Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 28 18:58:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rzz_10068/04_2023/6rzz_10068.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rzz_10068/04_2023/6rzz_10068.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/6rzz_10068/04_2023/6rzz_10068.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rzz_10068/04_2023/6rzz_10068.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rzz_10068/04_2023/6rzz_10068.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rzz_10068/04_2023/6rzz_10068.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.003 sd= 0.023 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 10 6.06 5 P 3419 5.49 5 S 148 5.16 5 C 71415 2.51 5 N 24656 2.21 5 O 34711 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 9": "NH1" <-> "NH2" Residue "B ARG 21": "NH1" <-> "NH2" Residue "B ARG 37": "NH1" <-> "NH2" Residue "B GLU 73": "OE1" <-> "OE2" Residue "B ARG 200": "NH1" <-> "NH2" Residue "C GLU 145": "OE1" <-> "OE2" Residue "C GLU 210": "OE1" <-> "OE2" Residue "C ARG 275": "NH1" <-> "NH2" Residue "C ARG 369": "NH1" <-> "NH2" Residue "D GLU 54": "OE1" <-> "OE2" Residue "D ARG 69": "NH1" <-> "NH2" Residue "D GLU 265": "OE1" <-> "OE2" Residue "D ARG 326": "NH1" <-> "NH2" Residue "D GLU 337": "OE1" <-> "OE2" Residue "D GLU 345": "OE1" <-> "OE2" Residue "D GLU 357": "OE1" <-> "OE2" Residue "E ARG 10": "NH1" <-> "NH2" Residue "E ARG 32": "NH1" <-> "NH2" Residue "E GLU 38": "OE1" <-> "OE2" Residue "E ARG 55": "NH1" <-> "NH2" Residue "E ARG 60": "NH1" <-> "NH2" Residue "E ARG 61": "NH1" <-> "NH2" Residue "E GLU 81": "OE1" <-> "OE2" Residue "E ARG 94": "NH1" <-> "NH2" Residue "F GLU 11": "OE1" <-> "OE2" Residue "F GLU 14": "OE1" <-> "OE2" Residue "F ARG 23": "NH1" <-> "NH2" Residue "F ARG 69": "NH1" <-> "NH2" Residue "F ARG 168": "NH1" <-> "NH2" Residue "G GLU 118": "OE1" <-> "OE2" Residue "G GLU 136": "OE1" <-> "OE2" Residue "H GLU 54": "OE1" <-> "OE2" Residue "H ARG 84": "NH1" <-> "NH2" Residue "H GLU 112": "OE1" <-> "OE2" Residue "H PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 185": "NH1" <-> "NH2" Residue "H ARG 204": "NH1" <-> "NH2" Residue "H GLU 208": "OE1" <-> "OE2" Residue "J GLU 45": "OE1" <-> "OE2" Residue "J PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 99": "OE1" <-> "OE2" Residue "J TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 149": "OE1" <-> "OE2" Residue "J ARG 162": "NH1" <-> "NH2" Residue "K ARG 42": "NH1" <-> "NH2" Residue "K ARG 49": "NH1" <-> "NH2" Residue "K ARG 104": "NH1" <-> "NH2" Residue "K GLU 107": "OE1" <-> "OE2" Residue "K ARG 128": "NH1" <-> "NH2" Residue "K GLU 136": "OE1" <-> "OE2" Residue "K ARG 157": "NH1" <-> "NH2" Residue "K ARG 171": "NH1" <-> "NH2" Residue "K ARG 174": "NH1" <-> "NH2" Residue "K GLU 176": "OE1" <-> "OE2" Residue "K ARG 180": "NH1" <-> "NH2" Residue "K GLU 184": "OE1" <-> "OE2" Residue "L ARG 32": "NH1" <-> "NH2" Residue "L ARG 70": "NH1" <-> "NH2" Residue "L ARG 88": "NH1" <-> "NH2" Residue "L GLU 96": "OE1" <-> "OE2" Residue "L ARG 128": "NH1" <-> "NH2" Residue "M ARG 19": "NH1" <-> "NH2" Residue "M GLU 37": "OE1" <-> "OE2" Residue "M GLU 92": "OE1" <-> "OE2" Residue "M GLU 107": "OE1" <-> "OE2" Residue "M ARG 108": "NH1" <-> "NH2" Residue "N GLU 84": "OE1" <-> "OE2" Residue "N GLU 97": "OE1" <-> "OE2" Residue "O GLU 9": "OE1" <-> "OE2" Residue "O ARG 20": "NH1" <-> "NH2" Residue "O ARG 49": "NH1" <-> "NH2" Residue "P GLU 123": "OE1" <-> "OE2" Residue "P GLU 126": "OE1" <-> "OE2" Residue "P GLU 130": "OE1" <-> "OE2" Residue "P ARG 140": "NH1" <-> "NH2" Residue "P ARG 158": "NH1" <-> "NH2" Residue "P GLU 209": "OE1" <-> "OE2" Residue "P GLU 210": "OE1" <-> "OE2" Residue "P ARG 218": "NH1" <-> "NH2" Residue "P GLU 257": "OE1" <-> "OE2" Residue "Q GLU 74": "OE1" <-> "OE2" Residue "Q ARG 92": "NH1" <-> "NH2" Residue "Q ARG 176": "NH1" <-> "NH2" Residue "R ARG 5": "NH1" <-> "NH2" Residue "R GLU 28": "OE1" <-> "OE2" Residue "R TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 17": "OE1" <-> "OE2" Residue "S ARG 28": "NH1" <-> "NH2" Residue "S ARG 80": "NH1" <-> "NH2" Residue "S GLU 93": "OE1" <-> "OE2" Residue "S GLU 104": "OE1" <-> "OE2" Residue "S ARG 117": "NH1" <-> "NH2" Residue "T ARG 8": "NH1" <-> "NH2" Residue "T ARG 136": "NH1" <-> "NH2" Residue "T GLU 137": "OE1" <-> "OE2" Residue "T ARG 139": "NH1" <-> "NH2" Residue "T GLU 144": "OE1" <-> "OE2" Residue "U ARG 3": "NH1" <-> "NH2" Residue "U ARG 18": "NH1" <-> "NH2" Residue "U GLU 40": "OE1" <-> "OE2" Residue "U ARG 56": "NH1" <-> "NH2" Residue "U ARG 126": "NH1" <-> "NH2" Residue "U ARG 128": "NH1" <-> "NH2" Residue "U ARG 135": "NH1" <-> "NH2" Residue "W ARG 33": "NH1" <-> "NH2" Residue "W ARG 56": "NH1" <-> "NH2" Residue "W GLU 70": "OE1" <-> "OE2" Residue "W GLU 101": "OE1" <-> "OE2" Residue "W GLU 104": "OE1" <-> "OE2" Residue "W TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 125": "NH1" <-> "NH2" Residue "W ARG 138": "NH1" <-> "NH2" Residue "X GLU 88": "OE1" <-> "OE2" Residue "X ARG 121": "NH1" <-> "NH2" Residue "Y ARG 84": "NH1" <-> "NH2" Residue "Y PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 27": "OE1" <-> "OE2" Residue "Z GLU 30": "OE1" <-> "OE2" Residue "a TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 29": "OE1" <-> "OE2" Residue "b ARG 30": "NH1" <-> "NH2" Residue "b GLU 59": "OE1" <-> "OE2" Residue "b ARG 67": "NH1" <-> "NH2" Residue "b ARG 100": "NH1" <-> "NH2" Residue "c ARG 52": "NH1" <-> "NH2" Residue "d TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 68": "OE1" <-> "OE2" Residue "d ARG 72": "NH1" <-> "NH2" Residue "d ARG 79": "NH1" <-> "NH2" Residue "e GLU 30": "OE1" <-> "OE2" Residue "e GLU 83": "OE1" <-> "OE2" Residue "f ARG 48": "NH1" <-> "NH2" Residue "f GLU 58": "OE1" <-> "OE2" Residue "f ARG 60": "NH1" <-> "NH2" Residue "f ARG 86": "NH1" <-> "NH2" Residue "g ARG 16": "NH1" <-> "NH2" Residue "g GLU 87": "OE1" <-> "OE2" Residue "g GLU 96": "OE1" <-> "OE2" Residue "h GLU 88": "OE1" <-> "OE2" Residue "h ARG 99": "NH1" <-> "NH2" Residue "i ARG 63": "NH1" <-> "NH2" Residue "j ARG 16": "NH1" <-> "NH2" Residue "j ARG 39": "NH1" <-> "NH2" Residue "l ARG 8": "NH1" <-> "NH2" Residue "l ARG 18": "NH1" <-> "NH2" Residue "l ARG 45": "NH1" <-> "NH2" Residue "l ARG 71": "NH1" <-> "NH2" Residue "l GLU 92": "OE1" <-> "OE2" Residue "m ARG 36": "NH1" <-> "NH2" Residue "m ARG 80": "NH1" <-> "NH2" Residue "n GLU 32": "OE1" <-> "OE2" Residue "n ARG 100": "NH1" <-> "NH2" Residue "n GLU 126": "OE1" <-> "OE2" Residue "n ARG 188": "NH1" <-> "NH2" Residue "n TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 141": "OE1" <-> "OE2" Residue "o GLU 186": "OE1" <-> "OE2" Residue "o GLU 196": "OE1" <-> "OE2" Residue "o ARG 197": "NH1" <-> "NH2" Residue "o ARG 208": "NH1" <-> "NH2" Residue "o ARG 214": "NH1" <-> "NH2" Residue "o ARG 220": "NH1" <-> "NH2" Residue "o ARG 228": "NH1" <-> "NH2" Residue "o ARG 246": "NH1" <-> "NH2" Residue "o GLU 426": "OE1" <-> "OE2" Residue "o ARG 427": "NH1" <-> "NH2" Residue "o ARG 446": "NH1" <-> "NH2" Residue "o ARG 466": "NH1" <-> "NH2" Residue "o ARG 468": "NH1" <-> "NH2" Residue "o GLU 480": "OE1" <-> "OE2" Residue "o ARG 482": "NH1" <-> "NH2" Residue "o ARG 485": "NH1" <-> "NH2" Residue "r ARG 29": "NH1" <-> "NH2" Residue "r ARG 75": "NH1" <-> "NH2" Residue "r GLU 107": "OE1" <-> "OE2" Residue "r ARG 134": "NH1" <-> "NH2" Residue "r GLU 165": "OE1" <-> "OE2" Residue "r GLU 205": "OE1" <-> "OE2" Residue "r ARG 224": "NH1" <-> "NH2" Residue "r ARG 232": "NH1" <-> "NH2" Residue "r ARG 243": "NH1" <-> "NH2" Residue "r GLU 338": "OE1" <-> "OE2" Residue "r ARG 362": "NH1" <-> "NH2" Residue "r PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 407": "OE1" <-> "OE2" Residue "r GLU 494": "OE1" <-> "OE2" Residue "r GLU 571": "OE1" <-> "OE2" Residue "s ARG 236": "NH1" <-> "NH2" Residue "s GLU 257": "OE1" <-> "OE2" Residue "s GLU 286": "OE1" <-> "OE2" Residue "s GLU 294": "OE1" <-> "OE2" Residue "u GLU 177": "OE1" <-> "OE2" Residue "u GLU 178": "OE1" <-> "OE2" Residue "u GLU 181": "OE1" <-> "OE2" Residue "u ARG 185": "NH1" <-> "NH2" Residue "u GLU 193": "OE1" <-> "OE2" Residue "u GLU 245": "OE1" <-> "OE2" Residue "u GLU 329": "OE1" <-> "OE2" Residue "u PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 366": "OE1" <-> "OE2" Residue "v GLU 4": "OE1" <-> "OE2" Residue "v ARG 17": "NH1" <-> "NH2" Residue "w ARG 51": "NH1" <-> "NH2" Residue "w ARG 63": "NH1" <-> "NH2" Residue "w ARG 73": "NH1" <-> "NH2" Residue "w GLU 77": "OE1" <-> "OE2" Residue "w ARG 79": "NH1" <-> "NH2" Residue "w GLU 80": "OE1" <-> "OE2" Residue "w ARG 87": "NH1" <-> "NH2" Residue "w ARG 88": "NH1" <-> "NH2" Residue "w ARG 96": "NH1" <-> "NH2" Residue "w GLU 106": "OE1" <-> "OE2" Residue "w ARG 111": "NH1" <-> "NH2" Residue "w GLU 135": "OE1" <-> "OE2" Residue "w ARG 148": "NH1" <-> "NH2" Residue "w ARG 156": "NH1" <-> "NH2" Residue "w ARG 162": "NH1" <-> "NH2" Residue "w ARG 303": "NH1" <-> "NH2" Residue "w ARG 330": "NH1" <-> "NH2" Residue "w ARG 333": "NH1" <-> "NH2" Residue "w ARG 342": "NH1" <-> "NH2" Residue "w ARG 404": "NH1" <-> "NH2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 134359 Number of models: 1 Model: "" Number of chains: 55 Chain: "A" Number of atoms: 67292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3146, 67292 Inner-chain residues flagged as termini: ['pdbres=" G A 494 "'] Classifications: {'RNA': 3146} Modifications used: {'5*END': 2, 'rna2p_pur': 320, 'rna2p_pyr': 202, 'rna3p_pur': 1428, 'rna3p_pyr': 1196} Link IDs: {'rna2p': 522, 'rna3p': 2623} Chain breaks: 3 Chain: "B" Number of atoms: 1878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1878 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain: "C" Number of atoms: 3039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3039 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 14, 'TRANS': 366} Chain: "D" Number of atoms: 2748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2748 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 17, 'TRANS': 343} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "E" Number of atoms: 1352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1352 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 5, 'TRANS': 163} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "F" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1502 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 4, 'TRANS': 184} Chain: "G" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1399 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 9, 'TRANS': 165} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1742 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 11, 'TRANS': 211} Chain: "J" Number of atoms: 1563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1563 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 8, 'TRANS': 188} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "K" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1486 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 9, 'TRANS': 176} Chain: "L" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1002 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 7, 'TRANS': 128} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "M" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1045 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 4, 'TRANS': 130} Chain: "N" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1172 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 7, 'TRANS': 140} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "O" Number of atoms: 1719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1719 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 7, 'TRANS': 195} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "P" Number of atoms: 2176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2176 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 10, 'TRANS': 258} Chain: "Q" Number of atoms: 1440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1440 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 9, 'TRANS': 175} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "R" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1209 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 2, 'TRANS': 147} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "S" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1436 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 7, 'TRANS': 163} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "T" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1275 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 6, 'TRANS': 152} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "U" Number of atoms: 1222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1222 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 5, 'TRANS': 148} Chain: "V" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 786 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 2, 'TRANS': 96} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "W" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 958 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "X" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 984 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "Y" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1091 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 6, 'TRANS': 128} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "Z" Number of atoms: 963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 963 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "a" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 415 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain: "b" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1760 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 10, 'TRANS': 208} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "c" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 741 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 1, 'TRANS': 95} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "d" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 872 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "e" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1020 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "f" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 849 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, 'TRANS': 101} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "g" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 812 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "h" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 763 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "i" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 665 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "j" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 611 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "k" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 435 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "l" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 756 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "m" Number of atoms: 680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 680 Classifications: {'peptide': 89} Link IDs: {'TRANS': 88} Chain: "n" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1691 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "o" Number of atoms: 2574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2574 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 17, 'TRANS': 302} Chain breaks: 2 Chain: "p" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1050 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 210} Link IDs: {'TRANS': 209} Unresolved non-hydrogen bonds: 420 Unresolved non-hydrogen angles: 630 Unresolved non-hydrogen dihedrals: 210 Planarities with less than four sites: {'UNK:plan-1': 210} Unresolved non-hydrogen planarities: 210 Chain: "r" Number of atoms: 3999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 3999 Classifications: {'peptide': 516} Link IDs: {'PTRANS': 25, 'TRANS': 490} Chain breaks: 3 Chain: "s" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 991 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 119} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "u" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1724 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 7, 'TRANS': 203} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 26 Chain: "v" Number of atoms: 500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 500 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain: "w" Number of atoms: 3076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3076 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 14, 'TRANS': 374} Chain: "x" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2576 Classifications: {'RNA': 121} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 8, 'rna3p_pur': 56, 'rna3p_pyr': 50} Link IDs: {'rna2p': 14, 'rna3p': 106} Chain: "y" Number of atoms: 3310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 3310 Classifications: {'RNA': 156} Modifications used: {'5*END': 1, 'rna2p_pur': 16, 'rna2p_pyr': 13, 'rna3p_pur': 62, 'rna3p_pyr': 65} Link IDs: {'rna2p': 29, 'rna3p': 126} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "m" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "s" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "u" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "w" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A06JQ SG CYS g 44 131.949 119.165 201.189 1.00 33.74 S ATOM A06K8 SG CYS g 47 127.439 118.762 200.316 1.00 37.28 S ATOM A06RA SG CYS g 81 129.750 119.722 204.410 1.00 35.91 S ATOM A06RT SG CYS g 84 130.513 116.415 203.196 1.00 37.35 S ATOM A07LJ SG CYS i 19 154.169 135.309 150.594 1.00 32.07 S ATOM A07M8 SG CYS i 22 154.243 137.251 146.799 1.00 20.32 S ATOM A07P0 SG CYS i 34 152.166 134.058 147.736 1.00 27.72 S ATOM A07PI SG CYS i 37 156.143 133.653 147.003 1.00 24.18 S ATOM A08VS SG CYS l 12 150.562 63.457 86.736 1.00 30.18 S ATOM A08WR SG CYS l 17 152.933 60.274 85.202 1.00 36.40 S ATOM A099N SG CYS l 74 149.704 59.886 87.795 1.00 28.12 S ATOM A09A9 SG CYS l 77 153.515 61.566 88.592 1.00 29.57 S ATOM A09MW SG CYS m 39 116.443 106.362 197.709 1.00 38.15 S ATOM A09NJ SG CYS m 42 115.317 109.004 200.235 1.00 38.95 S ATOM A09QK SG CYS m 57 116.086 110.965 197.253 1.00 34.29 S ATOM A09R2 SG CYS m 60 118.854 109.198 198.778 1.00 36.77 S ATOM A0HPY SG CYS s 326 27.060 120.770 108.982 1.00118.26 S ATOM A0IBG SG CYS u 217 78.248 188.316 194.393 1.00 90.26 S ATOM A0IC1 SG CYS u 220 78.522 186.184 190.426 1.00 89.92 S ATOM A0HZ3 SG CYS u 164 79.610 187.699 208.729 1.00104.27 S ATOM A0HZS SG CYS u 167 77.157 185.228 209.809 1.00107.67 S ATOM A0JTW SG CYS w 58 74.035 98.288 111.186 1.00114.33 S ATOM A0JUL SG CYS w 61 76.843 97.246 113.791 1.00115.69 S ATOM A0JM0 SG CYS w 19 30.754 125.037 130.056 1.00 93.63 S ATOM A0JMK SG CYS w 22 28.057 123.046 128.727 1.00 93.42 S ATOM A0JPM SG CYS w 38 31.966 123.092 127.195 1.00102.89 S Time building chain proxies: 50.85, per 1000 atoms: 0.38 Number of scatterers: 134359 At special positions: 0 Unit cell: (238.56, 244.95, 249.21, 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 10 29.99 S 148 16.00 P 3419 15.00 O 34711 8.00 N 24656 7.00 C 71415 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: 47.88 Conformation dependent library (CDL) restraints added in 7.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN g 201 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 44 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 84 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 81 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 47 " pdb=" ZN i 101 " pdb="ZN ZN i 101 " - pdb=" SG CYS i 34 " pdb="ZN ZN i 101 " - pdb=" SG CYS i 22 " pdb="ZN ZN i 101 " - pdb=" SG CYS i 19 " pdb="ZN ZN i 101 " - pdb=" SG CYS i 37 " pdb=" ZN l 201 " pdb="ZN ZN l 201 " - pdb=" SG CYS l 12 " pdb="ZN ZN l 201 " - pdb=" SG CYS l 74 " pdb="ZN ZN l 201 " - pdb=" SG CYS l 77 " pdb="ZN ZN l 201 " - pdb=" SG CYS l 17 " pdb=" ZN m 101 " pdb="ZN ZN m 101 " - pdb=" SG CYS m 39 " pdb="ZN ZN m 101 " - pdb=" SG CYS m 57 " pdb="ZN ZN m 101 " - pdb=" SG CYS m 42 " pdb="ZN ZN m 101 " - pdb=" SG CYS m 60 " pdb=" ZN s 402 " pdb="ZN ZN s 402 " - pdb=" SG CYS s 326 " pdb=" ZN u 401 " pdb="ZN ZN u 401 " - pdb=" NE2 HIS u 233 " pdb="ZN ZN u 401 " - pdb=" ND1 HIS u 239 " pdb="ZN ZN u 401 " - pdb=" SG CYS u 220 " pdb="ZN ZN u 401 " - pdb=" SG CYS u 217 " pdb=" ZN u 402 " pdb="ZN ZN u 402 " - pdb=" NE2 HIS u 187 " pdb="ZN ZN u 402 " - pdb=" SG CYS u 164 " pdb="ZN ZN u 402 " - pdb=" SG CYS u 167 " pdb=" ZN w 601 " pdb="ZN ZN w 601 " - pdb=" SG CYS w 58 " pdb="ZN ZN w 601 " - pdb=" SG CYS w 61 " pdb=" ZN w 602 " pdb="ZN ZN w 602 " - pdb=" SG CYS w 19 " pdb="ZN ZN w 602 " - pdb=" SG CYS w 22 " pdb="ZN ZN w 602 " - pdb=" SG CYS w 38 " Number of angles added : 25 14972 Ramachandran restraints generated. 7486 Oldfield, 0 Emsley, 7486 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14572 Finding SS restraints... Secondary structure from input PDB file: 253 helices and 86 sheets defined 33.6% alpha, 15.1% beta 985 base pairs and 1848 stacking pairs defined. Time for finding SS restraints: 40.39 Creating SS restraints... Processing helix chain 'B' and resid 5 through 10 Processing helix chain 'B' and resid 33 through 38 Processing helix chain 'B' and resid 173 through 177 removed outlier: 3.921A pdb=" N LYS B 177 " --> pdb=" O ARG B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 190 Processing helix chain 'B' and resid 200 through 204 removed outlier: 3.537A pdb=" N MET B 204 " --> pdb=" O GLY B 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 17 removed outlier: 3.640A pdb=" N PHE C 16 " --> pdb=" O HIS C 13 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU C 17 " --> pdb=" O LEU C 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 13 through 17' Processing helix chain 'C' and resid 111 through 116 Processing helix chain 'C' and resid 117 through 119 No H-bonds generated for 'chain 'C' and resid 117 through 119' Processing helix chain 'C' and resid 134 through 139 removed outlier: 3.954A pdb=" N ALA C 138 " --> pdb=" O SER C 134 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN C 139 " --> pdb=" O ALA C 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 134 through 139' Processing helix chain 'C' and resid 141 through 155 removed outlier: 4.123A pdb=" N GLU C 147 " --> pdb=" O GLY C 143 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR C 154 " --> pdb=" O ARG C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 198 removed outlier: 3.541A pdb=" N ASP C 193 " --> pdb=" O SER C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 208 removed outlier: 3.550A pdb=" N SER C 207 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 233 Processing helix chain 'C' and resid 372 through 381 Processing helix chain 'D' and resid 24 through 28 Processing helix chain 'D' and resid 31 through 43 removed outlier: 4.028A pdb=" N THR D 37 " --> pdb=" O ASP D 33 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER D 41 " --> pdb=" O THR D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 131 through 137 Processing helix chain 'D' and resid 153 through 159 Processing helix chain 'D' and resid 161 through 173 Processing helix chain 'D' and resid 174 through 183 removed outlier: 3.750A pdb=" N VAL D 181 " --> pdb=" O ASP D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 195 removed outlier: 3.605A pdb=" N TYR D 194 " --> pdb=" O LYS D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 219 Processing helix chain 'D' and resid 234 through 239 Processing helix chain 'D' and resid 240 through 243 Processing helix chain 'D' and resid 252 through 256 removed outlier: 3.771A pdb=" N THR D 256 " --> pdb=" O GLU D 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 252 through 256' Processing helix chain 'D' and resid 257 through 263 Processing helix chain 'D' and resid 286 through 291 Processing helix chain 'D' and resid 292 through 297 removed outlier: 3.703A pdb=" N GLN D 296 " --> pdb=" O SER D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 328 Processing helix chain 'D' and resid 329 through 331 No H-bonds generated for 'chain 'D' and resid 329 through 331' Processing helix chain 'D' and resid 332 through 337 Processing helix chain 'D' and resid 338 through 342 removed outlier: 4.041A pdb=" N LYS D 342 " --> pdb=" O LEU D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 361 removed outlier: 3.621A pdb=" N THR D 356 " --> pdb=" O ALA D 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 42 removed outlier: 3.565A pdb=" N LYS E 35 " --> pdb=" O THR E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 85 removed outlier: 3.812A pdb=" N GLU E 78 " --> pdb=" O PRO E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 141 removed outlier: 3.799A pdb=" N ARG E 140 " --> pdb=" O ALA E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 166 Processing helix chain 'F' and resid 63 through 84 removed outlier: 4.042A pdb=" N ARG F 69 " --> pdb=" O VAL F 65 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR F 70 " --> pdb=" O ALA F 66 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL F 82 " --> pdb=" O MET F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 120 Processing helix chain 'F' and resid 150 through 160 Processing helix chain 'G' and resid 68 through 73 Processing helix chain 'G' and resid 92 through 96 removed outlier: 4.200A pdb=" N GLY G 95 " --> pdb=" O SER G 92 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL G 96 " --> pdb=" O VAL G 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 92 through 96' Processing helix chain 'G' and resid 102 through 107 removed outlier: 3.692A pdb=" N PHE G 106 " --> pdb=" O ASN G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 144 removed outlier: 3.760A pdb=" N VAL G 135 " --> pdb=" O LYS G 131 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU G 136 " --> pdb=" O ALA G 132 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ASP G 137 " --> pdb=" O GLU G 133 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL G 140 " --> pdb=" O GLU G 136 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL G 141 " --> pdb=" O ASP G 137 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASP G 142 " --> pdb=" O GLN G 138 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA G 144 " --> pdb=" O VAL G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 150 Processing helix chain 'G' and resid 154 through 161 Processing helix chain 'H' and resid 46 through 50 removed outlier: 3.849A pdb=" N VAL H 50 " --> pdb=" O SER H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 69 removed outlier: 4.092A pdb=" N LYS H 63 " --> pdb=" O GLN H 59 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE H 67 " --> pdb=" O LYS H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 80 removed outlier: 3.695A pdb=" N TYR H 80 " --> pdb=" O GLN H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 96 removed outlier: 3.623A pdb=" N LYS H 92 " --> pdb=" O ALA H 88 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU H 93 " --> pdb=" O GLU H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 114 removed outlier: 3.549A pdb=" N LYS H 106 " --> pdb=" O ALA H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 145 removed outlier: 3.702A pdb=" N ALA H 141 " --> pdb=" O ASN H 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 163 Processing helix chain 'H' and resid 165 through 174 Processing helix chain 'H' and resid 182 through 189 removed outlier: 3.646A pdb=" N LEU H 189 " --> pdb=" O ARG H 185 " (cutoff:3.500A) Processing helix chain 'H' and resid 207 through 220 removed outlier: 3.974A pdb=" N ALA H 220 " --> pdb=" O SER H 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 225 through 230 Processing helix chain 'H' and resid 239 through 247 removed outlier: 3.792A pdb=" N LYS H 245 " --> pdb=" O LYS H 241 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 29 removed outlier: 3.534A pdb=" N SER J 20 " --> pdb=" O GLY J 16 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N THR J 21 " --> pdb=" O ARG J 17 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU J 27 " --> pdb=" O ALA J 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 39 removed outlier: 3.888A pdb=" N ALA J 39 " --> pdb=" O ARG J 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 36 through 39' Processing helix chain 'J' and resid 45 through 57 Processing helix chain 'J' and resid 64 through 68 Processing helix chain 'J' and resid 74 through 85 Processing helix chain 'J' and resid 91 through 98 Processing helix chain 'J' and resid 119 through 122 Processing helix chain 'J' and resid 123 through 128 Processing helix chain 'J' and resid 137 through 145 Processing helix chain 'J' and resid 150 through 181 removed outlier: 3.571A pdb=" N GLU J 156 " --> pdb=" O VAL J 152 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP J 157 " --> pdb=" O ALA J 153 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS J 158 " --> pdb=" O LYS J 154 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG J 159 " --> pdb=" O LEU J 155 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG J 162 " --> pdb=" O LYS J 158 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA J 168 " --> pdb=" O ALA J 164 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS J 169 " --> pdb=" O GLU J 165 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA J 180 " --> pdb=" O LYS J 176 " (cutoff:3.500A) Processing helix chain 'J' and resid 182 through 184 No H-bonds generated for 'chain 'J' and resid 182 through 184' Processing helix chain 'J' and resid 187 through 194 Processing helix chain 'J' and resid 195 through 197 No H-bonds generated for 'chain 'J' and resid 195 through 197' Processing helix chain 'K' and resid 27 through 46 removed outlier: 3.679A pdb=" N VAL K 33 " --> pdb=" O ALA K 29 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER K 34 " --> pdb=" O GLY K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 83 Processing helix chain 'K' and resid 88 through 93 removed outlier: 3.898A pdb=" N THR K 92 " --> pdb=" O ALA K 88 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE K 93 " --> pdb=" O TYR K 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 88 through 93' Processing helix chain 'K' and resid 105 through 122 Processing helix chain 'K' and resid 165 through 186 removed outlier: 3.597A pdb=" N SER K 175 " --> pdb=" O ARG K 171 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS K 177 " --> pdb=" O ALA K 173 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N GLY K 181 " --> pdb=" O LYS K 177 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N ILE K 182 " --> pdb=" O LYS K 178 " (cutoff:3.500A) Processing helix chain 'L' and resid 119 through 124 Processing helix chain 'L' and resid 126 through 132 Processing helix chain 'M' and resid 77 through 89 removed outlier: 3.600A pdb=" N ALA M 86 " --> pdb=" O SER M 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 89 through 94 Processing helix chain 'M' and resid 97 through 111 removed outlier: 3.725A pdb=" N ALA M 111 " --> pdb=" O GLU M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 113 through 135 removed outlier: 3.617A pdb=" N VAL M 120 " --> pdb=" O GLU M 116 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR M 130 " --> pdb=" O GLN M 126 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS M 133 " --> pdb=" O TYR M 129 " (cutoff:3.500A) Processing helix chain 'N' and resid 41 through 46 Processing helix chain 'N' and resid 78 through 82 removed outlier: 3.558A pdb=" N ILE N 82 " --> pdb=" O TRP N 79 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 92 removed outlier: 3.981A pdb=" N ASP N 88 " --> pdb=" O GLU N 84 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLN N 89 " --> pdb=" O ASP N 85 " (cutoff:3.500A) Processing helix chain 'N' and resid 131 through 141 removed outlier: 3.779A pdb=" N ALA N 141 " --> pdb=" O LYS N 137 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 12 removed outlier: 3.719A pdb=" N LEU O 7 " --> pdb=" O ALA O 3 " (cutoff:3.500A) Processing helix chain 'O' and resid 16 through 32 removed outlier: 3.964A pdb=" N TRP O 28 " --> pdb=" O ARG O 24 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 52 Processing helix chain 'O' and resid 97 through 110 Processing helix chain 'O' and resid 139 through 144 Processing helix chain 'O' and resid 148 through 157 removed outlier: 3.727A pdb=" N ILE O 151 " --> pdb=" O TYR O 148 " (cutoff:3.500A) Proline residue: O 154 - end of helix removed outlier: 3.700A pdb=" N LYS O 157 " --> pdb=" O PRO O 154 " (cutoff:3.500A) Processing helix chain 'O' and resid 165 through 173 Processing helix chain 'O' and resid 186 through 195 removed outlier: 3.540A pdb=" N TRP O 191 " --> pdb=" O ARG O 187 " (cutoff:3.500A) Processing helix chain 'P' and resid 9 through 16 removed outlier: 3.578A pdb=" N ARG P 15 " --> pdb=" O ALA P 11 " (cutoff:3.500A) Processing helix chain 'P' and resid 20 through 25 Processing helix chain 'P' and resid 29 through 38 removed outlier: 4.084A pdb=" N ARG P 35 " --> pdb=" O TYR P 31 " (cutoff:3.500A) Processing helix chain 'P' and resid 81 through 86 Proline residue: P 84 - end of helix No H-bonds generated for 'chain 'P' and resid 81 through 86' Processing helix chain 'P' and resid 94 through 114 Processing helix chain 'P' and resid 158 through 170 removed outlier: 3.621A pdb=" N ALA P 162 " --> pdb=" O ARG P 158 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU P 163 " --> pdb=" O VAL P 159 " (cutoff:3.500A) Processing helix chain 'P' and resid 191 through 200 removed outlier: 3.867A pdb=" N SER P 197 " --> pdb=" O GLU P 193 " (cutoff:3.500A) Processing helix chain 'P' and resid 202 through 215 removed outlier: 3.795A pdb=" N TYR P 207 " --> pdb=" O HIS P 203 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP P 213 " --> pdb=" O GLU P 209 " (cutoff:3.500A) Processing helix chain 'P' and resid 217 through 223 Processing helix chain 'P' and resid 223 through 229 Processing helix chain 'P' and resid 235 through 250 removed outlier: 3.553A pdb=" N SER P 242 " --> pdb=" O ASP P 238 " (cutoff:3.500A) Processing helix chain 'P' and resid 263 through 270 Processing helix chain 'Q' and resid 23 through 40 removed outlier: 3.701A pdb=" N LEU Q 29 " --> pdb=" O TYR Q 25 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE Q 35 " --> pdb=" O LYS Q 31 " (cutoff:3.500A) Processing helix chain 'Q' and resid 42 through 53 removed outlier: 4.210A pdb=" N LYS Q 46 " --> pdb=" O ALA Q 42 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE Q 53 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 64 through 71 Processing helix chain 'Q' and resid 107 through 118 removed outlier: 3.505A pdb=" N ALA Q 112 " --> pdb=" O ALA Q 108 " (cutoff:3.500A) Processing helix chain 'Q' and resid 149 through 153 removed outlier: 3.832A pdb=" N HIS Q 152 " --> pdb=" O ALA Q 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 16 removed outlier: 3.675A pdb=" N ARG R 9 " --> pdb=" O ARG R 5 " (cutoff:3.500A) Processing helix chain 'R' and resid 18 through 20 No H-bonds generated for 'chain 'R' and resid 18 through 20' Processing helix chain 'R' and resid 28 through 33 Processing helix chain 'R' and resid 38 through 47 Processing helix chain 'R' and resid 60 through 73 Processing helix chain 'R' and resid 77 through 81 removed outlier: 4.023A pdb=" N ARG R 81 " --> pdb=" O TYR R 78 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 89 Processing helix chain 'R' and resid 90 through 112 removed outlier: 3.691A pdb=" N VAL R 101 " --> pdb=" O ARG R 97 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG R 110 " --> pdb=" O LEU R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 129 removed outlier: 4.320A pdb=" N VAL R 122 " --> pdb=" O HIS R 118 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS R 125 " --> pdb=" O HIS R 121 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 149 removed outlier: 3.612A pdb=" N GLN R 144 " --> pdb=" O GLU R 140 " (cutoff:3.500A) Processing helix chain 'S' and resid 33 through 46 Processing helix chain 'S' and resid 98 through 114 removed outlier: 3.852A pdb=" N GLU S 104 " --> pdb=" O VAL S 100 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR S 105 " --> pdb=" O ALA S 101 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP S 109 " --> pdb=" O THR S 105 " (cutoff:3.500A) Processing helix chain 'S' and resid 117 through 119 No H-bonds generated for 'chain 'S' and resid 117 through 119' Processing helix chain 'S' and resid 137 through 142 Processing helix chain 'T' and resid 104 through 123 removed outlier: 3.539A pdb=" N ALA T 121 " --> pdb=" O ALA T 117 " (cutoff:3.500A) Processing helix chain 'U' and resid 10 through 12 No H-bonds generated for 'chain 'U' and resid 10 through 12' Processing helix chain 'U' and resid 25 through 36 removed outlier: 3.768A pdb=" N GLU U 31 " --> pdb=" O LYS U 27 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE U 36 " --> pdb=" O THR U 32 " (cutoff:3.500A) Processing helix chain 'U' and resid 40 through 53 removed outlier: 3.619A pdb=" N GLU U 49 " --> pdb=" O GLN U 45 " (cutoff:3.500A) Processing helix chain 'U' and resid 70 through 74 removed outlier: 3.859A pdb=" N GLY U 73 " --> pdb=" O THR U 70 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS U 74 " --> pdb=" O ALA U 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 70 through 74' Processing helix chain 'U' and resid 84 through 106 removed outlier: 3.565A pdb=" N LEU U 94 " --> pdb=" O PHE U 90 " (cutoff:3.500A) Processing helix chain 'V' and resid 19 through 24 removed outlier: 3.739A pdb=" N THR V 23 " --> pdb=" O VAL V 19 " (cutoff:3.500A) Processing helix chain 'V' and resid 29 through 41 Processing helix chain 'V' and resid 72 through 87 Processing helix chain 'W' and resid 58 through 62 Processing helix chain 'W' and resid 69 through 79 removed outlier: 3.545A pdb=" N LYS W 74 " --> pdb=" O GLU W 70 " (cutoff:3.500A) Processing helix chain 'W' and resid 93 through 104 Processing helix chain 'W' and resid 131 through 140 removed outlier: 3.623A pdb=" N ILE W 135 " --> pdb=" O ASP W 131 " (cutoff:3.500A) Processing helix chain 'X' and resid 11 through 21 Processing helix chain 'X' and resid 26 through 31 Processing helix chain 'X' and resid 36 through 44 removed outlier: 3.672A pdb=" N ALA X 41 " --> pdb=" O LYS X 37 " (cutoff:3.500A) Processing helix chain 'X' and resid 100 through 102 No H-bonds generated for 'chain 'X' and resid 100 through 102' Processing helix chain 'X' and resid 115 through 122 Processing helix chain 'Y' and resid 60 through 66 removed outlier: 3.586A pdb=" N THR Y 66 " --> pdb=" O VAL Y 62 " (cutoff:3.500A) Processing helix chain 'Y' and resid 97 through 101 removed outlier: 3.678A pdb=" N PHE Y 101 " --> pdb=" O THR Y 98 " (cutoff:3.500A) Processing helix chain 'Y' and resid 103 through 124 removed outlier: 3.547A pdb=" N ARG Y 107 " --> pdb=" O GLN Y 103 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU Y 108 " --> pdb=" O PRO Y 104 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU Y 109 " --> pdb=" O SER Y 105 " (cutoff:3.500A) Processing helix chain 'Z' and resid 5 through 11 removed outlier: 4.209A pdb=" N THR Z 11 " --> pdb=" O TYR Z 7 " (cutoff:3.500A) Processing helix chain 'Z' and resid 13 through 38 removed outlier: 3.691A pdb=" N VAL Z 22 " --> pdb=" O ALA Z 18 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP Z 23 " --> pdb=" O SER Z 19 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL Z 33 " --> pdb=" O ALA Z 29 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN Z 34 " --> pdb=" O GLU Z 30 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU Z 36 " --> pdb=" O LYS Z 32 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER Z 37 " --> pdb=" O VAL Z 33 " (cutoff:3.500A) Processing helix chain 'Z' and resid 42 through 70 removed outlier: 4.411A pdb=" N THR Z 46 " --> pdb=" O PRO Z 42 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU Z 64 " --> pdb=" O GLU Z 60 " (cutoff:3.500A) Processing helix chain 'Z' and resid 85 through 90 Processing helix chain 'Z' and resid 93 through 98 removed outlier: 3.659A pdb=" N SER Z 98 " --> pdb=" O LYS Z 94 " (cutoff:3.500A) Processing helix chain 'Z' and resid 101 through 111 Processing helix chain 'a' and resid 11 through 19 removed outlier: 4.296A pdb=" N ASN a 19 " --> pdb=" O LYS a 15 " (cutoff:3.500A) Processing helix chain 'a' and resid 36 through 56 removed outlier: 3.689A pdb=" N ASN a 42 " --> pdb=" O LYS a 38 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N HIS a 45 " --> pdb=" O ARG a 41 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA a 56 " --> pdb=" O LYS a 52 " (cutoff:3.500A) Processing helix chain 'b' and resid 27 through 73 removed outlier: 3.765A pdb=" N ALA b 32 " --> pdb=" O ALA b 28 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA b 35 " --> pdb=" O ALA b 31 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU b 39 " --> pdb=" O ALA b 35 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA b 50 " --> pdb=" O GLU b 46 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU b 59 " --> pdb=" O TYR b 55 " (cutoff:3.500A) Processing helix chain 'b' and resid 96 through 106 removed outlier: 3.545A pdb=" N GLN b 104 " --> pdb=" O ARG b 100 " (cutoff:3.500A) Processing helix chain 'b' and resid 120 through 128 removed outlier: 3.761A pdb=" N GLU b 125 " --> pdb=" O LYS b 121 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU b 126 " --> pdb=" O ALA b 122 " (cutoff:3.500A) Processing helix chain 'b' and resid 130 through 132 No H-bonds generated for 'chain 'b' and resid 130 through 132' Processing helix chain 'b' and resid 141 through 149 removed outlier: 3.573A pdb=" N GLN b 146 " --> pdb=" O SER b 142 " (cutoff:3.500A) Processing helix chain 'b' and resid 165 through 174 removed outlier: 3.925A pdb=" N ILE b 169 " --> pdb=" O ASP b 165 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN b 172 " --> pdb=" O ILE b 168 " (cutoff:3.500A) Processing helix chain 'b' and resid 175 through 177 No H-bonds generated for 'chain 'b' and resid 175 through 177' Processing helix chain 'b' and resid 180 through 190 Processing helix chain 'b' and resid 194 through 200 Processing helix chain 'b' and resid 235 through 241 Processing helix chain 'c' and resid 10 through 15 Processing helix chain 'c' and resid 27 through 36 removed outlier: 3.587A pdb=" N LYS c 32 " --> pdb=" O LYS c 28 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER c 33 " --> pdb=" O SER c 29 " (cutoff:3.500A) Processing helix chain 'c' and resid 49 through 64 Processing helix chain 'c' and resid 73 through 82 removed outlier: 3.633A pdb=" N THR c 79 " --> pdb=" O ASN c 75 " (cutoff:3.500A) Processing helix chain 'd' and resid 24 through 26 No H-bonds generated for 'chain 'd' and resid 24 through 26' Processing helix chain 'd' and resid 27 through 41 removed outlier: 3.798A pdb=" N LYS d 34 " --> pdb=" O PRO d 30 " (cutoff:3.500A) Processing helix chain 'd' and resid 52 through 60 removed outlier: 3.864A pdb=" N ALA d 58 " --> pdb=" O GLU d 54 " (cutoff:3.500A) Processing helix chain 'd' and resid 61 through 63 No H-bonds generated for 'chain 'd' and resid 61 through 63' Processing helix chain 'e' and resid 54 through 58 removed outlier: 3.732A pdb=" N TYR e 57 " --> pdb=" O LYS e 54 " (cutoff:3.500A) Processing helix chain 'e' and resid 78 through 83 Processing helix chain 'e' and resid 84 through 86 No H-bonds generated for 'chain 'e' and resid 84 through 86' Processing helix chain 'e' and resid 101 through 116 removed outlier: 3.726A pdb=" N VAL e 106 " --> pdb=" O ALA e 102 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL e 107 " --> pdb=" O LYS e 103 " (cutoff:3.500A) Processing helix chain 'f' and resid 41 through 45 removed outlier: 3.716A pdb=" N LEU f 45 " --> pdb=" O GLN f 42 " (cutoff:3.500A) Processing helix chain 'g' and resid 59 through 64 removed outlier: 3.511A pdb=" N THR g 64 " --> pdb=" O GLN g 61 " (cutoff:3.500A) Processing helix chain 'g' and resid 66 through 70 Processing helix chain 'g' and resid 82 through 104 removed outlier: 3.770A pdb=" N GLU g 96 " --> pdb=" O ALA g 92 " (cutoff:3.500A) Processing helix chain 'h' and resid 25 through 29 Processing helix chain 'h' and resid 34 through 49 removed outlier: 3.693A pdb=" N PHE h 39 " --> pdb=" O ASN h 35 " (cutoff:3.500A) Processing helix chain 'h' and resid 51 through 64 removed outlier: 3.727A pdb=" N ASP h 59 " --> pdb=" O ARG h 55 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU h 60 " --> pdb=" O ARG h 56 " (cutoff:3.500A) Processing helix chain 'h' and resid 65 through 78 removed outlier: 3.884A pdb=" N ALA h 69 " --> pdb=" O GLY h 65 " (cutoff:3.500A) Processing helix chain 'h' and resid 79 through 98 removed outlier: 3.598A pdb=" N ALA h 83 " --> pdb=" O SER h 79 " (cutoff:3.500A) Processing helix chain 'i' and resid 5 through 9 removed outlier: 3.579A pdb=" N PHE i 8 " --> pdb=" O THR i 5 " (cutoff:3.500A) Processing helix chain 'i' and resid 66 through 68 No H-bonds generated for 'chain 'i' and resid 66 through 68' Processing helix chain 'i' and resid 69 through 77 removed outlier: 3.656A pdb=" N ASN i 76 " --> pdb=" O ARG i 72 " (cutoff:3.500A) Processing helix chain 'j' and resid 7 through 15 removed outlier: 3.621A pdb=" N LEU j 12 " --> pdb=" O ILE j 8 " (cutoff:3.500A) Processing helix chain 'j' and resid 59 through 68 Processing helix chain 'k' and resid 6 through 19 removed outlier: 3.645A pdb=" N LYS k 12 " --> pdb=" O ARG k 8 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS k 15 " --> pdb=" O GLN k 11 " (cutoff:3.500A) Processing helix chain 'k' and resid 26 through 30 Processing helix chain 'l' and resid 37 through 48 removed outlier: 3.769A pdb=" N TYR l 43 " --> pdb=" O GLY l 39 " (cutoff:3.500A) Processing helix chain 'm' and resid 8 through 14 removed outlier: 3.564A pdb=" N GLY m 12 " --> pdb=" O GLY m 9 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS m 13 " --> pdb=" O ILE m 10 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR m 14 " --> pdb=" O THR m 11 " (cutoff:3.500A) Processing helix chain 'm' and resid 19 through 31 removed outlier: 4.147A pdb=" N GLN m 25 " --> pdb=" O SER m 21 " (cutoff:3.500A) Processing helix chain 'm' and resid 73 through 90 removed outlier: 3.734A pdb=" N ALA m 77 " --> pdb=" O THR m 73 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR m 78 " --> pdb=" O ALA m 74 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR m 82 " --> pdb=" O THR m 78 " (cutoff:3.500A) Processing helix chain 'n' and resid 12 through 16 removed outlier: 3.811A pdb=" N PHE n 16 " --> pdb=" O GLU n 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 12 through 16' Processing helix chain 'n' and resid 31 through 40 removed outlier: 3.990A pdb=" N PHE n 38 " --> pdb=" O PHE n 34 " (cutoff:3.500A) Processing helix chain 'n' and resid 78 through 86 removed outlier: 3.691A pdb=" N LEU n 84 " --> pdb=" O GLU n 80 " (cutoff:3.500A) Processing helix chain 'n' and resid 103 through 107 Processing helix chain 'n' and resid 124 through 134 removed outlier: 3.572A pdb=" N LEU n 128 " --> pdb=" O GLU n 124 " (cutoff:3.500A) Processing helix chain 'n' and resid 166 through 178 removed outlier: 3.744A pdb=" N GLU n 172 " --> pdb=" O GLN n 168 " (cutoff:3.500A) Processing helix chain 'n' and resid 192 through 197 removed outlier: 3.697A pdb=" N MET n 197 " --> pdb=" O VAL n 193 " (cutoff:3.500A) Processing helix chain 'n' and resid 211 through 223 removed outlier: 3.823A pdb=" N ILE n 221 " --> pdb=" O VAL n 217 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG n 223 " --> pdb=" O GLU n 219 " (cutoff:3.500A) Processing helix chain 'o' and resid 147 through 173 removed outlier: 3.766A pdb=" N GLU o 155 " --> pdb=" O LEU o 151 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TRP o 162 " --> pdb=" O ALA o 158 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER o 172 " --> pdb=" O HIS o 168 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN o 173 " --> pdb=" O LEU o 169 " (cutoff:3.500A) Processing helix chain 'o' and resid 184 through 193 removed outlier: 4.047A pdb=" N TRP o 188 " --> pdb=" O ASN o 184 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU o 191 " --> pdb=" O VAL o 187 " (cutoff:3.500A) Processing helix chain 'o' and resid 193 through 199 removed outlier: 3.820A pdb=" N ARG o 197 " --> pdb=" O ARG o 193 " (cutoff:3.500A) Processing helix chain 'o' and resid 215 through 220 removed outlier: 4.393A pdb=" N GLU o 219 " --> pdb=" O SER o 215 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG o 220 " --> pdb=" O VAL o 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 215 through 220' Processing helix chain 'o' and resid 242 through 256 removed outlier: 3.796A pdb=" N ILE o 247 " --> pdb=" O LYS o 243 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ALA o 248 " --> pdb=" O LYS o 244 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR o 252 " --> pdb=" O ALA o 248 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS o 256 " --> pdb=" O TYR o 252 " (cutoff:3.500A) Processing helix chain 'o' and resid 348 through 354 removed outlier: 3.671A pdb=" N ILE o 353 " --> pdb=" O LYS o 349 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN o 354 " --> pdb=" O SER o 350 " (cutoff:3.500A) Processing helix chain 'o' and resid 418 through 427 removed outlier: 4.035A pdb=" N ARG o 427 " --> pdb=" O LEU o 423 " (cutoff:3.500A) Processing helix chain 'o' and resid 429 through 438 Processing helix chain 'o' and resid 460 through 469 removed outlier: 3.838A pdb=" N ALA o 467 " --> pdb=" O ALA o 463 " (cutoff:3.500A) Processing helix chain 'o' and resid 479 through 492 removed outlier: 4.708A pdb=" N ARG o 485 " --> pdb=" O PRO o 481 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N TYR o 486 " --> pdb=" O ARG o 482 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP o 490 " --> pdb=" O TYR o 486 " (cutoff:3.500A) Processing helix chain 'p' and resid 66 through 71 Processing helix chain 'p' and resid 96 through 100 Processing helix chain 'p' and resid 140 through 145 Processing helix chain 'p' and resid 178 through 182 removed outlier: 3.534A pdb=" N UNK p 181 " --> pdb=" O UNK p 178 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N UNK p 182 " --> pdb=" O UNK p 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 178 through 182' Processing helix chain 'r' and resid 21 through 28 Processing helix chain 'r' and resid 30 through 43 removed outlier: 3.712A pdb=" N ILE r 34 " --> pdb=" O THR r 30 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA r 35 " --> pdb=" O ALA r 31 " (cutoff:3.500A) Processing helix chain 'r' and resid 60 through 74 removed outlier: 3.856A pdb=" N LEU r 66 " --> pdb=" O PRO r 62 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU r 67 " --> pdb=" O GLU r 63 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR r 68 " --> pdb=" O LEU r 64 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASP r 69 " --> pdb=" O CYS r 65 " (cutoff:3.500A) Processing helix chain 'r' and resid 110 through 118 removed outlier: 3.842A pdb=" N LEU r 115 " --> pdb=" O THR r 111 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ASN r 116 " --> pdb=" O GLN r 112 " (cutoff:3.500A) Processing helix chain 'r' and resid 125 through 130 Processing helix chain 'r' and resid 180 through 201 removed outlier: 3.879A pdb=" N ILE r 189 " --> pdb=" O ALA r 185 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA r 190 " --> pdb=" O ALA r 186 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU r 192 " --> pdb=" O HIS r 188 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL r 194 " --> pdb=" O ALA r 190 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL r 195 " --> pdb=" O MET r 191 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LEU r 197 " --> pdb=" O THR r 193 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N CYS r 200 " --> pdb=" O ALA r 196 " (cutoff:3.500A) Processing helix chain 'r' and resid 219 through 234 removed outlier: 3.601A pdb=" N ILE r 223 " --> pdb=" O THR r 219 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA r 231 " --> pdb=" O VAL r 227 " (cutoff:3.500A) Processing helix chain 'r' and resid 257 through 261 removed outlier: 3.574A pdb=" N GLU r 261 " --> pdb=" O ILE r 258 " (cutoff:3.500A) Processing helix chain 'r' and resid 372 through 379 Processing helix chain 'r' and resid 406 through 429 removed outlier: 3.749A pdb=" N GLN r 410 " --> pdb=" O GLU r 406 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N SER r 418 " --> pdb=" O LYS r 414 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU r 421 " --> pdb=" O LYS r 417 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLU r 425 " --> pdb=" O LEU r 421 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE r 426 " --> pdb=" O GLY r 422 " (cutoff:3.500A) Processing helix chain 'r' and resid 445 through 450 Processing helix chain 'r' and resid 481 through 489 removed outlier: 3.842A pdb=" N SER r 487 " --> pdb=" O ILE r 483 " (cutoff:3.500A) Processing helix chain 'r' and resid 549 through 562 removed outlier: 3.937A pdb=" N GLN r 555 " --> pdb=" O GLN r 551 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP r 562 " --> pdb=" O THR r 558 " (cutoff:3.500A) Processing helix chain 's' and resid 291 through 297 Processing helix chain 'u' and resid 146 through 154 removed outlier: 4.001A pdb=" N GLU u 151 " --> pdb=" O ARG u 147 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS u 152 " --> pdb=" O VAL u 148 " (cutoff:3.500A) Processing helix chain 'u' and resid 175 through 186 removed outlier: 3.667A pdb=" N GLU u 181 " --> pdb=" O GLU u 177 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE u 184 " --> pdb=" O LEU u 180 " (cutoff:3.500A) Processing helix chain 'u' and resid 193 through 197 removed outlier: 3.754A pdb=" N LEU u 197 " --> pdb=" O GLN u 194 " (cutoff:3.500A) Processing helix chain 'u' and resid 199 through 213 removed outlier: 4.197A pdb=" N VAL u 204 " --> pdb=" O LYS u 200 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS u 205 " --> pdb=" O ILE u 201 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU u 213 " --> pdb=" O GLU u 209 " (cutoff:3.500A) Processing helix chain 'u' and resid 226 through 237 Processing helix chain 'u' and resid 246 through 255 removed outlier: 5.102A pdb=" N GLU u 252 " --> pdb=" O ASP u 248 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ILE u 253 " --> pdb=" O GLU u 249 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLU u 255 " --> pdb=" O LEU u 251 " (cutoff:3.500A) Processing helix chain 'u' and resid 316 through 322 removed outlier: 4.927A pdb=" N ARG u 320 " --> pdb=" O SER u 317 " (cutoff:3.500A) Processing helix chain 'u' and resid 333 through 341 removed outlier: 3.940A pdb=" N GLY u 337 " --> pdb=" O THR u 333 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR u 338 " --> pdb=" O GLU u 334 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU u 339 " --> pdb=" O GLY u 335 " (cutoff:3.500A) Processing helix chain 'u' and resid 358 through 375 removed outlier: 3.680A pdb=" N VAL u 362 " --> pdb=" O THR u 358 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN u 364 " --> pdb=" O GLN u 360 " (cutoff:3.500A) Processing helix chain 'v' and resid 33 through 42 Processing helix chain 'v' and resid 52 through 59 removed outlier: 3.780A pdb=" N ARG v 56 " --> pdb=" O THR v 52 " (cutoff:3.500A) Processing helix chain 'w' and resid 35 through 42 Processing helix chain 'w' and resid 79 through 88 removed outlier: 3.940A pdb=" N ALA w 83 " --> pdb=" O ARG w 79 " (cutoff:3.500A) Processing helix chain 'w' and resid 143 through 151 removed outlier: 3.967A pdb=" N SER w 149 " --> pdb=" O ASP w 145 " (cutoff:3.500A) Processing helix chain 'w' and resid 168 through 182 removed outlier: 4.185A pdb=" N LEU w 179 " --> pdb=" O GLU w 175 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS w 180 " --> pdb=" O GLN w 176 " (cutoff:3.500A) Processing helix chain 'w' and resid 203 through 215 removed outlier: 3.827A pdb=" N ALA w 207 " --> pdb=" O GLN w 203 " (cutoff:3.500A) Processing helix chain 'w' and resid 260 through 267 Processing helix chain 'w' and resid 297 through 302 Processing helix chain 'w' and resid 311 through 315 Processing helix chain 'w' and resid 381 through 386 Processing sheet with id=AA1, first strand: chain 'B' and resid 71 through 77 removed outlier: 6.062A pdb=" N LEU B 58 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ILE B 48 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LYS B 60 " --> pdb=" O LYS B 46 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ARG B 64 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ARG B 42 " --> pdb=" O ARG B 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 101 through 103 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 5.229A pdb=" N VAL C 158 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N HIS C 163 " --> pdb=" O VAL C 86 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N VAL C 86 " --> pdb=" O HIS C 163 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N VAL C 87 " --> pdb=" O TRP C 106 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N TRP C 106 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL C 89 " --> pdb=" O THR C 104 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N THR C 104 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N GLY C 91 " --> pdb=" O LEU C 102 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 5.229A pdb=" N VAL C 158 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N HIS C 163 " --> pdb=" O VAL C 86 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N VAL C 86 " --> pdb=" O HIS C 163 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS C 201 " --> pdb=" O VAL C 86 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 356 through 359 removed outlier: 6.528A pdb=" N VAL C 57 " --> pdb=" O LYS C 357 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ILE C 359 " --> pdb=" O THR C 55 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N THR C 55 " --> pdb=" O ILE C 359 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ILE C 335 " --> pdb=" O VAL C 220 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N VAL C 220 " --> pdb=" O ILE C 335 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ILE C 215 " --> pdb=" O ASN C 279 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LYS C 281 " --> pdb=" O LYS C 325 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N MET C 323 " --> pdb=" O TYR C 283 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N VAL C 285 " --> pdb=" O PHE C 321 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N PHE C 321 " --> pdb=" O VAL C 285 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N ASP C 80 " --> pdb=" O LYS C 50 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N LYS C 50 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 226 through 227 Processing sheet with id=AA7, first strand: chain 'D' and resid 5 through 9 removed outlier: 3.689A pdb=" N VAL D 8 " --> pdb=" O ASN D 18 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N ASN D 18 " --> pdb=" O VAL D 8 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 62 through 64 Processing sheet with id=AA9, first strand: chain 'D' and resid 150 through 152 removed outlier: 4.192A pdb=" N LEU D 150 " --> pdb=" O VAL D 248 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU D 206 " --> pdb=" O ILE D 249 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N THR D 251 " --> pdb=" O LEU D 206 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N VAL D 208 " --> pdb=" O THR D 251 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL D 207 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 186 through 187 Processing sheet with id=AB2, first strand: chain 'E' and resid 46 through 48 removed outlier: 3.733A pdb=" N ALA E 66 " --> pdb=" O SER E 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 5 through 11 Processing sheet with id=AB4, first strand: chain 'F' and resid 17 through 21 Processing sheet with id=AB5, first strand: chain 'F' and resid 133 through 136 removed outlier: 6.846A pdb=" N LYS F 87 " --> pdb=" O LYS F 184 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LYS F 184 " --> pdb=" O LYS F 87 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LYS F 89 " --> pdb=" O SER F 182 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 100 through 103 Processing sheet with id=AB7, first strand: chain 'G' and resid 77 through 79 removed outlier: 6.726A pdb=" N LEU G 64 " --> pdb=" O LEU G 55 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N THR G 38 " --> pdb=" O TYR G 54 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N VAL G 39 " --> pdb=" O THR G 87 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 70 through 71 Processing sheet with id=AB9, first strand: chain 'H' and resid 177 through 179 removed outlier: 3.531A pdb=" N LEU H 150 " --> pdb=" O LEU H 200 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 5 through 9 removed outlier: 5.890A pdb=" N VAL J 6 " --> pdb=" O VAL J 33 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL J 35 " --> pdb=" O VAL J 6 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N ILE J 8 " --> pdb=" O VAL J 35 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 41 through 43 Processing sheet with id=AC3, first strand: chain 'K' and resid 22 through 24 removed outlier: 6.084A pdb=" N LYS K 23 " --> pdb=" O LEU O 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'K' and resid 57 through 59 Processing sheet with id=AC5, first strand: chain 'K' and resid 123 through 125 Processing sheet with id=AC6, first strand: chain 'K' and resid 157 through 158 Processing sheet with id=AC7, first strand: chain 'L' and resid 17 through 18 Processing sheet with id=AC8, first strand: chain 'L' and resid 22 through 25 removed outlier: 6.667A pdb=" N ASN L 33 " --> pdb=" O LYS L 63 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N MET L 59 " --> pdb=" O ILE L 37 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N VAL L 39 " --> pdb=" O MET L 57 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N MET L 57 " --> pdb=" O VAL L 39 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N VAL L 78 " --> pdb=" O VAL L 101 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL L 101 " --> pdb=" O VAL L 78 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N GLY L 100 " --> pdb=" O ILE L 22 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ASN L 24 " --> pdb=" O GLY L 100 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ILE L 102 " --> pdb=" O ASN L 24 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 85 through 86 removed outlier: 6.435A pdb=" N PHE L 92 " --> pdb=" O LEU v 20 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N VAL v 22 " --> pdb=" O PHE L 92 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N TYR L 94 " --> pdb=" O VAL v 22 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 114 through 118 removed outlier: 8.823A pdb=" N ILE L 114 " --> pdb=" O GLY L 134 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N VAL L 136 " --> pdb=" O ILE L 114 " (cutoff:3.500A) removed outlier: 10.581A pdb=" N GLY L 116 " --> pdb=" O VAL L 136 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'M' and resid 15 through 16 Processing sheet with id=AD3, first strand: chain 'M' and resid 56 through 59 removed outlier: 7.499A pdb=" N LYS M 43 " --> pdb=" O ILE M 38 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ILE M 38 " --> pdb=" O LYS M 43 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU M 45 " --> pdb=" O VAL M 36 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ARG M 19 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N VAL M 20 " --> pdb=" O THR M 66 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 101 through 103 removed outlier: 6.088A pdb=" N VAL N 125 " --> pdb=" O GLU N 146 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 111 through 112 Processing sheet with id=AD6, first strand: chain 'O' and resid 36 through 39 removed outlier: 4.324A pdb=" N ILE O 61 " --> pdb=" O ALA O 39 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N TYR O 129 " --> pdb=" O TRP O 120 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N TRP O 120 " --> pdb=" O TYR O 129 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLU O 131 " --> pdb=" O SER O 118 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N SER O 118 " --> pdb=" O GLU O 131 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE O 133 " --> pdb=" O LEU O 116 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'P' and resid 71 through 79 removed outlier: 3.564A pdb=" N GLY P 71 " --> pdb=" O THR P 68 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE P 64 " --> pdb=" O LEU P 75 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ALA P 77 " --> pdb=" O CYS P 62 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N CYS P 62 " --> pdb=" O ALA P 77 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N TYR P 79 " --> pdb=" O ILE P 60 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE P 60 " --> pdb=" O TYR P 79 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TYR P 49 " --> pdb=" O PHE P 145 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ASP P 147 " --> pdb=" O TYR P 49 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU P 51 " --> pdb=" O ASP P 147 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'P' and resid 183 through 184 Processing sheet with id=AD9, first strand: chain 'Q' and resid 62 through 63 Processing sheet with id=AE1, first strand: chain 'Q' and resid 120 through 122 removed outlier: 6.361A pdb=" N VAL Q 81 " --> pdb=" O ALA Q 102 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'R' and resid 22 through 24 Processing sheet with id=AE3, first strand: chain 'S' and resid 56 through 63 removed outlier: 6.650A pdb=" N ILE S 10 " --> pdb=" O VAL S 59 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE S 61 " --> pdb=" O GLN S 8 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLN S 8 " --> pdb=" O ILE S 61 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N GLN S 63 " --> pdb=" O GLU S 6 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N GLU S 6 " --> pdb=" O GLN S 63 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'S' and resid 87 through 94 removed outlier: 6.770A pdb=" N ARG S 80 " --> pdb=" O ILE S 123 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ILE S 123 " --> pdb=" O ARG S 80 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N ASP S 82 " --> pdb=" O ILE S 121 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ILE S 121 " --> pdb=" O ASP S 82 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'T' and resid 83 through 92 removed outlier: 3.526A pdb=" N SER T 71 " --> pdb=" O THR T 68 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN T 66 " --> pdb=" O GLY T 73 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE T 75 " --> pdb=" O VAL T 64 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N VAL T 64 " --> pdb=" O ILE T 75 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N ASN T 77 " --> pdb=" O GLY T 62 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N GLY T 62 " --> pdb=" O ASN T 77 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'T' and resid 139 through 141 Processing sheet with id=AE7, first strand: chain 'U' and resid 14 through 22 removed outlier: 3.989A pdb=" N TYR U 21 " --> pdb=" O SER U 144 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N SER U 144 " --> pdb=" O TYR U 21 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N HIS U 145 " --> pdb=" O VAL U 119 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL U 119 " --> pdb=" O HIS U 145 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLU U 147 " --> pdb=" O ILE U 117 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ILE U 117 " --> pdb=" O GLU U 147 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL U 149 " --> pdb=" O SER U 115 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'U' and resid 58 through 59 Processing sheet with id=AE9, first strand: chain 'U' and resid 128 through 131 removed outlier: 3.562A pdb=" N THR U 129 " --> pdb=" O ASN U 137 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG U 135 " --> pdb=" O ARG U 131 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'V' and resid 54 through 58 removed outlier: 8.048A pdb=" N TYR V 103 " --> pdb=" O THR V 14 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N THR V 16 " --> pdb=" O TYR V 103 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N LEU V 105 " --> pdb=" O THR V 16 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ASP V 18 " --> pdb=" O LEU V 105 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N GLU V 102 " --> pdb=" O THR V 98 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'V' and resid 42 through 43 Processing sheet with id=AF3, first strand: chain 'W' and resid 63 through 66 removed outlier: 3.997A pdb=" N LYS W 120 " --> pdb=" O VAL W 86 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS W 109 " --> pdb=" O ARG W 125 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'X' and resid 32 through 34 Processing sheet with id=AF5, first strand: chain 'X' and resid 94 through 99 removed outlier: 10.563A pdb=" N VAL X 95 " --> pdb=" O LYS X 84 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N LYS X 84 " --> pdb=" O VAL X 95 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N ILE X 97 " --> pdb=" O VAL X 82 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL X 82 " --> pdb=" O ILE X 97 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ALA X 79 " --> pdb=" O VAL X 73 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N VAL X 73 " --> pdb=" O ALA X 79 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLN X 81 " --> pdb=" O SER X 71 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LYS X 69 " --> pdb=" O ASP X 83 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N VAL X 85 " --> pdb=" O GLU X 67 " (cutoff:3.500A) removed outlier: 9.758A pdb=" N GLU X 67 " --> pdb=" O VAL X 85 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLU X 55 " --> pdb=" O THR X 107 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Y' and resid 69 through 76 removed outlier: 7.136A pdb=" N LYS Y 69 " --> pdb=" O GLU Y 47 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N HIS Y 40 " --> pdb=" O PRO Y 28 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU Y 42 " --> pdb=" O VAL Y 26 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE Y 46 " --> pdb=" O LYS Y 22 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N LYS Y 22 " --> pdb=" O ILE Y 46 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LYS Y 9 " --> pdb=" O ILE Y 25 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N VAL Y 10 " --> pdb=" O THR Y 83 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'b' and resid 205 through 206 removed outlier: 4.209A pdb=" N SER b 113 " --> pdb=" O ARG b 88 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL b 134 " --> pdb=" O GLY b 230 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'b' and resid 153 through 156 Processing sheet with id=AF9, first strand: chain 'c' and resid 23 through 25 removed outlier: 3.674A pdb=" N LEU c 41 " --> pdb=" O ILE c 92 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'd' and resid 49 through 51 removed outlier: 6.826A pdb=" N ARG d 50 " --> pdb=" O VAL d 93 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'e' and resid 72 through 76 Processing sheet with id=AG3, first strand: chain 'f' and resid 9 through 18 removed outlier: 9.612A pdb=" N VAL f 9 " --> pdb=" O ILE f 32 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ILE f 32 " --> pdb=" O VAL f 9 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N GLY f 11 " --> pdb=" O ILE f 30 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N ILE f 30 " --> pdb=" O GLY f 11 " (cutoff:3.500A) removed outlier: 8.803A pdb=" N HIS f 13 " --> pdb=" O SER f 28 " (cutoff:3.500A) removed outlier: 9.674A pdb=" N SER f 28 " --> pdb=" O HIS f 13 " (cutoff:3.500A) removed outlier: 11.364A pdb=" N SER f 15 " --> pdb=" O ASN f 26 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N ASN f 26 " --> pdb=" O SER f 15 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN f 17 " --> pdb=" O ASN f 24 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N ASN f 26 " --> pdb=" O PHE f 85 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N PHE f 85 " --> pdb=" O ASN f 26 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N VAL f 80 " --> pdb=" O THR f 74 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N THR f 74 " --> pdb=" O VAL f 80 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ARG f 82 " --> pdb=" O THR f 72 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N LYS f 63 " --> pdb=" O ALA f 55 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N VAL f 52 " --> pdb=" O SER f 97 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N SER f 97 " --> pdb=" O VAL f 52 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'g' and resid 19 through 24 removed outlier: 4.479A pdb=" N LYS g 19 " --> pdb=" O VAL g 35 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'i' and resid 16 through 18 Processing sheet with id=AG6, first strand: chain 'j' and resid 3 through 4 removed outlier: 4.784A pdb=" N THR j 22 " --> pdb=" O ARG j 46 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ALA j 23 " --> pdb=" O ASN j 76 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'l' and resid 3 through 5 removed outlier: 6.778A pdb=" N VAL l 4 " --> pdb=" O GLY l 94 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'l' and resid 7 through 12 removed outlier: 6.999A pdb=" N LYS l 66 " --> pdb=" O ARG l 87 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ARG l 87 " --> pdb=" O LYS l 66 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N VAL l 68 " --> pdb=" O LEU l 85 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'm' and resid 37 through 38 Processing sheet with id=AH1, first strand: chain 'n' and resid 2 through 5 removed outlier: 6.088A pdb=" N THR n 3 " --> pdb=" O THR n 206 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'n' and resid 17 through 19 Processing sheet with id=AH3, first strand: chain 'n' and resid 70 through 72 removed outlier: 5.918A pdb=" N LEU n 70 " --> pdb=" O GLN n 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH3 Processing sheet with id=AH4, first strand: chain 'n' and resid 108 through 110 Processing sheet with id=AH5, first strand: chain 'n' and resid 152 through 154 Processing sheet with id=AH6, first strand: chain 'o' and resid 201 through 203 removed outlier: 5.803A pdb=" N ILE o 339 " --> pdb=" O CYS o 386 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'o' and resid 205 through 206 removed outlier: 5.671A pdb=" N VAL o 205 " --> pdb=" O ASN o 236 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH7 Processing sheet with id=AH8, first strand: chain 'r' and resid 94 through 97 Processing sheet with id=AH9, first strand: chain 'r' and resid 236 through 238 removed outlier: 4.102A pdb=" N VAL r 316 " --> pdb=" O ILE r 247 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N SER r 242 " --> pdb=" O TRP r 269 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'r' and resid 236 through 238 removed outlier: 3.904A pdb=" N THR r 506 " --> pdb=" O LEU r 525 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'r' and resid 334 through 340 removed outlier: 3.605A pdb=" N THR r 336 " --> pdb=" O ARG r 441 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG r 441 " --> pdb=" O THR r 336 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ILE r 437 " --> pdb=" O VAL r 340 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE r 496 " --> pdb=" O TRP r 442 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'r' and resid 360 through 362 Processing sheet with id=AI4, first strand: chain 's' and resid 238 through 241 removed outlier: 7.253A pdb=" N LYS s 238 " --> pdb=" O CYS s 232 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N CYS s 232 " --> pdb=" O LYS s 238 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 's' and resid 282 through 285 removed outlier: 4.060A pdb=" N ILE s 334 " --> pdb=" O ILE s 285 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 's' and resid 305 through 306 removed outlier: 3.808A pdb=" N GLY s 315 " --> pdb=" O PHE s 305 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'u' and resid 304 through 306 Processing sheet with id=AI8, first strand: chain 'v' and resid 4 through 5 Processing sheet with id=AI9, first strand: chain 'w' and resid 52 through 55 removed outlier: 5.795A pdb=" N ALA w 53 " --> pdb=" O ILE w 137 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ARG w 113 " --> pdb=" O ILE w 103 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'w' and resid 189 through 192 removed outlier: 4.099A pdb=" N SER w 189 " --> pdb=" O PHE w 200 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE w 200 " --> pdb=" O SER w 189 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N THR w 158 " --> pdb=" O TYR w 244 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N VAL w 246 " --> pdb=" O THR w 158 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N GLN w 160 " --> pdb=" O VAL w 246 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ILE w 248 " --> pdb=" O GLN w 160 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ARG w 162 " --> pdb=" O ILE w 248 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'w' and resid 189 through 192 removed outlier: 4.099A pdb=" N SER w 189 " --> pdb=" O PHE w 200 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE w 200 " --> pdb=" O SER w 189 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N THR w 158 " --> pdb=" O TYR w 244 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N VAL w 246 " --> pdb=" O THR w 158 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N GLN w 160 " --> pdb=" O VAL w 246 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ILE w 248 " --> pdb=" O GLN w 160 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ARG w 162 " --> pdb=" O ILE w 248 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'w' and resid 256 through 258 removed outlier: 6.851A pdb=" N GLN w 284 " --> pdb=" O SER w 277 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLN w 292 " --> pdb=" O ASP w 287 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'w' and resid 353 through 354 removed outlier: 6.349A pdb=" N THR w 339 " --> pdb=" O LEU w 321 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N SER w 368 " --> pdb=" O LYS w 400 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N LYS w 400 " --> pdb=" O SER w 368 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N MET w 370 " --> pdb=" O VAL w 398 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'w' and resid 329 through 330 removed outlier: 3.598A pdb=" N ARG w 330 " --> pdb=" O ARG w 333 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG w 333 " --> pdb=" O ARG w 330 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ5 1933 hydrogen bonds defined for protein. 5442 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2441 hydrogen bonds 3904 hydrogen bond angles 0 basepair planarities 985 basepair parallelities 1848 stacking parallelities Total time for adding SS restraints: 218.55 Time building geometry restraints manager: 52.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 16346 1.32 - 1.45: 58767 1.45 - 1.57: 62013 1.57 - 1.70: 6834 1.70 - 1.83: 223 Bond restraints: 144183 Sorted by residual: bond pdb=" C1' U A2258 " pdb=" N1 U A2258 " ideal model delta sigma weight residual 1.480 1.572 -0.092 1.50e-02 4.44e+03 3.78e+01 bond pdb=" C PRO s 250 " pdb=" N PRO s 251 " ideal model delta sigma weight residual 1.333 1.386 -0.053 1.20e-02 6.94e+03 1.96e+01 bond pdb=" C ALA o 167 " pdb=" O ALA o 167 " ideal model delta sigma weight residual 1.237 1.287 -0.050 1.17e-02 7.31e+03 1.83e+01 bond pdb=" N CYS g 81 " pdb=" CA CYS g 81 " ideal model delta sigma weight residual 1.457 1.508 -0.051 1.29e-02 6.01e+03 1.56e+01 bond pdb=" C THR w 24 " pdb=" N PRO w 25 " ideal model delta sigma weight residual 1.334 1.377 -0.043 1.11e-02 8.12e+03 1.50e+01 ... (remaining 144178 not shown) Histogram of bond angle deviations from ideal: 97.04 - 105.44: 17390 105.44 - 113.83: 90085 113.83 - 122.23: 74346 122.23 - 130.63: 28150 130.63 - 139.02: 1558 Bond angle restraints: 211529 Sorted by residual: angle pdb=" CA PRO C 18 " pdb=" N PRO C 18 " pdb=" CD PRO C 18 " ideal model delta sigma weight residual 112.00 98.57 13.43 1.40e+00 5.10e-01 9.21e+01 angle pdb=" C GLU o 171 " pdb=" N SER o 172 " pdb=" CA SER o 172 " ideal model delta sigma weight residual 121.54 139.02 -17.48 1.91e+00 2.74e-01 8.38e+01 angle pdb=" C PRO C 18 " pdb=" CA PRO C 18 " pdb=" CB PRO C 18 " ideal model delta sigma weight residual 111.56 126.25 -14.69 1.65e+00 3.67e-01 7.92e+01 angle pdb=" C THR r 55 " pdb=" N GLN r 56 " pdb=" CA GLN r 56 " ideal model delta sigma weight residual 121.54 133.74 -12.20 1.91e+00 2.74e-01 4.08e+01 angle pdb=" C CYS u 220 " pdb=" N ASN u 221 " pdb=" CA ASN u 221 " ideal model delta sigma weight residual 121.54 133.54 -12.00 1.91e+00 2.74e-01 3.95e+01 ... (remaining 211524 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 76121 35.89 - 71.79: 2887 71.79 - 107.68: 219 107.68 - 143.57: 15 143.57 - 179.47: 45 Dihedral angle restraints: 79287 sinusoidal: 56712 harmonic: 22575 Sorted by residual: dihedral pdb=" O4' U A3306 " pdb=" C1' U A3306 " pdb=" N1 U A3306 " pdb=" C2 U A3306 " ideal model delta sinusoidal sigma weight residual 200.00 20.92 179.08 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U A2506 " pdb=" C1' U A2506 " pdb=" N1 U A2506 " pdb=" C2 U A2506 " ideal model delta sinusoidal sigma weight residual -160.00 14.12 -174.12 1 1.50e+01 4.44e-03 8.51e+01 dihedral pdb=" O4' U A 252 " pdb=" C1' U A 252 " pdb=" N1 U A 252 " pdb=" C2 U A 252 " ideal model delta sinusoidal sigma weight residual 200.00 26.24 173.76 1 1.50e+01 4.44e-03 8.51e+01 ... (remaining 79284 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 25303 0.109 - 0.218: 1110 0.218 - 0.327: 64 0.327 - 0.436: 5 0.436 - 0.545: 4 Chirality restraints: 26486 Sorted by residual: chirality pdb=" CA HIS C 256 " pdb=" N HIS C 256 " pdb=" C HIS C 256 " pdb=" CB HIS C 256 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.41e+00 chirality pdb=" CB ILE D 148 " pdb=" CA ILE D 148 " pdb=" CG1 ILE D 148 " pdb=" CG2 ILE D 148 " both_signs ideal model delta sigma weight residual False 2.64 2.11 0.54 2.00e-01 2.50e+01 7.18e+00 chirality pdb=" CA SER b 228 " pdb=" N SER b 228 " pdb=" C SER b 228 " pdb=" CB SER b 228 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.65e+00 ... (remaining 26483 not shown) Planarity restraints: 14105 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS g 81 " -0.025 2.00e-02 2.50e+03 5.11e-02 2.61e+01 pdb=" C CYS g 81 " 0.088 2.00e-02 2.50e+03 pdb=" O CYS g 81 " -0.033 2.00e-02 2.50e+03 pdb=" N ALA g 82 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 17 " -0.077 5.00e-02 4.00e+02 1.10e-01 1.93e+01 pdb=" N PRO C 18 " 0.190 5.00e-02 4.00e+02 pdb=" CA PRO C 18 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO C 18 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G A 406 " -0.053 2.00e-02 2.50e+03 2.31e-02 1.59e+01 pdb=" N9 G A 406 " 0.052 2.00e-02 2.50e+03 pdb=" C8 G A 406 " 0.006 2.00e-02 2.50e+03 pdb=" N7 G A 406 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G A 406 " -0.000 2.00e-02 2.50e+03 pdb=" C6 G A 406 " -0.011 2.00e-02 2.50e+03 pdb=" O6 G A 406 " -0.011 2.00e-02 2.50e+03 pdb=" N1 G A 406 " -0.001 2.00e-02 2.50e+03 pdb=" C2 G A 406 " -0.011 2.00e-02 2.50e+03 pdb=" N2 G A 406 " 0.009 2.00e-02 2.50e+03 pdb=" N3 G A 406 " 0.016 2.00e-02 2.50e+03 pdb=" C4 G A 406 " 0.004 2.00e-02 2.50e+03 ... (remaining 14102 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.23: 13 2.23 - 2.90: 49693 2.90 - 3.57: 187745 3.57 - 4.23: 400707 4.23 - 4.90: 566135 Nonbonded interactions: 1204293 Sorted by model distance: nonbonded pdb=" CG PRO G 7 " pdb=" CE1 TYR G 10 " model vdw 1.568 3.740 nonbonded pdb=" CD ARG o 163 " pdb=" NH1 ARG o 183 " model vdw 2.015 3.520 nonbonded pdb=" NH2 ARG w 96 " pdb=" OE2 GLU w 121 " model vdw 2.028 2.520 nonbonded pdb=" NH2 ARG i 21 " pdb=" O ALA i 41 " model vdw 2.060 2.520 nonbonded pdb=" CD PRO G 7 " pdb=" CE1 TYR G 10 " model vdw 2.127 3.740 ... (remaining 1204288 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 18.540 Check model and map are aligned: 1.490 Set scattering table: 0.860 Process input model: 476.850 Find NCS groups from input model: 3.010 Set up NCS constraints: 0.370 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: 0.030 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 505.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 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 0.092 144183 Z= 0.456 Angle : 0.889 17.482 211529 Z= 0.460 Chirality : 0.051 0.545 26486 Planarity : 0.007 0.110 14105 Dihedral : 16.096 179.468 64715 Min Nonbonded Distance : 1.568 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.28 % Favored : 93.59 % Rotamer Outliers : 1.18 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.04 (0.08), residues: 7486 helix: -3.11 (0.07), residues: 2346 sheet: -1.81 (0.14), residues: 1081 loop : -2.69 (0.08), residues: 4059 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14972 Ramachandran restraints generated. 7486 Oldfield, 0 Emsley, 7486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14972 Ramachandran restraints generated. 7486 Oldfield, 0 Emsley, 7486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1166 residues out of total 6428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 1090 time to evaluate : 7.281 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LYS E 174 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR J 198 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL L 137 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "VAL Q 186 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR S 172 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE T 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE W 142 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 76 outliers final: 49 residues processed: 1158 average time/residue: 1.3788 time to fit residues: 2721.1230 Evaluate side-chains 927 residues out of total 6428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 878 time to evaluate : 7.264 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "LYS E 174 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL L 137 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL Q 186 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR S 172 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE T 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE W 142 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. outliers start: 49 outliers final: 9 residues processed: 49 average time/residue: 1.0627 time to fit residues: 107.2713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1098 random chunks: chunk 927 optimal weight: 50.0000 chunk 832 optimal weight: 3.9990 chunk 461 optimal weight: 2.9990 chunk 284 optimal weight: 7.9990 chunk 561 optimal weight: 0.9990 chunk 444 optimal weight: 1.9990 chunk 860 optimal weight: 2.9990 chunk 333 optimal weight: 1.9990 chunk 523 optimal weight: 2.9990 chunk 640 optimal weight: 2.9990 chunk 997 optimal weight: 9.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 377 HIS D 59 GLN D 311 HIS E 47 GLN G 80 ASN G 97 ASN H 45 ASN H 240 ASN J 41 ASN K 28 GLN K 160 GLN M 56 GLN O 87 GLN ** P 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 141 HIS S 88 HIS ** U 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 81 GLN ** Y 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 43 HIS b 80 GLN b 146 GLN h 91 ASN j 67 GLN m 34 HIS n 9 ASN n 140 GLN o 170 GLN o 209 ASN o 245 GLN ** o 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 146 HIS s 248 HIS s 337 GLN u 390 GLN w 206 HIS w 332 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.0895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.086 144183 Z= 0.196 Angle : 0.560 11.750 211529 Z= 0.292 Chirality : 0.036 0.295 26486 Planarity : 0.005 0.157 14105 Dihedral : 15.037 179.930 49663 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.28 % Favored : 94.70 % Rotamer Outliers : 1.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.34 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.08), residues: 7486 helix: -1.69 (0.10), residues: 2344 sheet: -1.42 (0.14), residues: 1109 loop : -2.25 (0.08), residues: 4033 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14972 Ramachandran restraints generated. 7486 Oldfield, 0 Emsley, 7486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14972 Ramachandran restraints generated. 7486 Oldfield, 0 Emsley, 7486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1086 residues out of total 6428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 960 time to evaluate : 7.045 Fit side-chains TARDY: cannot create tardy model for: "LYS E 174 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR J 198 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL L 137 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "VAL Q 186 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR S 172 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE T 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE W 142 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 126 outliers final: 82 residues processed: 1037 average time/residue: 1.3030 time to fit residues: 2342.3968 Evaluate side-chains 965 residues out of total 6428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 883 time to evaluate : 7.206 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "LYS E 174 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL L 137 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL Q 186 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR S 172 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE T 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE W 142 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. outliers start: 82 outliers final: 7 residues processed: 82 average time/residue: 1.0723 time to fit residues: 173.7549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1098 random chunks: chunk 554 optimal weight: 3.9990 chunk 309 optimal weight: 10.0000 chunk 829 optimal weight: 7.9990 chunk 678 optimal weight: 0.8980 chunk 275 optimal weight: 10.0000 chunk 998 optimal weight: 50.0000 chunk 1079 optimal weight: 10.0000 chunk 889 optimal weight: 9.9990 chunk 990 optimal weight: 40.0000 chunk 340 optimal weight: 0.8980 chunk 801 optimal weight: 7.9990 overall best weight: 4.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 GLN C 319 ASN C 377 HIS D 115 HIS D 320 ASN F 183 HIS G 80 ASN K 25 HIS K 160 GLN ** P 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 154 HIS ** T 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 59 ASN b 146 GLN ** e 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 12 ASN h 91 ASN j 67 GLN l 59 HIS n 9 ASN n 75 GLN ** o 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 58 GLN u 163 GLN u 172 HIS u 357 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.074 144183 Z= 0.333 Angle : 0.593 10.585 211529 Z= 0.308 Chirality : 0.039 0.342 26486 Planarity : 0.005 0.157 14105 Dihedral : 14.996 179.391 49663 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.08 % Favored : 93.90 % Rotamer Outliers : 2.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.34 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.09), residues: 7486 helix: -1.06 (0.10), residues: 2334 sheet: -1.22 (0.15), residues: 1084 loop : -2.02 (0.09), residues: 4068 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14972 Ramachandran restraints generated. 7486 Oldfield, 0 Emsley, 7486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14972 Ramachandran restraints generated. 7486 Oldfield, 0 Emsley, 7486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1081 residues out of total 6428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 925 time to evaluate : 7.365 Fit side-chains TARDY: cannot create tardy model for: "LYS E 174 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR J 198 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL L 137 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL Q 186 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR S 172 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE T 160 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 156 outliers final: 104 residues processed: 1034 average time/residue: 1.2443 time to fit residues: 2238.1981 Evaluate side-chains 981 residues out of total 6428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 877 time to evaluate : 7.389 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "LYS E 174 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL L 137 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL Q 186 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR S 172 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE T 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. outliers start: 104 outliers final: 6 residues processed: 104 average time/residue: 1.0069 time to fit residues: 206.6163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1098 random chunks: chunk 986 optimal weight: 4.9990 chunk 751 optimal weight: 0.9990 chunk 518 optimal weight: 7.9990 chunk 110 optimal weight: 7.9990 chunk 476 optimal weight: 9.9990 chunk 670 optimal weight: 5.9990 chunk 1002 optimal weight: 0.6980 chunk 1061 optimal weight: 5.9990 chunk 523 optimal weight: 0.9990 chunk 950 optimal weight: 10.0000 chunk 286 optimal weight: 8.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 HIS C 377 HIS E 47 GLN G 80 ASN H 240 ASN K 12 ASN K 160 GLN ** P 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 87 ASN ** Y 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 80 GLN b 146 GLN ** e 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 5 HIS h 12 ASN h 91 ASN j 67 GLN l 59 HIS n 9 ASN ** o 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 505 ASN u 357 GLN ** w 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.069 144183 Z= 0.231 Angle : 0.553 9.808 211529 Z= 0.288 Chirality : 0.036 0.313 26486 Planarity : 0.004 0.154 14105 Dihedral : 14.946 179.145 49663 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.73 % Favored : 94.24 % Rotamer Outliers : 1.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.34 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.09), residues: 7486 helix: -0.75 (0.10), residues: 2343 sheet: -1.10 (0.15), residues: 1086 loop : -1.90 (0.09), residues: 4057 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14972 Ramachandran restraints generated. 7486 Oldfield, 0 Emsley, 7486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14972 Ramachandran restraints generated. 7486 Oldfield, 0 Emsley, 7486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1042 residues out of total 6428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 922 time to evaluate : 7.490 Fit side-chains TARDY: cannot create tardy model for: "LYS E 174 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR J 198 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL L 137 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL Q 186 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR S 172 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE T 160 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 120 outliers final: 81 residues processed: 993 average time/residue: 1.2831 time to fit residues: 2203.3533 Evaluate side-chains 958 residues out of total 6428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 877 time to evaluate : 7.283 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "LYS E 174 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL L 137 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL Q 186 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR S 172 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE T 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. outliers start: 81 outliers final: 6 residues processed: 81 average time/residue: 1.0564 time to fit residues: 167.7159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1098 random chunks: chunk 883 optimal weight: 20.0000 chunk 602 optimal weight: 0.9990 chunk 15 optimal weight: 20.0000 chunk 790 optimal weight: 7.9990 chunk 437 optimal weight: 10.0000 chunk 905 optimal weight: 6.9990 chunk 733 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 chunk 541 optimal weight: 9.9990 chunk 952 optimal weight: 0.9990 chunk 267 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 319 ASN G 80 ASN H 45 ASN ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 120 GLN K 160 GLN ** P 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 46 GLN S 114 HIS T 98 HIS ** Y 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 80 GLN b 146 GLN d 15 ASN e 52 GLN f 88 ASN h 91 ASN l 59 HIS ** o 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 413 GLN r 116 ASN r 505 ASN v 32 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.083 144183 Z= 0.389 Angle : 0.614 12.851 211529 Z= 0.317 Chirality : 0.040 0.379 26486 Planarity : 0.005 0.154 14105 Dihedral : 15.001 179.595 49663 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.61 % Favored : 93.36 % Rotamer Outliers : 2.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.34 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.09), residues: 7486 helix: -0.64 (0.10), residues: 2341 sheet: -1.14 (0.15), residues: 1108 loop : -1.85 (0.09), residues: 4037 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14972 Ramachandran restraints generated. 7486 Oldfield, 0 Emsley, 7486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14972 Ramachandran restraints generated. 7486 Oldfield, 0 Emsley, 7486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1040 residues out of total 6428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 901 time to evaluate : 7.428 Fit side-chains TARDY: cannot create tardy model for: "LYS E 174 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR J 198 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL L 137 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL Q 186 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR S 172 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE T 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 139 outliers final: 91 residues processed: 1002 average time/residue: 1.2667 time to fit residues: 2204.7638 Evaluate side-chains 969 residues out of total 6428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 878 time to evaluate : 7.302 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "LYS E 174 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL L 137 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL Q 186 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR S 172 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE T 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. outliers start: 91 outliers final: 6 residues processed: 91 average time/residue: 0.9832 time to fit residues: 178.4475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1098 random chunks: chunk 357 optimal weight: 2.9990 chunk 955 optimal weight: 40.0000 chunk 209 optimal weight: 10.0000 chunk 623 optimal weight: 0.9990 chunk 262 optimal weight: 50.0000 chunk 1062 optimal weight: 6.9990 chunk 881 optimal weight: 5.9990 chunk 491 optimal weight: 0.9990 chunk 88 optimal weight: 6.9990 chunk 351 optimal weight: 4.9990 chunk 557 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 HIS B 86 GLN D 311 HIS E 47 GLN G 80 ASN H 45 ASN ** H 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 120 GLN K 160 GLN N 89 GLN ** P 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 46 GLN ** Y 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 146 GLN d 15 ASN h 91 ASN l 59 HIS ** n 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 144183 Z= 0.256 Angle : 0.555 11.642 211529 Z= 0.288 Chirality : 0.037 0.302 26486 Planarity : 0.004 0.150 14105 Dihedral : 14.906 179.301 49663 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.86 % Favored : 94.11 % Rotamer Outliers : 1.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.34 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.09), residues: 7486 helix: -0.42 (0.11), residues: 2341 sheet: -1.01 (0.15), residues: 1076 loop : -1.73 (0.09), residues: 4069 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14972 Ramachandran restraints generated. 7486 Oldfield, 0 Emsley, 7486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14972 Ramachandran restraints generated. 7486 Oldfield, 0 Emsley, 7486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1022 residues out of total 6428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 920 time to evaluate : 7.377 Fit side-chains TARDY: cannot create tardy model for: "LYS E 174 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR J 198 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL L 137 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL Q 186 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR S 172 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE T 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 102 outliers final: 63 residues processed: 984 average time/residue: 1.3243 time to fit residues: 2266.6015 Evaluate side-chains 949 residues out of total 6428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 886 time to evaluate : 7.333 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "LYS E 174 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL L 137 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL Q 186 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR S 172 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE T 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. outliers start: 63 outliers final: 6 residues processed: 63 average time/residue: 1.0403 time to fit residues: 131.9788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1098 random chunks: chunk 1024 optimal weight: 10.0000 chunk 119 optimal weight: 50.0000 chunk 605 optimal weight: 2.9990 chunk 775 optimal weight: 2.9990 chunk 601 optimal weight: 2.9990 chunk 894 optimal weight: 0.2980 chunk 593 optimal weight: 2.9990 chunk 1058 optimal weight: 0.0970 chunk 662 optimal weight: 1.9990 chunk 645 optimal weight: 1.9990 chunk 488 optimal weight: 4.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 GLN ** E 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 ASN H 240 ASN J 89 HIS K 120 GLN N 89 GLN O 15 GLN ** P 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 46 GLN V 87 ASN ** Y 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 80 GLN b 146 GLN e 52 GLN h 91 ASN n 9 ASN ** n 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 205 ASN ** w 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.073 144183 Z= 0.152 Angle : 0.531 11.089 211529 Z= 0.278 Chirality : 0.034 0.292 26486 Planarity : 0.004 0.146 14105 Dihedral : 14.891 179.548 49663 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.80 % Favored : 94.18 % Rotamer Outliers : 1.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.34 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.09), residues: 7486 helix: -0.30 (0.11), residues: 2343 sheet: -0.96 (0.15), residues: 1083 loop : -1.65 (0.09), residues: 4060 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14972 Ramachandran restraints generated. 7486 Oldfield, 0 Emsley, 7486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14972 Ramachandran restraints generated. 7486 Oldfield, 0 Emsley, 7486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1006 residues out of total 6428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 935 time to evaluate : 7.466 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LYS E 174 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR J 198 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL L 137 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL Q 186 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR S 172 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE T 160 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 71 outliers final: 38 residues processed: 980 average time/residue: 1.2433 time to fit residues: 2107.0032 Evaluate side-chains 943 residues out of total 6428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 905 time to evaluate : 7.264 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "LYS E 174 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL L 137 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL Q 186 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR S 172 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE T 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. outliers start: 38 outliers final: 6 residues processed: 38 average time/residue: 1.0830 time to fit residues: 83.6018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1098 random chunks: chunk 654 optimal weight: 0.1980 chunk 422 optimal weight: 0.7980 chunk 632 optimal weight: 6.9990 chunk 318 optimal weight: 5.9990 chunk 207 optimal weight: 10.0000 chunk 205 optimal weight: 10.0000 chunk 672 optimal weight: 3.9990 chunk 721 optimal weight: 20.0000 chunk 523 optimal weight: 3.9990 chunk 98 optimal weight: 50.0000 chunk 831 optimal weight: 1.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 HIS C 121 ASN C 319 ASN ** E 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 ASN ** P 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 46 GLN ** Y 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 80 GLN b 146 GLN e 52 GLN h 91 ASN ** n 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 505 ASN w 181 HIS w 205 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 144183 Z= 0.194 Angle : 0.526 13.467 211529 Z= 0.273 Chirality : 0.035 0.343 26486 Planarity : 0.004 0.146 14105 Dihedral : 14.797 179.804 49663 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.74 % Favored : 94.23 % Rotamer Outliers : 1.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.34 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.09), residues: 7486 helix: -0.16 (0.11), residues: 2356 sheet: -0.92 (0.15), residues: 1081 loop : -1.57 (0.09), residues: 4049 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14972 Ramachandran restraints generated. 7486 Oldfield, 0 Emsley, 7486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14972 Ramachandran restraints generated. 7486 Oldfield, 0 Emsley, 7486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 982 residues out of total 6428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 915 time to evaluate : 9.500 Fit side-chains TARDY: cannot create tardy model for: "LYS E 174 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR J 198 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL L 137 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL Q 186 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR S 172 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE T 160 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 67 outliers final: 48 residues processed: 954 average time/residue: 1.2915 time to fit residues: 2122.2432 Evaluate side-chains 946 residues out of total 6428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 898 time to evaluate : 7.268 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "LYS E 174 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL L 137 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL Q 186 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR S 172 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE T 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. outliers start: 48 outliers final: 6 residues processed: 48 average time/residue: 0.9789 time to fit residues: 96.1723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1098 random chunks: chunk 962 optimal weight: 50.0000 chunk 1013 optimal weight: 7.9990 chunk 925 optimal weight: 30.0000 chunk 986 optimal weight: 20.0000 chunk 593 optimal weight: 1.9990 chunk 429 optimal weight: 3.9990 chunk 774 optimal weight: 10.0000 chunk 302 optimal weight: 20.0000 chunk 891 optimal weight: 0.1980 chunk 932 optimal weight: 50.0000 chunk 982 optimal weight: 10.0000 overall best weight: 4.8390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 GLN D 311 HIS ** E 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 ASN H 240 ASN K 120 GLN K 160 GLN N 89 GLN O 15 GLN ** P 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 46 GLN V 87 ASN ** Y 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 10 HIS b 146 GLN l 27 GLN ** n 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.078 144183 Z= 0.364 Angle : 0.599 11.458 211529 Z= 0.309 Chirality : 0.039 0.359 26486 Planarity : 0.005 0.149 14105 Dihedral : 14.887 179.565 49663 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.48 % Favored : 93.49 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.34 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.09), residues: 7486 helix: -0.21 (0.11), residues: 2350 sheet: -0.98 (0.15), residues: 1080 loop : -1.63 (0.09), residues: 4056 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14972 Ramachandran restraints generated. 7486 Oldfield, 0 Emsley, 7486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14972 Ramachandran restraints generated. 7486 Oldfield, 0 Emsley, 7486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 932 residues out of total 6428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 894 time to evaluate : 7.331 Fit side-chains TARDY: cannot create tardy model for: "LYS E 174 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR J 198 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL L 137 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL Q 186 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR S 172 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE T 160 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 38 outliers final: 24 residues processed: 918 average time/residue: 1.2782 time to fit residues: 2031.3437 Evaluate side-chains 902 residues out of total 6428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 878 time to evaluate : 9.245 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "LYS E 174 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL L 137 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL Q 186 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR S 172 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE T 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. outliers start: 24 outliers final: 6 residues processed: 24 average time/residue: 1.0273 time to fit residues: 55.2104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1098 random chunks: chunk 647 optimal weight: 0.8980 chunk 1042 optimal weight: 20.0000 chunk 636 optimal weight: 0.8980 chunk 494 optimal weight: 5.9990 chunk 724 optimal weight: 6.9990 chunk 1093 optimal weight: 7.9990 chunk 1006 optimal weight: 20.0000 chunk 871 optimal weight: 3.9990 chunk 90 optimal weight: 8.9990 chunk 672 optimal weight: 7.9990 chunk 534 optimal weight: 0.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 GLN C 173 GLN ** E 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 ASN K 19 GLN ** P 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 46 GLN ** Y 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 80 GLN b 146 GLN e 52 GLN h 91 ASN j 67 GLN l 27 GLN ** n 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 505 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.091 144183 Z= 0.211 Angle : 0.556 12.820 211529 Z= 0.289 Chirality : 0.036 0.344 26486 Planarity : 0.004 0.146 14105 Dihedral : 14.870 179.874 49663 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.08 % Favored : 93.90 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.34 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.09), residues: 7486 helix: -0.17 (0.11), residues: 2355 sheet: -0.93 (0.15), residues: 1068 loop : -1.59 (0.09), residues: 4063 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14972 Ramachandran restraints generated. 7486 Oldfield, 0 Emsley, 7486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14972 Ramachandran restraints generated. 7486 Oldfield, 0 Emsley, 7486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 925 residues out of total 6428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 893 time to evaluate : 7.288 Fit side-chains TARDY: cannot create tardy model for: "LYS E 174 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR J 198 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL L 137 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL Q 186 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR S 172 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE T 160 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 32 outliers final: 27 residues processed: 911 average time/residue: 1.2656 time to fit residues: 1991.2093 Evaluate side-chains 910 residues out of total 6428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 883 time to evaluate : 7.355 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "LYS E 174 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL L 137 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL Q 186 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR S 172 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE T 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. outliers start: 27 outliers final: 6 residues processed: 27 average time/residue: 1.1059 time to fit residues: 62.7684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1098 random chunks: chunk 691 optimal weight: 7.9990 chunk 927 optimal weight: 50.0000 chunk 266 optimal weight: 10.0000 chunk 803 optimal weight: 10.0000 chunk 128 optimal weight: 8.9990 chunk 242 optimal weight: 10.0000 chunk 872 optimal weight: 30.0000 chunk 365 optimal weight: 3.9990 chunk 895 optimal weight: 3.9990 chunk 110 optimal weight: 7.9990 chunk 160 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 GLN E 7 ASN ** E 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 ASN H 240 ASN K 120 GLN K 160 GLN N 62 HIS O 15 GLN ** P 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 46 GLN V 87 ASN ** Y 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 146 GLN h 91 ASN j 67 GLN l 27 GLN l 59 HIS ** n 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 51 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.125799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.081988 restraints weight = 207514.880| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 1.56 r_work: 0.2587 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2471 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.090 144183 Z= 0.486 Angle : 0.670 11.788 211529 Z= 0.344 Chirality : 0.044 0.446 26486 Planarity : 0.005 0.150 14105 Dihedral : 15.032 179.865 49663 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.01 % Favored : 92.96 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.34 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.09), residues: 7486 helix: -0.35 (0.11), residues: 2352 sheet: -0.96 (0.15), residues: 1064 loop : -1.71 (0.09), residues: 4070 =============================================================================== Job complete usr+sys time: 33567.37 seconds wall clock time: 588 minutes 13.42 seconds (35293.42 seconds total)