cc_final: 0.6398 (m-10) REVERT: Z 972 TYR cc_start: 0.8158 (OUTLIER) cc_final: 0.7554 (m-10) REVERT: Z 1126 ILE cc_start: 0.7531 (OUTLIER) cc_final: 0.7079 (tt) REVERT: Z 1129 ARG cc_start: 0.7229 (mtt180) cc_final: 0.6661 (ptt90) REVERT: Z 1130 ARG cc_start: 0.6366 (tpp80) cc_final: 0.5837 (tpt170) REVERT: Z 1145 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.6179 (tt0) REVERT: b 66 LYS cc_start: 0.8042 (mmtt) cc_final: 0.7641 (mtpp) REVERT: b 109 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8440 (mp) REVERT: b 117 LEU cc_start: 0.7139 (OUTLIER) cc_final: 0.6894 (mp) REVERT: c 502 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8501 (mm) REVERT: c 676 MET cc_start: 0.6852 (ptp) cc_final: 0.4576 (mmt) REVERT: d 184 HIS cc_start: 0.6658 (OUTLIER) cc_final: 0.6037 (p-80) REVERT: d 298 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.8007 (mp) REVERT: d 395 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7261 (mmt90) REVERT: d 397 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8091 (pp) REVERT: e 92 THR cc_start: 0.4925 (p) cc_final: 0.4696 (t) REVERT: e 113 TYR cc_start: 0.7091 (m-80) cc_final: 0.6420 (m-80) REVERT: g 64 LYS cc_start: 0.7319 (tptt) cc_final: 0.6667 (pttp) REVERT: g 135 ARG cc_start: 0.6066 (ttm110) cc_final: 0.5549 (mmt180) REVERT: g 142 ARG cc_start: 0.5453 (mtt180) cc_final: 0.4925 (mtp85) REVERT: g 183 ARG cc_start: 0.6627 (OUTLIER) cc_final: 0.5879 (mtp85) REVERT: g 204 LYS cc_start: 0.7865 (mttt) cc_final: 0.7390 (mmtt) REVERT: h 148 MET cc_start: 0.6050 (tmm) cc_final: 0.5612 (tmm) REVERT: h 206 LYS cc_start: 0.6790 (tptt) cc_final: 0.6026 (ttmt) REVERT: h 246 ASN cc_start: 0.6380 (OUTLIER) cc_final: 0.6105 (m110) REVERT: m 182 MET cc_start: 0.7453 (tpp) cc_final: 0.7090 (tpp) REVERT: p 151 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.7491 (ttm-80) REVERT: r 133 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7009 (ptt-90) REVERT: v 127 MET cc_start: 0.3541 (tmm) cc_final: 0.3326 (tmm) REVERT: w 117 ARG cc_start: 0.7595 (ttm110) cc_final: 0.6955 (mtt90) REVERT: w 121 VAL cc_start: 0.8410 (t) cc_final: 0.8203 (p) REVERT: x 107 PHE cc_start: 0.6994 (OUTLIER) cc_final: 0.6549 (m-80) REVERT: z 23 ARG cc_start: 0.6863 (OUTLIER) cc_final: 0.6489 (ttt90) outliers start: 543 outliers final: 381 residues processed: 1950 average time/residue: 1.1378 time to fit residues: 3861.3333 Evaluate side-chains 1951 residues out of total 11710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 422 poor density : 1529 time to evaluate : 9.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 147 HIS Chi-restraints excluded: chain A residue 150 HIS Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 243 TRP Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 250 PHE Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 417 PHE Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 533 GLN Chi-restraints excluded: chain A residue 543 GLN Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 738 PHE Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 772 ARG Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 103 PHE Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 195 GLN Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 249 ILE Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain E residue 23 GLU Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 300 PHE Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 172 CYS Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 211 HIS Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 318 THR Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 338 SER Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 353 THR Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 363 HIS Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 401 CYS Chi-restraints excluded: chain F residue 406 ILE Chi-restraints excluded: chain F residue 420 VAL Chi-restraints excluded: chain F residue 427 ASN Chi-restraints excluded: chain F residue 438 THR Chi-restraints excluded: chain F residue 442 ARG Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 51 GLN Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 153 SER Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain G residue 191 ASP Chi-restraints excluded: chain G residue 267 ILE Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 129 ARG Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain I residue 862 ASN Chi-restraints excluded: chain I residue 871 VAL Chi-restraints excluded: chain I residue 877 ILE Chi-restraints excluded: chain I residue 906 LEU Chi-restraints excluded: chain I residue 921 ILE Chi-restraints excluded: chain J residue 755 ARG Chi-restraints excluded: chain J residue 789 THR Chi-restraints excluded: chain J residue 860 LEU Chi-restraints excluded: chain J residue 863 ILE Chi-restraints excluded: chain J residue 867 THR Chi-restraints excluded: chain K residue 329 THR Chi-restraints excluded: chain K residue 343 LEU Chi-restraints excluded: chain K residue 369 LEU Chi-restraints excluded: chain K residue 905 VAL Chi-restraints excluded: chain L residue 86 ILE Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 150 THR Chi-restraints excluded: chain L residue 158 THR Chi-restraints excluded: chain L residue 190 VAL Chi-restraints excluded: chain L residue 239 LEU Chi-restraints excluded: chain L residue 246 THR Chi-restraints excluded: chain L residue 334 LEU Chi-restraints excluded: chain L residue 347 THR Chi-restraints excluded: chain M residue 111 ILE Chi-restraints excluded: chain M residue 148 LEU Chi-restraints excluded: chain M residue 162 ASP Chi-restraints excluded: chain M residue 170 TRP Chi-restraints excluded: chain M residue 219 ILE Chi-restraints excluded: chain M residue 312 ILE Chi-restraints excluded: chain M residue 325 VAL Chi-restraints excluded: chain M residue 399 ILE Chi-restraints excluded: chain M residue 425 THR Chi-restraints excluded: chain M residue 432 MET Chi-restraints excluded: chain N residue 51 GLU Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 144 LEU Chi-restraints excluded: chain N residue 157 LEU Chi-restraints excluded: chain N residue 260 THR Chi-restraints excluded: chain N residue 279 SER Chi-restraints excluded: chain N residue 317 SER Chi-restraints excluded: chain N residue 323 THR Chi-restraints excluded: chain N residue 448 THR Chi-restraints excluded: chain N residue 449 ARG Chi-restraints excluded: chain N residue 466 MET Chi-restraints excluded: chain N residue 575 THR Chi-restraints excluded: chain O residue 40 THR Chi-restraints excluded: chain O residue 85 VAL Chi-restraints excluded: chain O residue 145 LEU Chi-restraints excluded: chain O residue 151 ILE Chi-restraints excluded: chain O residue 161 VAL Chi-restraints excluded: chain O residue 185 LEU Chi-restraints excluded: chain O residue 254 VAL Chi-restraints excluded: chain O residue 279 ILE Chi-restraints excluded: chain O residue 286 LEU Chi-restraints excluded: chain O residue 340 ILE Chi-restraints excluded: chain O residue 369 SER Chi-restraints excluded: chain O residue 486 MET Chi-restraints excluded: chain O residue 506 THR Chi-restraints excluded: chain O residue 546 THR Chi-restraints excluded: chain O residue 554 THR Chi-restraints excluded: chain O residue 557 LEU Chi-restraints excluded: chain O residue 560 SER Chi-restraints excluded: chain O residue 629 VAL Chi-restraints excluded: chain O residue 630 VAL Chi-restraints excluded: chain O residue 640 CYS Chi-restraints excluded: chain O residue 660 ILE Chi-restraints excluded: chain O residue 718 ASP Chi-restraints excluded: chain O residue 733 VAL Chi-restraints excluded: chain O residue 756 PHE Chi-restraints excluded: chain O residue 771 LEU Chi-restraints excluded: chain O residue 773 VAL Chi-restraints excluded: chain O residue 785 VAL Chi-restraints excluded: chain O residue 840 MET Chi-restraints excluded: chain O residue 843 LEU Chi-restraints excluded: chain O residue 854 LEU Chi-restraints excluded: chain O residue 859 ILE Chi-restraints excluded: chain O residue 943 HIS Chi-restraints excluded: chain O residue 1006 ILE Chi-restraints excluded: chain P residue 6 ILE Chi-restraints excluded: chain P residue 15 LYS Chi-restraints excluded: chain P residue 42 SER Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 128 THR Chi-restraints excluded: chain P residue 168 VAL Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 203 VAL Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 256 SER Chi-restraints excluded: chain R residue 260 SER Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain S residue 183 VAL Chi-restraints excluded: chain S residue 203 VAL Chi-restraints excluded: chain S residue 225 VAL Chi-restraints excluded: chain S residue 292 LEU Chi-restraints excluded: chain T residue 8 LEU Chi-restraints excluded: chain T residue 19 GLU Chi-restraints excluded: chain T residue 52 SER Chi-restraints excluded: chain T residue 108 GLU Chi-restraints excluded: chain T residue 173 ASN Chi-restraints excluded: chain T residue 184 LEU Chi-restraints excluded: chain T residue 274 VAL Chi-restraints excluded: chain T residue 295 LEU Chi-restraints excluded: chain T residue 312 THR Chi-restraints excluded: chain T residue 321 HIS Chi-restraints excluded: chain T residue 334 SER Chi-restraints excluded: chain U residue 166 VAL Chi-restraints excluded: chain U residue 169 VAL Chi-restraints excluded: chain U residue 237 VAL Chi-restraints excluded: chain U residue 341 TYR Chi-restraints excluded: chain U residue 348 SER Chi-restraints excluded: chain U residue 441 ASN Chi-restraints excluded: chain V residue 17 LEU Chi-restraints excluded: chain V residue 52 LEU Chi-restraints excluded: chain V residue 95 SER Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain W residue 18 VAL Chi-restraints excluded: chain W residue 71 ILE Chi-restraints excluded: chain W residue 94 VAL Chi-restraints excluded: chain W residue 102 SER Chi-restraints excluded: chain W residue 103 LEU Chi-restraints excluded: chain X residue 182 TYR Chi-restraints excluded: chain X residue 227 ILE Chi-restraints excluded: chain X residue 270 LEU Chi-restraints excluded: chain X residue 286 GLN Chi-restraints excluded: chain X residue 312 VAL Chi-restraints excluded: chain X residue 403 MET Chi-restraints excluded: chain X residue 432 ILE Chi-restraints excluded: chain X residue 502 VAL Chi-restraints excluded: chain X residue 580 VAL Chi-restraints excluded: chain X residue 582 THR Chi-restraints excluded: chain Y residue 65 ILE Chi-restraints excluded: chain Y residue 75 ILE Chi-restraints excluded: chain Y residue 98 ILE Chi-restraints excluded: chain Y residue 102 ILE Chi-restraints excluded: chain Y residue 111 THR Chi-restraints excluded: chain Y residue 114 LEU Chi-restraints excluded: chain Y residue 128 LEU Chi-restraints excluded: chain Y residue 142 THR Chi-restraints excluded: chain Y residue 152 THR Chi-restraints excluded: chain Y residue 164 PHE Chi-restraints excluded: chain Y residue 305 VAL Chi-restraints excluded: chain Y residue 318 LEU Chi-restraints excluded: chain Y residue 334 THR Chi-restraints excluded: chain Y residue 396 VAL Chi-restraints excluded: chain Y residue 401 THR Chi-restraints excluded: chain Z residue 84 LEU Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain Z residue 140 ILE Chi-restraints excluded: chain Z residue 156 ILE Chi-restraints excluded: chain Z residue 166 VAL Chi-restraints excluded: chain Z residue 175 LEU Chi-restraints excluded: chain Z residue 176 PHE Chi-restraints excluded: chain Z residue 195 THR Chi-restraints excluded: chain Z residue 205 TYR Chi-restraints excluded: chain Z residue 271 SER Chi-restraints excluded: chain Z residue 799 LEU Chi-restraints excluded: chain Z residue 836 SER Chi-restraints excluded: chain Z residue 842 PHE Chi-restraints excluded: chain Z residue 845 LEU Chi-restraints excluded: chain Z residue 867 MET Chi-restraints excluded: chain Z residue 878 ILE Chi-restraints excluded: chain Z residue 881 ASN Chi-restraints excluded: chain Z residue 886 CYS Chi-restraints excluded: chain Z residue 902 THR Chi-restraints excluded: chain Z residue 906 LEU Chi-restraints excluded: chain Z residue 914 ILE Chi-restraints excluded: chain Z residue 915 VAL Chi-restraints excluded: chain Z residue 923 THR Chi-restraints excluded: chain Z residue 952 ILE Chi-restraints excluded: chain Z residue 972 TYR Chi-restraints excluded: chain Z residue 988 ILE Chi-restraints excluded: chain Z residue 1058 LEU Chi-restraints excluded: chain Z residue 1093 LEU Chi-restraints excluded: chain Z residue 1126 ILE Chi-restraints excluded: chain Z residue 1145 GLU Chi-restraints excluded: chain a residue 30 HIS Chi-restraints excluded: chain a residue 51 CYS Chi-restraints excluded: chain a residue 62 SER Chi-restraints excluded: chain a residue 85 MET Chi-restraints excluded: chain a residue 95 SER Chi-restraints excluded: chain a residue 103 VAL Chi-restraints excluded: chain a residue 113 VAL Chi-restraints excluded: chain a residue 136 VAL Chi-restraints excluded: chain a residue 158 VAL Chi-restraints excluded: chain a residue 162 VAL Chi-restraints excluded: chain b residue 107 ILE Chi-restraints excluded: chain b residue 109 LEU Chi-restraints excluded: chain b residue 117 LEU Chi-restraints excluded: chain b residue 121 ASN Chi-restraints excluded: chain b residue 130 SER Chi-restraints excluded: chain b residue 139 ILE Chi-restraints excluded: chain b residue 156 HIS Chi-restraints excluded: chain b residue 184 VAL Chi-restraints excluded: chain b residue 205 VAL Chi-restraints excluded: chain b residue 231 VAL Chi-restraints excluded: chain b residue 239 VAL Chi-restraints excluded: chain b residue 262 THR Chi-restraints excluded: chain b residue 263 MET Chi-restraints excluded: chain b residue 290 THR Chi-restraints excluded: chain c residue 494 LEU Chi-restraints excluded: chain c residue 501 THR Chi-restraints excluded: chain c residue 502 LEU Chi-restraints excluded: chain c residue 526 VAL Chi-restraints excluded: chain c residue 619 ILE Chi-restraints excluded: chain c residue 633 LEU Chi-restraints excluded: chain d residue 6 LEU Chi-restraints excluded: chain d residue 90 VAL Chi-restraints excluded: chain d residue 105 ARG Chi-restraints excluded: chain d residue 132 ILE Chi-restraints excluded: chain d residue 147 ILE Chi-restraints excluded: chain d residue 184 HIS Chi-restraints excluded: chain d residue 185 SER Chi-restraints excluded: chain d residue 200 ILE Chi-restraints excluded: chain d residue 201 THR Chi-restraints excluded: chain d residue 215 SER Chi-restraints excluded: chain d residue 233 VAL Chi-restraints excluded: chain d residue 236 THR Chi-restraints excluded: chain d residue 292 SER Chi-restraints excluded: chain d residue 298 LEU Chi-restraints excluded: chain d residue 300 SER Chi-restraints excluded: chain d residue 302 SER Chi-restraints excluded: chain d residue 363 VAL Chi-restraints excluded: chain d residue 395 ARG Chi-restraints excluded: chain d residue 397 LEU Chi-restraints excluded: chain d residue 441 VAL Chi-restraints excluded: chain e residue 183 ASP Chi-restraints excluded: chain e residue 195 THR Chi-restraints excluded: chain e residue 245 CYS Chi-restraints excluded: chain f residue 229 ASN Chi-restraints excluded: chain g residue 73 ILE Chi-restraints excluded: chain g residue 99 ILE Chi-restraints excluded: chain g residue 130 VAL Chi-restraints excluded: chain g residue 156 LEU Chi-restraints excluded: chain g residue 183 ARG Chi-restraints excluded: chain g residue 201 LEU Chi-restraints excluded: chain h residue 87 ILE Chi-restraints excluded: chain h residue 161 LEU Chi-restraints excluded: chain h residue 219 LEU Chi-restraints excluded: chain h residue 246 ASN Chi-restraints excluded: chain k residue 86 THR Chi-restraints excluded: chain k residue 108 LEU Chi-restraints excluded: chain k residue 172 SER Chi-restraints excluded: chain l residue 67 GLU Chi-restraints excluded: chain l residue 68 VAL Chi-restraints excluded: chain l residue 181 LEU Chi-restraints excluded: chain m residue 40 ASP Chi-restraints excluded: chain m residue 79 ASP Chi-restraints excluded: chain m residue 90 ILE Chi-restraints excluded: chain m residue 111 VAL Chi-restraints excluded: chain m residue 114 ILE Chi-restraints excluded: chain m residue 176 ASP Chi-restraints excluded: chain m residue 189 MET Chi-restraints excluded: chain m residue 202 ASP Chi-restraints excluded: chain n residue 34 SER Chi-restraints excluded: chain n residue 38 ILE Chi-restraints excluded: chain n residue 86 MET Chi-restraints excluded: chain n residue 174 VAL Chi-restraints excluded: chain n residue 193 SER Chi-restraints excluded: chain o residue 32 MET Chi-restraints excluded: chain o residue 52 ILE Chi-restraints excluded: chain o residue 63 MET Chi-restraints excluded: chain o residue 162 VAL Chi-restraints excluded: chain p residue 151 ARG Chi-restraints excluded: chain p residue 192 THR Chi-restraints excluded: chain q residue 44 HIS Chi-restraints excluded: chain q residue 60 LEU Chi-restraints excluded: chain q residue 136 VAL Chi-restraints excluded: chain q residue 141 SER Chi-restraints excluded: chain r residue 83 VAL Chi-restraints excluded: chain r residue 108 GLN Chi-restraints excluded: chain r residue 125 VAL Chi-restraints excluded: chain r residue 132 ILE Chi-restraints excluded: chain r residue 133 ARG Chi-restraints excluded: chain r residue 171 ARG Chi-restraints excluded: chain t residue 53 CYS Chi-restraints excluded: chain t residue 61 VAL Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain u residue 7 VAL Chi-restraints excluded: chain u residue 9 VAL Chi-restraints excluded: chain u residue 17 THR Chi-restraints excluded: chain u residue 23 VAL Chi-restraints excluded: chain u residue 48 LEU Chi-restraints excluded: chain u residue 66 ARG Chi-restraints excluded: chain u residue 69 VAL Chi-restraints excluded: chain u residue 95 LYS Chi-restraints excluded: chain u residue 97 VAL Chi-restraints excluded: chain v residue 21 LEU Chi-restraints excluded: chain v residue 66 THR Chi-restraints excluded: chain w residue 105 THR Chi-restraints excluded: chain w residue 126 ILE Chi-restraints excluded: chain x residue 52 ILE Chi-restraints excluded: chain x residue 83 VAL Chi-restraints excluded: chain x residue 107 PHE Chi-restraints excluded: chain y residue 337 THR Chi-restraints excluded: chain y residue 391 LEU Chi-restraints excluded: chain z residue 23 ARG Chi-restraints excluded: chain z residue 37 THR Chi-restraints excluded: chain z residue 57 LEU Chi-restraints excluded: chain z residue 66 ARG Chi-restraints excluded: chain 0 residue 164 LEU Chi-restraints excluded: chain 0 residue 184 SER Chi-restraints excluded: chain 0 residue 192 ASN Chi-restraints excluded: chain 0 residue 219 ILE Chi-restraints excluded: chain 0 residue 227 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1508 random chunks: chunk 1406 optimal weight: 20.0000 chunk 164 optimal weight: 0.9990 chunk 831 optimal weight: 0.6980 chunk 1065 optimal weight: 50.0000 chunk 825 optimal weight: 3.9990 chunk 1228 optimal weight: 0.0870 chunk 814 optimal weight: 2.9990 chunk 1453 optimal weight: 10.0000 chunk 909 optimal weight: 20.0000 chunk 886 optimal weight: 3.9990 chunk 671 optimal weight: 4.9990 overall best weight: 1.7564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 HIS ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 GLN D 273 GLN E 158 GLN ** F 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 HIS H 117 ASN ** J 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 333 ASN ** K 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 117 GLN ** O 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 505 ASN O 636 HIS ** T 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 176 HIS U 336 HIS ** U 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 27 GLN X 286 GLN ** X 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z1030 ASN a 30 HIS ** b 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 232 ASN l 92 GLN m 112 HIS ** m 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 179 GLN r 36 ASN ** r 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 151 GLN ** v 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 39 GLN ** w 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 44 HIS x 65 ASN ** y 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 192 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6241 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 140828 Z= 0.269 Angle : 0.701 40.213 198339 Z= 0.353 Chirality : 0.043 0.347 24279 Planarity : 0.005 0.110 19356 Dihedral : 21.338 179.795 39625 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.01 % Favored : 91.90 % Rotamer: Outliers : 5.32 % Allowed : 19.66 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.02 % Twisted Proline : 0.50 % Twisted General : 0.07 % 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: -1.55 (0.07), residues: 13489 helix: 0.64 (0.08), residues: 4720 sheet: -1.34 (0.10), residues: 2669 loop : -2.25 (0.08), residues: 6100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP N 426 HIS 0.018 0.001 HIS a 30 PHE 0.044 0.002 PHE A 687 TYR 0.039 0.002 TYR T 219 ARG 0.014 0.001 ARG W 119 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26978 Ramachandran restraints generated. 13489 Oldfield, 0 Emsley, 13489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26978 Ramachandran restraints generated. 13489 Oldfield, 0 Emsley, 13489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2130 residues out of total 11710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 511 poor density : 1619 time to evaluate : 9.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ILE cc_start: 0.8140 (OUTLIER) cc_final: 0.7581 (mm) REVERT: A 81 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7435 (tt) REVERT: A 354 ARG cc_start: 0.6889 (mtm-85) cc_final: 0.6547 (mtm180) REVERT: A 459 GLN cc_start: 0.7831 (pt0) cc_final: 0.7070 (mm110) REVERT: A 827 ARG cc_start: 0.7607 (ttp80) cc_final: 0.7305 (ttm170) REVERT: B 861 ARG cc_start: 0.8144 (mtm-85) cc_final: 0.7079 (mtm-85) REVERT: B 894 ASN cc_start: 0.7643 (t0) cc_final: 0.7336 (t0) REVERT: B 900 LYS cc_start: 0.7889 (tptp) cc_final: 0.7314 (mtmt) REVERT: D 80 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8283 (pp) REVERT: D 195 GLN cc_start: 0.6811 (OUTLIER) cc_final: 0.6572 (tp40) REVERT: D 292 ILE cc_start: 0.8414 (mm) cc_final: 0.8113 (mm) REVERT: D 323 GLN cc_start: 0.7732 (tp40) cc_final: 0.7439 (mm-40) REVERT: E 191 ARG cc_start: 0.6788 (mtp180) cc_final: 0.6337 (mtt-85) REVERT: E 300 PHE cc_start: 0.7603 (OUTLIER) cc_final: 0.7068 (t80) REVERT: F 106 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7305 (tt) REVERT: F 326 ILE cc_start: 0.8026 (OUTLIER) cc_final: 0.7802 (pt) REVERT: F 442 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7053 (ttp-170) REVERT: G 51 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.7566 (mt0) REVERT: H 34 TYR cc_start: 0.7703 (t80) cc_final: 0.7256 (t80) REVERT: H 69 SER cc_start: 0.8813 (p) cc_final: 0.8592 (m) REVERT: I 790 MET cc_start: 0.4189 (tpp) cc_final: 0.3295 (mmt) REVERT: I 877 ILE cc_start: 0.7544 (OUTLIER) cc_final: 0.7139 (pt) REVERT: L 137 LEU cc_start: 0.7296 (OUTLIER) cc_final: 0.6830 (mp) REVERT: L 138 LYS cc_start: 0.6974 (ptpp) cc_final: 0.5738 (ttmm) REVERT: L 298 LYS cc_start: 0.4021 (tptt) cc_final: 0.3166 (tmtt) REVERT: M 262 HIS cc_start: 0.7304 (m-70) cc_final: 0.7076 (m170) REVERT: M 938 MET cc_start: 0.8027 (tpp) cc_final: 0.7386 (ttm) REVERT: N 52 GLU cc_start: 0.7810 (tm-30) cc_final: 0.7514 (tm-30) REVERT: N 63 LYS cc_start: 0.7832 (mtpt) cc_final: 0.7411 (pttm) REVERT: N 144 LEU cc_start: 0.5953 (OUTLIER) cc_final: 0.5559 (tm) REVERT: N 157 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8388 (pp) REVERT: N 164 ASP cc_start: 0.7884 (OUTLIER) cc_final: 0.7550 (t0) REVERT: N 239 SER cc_start: 0.8464 (OUTLIER) cc_final: 0.7967 (m) REVERT: N 393 LYS cc_start: 0.7694 (tptt) cc_final: 0.7411 (tttt) REVERT: N 397 MET cc_start: 0.6906 (pmm) cc_final: 0.6559 (pmm) REVERT: O 105 TYR cc_start: 0.8584 (OUTLIER) cc_final: 0.8067 (m-80) REVERT: O 222 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.7736 (pp) REVERT: O 861 LYS cc_start: 0.6279 (mttt) cc_final: 0.5851 (mmtt) REVERT: O 1006 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7473 (pp) REVERT: O 1007 MET cc_start: 0.8008 (ttm) cc_final: 0.7687 (ttm) REVERT: P 28 LYS cc_start: 0.7811 (mttt) cc_final: 0.7461 (tptm) REVERT: P 65 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7799 (mt) REVERT: P 84 TYR cc_start: 0.7457 (m-80) cc_final: 0.7218 (m-10) REVERT: P 118 TRP cc_start: 0.7036 (m-10) cc_final: 0.6227 (m-10) REVERT: P 122 THR cc_start: 0.8476 (t) cc_final: 0.8011 (p) REVERT: P 155 ARG cc_start: 0.8172 (ttm170) cc_final: 0.6654 (ttt-90) REVERT: S 109 ILE cc_start: 0.4102 (pt) cc_final: 0.3564 (pt) REVERT: T 83 GLU cc_start: 0.7252 (tm-30) cc_final: 0.7028 (tm-30) REVERT: T 262 MET cc_start: 0.4661 (mpp) cc_final: 0.4440 (mpp) REVERT: T 377 ARG cc_start: 0.7762 (ttp-110) cc_final: 0.7227 (ttp-170) REVERT: T 392 ILE cc_start: 0.8502 (tp) cc_final: 0.8267 (pt) REVERT: T 398 LYS cc_start: 0.8282 (ttpt) cc_final: 0.7911 (pttm) REVERT: U 65 LEU cc_start: 0.6985 (OUTLIER) cc_final: 0.6777 (tt) REVERT: U 133 MET cc_start: 0.0871 (ttt) cc_final: -0.0556 (mmt) REVERT: U 179 LEU cc_start: 0.8336 (tt) cc_final: 0.7922 (mp) REVERT: W 35 LYS cc_start: 0.8171 (mmtm) cc_final: 0.7810 (mmtt) REVERT: W 90 ARG cc_start: 0.8220 (ptm160) cc_final: 0.7955 (mtp-110) REVERT: W 119 ARG cc_start: 0.7973 (mtm110) cc_final: 0.7648 (mtp-110) REVERT: X 182 TYR cc_start: 0.5886 (OUTLIER) cc_final: 0.3849 (t80) REVERT: X 462 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.7840 (mt0) REVERT: X 557 ARG cc_start: 0.5906 (OUTLIER) cc_final: 0.5685 (mmt180) REVERT: Y 111 THR cc_start: 0.7640 (OUTLIER) cc_final: 0.7302 (m) REVERT: Y 359 GLU cc_start: 0.4644 (mm-30) cc_final: 0.4375 (mm-30) REVERT: Z 176 PHE cc_start: 0.7543 (OUTLIER) cc_final: 0.6481 (m-10) REVERT: Z 972 TYR cc_start: 0.8055 (OUTLIER) cc_final: 0.7450 (m-10) REVERT: Z 1038 ILE cc_start: 0.8231 (OUTLIER) cc_final: 0.7864 (mp) REVERT: Z 1129 ARG cc_start: 0.7206 (mtt180) cc_final: 0.6660 (ptt90) REVERT: Z 1130 ARG cc_start: 0.6403 (tpp80) cc_final: 0.5795 (tpt170) REVERT: Z 1145 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.6165 (tt0) REVERT: b 66 LYS cc_start: 0.7985 (mmtt) cc_final: 0.7573 (mtpp) REVERT: b 109 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8384 (mp) REVERT: b 117 LEU cc_start: 0.7144 (OUTLIER) cc_final: 0.6940 (mp) REVERT: b 146 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.6882 (mtp180) REVERT: c 502 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8504 (mm) REVERT: c 676 MET cc_start: 0.6815 (ptp) cc_final: 0.4462 (mmt) REVERT: d 25 ARG cc_start: 0.7033 (ptm-80) cc_final: 0.6809 (ptm-80) REVERT: d 250 MET cc_start: 0.8685 (mmm) cc_final: 0.7856 (mmm) REVERT: d 395 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7139 (mmt90) REVERT: d 397 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8035 (pp) REVERT: e 92 THR cc_start: 0.4893 (p) cc_final: 0.4691 (t) REVERT: e 113 TYR cc_start: 0.7006 (m-80) cc_final: 0.6408 (m-80) REVERT: e 151 LYS cc_start: 0.6740 (OUTLIER) cc_final: 0.6045 (tttp) REVERT: f 77 MET cc_start: 0.5839 (mmp) cc_final: 0.5415 (tmm) REVERT: g 64 LYS cc_start: 0.7304 (tptt) cc_final: 0.6691 (pttp) REVERT: g 135 ARG cc_start: 0.6089 (ttm110) cc_final: 0.5545 (mmt180) REVERT: g 142 ARG cc_start: 0.5438 (mtt180) cc_final: 0.4939 (mtp85) REVERT: g 183 ARG cc_start: 0.6622 (OUTLIER) cc_final: 0.5833 (mtp85) REVERT: g 204 LYS cc_start: 0.7731 (mttt) cc_final: 0.7315 (mmtt) REVERT: h 148 MET cc_start: 0.6120 (tmm) cc_final: 0.5601 (tpt) REVERT: h 206 LYS cc_start: 0.6756 (tptt) cc_final: 0.6071 (ttmt) REVERT: h 246 ASN cc_start: 0.6328 (OUTLIER) cc_final: 0.6053 (m110) REVERT: m 42 MET cc_start: 0.5402 (mmm) cc_final: 0.4578 (mtt) REVERT: p 151 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.7479 (ttm-80) REVERT: r 133 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7016 (ptt-90) REVERT: r 136 LYS cc_start: 0.5114 (pttt) cc_final: 0.4630 (pttt) REVERT: u 111 GLN cc_start: 0.7529 (mm-40) cc_final: 0.7314 (mm-40) REVERT: w 82 ARG cc_start: 0.7036 (ptt90) cc_final: 0.6733 (ptt90) REVERT: w 117 ARG cc_start: 0.7492 (ttm110) cc_final: 0.6867 (mtt90) REVERT: x 78 LYS cc_start: 0.7842 (mmtt) cc_final: 0.7638 (mmtt) REVERT: x 107 PHE cc_start: 0.7015 (OUTLIER) cc_final: 0.6646 (m-80) outliers start: 511 outliers final: 389 residues processed: 1952 average time/residue: 1.1617 time to fit residues: 3945.9706 Evaluate side-chains 1984 residues out of total 11710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 429 poor density : 1555 time to evaluate : 8.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 147 HIS Chi-restraints excluded: chain A residue 150 HIS Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 243 TRP Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 250 PHE Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 417 PHE Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 533 GLN Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 738 PHE Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 772 ARG Chi-restraints excluded: chain B residue 903 ARG Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 103 PHE Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain D residue 195 GLN Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 249 ILE Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 300 PHE Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 172 CYS Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 211 HIS Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 318 THR Chi-restraints excluded: chain F residue 326 ILE Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 338 SER Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 353 THR Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 401 CYS Chi-restraints excluded: chain F residue 406 ILE Chi-restraints excluded: chain F residue 420 VAL Chi-restraints excluded: chain F residue 427 ASN Chi-restraints excluded: chain F residue 438 THR Chi-restraints excluded: chain F residue 442 ARG Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 51 GLN Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 153 SER Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain G residue 191 ASP Chi-restraints excluded: chain G residue 267 ILE Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 223 VAL Chi-restraints excluded: chain I residue 862 ASN Chi-restraints excluded: chain I residue 871 VAL Chi-restraints excluded: chain I residue 877 ILE Chi-restraints excluded: chain I residue 906 LEU Chi-restraints excluded: chain I residue 921 ILE Chi-restraints excluded: chain J residue 755 ARG Chi-restraints excluded: chain J residue 789 THR Chi-restraints excluded: chain J residue 806 ILE Chi-restraints excluded: chain J residue 829 VAL Chi-restraints excluded: chain J residue 860 LEU Chi-restraints excluded: chain J residue 863 ILE Chi-restraints excluded: chain K residue 329 THR Chi-restraints excluded: chain K residue 343 LEU Chi-restraints excluded: chain K residue 369 LEU Chi-restraints excluded: chain K residue 370 GLU Chi-restraints excluded: chain K residue 905 VAL Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 86 ILE Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 150 THR Chi-restraints excluded: chain L residue 158 THR Chi-restraints excluded: chain L residue 190 VAL Chi-restraints excluded: chain L residue 239 LEU Chi-restraints excluded: chain L residue 281 LEU Chi-restraints excluded: chain L residue 334 LEU Chi-restraints excluded: chain L residue 347 THR Chi-restraints excluded: chain M residue 111 ILE Chi-restraints excluded: chain M residue 148 LEU Chi-restraints excluded: chain M residue 162 ASP Chi-restraints excluded: chain M residue 170 TRP Chi-restraints excluded: chain M residue 219 ILE Chi-restraints excluded: chain M residue 244 LEU Chi-restraints excluded: chain M residue 312 ILE Chi-restraints excluded: chain M residue 325 VAL Chi-restraints excluded: chain M residue 425 THR Chi-restraints excluded: chain M residue 432 MET Chi-restraints excluded: chain N residue 51 GLU Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 144 LEU Chi-restraints excluded: chain N residue 157 LEU Chi-restraints excluded: chain N residue 164 ASP Chi-restraints excluded: chain N residue 239 SER Chi-restraints excluded: chain N residue 260 THR Chi-restraints excluded: chain N residue 293 SER Chi-restraints excluded: chain N residue 323 THR Chi-restraints excluded: chain N residue 448 THR Chi-restraints excluded: chain N residue 466 MET Chi-restraints excluded: chain N residue 528 LYS Chi-restraints excluded: chain N residue 575 THR Chi-restraints excluded: chain O residue 40 THR Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain O residue 85 VAL Chi-restraints excluded: chain O residue 105 TYR Chi-restraints excluded: chain O residue 145 LEU Chi-restraints excluded: chain O residue 151 ILE Chi-restraints excluded: chain O residue 161 VAL Chi-restraints excluded: chain O residue 222 LEU Chi-restraints excluded: chain O residue 254 VAL Chi-restraints excluded: chain O residue 279 ILE Chi-restraints excluded: chain O residue 286 LEU Chi-restraints excluded: chain O residue 351 VAL Chi-restraints excluded: chain O residue 369 SER Chi-restraints excluded: chain O residue 439 LYS Chi-restraints excluded: chain O residue 506 THR Chi-restraints excluded: chain O residue 546 THR Chi-restraints excluded: chain O residue 554 THR Chi-restraints excluded: chain O residue 557 LEU Chi-restraints excluded: chain O residue 560 SER Chi-restraints excluded: chain O residue 629 VAL Chi-restraints excluded: chain O residue 630 VAL Chi-restraints excluded: chain O residue 638 VAL Chi-restraints excluded: chain O residue 640 CYS Chi-restraints excluded: chain O residue 660 ILE Chi-restraints excluded: chain O residue 718 ASP Chi-restraints excluded: chain O residue 733 VAL Chi-restraints excluded: chain O residue 756 PHE Chi-restraints excluded: chain O residue 771 LEU Chi-restraints excluded: chain O residue 773 VAL Chi-restraints excluded: chain O residue 785 VAL Chi-restraints excluded: chain O residue 840 MET Chi-restraints excluded: chain O residue 854 LEU Chi-restraints excluded: chain O residue 859 ILE Chi-restraints excluded: chain O residue 943 HIS Chi-restraints excluded: chain O residue 1006 ILE Chi-restraints excluded: chain O residue 1012 LEU Chi-restraints excluded: chain O residue 1030 LEU Chi-restraints excluded: chain P residue 6 ILE Chi-restraints excluded: chain P residue 15 LYS Chi-restraints excluded: chain P residue 42 SER Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 168 VAL Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 203 VAL Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 256 SER Chi-restraints excluded: chain R residue 260 SER Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain S residue 183 VAL Chi-restraints excluded: chain S residue 203 VAL Chi-restraints excluded: chain S residue 225 VAL Chi-restraints excluded: chain S residue 292 LEU Chi-restraints excluded: chain T residue 8 LEU Chi-restraints excluded: chain T residue 19 GLU Chi-restraints excluded: chain T residue 52 SER Chi-restraints excluded: chain T residue 173 ASN Chi-restraints excluded: chain T residue 184 LEU Chi-restraints excluded: chain T residue 187 LEU Chi-restraints excluded: chain T residue 274 VAL Chi-restraints excluded: chain T residue 295 LEU Chi-restraints excluded: chain T residue 312 THR Chi-restraints excluded: chain T residue 321 HIS Chi-restraints excluded: chain T residue 334 SER Chi-restraints excluded: chain T residue 338 ILE Chi-restraints excluded: chain U residue 65 LEU Chi-restraints excluded: chain U residue 169 VAL Chi-restraints excluded: chain U residue 237 VAL Chi-restraints excluded: chain U residue 251 THR Chi-restraints excluded: chain U residue 341 TYR Chi-restraints excluded: chain U residue 348 SER Chi-restraints excluded: chain V residue 17 LEU Chi-restraints excluded: chain V residue 95 SER Chi-restraints excluded: chain V residue 105 SER Chi-restraints excluded: chain V residue 125 LEU Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain W residue 18 VAL Chi-restraints excluded: chain W residue 71 ILE Chi-restraints excluded: chain W residue 94 VAL Chi-restraints excluded: chain W residue 102 SER Chi-restraints excluded: chain W residue 103 LEU Chi-restraints excluded: chain X residue 182 TYR Chi-restraints excluded: chain X residue 227 ILE Chi-restraints excluded: chain X residue 270 LEU Chi-restraints excluded: chain X residue 312 VAL Chi-restraints excluded: chain X residue 403 MET Chi-restraints excluded: chain X residue 432 ILE Chi-restraints excluded: chain X residue 462 GLN Chi-restraints excluded: chain X residue 502 VAL Chi-restraints excluded: chain X residue 557 ARG Chi-restraints excluded: chain X residue 579 VAL Chi-restraints excluded: chain X residue 580 VAL Chi-restraints excluded: chain X residue 582 THR Chi-restraints excluded: chain X residue 604 PHE Chi-restraints excluded: chain X residue 606 VAL Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Y residue 65 ILE Chi-restraints excluded: chain Y residue 98 ILE Chi-restraints excluded: chain Y residue 102 ILE Chi-restraints excluded: chain Y residue 111 THR Chi-restraints excluded: chain Y residue 114 LEU Chi-restraints excluded: chain Y residue 128 LEU Chi-restraints excluded: chain Y residue 142 THR Chi-restraints excluded: chain Y residue 305 VAL Chi-restraints excluded: chain Y residue 318 LEU Chi-restraints excluded: chain Y residue 334 THR Chi-restraints excluded: chain Y residue 396 VAL Chi-restraints excluded: chain Z residue 84 LEU Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain Z residue 166 VAL Chi-restraints excluded: chain Z residue 175 LEU Chi-restraints excluded: chain Z residue 176 PHE Chi-restraints excluded: chain Z residue 205 TYR Chi-restraints excluded: chain Z residue 222 LEU Chi-restraints excluded: chain Z residue 271 SER Chi-restraints excluded: chain Z residue 789 CYS Chi-restraints excluded: chain Z residue 799 LEU Chi-restraints excluded: chain Z residue 836 SER Chi-restraints excluded: chain Z residue 842 PHE Chi-restraints excluded: chain Z residue 845 LEU Chi-restraints excluded: chain Z residue 867 MET Chi-restraints excluded: chain Z residue 878 ILE Chi-restraints excluded: chain Z residue 886 CYS Chi-restraints excluded: chain Z residue 902 THR Chi-restraints excluded: chain Z residue 904 THR Chi-restraints excluded: chain Z residue 906 LEU Chi-restraints excluded: chain Z residue 914 ILE Chi-restraints excluded: chain Z residue 915 VAL Chi-restraints excluded: chain Z residue 923 THR Chi-restraints excluded: chain Z residue 952 ILE Chi-restraints excluded: chain Z residue 972 TYR Chi-restraints excluded: chain Z residue 988 ILE Chi-restraints excluded: chain Z residue 1038 ILE Chi-restraints excluded: chain Z residue 1058 LEU Chi-restraints excluded: chain Z residue 1093 LEU Chi-restraints excluded: chain Z residue 1145 GLU Chi-restraints excluded: chain a residue 30 HIS Chi-restraints excluded: chain a residue 51 CYS Chi-restraints excluded: chain a residue 62 SER Chi-restraints excluded: chain a residue 95 SER Chi-restraints excluded: chain a residue 103 VAL Chi-restraints excluded: chain a residue 113 VAL Chi-restraints excluded: chain a residue 136 VAL Chi-restraints excluded: chain a residue 149 LEU Chi-restraints excluded: chain a residue 158 VAL Chi-restraints excluded: chain a residue 162 VAL Chi-restraints excluded: chain b residue 38 SER Chi-restraints excluded: chain b residue 92 THR Chi-restraints excluded: chain b residue 109 LEU Chi-restraints excluded: chain b residue 117 LEU Chi-restraints excluded: chain b residue 121 ASN Chi-restraints excluded: chain b residue 127 LEU Chi-restraints excluded: chain b residue 130 SER Chi-restraints excluded: chain b residue 139 ILE Chi-restraints excluded: chain b residue 146 ARG Chi-restraints excluded: chain b residue 156 HIS Chi-restraints excluded: chain b residue 184 VAL Chi-restraints excluded: chain b residue 205 VAL Chi-restraints excluded: chain b residue 231 VAL Chi-restraints excluded: chain b residue 232 ASN Chi-restraints excluded: chain b residue 239 VAL Chi-restraints excluded: chain b residue 263 MET Chi-restraints excluded: chain b residue 290 THR Chi-restraints excluded: chain c residue 494 LEU Chi-restraints excluded: chain c residue 501 THR Chi-restraints excluded: chain c residue 502 LEU Chi-restraints excluded: chain c residue 557 VAL Chi-restraints excluded: chain c residue 619 ILE Chi-restraints excluded: chain c residue 633 LEU Chi-restraints excluded: chain d residue 6 LEU Chi-restraints excluded: chain d residue 90 VAL Chi-restraints excluded: chain d residue 105 ARG Chi-restraints excluded: chain d residue 147 ILE Chi-restraints excluded: chain d residue 160 SER Chi-restraints excluded: chain d residue 184 HIS Chi-restraints excluded: chain d residue 185 SER Chi-restraints excluded: chain d residue 200 ILE Chi-restraints excluded: chain d residue 201 THR Chi-restraints excluded: chain d residue 215 SER Chi-restraints excluded: chain d residue 236 THR Chi-restraints excluded: chain d residue 283 VAL Chi-restraints excluded: chain d residue 298 LEU Chi-restraints excluded: chain d residue 300 SER Chi-restraints excluded: chain d residue 302 SER Chi-restraints excluded: chain d residue 363 VAL Chi-restraints excluded: chain d residue 395 ARG Chi-restraints excluded: chain d residue 397 LEU Chi-restraints excluded: chain d residue 441 VAL Chi-restraints excluded: chain e residue 151 LYS Chi-restraints excluded: chain e residue 195 THR Chi-restraints excluded: chain e residue 245 CYS Chi-restraints excluded: chain e residue 250 ASP Chi-restraints excluded: chain f residue 181 SER Chi-restraints excluded: chain f residue 229 ASN Chi-restraints excluded: chain g residue 41 THR Chi-restraints excluded: chain g residue 73 ILE Chi-restraints excluded: chain g residue 130 VAL Chi-restraints excluded: chain g residue 156 LEU Chi-restraints excluded: chain g residue 183 ARG Chi-restraints excluded: chain g residue 201 LEU Chi-restraints excluded: chain h residue 87 ILE Chi-restraints excluded: chain h residue 161 LEU Chi-restraints excluded: chain h residue 219 LEU Chi-restraints excluded: chain h residue 222 PHE Chi-restraints excluded: chain h residue 246 ASN Chi-restraints excluded: chain k residue 86 THR Chi-restraints excluded: chain k residue 108 LEU Chi-restraints excluded: chain k residue 110 ARG Chi-restraints excluded: chain l residue 59 ASP Chi-restraints excluded: chain l residue 67 GLU Chi-restraints excluded: chain l residue 68 VAL Chi-restraints excluded: chain l residue 181 LEU Chi-restraints excluded: chain m residue 40 ASP Chi-restraints excluded: chain m residue 79 ASP Chi-restraints excluded: chain m residue 111 VAL Chi-restraints excluded: chain m residue 172 PHE Chi-restraints excluded: chain m residue 189 MET Chi-restraints excluded: chain n residue 34 SER Chi-restraints excluded: chain n residue 86 MET Chi-restraints excluded: chain n residue 193 SER Chi-restraints excluded: chain o residue 32 MET Chi-restraints excluded: chain o residue 52 ILE Chi-restraints excluded: chain o residue 76 LEU Chi-restraints excluded: chain o residue 162 VAL Chi-restraints excluded: chain p residue 151 ARG Chi-restraints excluded: chain p residue 162 VAL Chi-restraints excluded: chain q residue 44 HIS Chi-restraints excluded: chain q residue 60 LEU Chi-restraints excluded: chain q residue 136 VAL Chi-restraints excluded: chain q residue 141 SER Chi-restraints excluded: chain r residue 36 ASN Chi-restraints excluded: chain r residue 108 GLN Chi-restraints excluded: chain r residue 125 VAL Chi-restraints excluded: chain r residue 132 ILE Chi-restraints excluded: chain r residue 133 ARG Chi-restraints excluded: chain r residue 171 ARG Chi-restraints excluded: chain s residue 125 LEU Chi-restraints excluded: chain t residue 53 CYS Chi-restraints excluded: chain t residue 61 VAL Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain u residue 7 VAL Chi-restraints excluded: chain u residue 9 VAL Chi-restraints excluded: chain u residue 17 THR Chi-restraints excluded: chain u residue 44 LEU Chi-restraints excluded: chain u residue 48 LEU Chi-restraints excluded: chain u residue 66 ARG Chi-restraints excluded: chain u residue 69 VAL Chi-restraints excluded: chain u residue 95 LYS Chi-restraints excluded: chain u residue 97 VAL Chi-restraints excluded: chain v residue 66 THR Chi-restraints excluded: chain w residue 39 GLN Chi-restraints excluded: chain w residue 105 THR Chi-restraints excluded: chain w residue 126 ILE Chi-restraints excluded: chain x residue 52 ILE Chi-restraints excluded: chain x residue 59 VAL Chi-restraints excluded: chain x residue 83 VAL Chi-restraints excluded: chain x residue 107 PHE Chi-restraints excluded: chain y residue 337 THR Chi-restraints excluded: chain y residue 391 LEU Chi-restraints excluded: chain z residue 37 THR Chi-restraints excluded: chain z residue 40 SER Chi-restraints excluded: chain z residue 57 LEU Chi-restraints excluded: chain z residue 66 ARG Chi-restraints excluded: chain 0 residue 164 LEU Chi-restraints excluded: chain 0 residue 184 SER Chi-restraints excluded: chain 0 residue 227 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1508 random chunks: chunk 899 optimal weight: 0.7980 chunk 580 optimal weight: 0.6980 chunk 868 optimal weight: 0.9990 chunk 437 optimal weight: 2.9990 chunk 285 optimal weight: 4.9990 chunk 281 optimal weight: 0.9990 chunk 924 optimal weight: 1.9990 chunk 990 optimal weight: 30.0000 chunk 718 optimal weight: 0.0770 chunk 135 optimal weight: 0.7980 chunk 1142 optimal weight: 0.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 HIS ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 273 GLN E 158 GLN ** F 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 HIS J 741 GLN ** J 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 333 ASN ** K 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 117 GLN O 191 ASN ** O 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 505 ASN O 636 HIS P 149 ASN ** T 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 336 HIS ** U 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 27 GLN ** Z 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 239 ASN Z1030 ASN a 30 HIS a 74 HIS ** b 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 202 GLN ** c 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 132 HIS r 36 ASN ** r 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 151 GLN ** v 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 65 ASN ** y 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6174 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 140828 Z= 0.180 Angle : 0.659 40.458 198339 Z= 0.330 Chirality : 0.041 0.318 24279 Planarity : 0.005 0.102 19356 Dihedral : 21.222 179.827 39625 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.54 % Favored : 92.39 % Rotamer: Outliers : 4.54 % Allowed : 20.69 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.02 % Twisted Proline : 0.50 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.07), residues: 13489 helix: 0.92 (0.08), residues: 4738 sheet: -1.21 (0.10), residues: 2652 loop : -2.15 (0.08), residues: 6099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP N 426 HIS 0.021 0.001 HIS a 30 PHE 0.033 0.002 PHE A 687 TYR 0.023 0.001 TYR m 121 ARG 0.015 0.000 ARG r 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26978 Ramachandran restraints generated. 13489 Oldfield, 0 Emsley, 13489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26978 Ramachandran restraints generated. 13489 Oldfield, 0 Emsley, 13489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2098 residues out of total 11710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 436 poor density : 1662 time to evaluate : 12.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ILE cc_start: 0.7852 (OUTLIER) cc_final: 0.7264 (mm) REVERT: A 81 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7502 (tt) REVERT: A 459 GLN cc_start: 0.7823 (pt0) cc_final: 0.7102 (mm110) REVERT: A 698 TYR cc_start: 0.8004 (m-80) cc_final: 0.7795 (m-80) REVERT: A 827 ARG cc_start: 0.7462 (ttp80) cc_final: 0.7218 (ttm170) REVERT: B 861 ARG cc_start: 0.8124 (mtm-85) cc_final: 0.7094 (mtm-85) REVERT: D 80 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8200 (pp) REVERT: D 292 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.8052 (mm) REVERT: D 323 GLN cc_start: 0.7745 (tp40) cc_final: 0.7475 (mm-40) REVERT: E 191 ARG cc_start: 0.6791 (mtp180) cc_final: 0.6318 (mtt-85) REVERT: E 288 LYS cc_start: 0.7349 (pttt) cc_final: 0.6929 (tptp) REVERT: F 50 LYS cc_start: 0.7638 (mttt) cc_final: 0.7186 (tptt) REVERT: F 106 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7199 (tt) REVERT: F 363 HIS cc_start: 0.7964 (OUTLIER) cc_final: 0.6960 (p-80) REVERT: F 393 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.7492 (pt0) REVERT: F 442 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7067 (ttp-170) REVERT: H 34 TYR cc_start: 0.7524 (t80) cc_final: 0.7048 (t80) REVERT: H 124 LYS cc_start: 0.8622 (ttpt) cc_final: 0.8377 (ttmm) REVERT: I 877 ILE cc_start: 0.7513 (OUTLIER) cc_final: 0.7118 (pt) REVERT: I 895 MET cc_start: 0.6245 (mmp) cc_final: 0.5790 (tpt) REVERT: L 137 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.6959 (mp) REVERT: L 298 LYS cc_start: 0.3838 (tptt) cc_final: 0.3099 (tmtt) REVERT: M 262 HIS cc_start: 0.7239 (m-70) cc_final: 0.6941 (m170) REVERT: N 52 GLU cc_start: 0.7773 (tm-30) cc_final: 0.7549 (tm-30) REVERT: N 63 LYS cc_start: 0.7705 (mtpt) cc_final: 0.7310 (pttt) REVERT: N 144 LEU cc_start: 0.5784 (OUTLIER) cc_final: 0.5162 (tt) REVERT: N 157 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8424 (pp) REVERT: N 164 ASP cc_start: 0.7797 (OUTLIER) cc_final: 0.7475 (t0) REVERT: N 393 LYS cc_start: 0.7582 (tptt) cc_final: 0.7313 (tttt) REVERT: N 397 MET cc_start: 0.6992 (pmm) cc_final: 0.6681 (pmm) REVERT: O 105 TYR cc_start: 0.8521 (OUTLIER) cc_final: 0.8056 (m-80) REVERT: O 222 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.7675 (pp) REVERT: O 340 ILE cc_start: 0.7716 (OUTLIER) cc_final: 0.7365 (tt) REVERT: O 486 MET cc_start: 0.7453 (OUTLIER) cc_final: 0.6339 (ptp) REVERT: O 576 ARG cc_start: 0.8101 (mmm160) cc_final: 0.7840 (mmt-90) REVERT: O 861 LYS cc_start: 0.6121 (mttt) cc_final: 0.5862 (mmtt) REVERT: O 1006 ILE cc_start: 0.8039 (OUTLIER) cc_final: 0.7452 (pp) REVERT: O 1007 MET cc_start: 0.7980 (ttm) cc_final: 0.7531 (ttm) REVERT: P 28 LYS cc_start: 0.7808 (mttt) cc_final: 0.7453 (tptm) REVERT: P 65 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7677 (mt) REVERT: P 118 TRP cc_start: 0.7002 (m-10) cc_final: 0.6393 (m-10) REVERT: P 122 THR cc_start: 0.8423 (t) cc_final: 0.7980 (p) REVERT: P 155 ARG cc_start: 0.8094 (ttm170) cc_final: 0.6624 (ttt-90) REVERT: S 109 ILE cc_start: 0.3997 (OUTLIER) cc_final: 0.3458 (pt) REVERT: T 83 GLU cc_start: 0.7203 (tm-30) cc_final: 0.6993 (tm-30) REVERT: T 176 HIS cc_start: 0.6195 (OUTLIER) cc_final: 0.5705 (t70) REVERT: T 217 ILE cc_start: 0.8809 (pt) cc_final: 0.8284 (mt) REVERT: T 377 ARG cc_start: 0.7798 (ttp-110) cc_final: 0.7293 (ttp-170) REVERT: T 392 ILE cc_start: 0.8428 (tp) cc_final: 0.8083 (pt) REVERT: T 398 LYS cc_start: 0.8217 (ttpt) cc_final: 0.7777 (pttm) REVERT: U 114 MET cc_start: 0.4980 (ptp) cc_final: 0.4756 (ptp) REVERT: U 133 MET cc_start: 0.0844 (ttt) cc_final: -0.0520 (mmt) REVERT: U 179 LEU cc_start: 0.8239 (tt) cc_final: 0.7842 (mp) REVERT: W 35 LYS cc_start: 0.8132 (mmtm) cc_final: 0.7779 (mmtt) REVERT: X 462 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7711 (mt0) REVERT: Y 111 THR cc_start: 0.7596 (OUTLIER) cc_final: 0.7265 (m) REVERT: Y 359 GLU cc_start: 0.4641 (mm-30) cc_final: 0.4400 (mm-30) REVERT: Z 73 ILE cc_start: 0.7677 (mm) cc_final: 0.7421 (mm) REVERT: Z 176 PHE cc_start: 0.7551 (OUTLIER) cc_final: 0.6561 (m-10) REVERT: Z 229 MET cc_start: 0.5606 (mmm) cc_final: 0.5295 (mtm) REVERT: Z 972 TYR cc_start: 0.7810 (OUTLIER) cc_final: 0.7210 (m-10) REVERT: Z 1126 ILE cc_start: 0.7511 (OUTLIER) cc_final: 0.7039 (tt) REVERT: Z 1129 ARG cc_start: 0.7198 (mtt180) cc_final: 0.6752 (ptt90) REVERT: Z 1130 ARG cc_start: 0.6400 (tpp80) cc_final: 0.5770 (tpt170) REVERT: b 66 LYS cc_start: 0.7969 (mmtt) cc_final: 0.7495 (mtpp) REVERT: b 109 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8331 (mp) REVERT: b 146 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.6605 (mtp180) REVERT: b 262 THR cc_start: 0.6682 (OUTLIER) cc_final: 0.6147 (m) REVERT: c 502 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8541 (mm) REVERT: c 676 MET cc_start: 0.6522 (ptp) cc_final: 0.4406 (mmt) REVERT: d 250 MET cc_start: 0.8596 (mmm) cc_final: 0.7797 (mmm) REVERT: d 397 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7945 (pp) REVERT: e 92 THR cc_start: 0.4887 (p) cc_final: 0.4672 (t) REVERT: e 113 TYR cc_start: 0.6947 (m-80) cc_final: 0.6471 (m-80) REVERT: e 151 LYS cc_start: 0.6687 (OUTLIER) cc_final: 0.5958 (tttp) REVERT: f 77 MET cc_start: 0.5763 (mmp) cc_final: 0.5416 (tmm) REVERT: g 135 ARG cc_start: 0.6148 (ttm110) cc_final: 0.5558 (mmt180) REVERT: g 142 ARG cc_start: 0.5546 (mtt180) cc_final: 0.5051 (mtp85) REVERT: g 183 ARG cc_start: 0.6607 (OUTLIER) cc_final: 0.5848 (mtp85) REVERT: g 204 LYS cc_start: 0.7592 (mttt) cc_final: 0.7174 (mmtt) REVERT: h 148 MET cc_start: 0.6011 (tmm) cc_final: 0.5626 (tpt) REVERT: h 160 ARG cc_start: 0.6449 (ttp-170) cc_final: 0.5988 (tpp-160) REVERT: h 206 LYS cc_start: 0.6752 (tptt) cc_final: 0.6060 (ttmt) REVERT: h 246 ASN cc_start: 0.6406 (OUTLIER) cc_final: 0.6125 (m110) REVERT: m 6 LYS cc_start: 0.2978 (mttp) cc_final: 0.2775 (ttpt) REVERT: n 96 MET cc_start: 0.7804 (ttp) cc_final: 0.7599 (ttp) REVERT: o 142 ARG cc_start: 0.4664 (mtt-85) cc_final: 0.4464 (mtt-85) REVERT: p 16 ARG cc_start: 0.4772 (ptt180) cc_final: 0.4384 (mpt-90) REVERT: p 24 ARG cc_start: 0.6664 (ptp-170) cc_final: 0.5695 (ptp-170) REVERT: r 133 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7045 (ptt-90) REVERT: r 136 LYS cc_start: 0.5096 (pttt) cc_final: 0.4821 (pttt) REVERT: s 107 LYS cc_start: 0.5234 (pttm) cc_final: 0.4970 (pttm) REVERT: t 32 ILE cc_start: 0.6771 (OUTLIER) cc_final: 0.6553 (mt) REVERT: w 117 ARG cc_start: 0.7340 (ttm110) cc_final: 0.6800 (mtt90) REVERT: x 107 PHE cc_start: 0.6944 (OUTLIER) cc_final: 0.6580 (m-10) outliers start: 436 outliers final: 312 residues processed: 1931 average time/residue: 1.1584 time to fit residues: 3890.3681 Evaluate side-chains 1912 residues out of total 11710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 349 poor density : 1563 time to evaluate : 9.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 147 HIS Chi-restraints excluded: chain A residue 150 HIS Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 250 PHE Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain A residue 417 PHE Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 533 GLN Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 738 PHE Chi-restraints excluded: chain A residue 772 ARG Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain B residue 903 ARG Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 103 PHE Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 172 CYS Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 211 HIS Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 318 THR Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 338 SER Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 353 THR Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 363 HIS Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 393 GLN Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 401 CYS Chi-restraints excluded: chain F residue 406 ILE Chi-restraints excluded: chain F residue 420 VAL Chi-restraints excluded: chain F residue 427 ASN Chi-restraints excluded: chain F residue 442 ARG Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 191 ASP Chi-restraints excluded: chain G residue 300 TRP Chi-restraints excluded: chain G residue 304 THR Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain I residue 871 VAL Chi-restraints excluded: chain I residue 877 ILE Chi-restraints excluded: chain I residue 906 LEU Chi-restraints excluded: chain I residue 921 ILE Chi-restraints excluded: chain J residue 806 ILE Chi-restraints excluded: chain K residue 369 LEU Chi-restraints excluded: chain K residue 370 GLU Chi-restraints excluded: chain K residue 905 VAL Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 150 THR Chi-restraints excluded: chain L residue 158 THR Chi-restraints excluded: chain L residue 190 VAL Chi-restraints excluded: chain L residue 239 LEU Chi-restraints excluded: chain L residue 281 LEU Chi-restraints excluded: chain L residue 347 THR Chi-restraints excluded: chain M residue 111 ILE Chi-restraints excluded: chain M residue 148 LEU Chi-restraints excluded: chain M residue 170 TRP Chi-restraints excluded: chain M residue 219 ILE Chi-restraints excluded: chain M residue 312 ILE Chi-restraints excluded: chain M residue 399 ILE Chi-restraints excluded: chain M residue 432 MET Chi-restraints excluded: chain N residue 51 GLU Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 144 LEU Chi-restraints excluded: chain N residue 157 LEU Chi-restraints excluded: chain N residue 164 ASP Chi-restraints excluded: chain N residue 260 THR Chi-restraints excluded: chain N residue 293 SER Chi-restraints excluded: chain N residue 323 THR Chi-restraints excluded: chain N residue 528 LYS Chi-restraints excluded: chain N residue 575 THR Chi-restraints excluded: chain O residue 40 THR Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain O residue 105 TYR Chi-restraints excluded: chain O residue 151 ILE Chi-restraints excluded: chain O residue 161 VAL Chi-restraints excluded: chain O residue 222 LEU Chi-restraints excluded: chain O residue 254 VAL Chi-restraints excluded: chain O residue 286 LEU Chi-restraints excluded: chain O residue 340 ILE Chi-restraints excluded: chain O residue 351 VAL Chi-restraints excluded: chain O residue 369 SER Chi-restraints excluded: chain O residue 439 LYS Chi-restraints excluded: chain O residue 486 MET Chi-restraints excluded: chain O residue 506 THR Chi-restraints excluded: chain O residue 546 THR Chi-restraints excluded: chain O residue 554 THR Chi-restraints excluded: chain O residue 557 LEU Chi-restraints excluded: chain O residue 560 SER Chi-restraints excluded: chain O residue 638 VAL Chi-restraints excluded: chain O residue 640 CYS Chi-restraints excluded: chain O residue 660 ILE Chi-restraints excluded: chain O residue 718 ASP Chi-restraints excluded: chain O residue 733 VAL Chi-restraints excluded: chain O residue 756 PHE Chi-restraints excluded: chain O residue 771 LEU Chi-restraints excluded: chain O residue 773 VAL Chi-restraints excluded: chain O residue 785 VAL Chi-restraints excluded: chain O residue 840 MET Chi-restraints excluded: chain O residue 854 LEU Chi-restraints excluded: chain O residue 859 ILE Chi-restraints excluded: chain O residue 943 HIS Chi-restraints excluded: chain O residue 1006 ILE Chi-restraints excluded: chain O residue 1012 LEU Chi-restraints excluded: chain O residue 1030 LEU Chi-restraints excluded: chain P residue 6 ILE Chi-restraints excluded: chain P residue 15 LYS Chi-restraints excluded: chain P residue 42 SER Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 168 VAL Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 203 VAL Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 256 SER Chi-restraints excluded: chain R residue 312 GLU Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain S residue 109 ILE Chi-restraints excluded: chain S residue 183 VAL Chi-restraints excluded: chain S residue 203 VAL Chi-restraints excluded: chain S residue 204 ILE Chi-restraints excluded: chain S residue 225 VAL Chi-restraints excluded: chain S residue 292 LEU Chi-restraints excluded: chain T residue 8 LEU Chi-restraints excluded: chain T residue 19 GLU Chi-restraints excluded: chain T residue 52 SER Chi-restraints excluded: chain T residue 176 HIS Chi-restraints excluded: chain T residue 187 LEU Chi-restraints excluded: chain T residue 274 VAL Chi-restraints excluded: chain T residue 321 HIS Chi-restraints excluded: chain T residue 334 SER Chi-restraints excluded: chain T residue 338 ILE Chi-restraints excluded: chain U residue 169 VAL Chi-restraints excluded: chain U residue 237 VAL Chi-restraints excluded: chain U residue 251 THR Chi-restraints excluded: chain U residue 341 TYR Chi-restraints excluded: chain U residue 348 SER Chi-restraints excluded: chain V residue 17 LEU Chi-restraints excluded: chain V residue 95 SER Chi-restraints excluded: chain W residue 18 VAL Chi-restraints excluded: chain W residue 52 LEU Chi-restraints excluded: chain W residue 71 ILE Chi-restraints excluded: chain W residue 94 VAL Chi-restraints excluded: chain W residue 102 SER Chi-restraints excluded: chain W residue 103 LEU Chi-restraints excluded: chain X residue 227 ILE Chi-restraints excluded: chain X residue 270 LEU Chi-restraints excluded: chain X residue 292 THR Chi-restraints excluded: chain X residue 312 VAL Chi-restraints excluded: chain X residue 432 ILE Chi-restraints excluded: chain X residue 462 GLN Chi-restraints excluded: chain X residue 502 VAL Chi-restraints excluded: chain X residue 579 VAL Chi-restraints excluded: chain X residue 580 VAL Chi-restraints excluded: chain X residue 582 THR Chi-restraints excluded: chain X residue 604 PHE Chi-restraints excluded: chain X residue 606 VAL Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Y residue 98 ILE Chi-restraints excluded: chain Y residue 102 ILE Chi-restraints excluded: chain Y residue 111 THR Chi-restraints excluded: chain Y residue 114 LEU Chi-restraints excluded: chain Y residue 128 LEU Chi-restraints excluded: chain Y residue 164 PHE Chi-restraints excluded: chain Y residue 305 VAL Chi-restraints excluded: chain Y residue 318 LEU Chi-restraints excluded: chain Y residue 396 VAL Chi-restraints excluded: chain Z residue 84 LEU Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain Z residue 166 VAL Chi-restraints excluded: chain Z residue 176 PHE Chi-restraints excluded: chain Z residue 205 TYR Chi-restraints excluded: chain Z residue 222 LEU Chi-restraints excluded: chain Z residue 271 SER Chi-restraints excluded: chain Z residue 789 CYS Chi-restraints excluded: chain Z residue 799 LEU Chi-restraints excluded: chain Z residue 836 SER Chi-restraints excluded: chain Z residue 842 PHE Chi-restraints excluded: chain Z residue 845 LEU Chi-restraints excluded: chain Z residue 867 MET Chi-restraints excluded: chain Z residue 878 ILE Chi-restraints excluded: chain Z residue 886 CYS Chi-restraints excluded: chain Z residue 906 LEU Chi-restraints excluded: chain Z residue 915 VAL Chi-restraints excluded: chain Z residue 952 ILE Chi-restraints excluded: chain Z residue 972 TYR Chi-restraints excluded: chain Z residue 1058 LEU Chi-restraints excluded: chain Z residue 1093 LEU Chi-restraints excluded: chain Z residue 1126 ILE Chi-restraints excluded: chain a residue 30 HIS Chi-restraints excluded: chain a residue 51 CYS Chi-restraints excluded: chain a residue 103 VAL Chi-restraints excluded: chain a residue 113 VAL Chi-restraints excluded: chain a residue 114 VAL Chi-restraints excluded: chain a residue 136 VAL Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain a residue 149 LEU Chi-restraints excluded: chain a residue 158 VAL Chi-restraints excluded: chain a residue 162 VAL Chi-restraints excluded: chain b residue 31 LYS Chi-restraints excluded: chain b residue 109 LEU Chi-restraints excluded: chain b residue 130 SER Chi-restraints excluded: chain b residue 139 ILE Chi-restraints excluded: chain b residue 146 ARG Chi-restraints excluded: chain b residue 156 HIS Chi-restraints excluded: chain b residue 184 VAL Chi-restraints excluded: chain b residue 205 VAL Chi-restraints excluded: chain b residue 231 VAL Chi-restraints excluded: chain b residue 239 VAL Chi-restraints excluded: chain b residue 262 THR Chi-restraints excluded: chain b residue 290 THR Chi-restraints excluded: chain c residue 494 LEU Chi-restraints excluded: chain c residue 501 THR Chi-restraints excluded: chain c residue 502 LEU Chi-restraints excluded: chain c residue 557 VAL Chi-restraints excluded: chain c residue 619 ILE Chi-restraints excluded: chain c residue 633 LEU Chi-restraints excluded: chain d residue 90 VAL Chi-restraints excluded: chain d residue 132 ILE Chi-restraints excluded: chain d residue 147 ILE Chi-restraints excluded: chain d residue 160 SER Chi-restraints excluded: chain d residue 184 HIS Chi-restraints excluded: chain d residue 236 THR Chi-restraints excluded: chain d residue 292 SER Chi-restraints excluded: chain d residue 300 SER Chi-restraints excluded: chain d residue 397 LEU Chi-restraints excluded: chain d residue 441 VAL Chi-restraints excluded: chain e residue 151 LYS Chi-restraints excluded: chain e residue 195 THR Chi-restraints excluded: chain e residue 245 CYS Chi-restraints excluded: chain e residue 250 ASP Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain f residue 128 VAL Chi-restraints excluded: chain f residue 181 SER Chi-restraints excluded: chain f residue 229 ASN Chi-restraints excluded: chain g residue 73 ILE Chi-restraints excluded: chain g residue 130 VAL Chi-restraints excluded: chain g residue 156 LEU Chi-restraints excluded: chain g residue 183 ARG Chi-restraints excluded: chain g residue 201 LEU Chi-restraints excluded: chain h residue 87 ILE Chi-restraints excluded: chain h residue 219 LEU Chi-restraints excluded: chain h residue 222 PHE Chi-restraints excluded: chain h residue 246 ASN Chi-restraints excluded: chain k residue 108 LEU Chi-restraints excluded: chain l residue 59 ASP Chi-restraints excluded: chain l residue 67 GLU Chi-restraints excluded: chain l residue 68 VAL Chi-restraints excluded: chain l residue 181 LEU Chi-restraints excluded: chain m residue 40 ASP Chi-restraints excluded: chain m residue 79 ASP Chi-restraints excluded: chain m residue 172 PHE Chi-restraints excluded: chain m residue 189 MET Chi-restraints excluded: chain m residue 202 ASP Chi-restraints excluded: chain n residue 34 SER Chi-restraints excluded: chain n residue 193 SER Chi-restraints excluded: chain n residue 195 SER Chi-restraints excluded: chain o residue 32 MET Chi-restraints excluded: chain o residue 52 ILE Chi-restraints excluded: chain o residue 100 CYS Chi-restraints excluded: chain o residue 162 VAL Chi-restraints excluded: chain p residue 22 LEU Chi-restraints excluded: chain q residue 44 HIS Chi-restraints excluded: chain q residue 60 LEU Chi-restraints excluded: chain q residue 136 VAL Chi-restraints excluded: chain q residue 141 SER Chi-restraints excluded: chain r residue 36 ASN Chi-restraints excluded: chain r residue 132 ILE Chi-restraints excluded: chain r residue 133 ARG Chi-restraints excluded: chain s residue 125 LEU Chi-restraints excluded: chain t residue 32 ILE Chi-restraints excluded: chain t residue 53 CYS Chi-restraints excluded: chain t residue 61 VAL Chi-restraints excluded: chain u residue 7 VAL Chi-restraints excluded: chain u residue 9 VAL Chi-restraints excluded: chain u residue 23 VAL Chi-restraints excluded: chain u residue 48 LEU Chi-restraints excluded: chain u residue 66 ARG Chi-restraints excluded: chain u residue 69 VAL Chi-restraints excluded: chain u residue 95 LYS Chi-restraints excluded: chain u residue 97 VAL Chi-restraints excluded: chain v residue 66 THR Chi-restraints excluded: chain w residue 60 LYS Chi-restraints excluded: chain w residue 105 THR Chi-restraints excluded: chain x residue 59 VAL Chi-restraints excluded: chain x residue 107 PHE Chi-restraints excluded: chain y residue 337 THR Chi-restraints excluded: chain z residue 37 THR Chi-restraints excluded: chain z residue 57 LEU Chi-restraints excluded: chain z residue 66 ARG Chi-restraints excluded: chain 0 residue 164 LEU Chi-restraints excluded: chain 0 residue 184 SER Chi-restraints excluded: chain 0 residue 227 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1508 random chunks: chunk 1322 optimal weight: 0.4980 chunk 1392 optimal weight: 10.0000 chunk 1270 optimal weight: 10.0000 chunk 1354 optimal weight: 20.0000 chunk 815 optimal weight: 0.7980 chunk 590 optimal weight: 0.8980 chunk 1063 optimal weight: 40.0000 chunk 415 optimal weight: 3.9990 chunk 1223 optimal weight: 0.9990 chunk 1281 optimal weight: 0.0270 chunk 1349 optimal weight: 4.9990 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 HIS ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 GLN ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 GLN ** F 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 333 ASN ** K 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 117 GLN ** O 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 505 ASN O 636 HIS ** T 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 336 HIS ** U 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 27 GLN ** Z 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z1030 ASN a 30 HIS ** b 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 94 GLN e 146 HIS l 92 GLN m 112 HIS ** n 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 36 ASN v 16 GLN ** v 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 39 GLN ** w 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 65 ASN y 382 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6154 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 140828 Z= 0.175 Angle : 0.648 40.378 198339 Z= 0.323 Chirality : 0.040 0.351 24279 Planarity : 0.005 0.098 19356 Dihedral : 21.122 179.727 39625 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.01 % Favored : 92.93 % Rotamer: Outliers : 4.15 % Allowed : 21.11 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.02 % Twisted Proline : 0.50 % Twisted General : 0.05 % 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: -1.10 (0.07), residues: 13489 helix: 1.10 (0.08), residues: 4736 sheet: -1.10 (0.10), residues: 2656 loop : -2.08 (0.08), residues: 6097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.002 TRP N 426 HIS 0.022 0.001 HIS a 30 PHE 0.042 0.002 PHE A 687 TYR 0.024 0.001 TYR m 121 ARG 0.015 0.000 ARG r 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26978 Ramachandran restraints generated. 13489 Oldfield, 0 Emsley, 13489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26978 Ramachandran restraints generated. 13489 Oldfield, 0 Emsley, 13489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2037 residues out of total 11710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 399 poor density : 1638 time to evaluate : 9.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ILE cc_start: 0.7830 (OUTLIER) cc_final: 0.7253 (mm) REVERT: A 81 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7608 (tp) REVERT: A 97 SER cc_start: 0.7830 (OUTLIER) cc_final: 0.7303 (t) REVERT: A 459 GLN cc_start: 0.7778 (pt0) cc_final: 0.7150 (mm110) REVERT: A 827 ARG cc_start: 0.7369 (ttp80) cc_final: 0.7072 (ttm170) REVERT: B 861 ARG cc_start: 0.8114 (mtm-85) cc_final: 0.7052 (mtm-85) REVERT: B 900 LYS cc_start: 0.7780 (tptm) cc_final: 0.6866 (ttmm) REVERT: D 80 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8210 (pp) REVERT: D 292 ILE cc_start: 0.8280 (OUTLIER) cc_final: 0.8001 (mm) REVERT: D 323 GLN cc_start: 0.7716 (tp40) cc_final: 0.7460 (mm-40) REVERT: E 97 GLU cc_start: 0.7517 (mm-30) cc_final: 0.7295 (mm-30) REVERT: E 191 ARG cc_start: 0.6812 (mtp180) cc_final: 0.6413 (mtt-85) REVERT: E 288 LYS cc_start: 0.7195 (pttt) cc_final: 0.6896 (tptp) REVERT: F 50 LYS cc_start: 0.7750 (mttt) cc_final: 0.7287 (tptp) REVERT: F 106 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.7218 (tt) REVERT: F 363 HIS cc_start: 0.7956 (OUTLIER) cc_final: 0.6997 (p-80) REVERT: F 393 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.7491 (pt0) REVERT: F 442 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7113 (ttp-170) REVERT: H 34 TYR cc_start: 0.7502 (t80) cc_final: 0.6998 (t80) REVERT: H 124 LYS cc_start: 0.8638 (ttpt) cc_final: 0.8395 (ttmm) REVERT: I 877 ILE cc_start: 0.7525 (OUTLIER) cc_final: 0.7150 (pt) REVERT: I 895 MET cc_start: 0.6221 (mmp) cc_final: 0.5760 (tpt) REVERT: J 808 GLN cc_start: 0.7301 (OUTLIER) cc_final: 0.6371 (tm130) REVERT: K 320 ASN cc_start: 0.7750 (m-40) cc_final: 0.7253 (m-40) REVERT: K 368 GLU cc_start: 0.7005 (tp30) cc_final: 0.6763 (tp30) REVERT: L 137 LEU cc_start: 0.7385 (OUTLIER) cc_final: 0.7100 (mp) REVERT: L 298 LYS cc_start: 0.3773 (tptt) cc_final: 0.3116 (tmtt) REVERT: M 262 HIS cc_start: 0.7180 (m-70) cc_final: 0.6787 (m170) REVERT: N 63 LYS cc_start: 0.7574 (mtpt) cc_final: 0.7211 (pttt) REVERT: N 144 LEU cc_start: 0.5799 (OUTLIER) cc_final: 0.5237 (tt) REVERT: N 239 SER cc_start: 0.8349 (OUTLIER) cc_final: 0.7862 (m) REVERT: N 393 LYS cc_start: 0.7542 (tptt) cc_final: 0.7278 (tttt) REVERT: N 397 MET cc_start: 0.7066 (pmm) cc_final: 0.6798 (pmm) REVERT: O 340 ILE cc_start: 0.7708 (OUTLIER) cc_final: 0.7334 (tt) REVERT: O 486 MET cc_start: 0.7353 (OUTLIER) cc_final: 0.6211 (ptp) REVERT: O 576 ARG cc_start: 0.8092 (mmm160) cc_final: 0.7814 (mmt-90) REVERT: O 582 ARG cc_start: 0.6001 (mpp80) cc_final: 0.5759 (mtt90) REVERT: O 1006 ILE cc_start: 0.7979 (OUTLIER) cc_final: 0.7382 (pp) REVERT: O 1007 MET cc_start: 0.8021 (ttm) cc_final: 0.7564 (ttm) REVERT: P 28 LYS cc_start: 0.7805 (mttt) cc_final: 0.7441 (tptm) REVERT: P 65 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7649 (mt) REVERT: P 118 TRP cc_start: 0.6920 (m-10) cc_final: 0.6439 (m-10) REVERT: P 122 THR cc_start: 0.8408 (t) cc_final: 0.7977 (p) REVERT: P 155 ARG cc_start: 0.8028 (ttm170) cc_final: 0.6617 (ttt-90) REVERT: P 159 LYS cc_start: 0.7830 (mmtm) cc_final: 0.7592 (mmtm) REVERT: R 205 PRO cc_start: 0.7994 (Cg_endo) cc_final: 0.7737 (Cg_exo) REVERT: S 109 ILE cc_start: 0.3882 (pt) cc_final: 0.3351 (pt) REVERT: T 217 ILE cc_start: 0.8740 (pt) cc_final: 0.8207 (mt) REVERT: T 300 SER cc_start: 0.7811 (m) cc_final: 0.7226 (p) REVERT: T 377 ARG cc_start: 0.7861 (ttp-110) cc_final: 0.7325 (tmm160) REVERT: T 392 ILE cc_start: 0.8425 (tp) cc_final: 0.8092 (pt) REVERT: T 398 LYS cc_start: 0.8113 (ttpt) cc_final: 0.7657 (pttm) REVERT: U 114 MET cc_start: 0.4905 (ptp) cc_final: 0.4701 (ptp) REVERT: U 133 MET cc_start: 0.0774 (ttt) cc_final: -0.0505 (mmt) REVERT: U 273 GLN cc_start: 0.7490 (mt0) cc_final: 0.7083 (mt0) REVERT: W 35 LYS cc_start: 0.8152 (mmtm) cc_final: 0.7824 (mmtt) REVERT: W 76 ASN cc_start: 0.8863 (t0) cc_final: 0.8650 (t0) REVERT: X 462 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7656 (mt0) REVERT: Y 111 THR cc_start: 0.7598 (OUTLIER) cc_final: 0.7259 (m) REVERT: Z 229 MET cc_start: 0.5451 (mmm) cc_final: 0.5087 (mmm) REVERT: Z 972 TYR cc_start: 0.7803 (OUTLIER) cc_final: 0.7245 (m-10) REVERT: Z 1126 ILE cc_start: 0.7518 (OUTLIER) cc_final: 0.7043 (tt) REVERT: Z 1129 ARG cc_start: 0.7117 (mtt180) cc_final: 0.6638 (ptt90) REVERT: Z 1130 ARG cc_start: 0.6415 (tpp80) cc_final: 0.5767 (tpt170) REVERT: b 66 LYS cc_start: 0.7980 (mmtt) cc_final: 0.7498 (mtpp) REVERT: b 109 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8368 (mp) REVERT: b 126 ASP cc_start: 0.6597 (t0) cc_final: 0.6267 (t0) REVERT: b 262 THR cc_start: 0.6628 (OUTLIER) cc_final: 0.6143 (m) REVERT: c 491 GLU cc_start: 0.6211 (mt-10) cc_final: 0.5545 (mm-30) REVERT: c 511 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.7261 (ptm-80) REVERT: c 676 MET cc_start: 0.6273 (ptp) cc_final: 0.4416 (mmt) REVERT: d 250 MET cc_start: 0.8597 (mmm) cc_final: 0.7942 (mmm) REVERT: d 311 ARG cc_start: 0.7781 (ttm-80) cc_final: 0.7402 (mtm-85) REVERT: d 397 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7909 (pp) REVERT: e 113 TYR cc_start: 0.6954 (m-80) cc_final: 0.6454 (m-80) REVERT: e 151 LYS cc_start: 0.6813 (OUTLIER) cc_final: 0.6045 (tttp) REVERT: g 135 ARG cc_start: 0.6217 (ttm110) cc_final: 0.5596 (mmt180) REVERT: g 142 ARG cc_start: 0.5586 (mtt180) cc_final: 0.5132 (mtp85) REVERT: g 183 ARG cc_start: 0.6642 (OUTLIER) cc_final: 0.5884 (mtp85) REVERT: h 148 MET cc_start: 0.5931 (tmm) cc_final: 0.5588 (tpt) REVERT: h 160 ARG cc_start: 0.6413 (ttp-170) cc_final: 0.5957 (tpp-160) REVERT: h 206 LYS cc_start: 0.6666 (tptt) cc_final: 0.6052 (ttpt) REVERT: h 246 ASN cc_start: 0.6453 (OUTLIER) cc_final: 0.6077 (m110) REVERT: m 6 LYS cc_start: 0.3099 (mttp) cc_final: 0.2859 (ttpt) REVERT: p 16 ARG cc_start: 0.5116 (ptt180) cc_final: 0.4564 (mpt-90) REVERT: p 24 ARG cc_start: 0.6722 (ptp-170) cc_final: 0.5717 (ptp-170) REVERT: p 50 VAL cc_start: 0.2370 (p) cc_final: 0.1992 (t) REVERT: r 133 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.6929 (ptt-90) REVERT: r 136 LYS cc_start: 0.5130 (pttt) cc_final: 0.4663 (pttt) REVERT: s 107 LYS cc_start: 0.5328 (pttm) cc_final: 0.5089 (pttm) REVERT: v 68 MET cc_start: 0.2246 (mmm) cc_final: 0.1674 (mtm) REVERT: v 85 MET cc_start: 0.3182 (ppp) cc_final: 0.0912 (mtp) REVERT: w 117 ARG cc_start: 0.7298 (ttm110) cc_final: 0.6787 (mtt90) REVERT: x 107 PHE cc_start: 0.6965 (OUTLIER) cc_final: 0.6594 (m-10) outliers start: 399 outliers final: 310 residues processed: 1888 average time/residue: 1.1444 time to fit residues: 3750.8470 Evaluate side-chains 1910 residues out of total 11710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 341 poor density : 1569 time to evaluate : 9.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 147 HIS Chi-restraints excluded: chain A residue 150 HIS Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 250 PHE Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain A residue 417 PHE Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 533 GLN Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 738 PHE Chi-restraints excluded: chain A residue 772 ARG Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 103 PHE Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 172 CYS Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 211 HIS Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 318 THR Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 353 THR Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 363 HIS Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 393 GLN Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 401 CYS Chi-restraints excluded: chain F residue 406 ILE Chi-restraints excluded: chain F residue 420 VAL Chi-restraints excluded: chain F residue 427 ASN Chi-restraints excluded: chain F residue 442 ARG Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain G residue 191 ASP Chi-restraints excluded: chain G residue 300 TRP Chi-restraints excluded: chain G residue 304 THR Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain I residue 871 VAL Chi-restraints excluded: chain I residue 877 ILE Chi-restraints excluded: chain I residue 906 LEU Chi-restraints excluded: chain I residue 921 ILE Chi-restraints excluded: chain J residue 789 THR Chi-restraints excluded: chain J residue 808 GLN Chi-restraints excluded: chain J residue 829 VAL Chi-restraints excluded: chain J residue 863 ILE Chi-restraints excluded: chain K residue 369 LEU Chi-restraints excluded: chain K residue 370 GLU Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 150 THR Chi-restraints excluded: chain L residue 158 THR Chi-restraints excluded: chain L residue 190 VAL Chi-restraints excluded: chain L residue 239 LEU Chi-restraints excluded: chain L residue 281 LEU Chi-restraints excluded: chain L residue 347 THR Chi-restraints excluded: chain M residue 111 ILE Chi-restraints excluded: chain M residue 148 LEU Chi-restraints excluded: chain M residue 170 TRP Chi-restraints excluded: chain M residue 312 ILE Chi-restraints excluded: chain M residue 399 ILE Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 144 LEU Chi-restraints excluded: chain N residue 239 SER Chi-restraints excluded: chain N residue 260 THR Chi-restraints excluded: chain N residue 293 SER Chi-restraints excluded: chain N residue 323 THR Chi-restraints excluded: chain N residue 452 VAL Chi-restraints excluded: chain N residue 528 LYS Chi-restraints excluded: chain O residue 40 THR Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain O residue 151 ILE Chi-restraints excluded: chain O residue 161 VAL Chi-restraints excluded: chain O residue 254 VAL Chi-restraints excluded: chain O residue 286 LEU Chi-restraints excluded: chain O residue 304 VAL Chi-restraints excluded: chain O residue 340 ILE Chi-restraints excluded: chain O residue 351 VAL Chi-restraints excluded: chain O residue 369 SER Chi-restraints excluded: chain O residue 439 LYS Chi-restraints excluded: chain O residue 486 MET Chi-restraints excluded: chain O residue 506 THR Chi-restraints excluded: chain O residue 546 THR Chi-restraints excluded: chain O residue 554 THR Chi-restraints excluded: chain O residue 557 LEU Chi-restraints excluded: chain O residue 560 SER Chi-restraints excluded: chain O residue 621 HIS Chi-restraints excluded: chain O residue 630 VAL Chi-restraints excluded: chain O residue 638 VAL Chi-restraints excluded: chain O residue 640 CYS Chi-restraints excluded: chain O residue 718 ASP Chi-restraints excluded: chain O residue 733 VAL Chi-restraints excluded: chain O residue 771 LEU Chi-restraints excluded: chain O residue 773 VAL Chi-restraints excluded: chain O residue 785 VAL Chi-restraints excluded: chain O residue 840 MET Chi-restraints excluded: chain O residue 854 LEU Chi-restraints excluded: chain O residue 859 ILE Chi-restraints excluded: chain O residue 943 HIS Chi-restraints excluded: chain O residue 1006 ILE Chi-restraints excluded: chain O residue 1012 LEU Chi-restraints excluded: chain O residue 1013 LEU Chi-restraints excluded: chain P residue 6 ILE Chi-restraints excluded: chain P residue 15 LYS Chi-restraints excluded: chain P residue 42 SER Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 168 VAL Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 203 VAL Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 256 SER Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain S residue 183 VAL Chi-restraints excluded: chain S residue 203 VAL Chi-restraints excluded: chain S residue 204 ILE Chi-restraints excluded: chain S residue 225 VAL Chi-restraints excluded: chain S residue 292 LEU Chi-restraints excluded: chain T residue 8 LEU Chi-restraints excluded: chain T residue 19 GLU Chi-restraints excluded: chain T residue 52 SER Chi-restraints excluded: chain T residue 187 LEU Chi-restraints excluded: chain T residue 284 MET Chi-restraints excluded: chain T residue 309 ILE Chi-restraints excluded: chain T residue 321 HIS Chi-restraints excluded: chain T residue 334 SER Chi-restraints excluded: chain T residue 338 ILE Chi-restraints excluded: chain U residue 166 VAL Chi-restraints excluded: chain U residue 169 VAL Chi-restraints excluded: chain U residue 341 TYR Chi-restraints excluded: chain V residue 17 LEU Chi-restraints excluded: chain V residue 52 LEU Chi-restraints excluded: chain V residue 95 SER Chi-restraints excluded: chain V residue 105 SER Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain W residue 18 VAL Chi-restraints excluded: chain W residue 52 LEU Chi-restraints excluded: chain W residue 71 ILE Chi-restraints excluded: chain W residue 94 VAL Chi-restraints excluded: chain W residue 102 SER Chi-restraints excluded: chain W residue 103 LEU Chi-restraints excluded: chain X residue 227 ILE Chi-restraints excluded: chain X residue 270 LEU Chi-restraints excluded: chain X residue 292 THR Chi-restraints excluded: chain X residue 312 VAL Chi-restraints excluded: chain X residue 432 ILE Chi-restraints excluded: chain X residue 462 GLN Chi-restraints excluded: chain X residue 502 VAL Chi-restraints excluded: chain X residue 579 VAL Chi-restraints excluded: chain X residue 582 THR Chi-restraints excluded: chain X residue 604 PHE Chi-restraints excluded: chain X residue 606 VAL Chi-restraints excluded: chain Y residue 98 ILE Chi-restraints excluded: chain Y residue 102 ILE Chi-restraints excluded: chain Y residue 111 THR Chi-restraints excluded: chain Y residue 114 LEU Chi-restraints excluded: chain Y residue 128 LEU Chi-restraints excluded: chain Y residue 142 THR Chi-restraints excluded: chain Y residue 164 PHE Chi-restraints excluded: chain Y residue 305 VAL Chi-restraints excluded: chain Y residue 318 LEU Chi-restraints excluded: chain Y residue 396 VAL Chi-restraints excluded: chain Z residue 84 LEU Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain Z residue 166 VAL Chi-restraints excluded: chain Z residue 205 TYR Chi-restraints excluded: chain Z residue 222 LEU Chi-restraints excluded: chain Z residue 271 SER Chi-restraints excluded: chain Z residue 799 LEU Chi-restraints excluded: chain Z residue 836 SER Chi-restraints excluded: chain Z residue 842 PHE Chi-restraints excluded: chain Z residue 845 LEU Chi-restraints excluded: chain Z residue 867 MET Chi-restraints excluded: chain Z residue 878 ILE Chi-restraints excluded: chain Z residue 886 CYS Chi-restraints excluded: chain Z residue 902 THR Chi-restraints excluded: chain Z residue 906 LEU Chi-restraints excluded: chain Z residue 914 ILE Chi-restraints excluded: chain Z residue 915 VAL Chi-restraints excluded: chain Z residue 952 ILE Chi-restraints excluded: chain Z residue 972 TYR Chi-restraints excluded: chain Z residue 988 ILE Chi-restraints excluded: chain Z residue 1058 LEU Chi-restraints excluded: chain Z residue 1093 LEU Chi-restraints excluded: chain Z residue 1126 ILE Chi-restraints excluded: chain a residue 30 HIS Chi-restraints excluded: chain a residue 51 CYS Chi-restraints excluded: chain a residue 103 VAL Chi-restraints excluded: chain a residue 113 VAL Chi-restraints excluded: chain a residue 136 VAL Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain a residue 149 LEU Chi-restraints excluded: chain a residue 158 VAL Chi-restraints excluded: chain a residue 162 VAL Chi-restraints excluded: chain b residue 109 LEU Chi-restraints excluded: chain b residue 130 SER Chi-restraints excluded: chain b residue 139 ILE Chi-restraints excluded: chain b residue 156 HIS Chi-restraints excluded: chain b residue 184 VAL Chi-restraints excluded: chain b residue 205 VAL Chi-restraints excluded: chain b residue 231 VAL Chi-restraints excluded: chain b residue 239 VAL Chi-restraints excluded: chain b residue 262 THR Chi-restraints excluded: chain b residue 290 THR Chi-restraints excluded: chain c residue 501 THR Chi-restraints excluded: chain c residue 511 ARG Chi-restraints excluded: chain c residue 557 VAL Chi-restraints excluded: chain c residue 619 ILE Chi-restraints excluded: chain c residue 633 LEU Chi-restraints excluded: chain d residue 90 VAL Chi-restraints excluded: chain d residue 105 ARG Chi-restraints excluded: chain d residue 127 CYS Chi-restraints excluded: chain d residue 132 ILE Chi-restraints excluded: chain d residue 147 ILE Chi-restraints excluded: chain d residue 160 SER Chi-restraints excluded: chain d residue 184 HIS Chi-restraints excluded: chain d residue 236 THR Chi-restraints excluded: chain d residue 292 SER Chi-restraints excluded: chain d residue 300 SER Chi-restraints excluded: chain d residue 397 LEU Chi-restraints excluded: chain e residue 151 LYS Chi-restraints excluded: chain e residue 245 CYS Chi-restraints excluded: chain e residue 250 ASP Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain f residue 181 SER Chi-restraints excluded: chain f residue 229 ASN Chi-restraints excluded: chain g residue 73 ILE Chi-restraints excluded: chain g residue 130 VAL Chi-restraints excluded: chain g residue 156 LEU Chi-restraints excluded: chain g residue 183 ARG Chi-restraints excluded: chain g residue 201 LEU Chi-restraints excluded: chain h residue 219 LEU Chi-restraints excluded: chain h residue 222 PHE Chi-restraints excluded: chain h residue 246 ASN Chi-restraints excluded: chain k residue 108 LEU Chi-restraints excluded: chain l residue 59 ASP Chi-restraints excluded: chain l residue 67 GLU Chi-restraints excluded: chain l residue 68 VAL Chi-restraints excluded: chain l residue 181 LEU Chi-restraints excluded: chain m residue 40 ASP Chi-restraints excluded: chain m residue 78 THR Chi-restraints excluded: chain m residue 79 ASP Chi-restraints excluded: chain m residue 172 PHE Chi-restraints excluded: chain m residue 189 MET Chi-restraints excluded: chain n residue 34 SER Chi-restraints excluded: chain n residue 174 VAL Chi-restraints excluded: chain n residue 193 SER Chi-restraints excluded: chain o residue 32 MET Chi-restraints excluded: chain o residue 52 ILE Chi-restraints excluded: chain o residue 100 CYS Chi-restraints excluded: chain o residue 162 VAL Chi-restraints excluded: chain p residue 22 LEU Chi-restraints excluded: chain q residue 60 LEU Chi-restraints excluded: chain q residue 136 VAL Chi-restraints excluded: chain q residue 141 SER Chi-restraints excluded: chain r residue 36 ASN Chi-restraints excluded: chain r residue 132 ILE Chi-restraints excluded: chain r residue 133 ARG Chi-restraints excluded: chain t residue 53 CYS Chi-restraints excluded: chain t residue 61 VAL Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain u residue 7 VAL Chi-restraints excluded: chain u residue 9 VAL Chi-restraints excluded: chain u residue 17 THR Chi-restraints excluded: chain u residue 48 LEU Chi-restraints excluded: chain u residue 66 ARG Chi-restraints excluded: chain u residue 69 VAL Chi-restraints excluded: chain u residue 95 LYS Chi-restraints excluded: chain u residue 97 VAL Chi-restraints excluded: chain v residue 66 THR Chi-restraints excluded: chain w residue 60 LYS Chi-restraints excluded: chain w residue 105 THR Chi-restraints excluded: chain x residue 59 VAL Chi-restraints excluded: chain x residue 107 PHE Chi-restraints excluded: chain y residue 337 THR Chi-restraints excluded: chain z residue 37 THR Chi-restraints excluded: chain z residue 57 LEU Chi-restraints excluded: chain z residue 66 ARG Chi-restraints excluded: chain 0 residue 164 LEU Chi-restraints excluded: chain 0 residue 184 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1508 random chunks: chunk 889 optimal weight: 0.9980 chunk 1432 optimal weight: 7.9990 chunk 874 optimal weight: 4.9990 chunk 679 optimal weight: 8.9990 chunk 995 optimal weight: 40.0000 chunk 1502 optimal weight: 20.0000 chunk 1382 optimal weight: 20.0000 chunk 1196 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 924 optimal weight: 20.0000 chunk 733 optimal weight: 5.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 9 ASN ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 18 GLN ** I 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 930 GLN ** K 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 272 HIS ** M 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 117 GLN ** O 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 505 ASN O 636 HIS ** P 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 139 GLN ** T 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 273 GLN U 336 HIS U 346 HIS ** U 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 27 GLN X 286 GLN X 330 GLN ** X 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 561 ASN Y 231 HIS ** Z 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z1030 ASN a 30 HIS a 74 HIS ** b 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 21 GLN e 146 HIS f 115 GLN ** k 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 119 GLN o 185 GLN q 179 GLN ** r 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 151 GLN ** v 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 65 ASN ** x 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6363 moved from start: 0.4365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.134 140828 Z= 0.600 Angle : 0.923 39.282 198339 Z= 0.463 Chirality : 0.052 0.449 24279 Planarity : 0.007 0.097 19356 Dihedral : 21.369 179.581 39625 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.04 % Favored : 89.83 % Rotamer: Outliers : 4.55 % Allowed : 21.13 % Favored : 74.32 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.02 % Twisted Proline : 0.50 % Twisted General : 0.09 % 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: -1.78 (0.07), residues: 13489 helix: 0.30 (0.07), residues: 4714 sheet: -1.36 (0.10), residues: 2650 loop : -2.32 (0.08), residues: 6125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.115 0.004 TRP N 426 HIS 0.028 0.002 HIS F 363 PHE 0.074 0.003 PHE A 687 TYR 0.046 0.003 TYR k 193 ARG 0.023 0.001 ARG r 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26978 Ramachandran restraints generated. 13489 Oldfield, 0 Emsley, 13489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26978 Ramachandran restraints generated. 13489 Oldfield, 0 Emsley, 13489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1983 residues out of total 11710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 437 poor density : 1546 time to evaluate : 9.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ILE cc_start: 0.8490 (OUTLIER) cc_final: 0.7979 (mm) REVERT: A 81 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7847 (tt) REVERT: A 459 GLN cc_start: 0.7933 (pt0) cc_final: 0.6976 (mm110) REVERT: A 518 PHE cc_start: 0.8694 (OUTLIER) cc_final: 0.7638 (m-80) REVERT: B 861 ARG cc_start: 0.8192 (mtm-85) cc_final: 0.7194 (mtm-85) REVERT: B 894 ASN cc_start: 0.7659 (t0) cc_final: 0.7376 (t0) REVERT: B 900 LYS cc_start: 0.7901 (tptm) cc_final: 0.7248 (mtpp) REVERT: D 80 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8430 (pp) REVERT: D 292 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8095 (mm) REVERT: E 136 LEU cc_start: 0.8561 (mt) cc_final: 0.8293 (mt) REVERT: E 191 ARG cc_start: 0.6815 (mtp180) cc_final: 0.6378 (mtt-85) REVERT: F 50 LYS cc_start: 0.7909 (mttt) cc_final: 0.7453 (tttp) REVERT: F 106 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7542 (tt) REVERT: F 363 HIS cc_start: 0.8017 (OUTLIER) cc_final: 0.7215 (p-80) REVERT: F 442 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7006 (ttp-170) REVERT: H 34 TYR cc_start: 0.8027 (t80) cc_final: 0.7825 (t80) REVERT: H 69 SER cc_start: 0.8802 (p) cc_final: 0.8587 (m) REVERT: I 790 MET cc_start: 0.4581 (tpp) cc_final: 0.4244 (tpp) REVERT: I 877 ILE cc_start: 0.7732 (OUTLIER) cc_final: 0.7328 (pp) REVERT: I 917 MET cc_start: 0.8361 (mtt) cc_final: 0.8124 (mtt) REVERT: J 808 GLN cc_start: 0.7569 (OUTLIER) cc_final: 0.6586 (tm130) REVERT: J 828 ARG cc_start: 0.7817 (tpp80) cc_final: 0.7384 (tpp80) REVERT: K 370 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.6912 (mt-10) REVERT: L 137 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7178 (mp) REVERT: L 298 LYS cc_start: 0.4381 (tptt) cc_final: 0.3422 (tmtt) REVERT: M 157 TRP cc_start: 0.7913 (m100) cc_final: 0.7673 (m100) REVERT: M 262 HIS cc_start: 0.7329 (m-70) cc_final: 0.7115 (m170) REVERT: N 63 LYS cc_start: 0.7903 (mtpt) cc_final: 0.7538 (pttm) REVERT: N 144 LEU cc_start: 0.6147 (OUTLIER) cc_final: 0.5782 (tm) REVERT: N 239 SER cc_start: 0.8549 (OUTLIER) cc_final: 0.7967 (m) REVERT: N 393 LYS cc_start: 0.7765 (tptt) cc_final: 0.7469 (tttt) REVERT: N 397 MET cc_start: 0.7131 (pmm) cc_final: 0.6798 (pmm) REVERT: O 105 TYR cc_start: 0.8679 (OUTLIER) cc_final: 0.8213 (m-80) REVERT: O 191 ASN cc_start: 0.7976 (OUTLIER) cc_final: 0.7712 (p0) REVERT: O 222 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.7916 (pp) REVERT: O 340 ILE cc_start: 0.7653 (OUTLIER) cc_final: 0.7322 (tt) REVERT: O 439 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7261 (mttt) REVERT: O 486 MET cc_start: 0.7908 (OUTLIER) cc_final: 0.7271 (ptp) REVERT: O 1006 ILE cc_start: 0.8212 (OUTLIER) cc_final: 0.7483 (pp) REVERT: O 1007 MET cc_start: 0.7996 (ttm) cc_final: 0.7691 (ttm) REVERT: P 28 LYS cc_start: 0.7818 (mttt) cc_final: 0.7457 (tptm) REVERT: P 65 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7852 (mp) REVERT: P 84 TYR cc_start: 0.7340 (m-80) cc_final: 0.6953 (m-10) REVERT: P 122 THR cc_start: 0.8535 (t) cc_final: 0.8023 (p) REVERT: P 155 ARG cc_start: 0.8145 (ttm170) cc_final: 0.6730 (ttt-90) REVERT: S 109 ILE cc_start: 0.4099 (OUTLIER) cc_final: 0.3603 (pt) REVERT: S 218 MET cc_start: 0.2856 (OUTLIER) cc_final: 0.2454 (mtt) REVERT: T 84 MET cc_start: 0.7949 (tpp) cc_final: 0.7643 (ttp) REVERT: T 377 ARG cc_start: 0.7758 (ttp-110) cc_final: 0.7314 (tmm160) REVERT: T 392 ILE cc_start: 0.8366 (tp) cc_final: 0.8147 (pt) REVERT: T 398 LYS cc_start: 0.8233 (ttpt) cc_final: 0.7817 (pttm) REVERT: U 133 MET cc_start: 0.0433 (ttt) cc_final: -0.0903 (mmt) REVERT: W 35 LYS cc_start: 0.8317 (mmtm) cc_final: 0.7885 (mmtt) REVERT: W 119 ARG cc_start: 0.8100 (mtm110) cc_final: 0.7786 (mtp-110) REVERT: X 233 ASP cc_start: 0.5816 (OUTLIER) cc_final: 0.5352 (t0) REVERT: X 462 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.7896 (mt0) REVERT: Y 111 THR cc_start: 0.7622 (OUTLIER) cc_final: 0.7256 (m) REVERT: Y 341 MET cc_start: 0.7116 (mtt) cc_final: 0.6743 (mtt) REVERT: Z 176 PHE cc_start: 0.7521 (OUTLIER) cc_final: 0.6516 (m-10) REVERT: Z 229 MET cc_start: 0.5674 (mmm) cc_final: 0.5340 (mtm) REVERT: Z 972 TYR cc_start: 0.8292 (OUTLIER) cc_final: 0.7827 (m-10) REVERT: Z 1038 ILE cc_start: 0.8264 (OUTLIER) cc_final: 0.7879 (mp) REVERT: Z 1126 ILE cc_start: 0.7506 (OUTLIER) cc_final: 0.7029 (tt) REVERT: Z 1129 ARG cc_start: 0.7238 (mtt180) cc_final: 0.6676 (ptt90) REVERT: Z 1130 ARG cc_start: 0.6493 (tpp80) cc_final: 0.5906 (tpt170) REVERT: a 172 LYS cc_start: 0.7455 (ttmm) cc_final: 0.7174 (mtmt) REVERT: b 66 LYS cc_start: 0.8046 (mmtt) cc_final: 0.7590 (mtpp) REVERT: b 109 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8322 (mp) REVERT: b 117 LEU cc_start: 0.7361 (OUTLIER) cc_final: 0.7079 (mp) REVERT: b 121 ASN cc_start: 0.8268 (OUTLIER) cc_final: 0.7812 (p0) REVERT: b 146 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.6833 (mtp180) REVERT: c 511 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7189 (ptm-80) REVERT: c 676 MET cc_start: 0.7030 (ptp) cc_final: 0.4742 (mmt) REVERT: d 298 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.7937 (mp) REVERT: d 395 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7383 (mtt90) REVERT: d 397 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8217 (pp) REVERT: e 113 TYR cc_start: 0.7080 (m-80) cc_final: 0.6512 (m-80) REVERT: g 64 LYS cc_start: 0.7359 (tptt) cc_final: 0.6695 (pttp) REVERT: g 135 ARG cc_start: 0.6386 (ttm110) cc_final: 0.5552 (mmt180) REVERT: g 142 ARG cc_start: 0.5598 (mtt180) cc_final: 0.5155 (mtp85) REVERT: g 183 ARG cc_start: 0.6737 (OUTLIER) cc_final: 0.5753 (mtp85) REVERT: g 204 LYS cc_start: 0.7779 (mttt) cc_final: 0.7382 (mmtt) REVERT: h 206 LYS cc_start: 0.7030 (tptt) cc_final: 0.6288 (ttpt) REVERT: n 96 MET cc_start: 0.8222 (ttp) cc_final: 0.7839 (ttt) REVERT: p 16 ARG cc_start: 0.4887 (ptt180) cc_final: 0.4417 (mpt-90) REVERT: p 24 ARG cc_start: 0.6964 (ptp-170) cc_final: 0.5865 (ptp-170) REVERT: p 50 VAL cc_start: 0.2445 (OUTLIER) cc_final: 0.1947 (t) REVERT: p 151 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7588 (ttm-80) REVERT: r 133 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.6952 (ptt-90) REVERT: w 117 ARG cc_start: 0.7396 (ttm110) cc_final: 0.6883 (mtt90) outliers start: 437 outliers final: 341 residues processed: 1838 average time/residue: 1.1377 time to fit residues: 3632.2810 Evaluate side-chains 1879 residues out of total 11710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 384 poor density : 1495 time to evaluate : 9.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 147 HIS Chi-restraints excluded: chain A residue 150 HIS Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 250 PHE Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain A residue 417 PHE Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 533 GLN Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 738 PHE Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 772 ARG Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 103 PHE Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 172 CYS Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 211 HIS Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 318 THR Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 363 HIS Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 401 CYS Chi-restraints excluded: chain F residue 406 ILE Chi-restraints excluded: chain F residue 420 VAL Chi-restraints excluded: chain F residue 427 ASN Chi-restraints excluded: chain F residue 438 THR Chi-restraints excluded: chain F residue 442 ARG Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain G residue 191 ASP Chi-restraints excluded: chain G residue 267 ILE Chi-restraints excluded: chain G residue 300 TRP Chi-restraints excluded: chain G residue 304 THR Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 129 ARG Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain I residue 862 ASN Chi-restraints excluded: chain I residue 871 VAL Chi-restraints excluded: chain I residue 877 ILE Chi-restraints excluded: chain I residue 906 LEU Chi-restraints excluded: chain I residue 921 ILE Chi-restraints excluded: chain J residue 789 THR Chi-restraints excluded: chain J residue 808 GLN Chi-restraints excluded: chain J residue 829 VAL Chi-restraints excluded: chain J residue 863 ILE Chi-restraints excluded: chain K residue 329 THR Chi-restraints excluded: chain K residue 343 LEU Chi-restraints excluded: chain K residue 369 LEU Chi-restraints excluded: chain K residue 370 GLU Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 86 ILE Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 150 THR Chi-restraints excluded: chain L residue 158 THR Chi-restraints excluded: chain L residue 190 VAL Chi-restraints excluded: chain L residue 239 LEU Chi-restraints excluded: chain L residue 281 LEU Chi-restraints excluded: chain L residue 347 THR Chi-restraints excluded: chain M residue 111 ILE Chi-restraints excluded: chain M residue 170 TRP Chi-restraints excluded: chain M residue 219 ILE Chi-restraints excluded: chain M residue 244 LEU Chi-restraints excluded: chain M residue 399 ILE Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 144 LEU Chi-restraints excluded: chain N residue 239 SER Chi-restraints excluded: chain N residue 260 THR Chi-restraints excluded: chain N residue 279 SER Chi-restraints excluded: chain N residue 293 SER Chi-restraints excluded: chain N residue 323 THR Chi-restraints excluded: chain N residue 448 THR Chi-restraints excluded: chain N residue 528 LYS Chi-restraints excluded: chain N residue 575 THR Chi-restraints excluded: chain O residue 40 THR Chi-restraints excluded: chain O residue 41 ILE Chi-restraints excluded: chain O residue 85 VAL Chi-restraints excluded: chain O residue 105 TYR Chi-restraints excluded: chain O residue 151 ILE Chi-restraints excluded: chain O residue 161 VAL Chi-restraints excluded: chain O residue 185 LEU Chi-restraints excluded: chain O residue 191 ASN Chi-restraints excluded: chain O residue 222 LEU Chi-restraints excluded: chain O residue 254 VAL Chi-restraints excluded: chain O residue 286 LEU Chi-restraints excluded: chain O residue 340 ILE Chi-restraints excluded: chain O residue 351 VAL Chi-restraints excluded: chain O residue 369 SER Chi-restraints excluded: chain O residue 439 LYS Chi-restraints excluded: chain O residue 486 MET Chi-restraints excluded: chain O residue 506 THR Chi-restraints excluded: chain O residue 546 THR Chi-restraints excluded: chain O residue 554 THR Chi-restraints excluded: chain O residue 557 LEU Chi-restraints excluded: chain O residue 560 SER Chi-restraints excluded: chain O residue 629 VAL Chi-restraints excluded: chain O residue 630 VAL Chi-restraints excluded: chain O residue 638 VAL Chi-restraints excluded: chain O residue 640 CYS Chi-restraints excluded: chain O residue 660 ILE Chi-restraints excluded: chain O residue 718 ASP Chi-restraints excluded: chain O residue 733 VAL Chi-restraints excluded: chain O residue 771 LEU Chi-restraints excluded: chain O residue 773 VAL Chi-restraints excluded: chain O residue 785 VAL Chi-restraints excluded: chain O residue 840 MET Chi-restraints excluded: chain O residue 854 LEU Chi-restraints excluded: chain O residue 859 ILE Chi-restraints excluded: chain O residue 943 HIS Chi-restraints excluded: chain O residue 1006 ILE Chi-restraints excluded: chain O residue 1012 LEU Chi-restraints excluded: chain O residue 1013 LEU Chi-restraints excluded: chain P residue 6 ILE Chi-restraints excluded: chain P residue 15 LYS Chi-restraints excluded: chain P residue 42 SER Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 168 VAL Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 203 VAL Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 256 SER Chi-restraints excluded: chain R residue 260 SER Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain S residue 109 ILE Chi-restraints excluded: chain S residue 183 VAL Chi-restraints excluded: chain S residue 203 VAL Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 225 VAL Chi-restraints excluded: chain S residue 292 LEU Chi-restraints excluded: chain T residue 8 LEU Chi-restraints excluded: chain T residue 19 GLU Chi-restraints excluded: chain T residue 52 SER Chi-restraints excluded: chain T residue 173 ASN Chi-restraints excluded: chain T residue 274 VAL Chi-restraints excluded: chain T residue 309 ILE Chi-restraints excluded: chain T residue 321 HIS Chi-restraints excluded: chain T residue 334 SER Chi-restraints excluded: chain T residue 338 ILE Chi-restraints excluded: chain U residue 166 VAL Chi-restraints excluded: chain U residue 169 VAL Chi-restraints excluded: chain U residue 341 TYR Chi-restraints excluded: chain U residue 348 SER Chi-restraints excluded: chain V residue 17 LEU Chi-restraints excluded: chain V residue 52 LEU Chi-restraints excluded: chain V residue 71 ILE Chi-restraints excluded: chain V residue 95 SER Chi-restraints excluded: chain V residue 105 SER Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain W residue 18 VAL Chi-restraints excluded: chain W residue 52 LEU Chi-restraints excluded: chain W residue 94 VAL Chi-restraints excluded: chain W residue 102 SER Chi-restraints excluded: chain W residue 103 LEU Chi-restraints excluded: chain X residue 227 ILE Chi-restraints excluded: chain X residue 233 ASP Chi-restraints excluded: chain X residue 292 THR Chi-restraints excluded: chain X residue 312 VAL Chi-restraints excluded: chain X residue 403 MET Chi-restraints excluded: chain X residue 420 LEU Chi-restraints excluded: chain X residue 432 ILE Chi-restraints excluded: chain X residue 462 GLN Chi-restraints excluded: chain X residue 502 VAL Chi-restraints excluded: chain X residue 579 VAL Chi-restraints excluded: chain X residue 582 THR Chi-restraints excluded: chain X residue 604 PHE Chi-restraints excluded: chain X residue 606 VAL Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Y residue 98 ILE Chi-restraints excluded: chain Y residue 102 ILE Chi-restraints excluded: chain Y residue 111 THR Chi-restraints excluded: chain Y residue 114 LEU Chi-restraints excluded: chain Y residue 128 LEU Chi-restraints excluded: chain Y residue 142 THR Chi-restraints excluded: chain Y residue 164 PHE Chi-restraints excluded: chain Y residue 305 VAL Chi-restraints excluded: chain Y residue 318 LEU Chi-restraints excluded: chain Y residue 396 VAL Chi-restraints excluded: chain Z residue 84 LEU Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain Z residue 156 ILE Chi-restraints excluded: chain Z residue 166 VAL Chi-restraints excluded: chain Z residue 175 LEU Chi-restraints excluded: chain Z residue 176 PHE Chi-restraints excluded: chain Z residue 205 TYR Chi-restraints excluded: chain Z residue 222 LEU Chi-restraints excluded: chain Z residue 271 SER Chi-restraints excluded: chain Z residue 799 LEU Chi-restraints excluded: chain Z residue 836 SER Chi-restraints excluded: chain Z residue 842 PHE Chi-restraints excluded: chain Z residue 845 LEU Chi-restraints excluded: chain Z residue 859 MET Chi-restraints excluded: chain Z residue 867 MET Chi-restraints excluded: chain Z residue 878 ILE Chi-restraints excluded: chain Z residue 886 CYS Chi-restraints excluded: chain Z residue 902 THR Chi-restraints excluded: chain Z residue 904 THR Chi-restraints excluded: chain Z residue 906 LEU Chi-restraints excluded: chain Z residue 914 ILE Chi-restraints excluded: chain Z residue 915 VAL Chi-restraints excluded: chain Z residue 923 THR Chi-restraints excluded: chain Z residue 952 ILE Chi-restraints excluded: chain Z residue 972 TYR Chi-restraints excluded: chain Z residue 988 ILE Chi-restraints excluded: chain Z residue 1038 ILE Chi-restraints excluded: chain Z residue 1058 LEU Chi-restraints excluded: chain Z residue 1093 LEU Chi-restraints excluded: chain Z residue 1126 ILE Chi-restraints excluded: chain a residue 30 HIS Chi-restraints excluded: chain a residue 51 CYS Chi-restraints excluded: chain a residue 95 SER Chi-restraints excluded: chain a residue 103 VAL Chi-restraints excluded: chain a residue 113 VAL Chi-restraints excluded: chain a residue 136 VAL Chi-restraints excluded: chain a residue 149 LEU Chi-restraints excluded: chain a residue 158 VAL Chi-restraints excluded: chain a residue 162 VAL Chi-restraints excluded: chain b residue 109 LEU Chi-restraints excluded: chain b residue 117 LEU Chi-restraints excluded: chain b residue 121 ASN Chi-restraints excluded: chain b residue 130 SER Chi-restraints excluded: chain b residue 139 ILE Chi-restraints excluded: chain b residue 146 ARG Chi-restraints excluded: chain b residue 156 HIS Chi-restraints excluded: chain b residue 184 VAL Chi-restraints excluded: chain b residue 205 VAL Chi-restraints excluded: chain b residue 231 VAL Chi-restraints excluded: chain b residue 239 VAL Chi-restraints excluded: chain b residue 262 THR Chi-restraints excluded: chain b residue 290 THR Chi-restraints excluded: chain c residue 501 THR Chi-restraints excluded: chain c residue 511 ARG Chi-restraints excluded: chain c residue 526 VAL Chi-restraints excluded: chain c residue 557 VAL Chi-restraints excluded: chain c residue 619 ILE Chi-restraints excluded: chain c residue 633 LEU Chi-restraints excluded: chain d residue 90 VAL Chi-restraints excluded: chain d residue 105 ARG Chi-restraints excluded: chain d residue 127 CYS Chi-restraints excluded: chain d residue 132 ILE Chi-restraints excluded: chain d residue 147 ILE Chi-restraints excluded: chain d residue 160 SER Chi-restraints excluded: chain d residue 184 HIS Chi-restraints excluded: chain d residue 185 SER Chi-restraints excluded: chain d residue 200 ILE Chi-restraints excluded: chain d residue 201 THR Chi-restraints excluded: chain d residue 236 THR Chi-restraints excluded: chain d residue 292 SER Chi-restraints excluded: chain d residue 298 LEU Chi-restraints excluded: chain d residue 300 SER Chi-restraints excluded: chain d residue 343 THR Chi-restraints excluded: chain d residue 395 ARG Chi-restraints excluded: chain d residue 397 LEU Chi-restraints excluded: chain e residue 245 CYS Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain f residue 181 SER Chi-restraints excluded: chain f residue 229 ASN Chi-restraints excluded: chain g residue 73 ILE Chi-restraints excluded: chain g residue 130 VAL Chi-restraints excluded: chain g residue 156 LEU Chi-restraints excluded: chain g residue 183 ARG Chi-restraints excluded: chain g residue 201 LEU Chi-restraints excluded: chain h residue 87 ILE Chi-restraints excluded: chain h residue 222 PHE Chi-restraints excluded: chain h residue 246 ASN Chi-restraints excluded: chain k residue 86 THR Chi-restraints excluded: chain k residue 108 LEU Chi-restraints excluded: chain l residue 67 GLU Chi-restraints excluded: chain l residue 68 VAL Chi-restraints excluded: chain m residue 40 ASP Chi-restraints excluded: chain m residue 45 ILE Chi-restraints excluded: chain m residue 78 THR Chi-restraints excluded: chain m residue 79 ASP Chi-restraints excluded: chain m residue 90 ILE Chi-restraints excluded: chain m residue 172 PHE Chi-restraints excluded: chain m residue 189 MET Chi-restraints excluded: chain n residue 34 SER Chi-restraints excluded: chain n residue 81 THR Chi-restraints excluded: chain n residue 86 MET Chi-restraints excluded: chain n residue 174 VAL Chi-restraints excluded: chain n residue 193 SER Chi-restraints excluded: chain o residue 32 MET Chi-restraints excluded: chain o residue 52 ILE Chi-restraints excluded: chain o residue 100 CYS Chi-restraints excluded: chain o residue 119 GLN Chi-restraints excluded: chain o residue 162 VAL Chi-restraints excluded: chain p residue 50 VAL Chi-restraints excluded: chain p residue 151 ARG Chi-restraints excluded: chain q residue 44 HIS Chi-restraints excluded: chain q residue 60 LEU Chi-restraints excluded: chain q residue 136 VAL Chi-restraints excluded: chain q residue 141 SER Chi-restraints excluded: chain r residue 132 ILE Chi-restraints excluded: chain r residue 133 ARG Chi-restraints excluded: chain t residue 32 ILE Chi-restraints excluded: chain t residue 53 CYS Chi-restraints excluded: chain t residue 61 VAL Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain u residue 7 VAL Chi-restraints excluded: chain u residue 9 VAL Chi-restraints excluded: chain u residue 17 THR Chi-restraints excluded: chain u residue 23 VAL Chi-restraints excluded: chain u residue 44 LEU Chi-restraints excluded: chain u residue 48 LEU Chi-restraints excluded: chain u residue 66 ARG Chi-restraints excluded: chain u residue 69 VAL Chi-restraints excluded: chain u residue 95 LYS Chi-restraints excluded: chain u residue 97 VAL Chi-restraints excluded: chain v residue 66 THR Chi-restraints excluded: chain w residue 105 THR Chi-restraints excluded: chain x residue 59 VAL Chi-restraints excluded: chain x residue 65 ASN Chi-restraints excluded: chain x residue 103 LEU Chi-restraints excluded: chain y residue 337 THR Chi-restraints excluded: chain z residue 11 VAL Chi-restraints excluded: chain z residue 37 THR Chi-restraints excluded: chain z residue 40 SER Chi-restraints excluded: chain z residue 57 LEU Chi-restraints excluded: chain z residue 66 ARG Chi-restraints excluded: chain 0 residue 164 LEU Chi-restraints excluded: chain 0 residue 184 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1508 random chunks: chunk 950 optimal weight: 5.9990 chunk 1274 optimal weight: 8.9990 chunk 366 optimal weight: 0.6980 chunk 1103 optimal weight: 40.0000 chunk 176 optimal weight: 3.9990 chunk 332 optimal weight: 4.9990 chunk 1198 optimal weight: 1.9990 chunk 501 optimal weight: 0.2980 chunk 1230 optimal weight: 20.0000 chunk 151 optimal weight: 0.9990 chunk 220 optimal weight: 0.7980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 9 ASN ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 273 GLN D 323 GLN F 196 GLN ** F 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 333 ASN ** K 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 62 GLN O 117 GLN ** O 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 505 ASN O 636 HIS P 119 GLN ** T 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 176 HIS ** T 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 336 HIS ** U 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 27 GLN ** W 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 316 GLN ** Z 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z1030 ASN a 30 HIS a 74 HIS ** b 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 21 GLN ** m 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 179 GLN ** r 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 151 GLN v 16 GLN ** v 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 65 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.222608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.176837 restraints weight = 193599.543| |-----------------------------------------------------------------------------| r_work (start): 0.4039 rms_B_bonded: 3.59 r_work: 0.3570 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3572 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3572 r_free = 0.3572 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3571 r_free = 0.3571 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3571 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 140828 Z= 0.209 Angle : 0.697 40.464 198339 Z= 0.348 Chirality : 0.042 0.328 24279 Planarity : 0.005 0.115 19356 Dihedral : 21.203 179.842 39625 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.17 % Favored : 92.76 % Rotamer: Outliers : 3.87 % Allowed : 22.22 % Favored : 73.91 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.02 % Twisted Proline : 0.50 % Twisted General : 0.06 % 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: -1.33 (0.07), residues: 13489 helix: 0.85 (0.08), residues: 4731 sheet: -1.25 (0.10), residues: 2677 loop : -2.13 (0.08), residues: 6081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.086 0.002 TRP N 426 HIS 0.019 0.001 HIS e 243 PHE 0.048 0.002 PHE A 687 TYR 0.030 0.002 TYR X 273 ARG 0.017 0.001 ARG O 582 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 56657.98 seconds wall clock time: 976 minutes 41.12 seconds (58601.12 seconds total)