Starting phenix.real_space_refine (version: dev) on Fri Apr 8 07:36:26 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oi9_12922/04_2022/7oi9_12922_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oi9_12922/04_2022/7oi9_12922.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oi9_12922/04_2022/7oi9_12922_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oi9_12922/04_2022/7oi9_12922_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oi9_12922/04_2022/7oi9_12922_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oi9_12922/04_2022/7oi9_12922.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oi9_12922/04_2022/7oi9_12922.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oi9_12922/04_2022/7oi9_12922_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oi9_12922/04_2022/7oi9_12922_updated.pdb" } resolution = 3.3 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= 0.001 sd= 0.021 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "D TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 86": "OD1" <-> "OD2" Residue "D GLU 197": "OE1" <-> "OE2" Residue "D TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 50": "OD1" <-> "OD2" Residue "E GLU 56": "OE1" <-> "OE2" Residue "E GLU 163": "OE1" <-> "OE2" Residue "E ASP 205": "OD1" <-> "OD2" Residue "E TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 335": "OE1" <-> "OE2" Residue "F PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 73": "OE1" <-> "OE2" Residue "F ASP 81": "OD1" <-> "OD2" Residue "F ASP 94": "OD1" <-> "OD2" Residue "F ASP 185": "OD1" <-> "OD2" Residue "F ASP 191": "OD1" <-> "OD2" Residue "F ASP 199": "OD1" <-> "OD2" Residue "F GLU 205": "OE1" <-> "OE2" Residue "F GLU 232": "OE1" <-> "OE2" Residue "F ASP 271": "OD1" <-> "OD2" Residue "F ASP 277": "OD1" <-> "OD2" Residue "H GLU 57": "OE1" <-> "OE2" Residue "H GLU 67": "OE1" <-> "OE2" Residue "H ASP 85": "OD1" <-> "OD2" Residue "H GLU 142": "OE1" <-> "OE2" Residue "K ASP 52": "OD1" <-> "OD2" Residue "K TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 71": "OD1" <-> "OD2" Residue "L TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 14": "OD1" <-> "OD2" Residue "M GLU 37": "OE1" <-> "OE2" Residue "M GLU 56": "OE1" <-> "OE2" Residue "M GLU 68": "OE1" <-> "OE2" Residue "M TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 135": "OD1" <-> "OD2" Residue "M TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 168": "OE1" <-> "OE2" Residue "M ASP 246": "OD1" <-> "OD2" Residue "M ASP 261": "OD1" <-> "OD2" Residue "M PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 288": "OE1" <-> "OE2" Residue "N PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 65": "OE1" <-> "OE2" Residue "N GLU 78": "OE1" <-> "OE2" Residue "N GLU 81": "OE1" <-> "OE2" Residue "N TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 168": "OE1" <-> "OE2" Residue "N GLU 196": "OE1" <-> "OE2" Residue "N GLU 203": "OE1" <-> "OE2" Residue "N TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 43": "OE1" <-> "OE2" Residue "O ASP 99": "OD1" <-> "OD2" Residue "P GLU 47": "OE1" <-> "OE2" Residue "P GLU 65": "OE1" <-> "OE2" Residue "P GLU 76": "OE1" <-> "OE2" Residue "P GLU 174": "OE1" <-> "OE2" Residue "Q GLU 79": "OE1" <-> "OE2" Residue "Q PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 88": "OD1" <-> "OD2" Residue "Q TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 161": "OE1" <-> "OE2" Residue "Q GLU 165": "OE1" <-> "OE2" Residue "Q TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 180": "OE1" <-> "OE2" Residue "Q GLU 196": "OE1" <-> "OE2" Residue "Q GLU 234": "OE1" <-> "OE2" Residue "Q GLU 272": "OE1" <-> "OE2" Residue "R TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 109": "OE1" <-> "OE2" Residue "S GLU 71": "OE1" <-> "OE2" Residue "S PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 119": "OE1" <-> "OE2" Residue "S ASP 139": "OD1" <-> "OD2" Residue "S GLU 157": "OE1" <-> "OE2" Residue "S GLU 199": "OE1" <-> "OE2" Residue "U PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 37": "OE1" <-> "OE2" Residue "U PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 47": "OE1" <-> "OE2" Residue "U ASP 52": "OD1" <-> "OD2" Residue "U TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 58": "OE1" <-> "OE2" Residue "U ASP 91": "OD1" <-> "OD2" Residue "U TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 109": "OD1" <-> "OD2" Residue "V TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 63": "OE1" <-> "OE2" Residue "V ASP 172": "OD1" <-> "OD2" Residue "V GLU 196": "OE1" <-> "OE2" Residue "W TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 63": "OE1" <-> "OE2" Residue "X ASP 95": "OD1" <-> "OD2" Residue "X PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 133": "OD1" <-> "OD2" Residue "X ASP 136": "OD1" <-> "OD2" Residue "X GLU 137": "OE1" <-> "OE2" Residue "X TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 151": "OE1" <-> "OE2" Residue "X ASP 152": "OD1" <-> "OD2" Residue "X ASP 180": "OD1" <-> "OD2" Residue "X TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 193": "OE1" <-> "OE2" Residue "X GLU 199": "OE1" <-> "OE2" Residue "X GLU 210": "OE1" <-> "OE2" Residue "Y GLU 66": "OE1" <-> "OE2" Residue "Y PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 108": "OE1" <-> "OE2" Residue "Y ASP 133": "OD1" <-> "OD2" Residue "Y GLU 214": "OE1" <-> "OE2" Residue "Y GLU 227": "OE1" <-> "OE2" Residue "Z GLU 82": "OE1" <-> "OE2" Residue "0 GLU 88": "OE1" <-> "OE2" Residue "0 GLU 133": "OE1" <-> "OE2" Residue "0 PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 39": "OE1" <-> "OE2" Residue "1 PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 58": "OE1" <-> "OE2" Residue "3 TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 175": "OD1" <-> "OD2" Residue "3 TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 47": "OD1" <-> "OD2" Residue "5 GLU 56": "OE1" <-> "OE2" Residue "5 ASP 84": "OD1" <-> "OD2" Residue "5 GLU 152": "OE1" <-> "OE2" Residue "5 GLU 174": "OE1" <-> "OE2" Residue "5 GLU 246": "OE1" <-> "OE2" Residue "5 ASP 276": "OD1" <-> "OD2" Residue "5 TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 46": "OE1" <-> "OE2" Residue "6 ASP 55": "OD1" <-> "OD2" Residue "6 GLU 62": "OE1" <-> "OE2" Residue "6 GLU 76": "OE1" <-> "OE2" Residue "6 ASP 133": "OD1" <-> "OD2" Residue "6 TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 197": "OE1" <-> "OE2" Residue "6 GLU 227": "OE1" <-> "OE2" Residue "6 TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 336": "OD1" <-> "OD2" Residue "6 PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 51": "OE1" <-> "OE2" Residue "7 TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 171": "OE1" <-> "OE2" Residue "7 PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 279": "OE1" <-> "OE2" Residue "7 GLU 318": "OE1" <-> "OE2" Residue "8 PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 101": "OE1" <-> "OE2" Residue "9 PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 50": "OE1" <-> "OE2" Residue "b PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 106": "OD1" <-> "OD2" Residue "b PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 46": "OE1" <-> "OE2" Residue "c GLU 101": "OE1" <-> "OE2" Residue "c TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 183": "OE1" <-> "OE2" Residue "c GLU 230": "OE1" <-> "OE2" Residue "c GLU 243": "OE1" <-> "OE2" Residue "c GLU 244": "OE1" <-> "OE2" Residue "c ASP 277": "OD1" <-> "OD2" Residue "c GLU 295": "OE1" <-> "OE2" Residue "c TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 86": "OD1" <-> "OD2" Residue "f GLU 87": "OE1" <-> "OE2" Residue "g ASP 116": "OD1" <-> "OD2" Residue "g ASP 126": "OD1" <-> "OD2" Residue "h ASP 65": "OD1" <-> "OD2" Residue "h TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 76": "OE1" <-> "OE2" Residue "i GLU 67": "OE1" <-> "OE2" Residue "j GLU 69": "OE1" <-> "OE2" Residue "j GLU 71": "OE1" <-> "OE2" Residue "m GLU 70": "OE1" <-> "OE2" Residue "o TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 57": "OE1" <-> "OE2" Residue "o GLU 72": "OE1" <-> "OE2" Residue "o ASP 93": "OD1" <-> "OD2" Residue "p ASP 46": "OD1" <-> "OD2" Residue "p ASP 74": "OD1" <-> "OD2" Residue "p GLU 109": "OE1" <-> "OE2" Residue "p TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ASP 41": "OD1" <-> "OD2" Residue "q ASP 44": "OD1" <-> "OD2" Residue "q GLU 86": "OE1" <-> "OE2" Residue "q GLU 89": "OE1" <-> "OE2" Residue "q GLU 101": "OE1" <-> "OE2" Residue "q GLU 110": "OE1" <-> "OE2" Residue "q GLU 116": "OE1" <-> "OE2" Residue "r ASP 84": "OD1" <-> "OD2" Residue "r PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 54": "OD1" <-> "OD2" Residue "s GLU 74": "OE1" <-> "OE2" Residue "s GLU 78": "OE1" <-> "OE2" Residue "s PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 103": "OD1" <-> "OD2" Residue "s PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 153": "OE1" <-> "OE2" Residue "s TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 201": "OD1" <-> "OD2" Residue "s ASP 227": "OD1" <-> "OD2" Residue "s ASP 228": "OD1" <-> "OD2" Residue "s TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 260": "OE1" <-> "OE2" Residue "s GLU 348": "OE1" <-> "OE2" Residue "s TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ASP 165": "OD1" <-> "OD2" Residue "u ASP 166": "OD1" <-> "OD2" Residue "u ASP 171": "OD1" <-> "OD2" Residue "u GLU 191": "OE1" <-> "OE2" Residue "w ASP 132": "OD1" <-> "OD2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 90599 Number of models: 1 Model: "" Number of chains: 60 Chain: "D" Number of atoms: 1706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1706 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 11, 'TRANS': 208} Chain breaks: 1 Chain: "E" Number of atoms: 2258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2258 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 22, 'TRANS': 262} Chain breaks: 1 Chain: "F" Number of atoms: 2013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 2013 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 21, 'TRANS': 228} Chain: "H" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 784 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "I" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1283 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 11, 'TRANS': 146} Chain breaks: 1 Chain: "J" Number of atoms: 1061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1061 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 9, 'TRANS': 130} Chain: "K" Number of atoms: 1451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1451 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 15, 'TRANS': 161} Chain: "L" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 889 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "M" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2305 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 26, 'TRANS': 260} Chain: "N" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1654 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 14, 'TRANS': 190} Chain: "O" Number of atoms: 1245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1245 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 9, 'TRANS': 142} Chain: "P" Number of atoms: 1148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1148 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 134, 'PCIS': 1} Chain: "Q" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1805 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 14, 'TRANS': 202} Chain: "R" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1153 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "S" Number of atoms: 1251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1251 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 9, 'TRANS': 145, 'PCIS': 1} Chain: "T" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1305 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 12, 'TRANS': 146} Chain breaks: 1 Chain: "U" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1154 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 11, 'TRANS': 127} Chain breaks: 1 Chain: "V" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1575 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 16, 'TRANS': 175} Chain breaks: 1 Chain: "W" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 859 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "X" Number of atoms: 2035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 2035 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 18, 'TRANS': 224} Chain: "Y" Number of atoms: 1517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1517 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 7, 'TRANS': 168} Chain: "Z" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 978 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 11, 'TRANS': 108} Chain: "0" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 880 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "1" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 433 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 1, 'TRANS': 50} Chain: "2" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Chain: "3" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 831 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "5" Number of atoms: 3156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3156 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 31, 'TRANS': 354, 'PCIS': 1} Chain breaks: 1 Chain: "6" Number of atoms: 2640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2640 Classifications: {'peptide': 324} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 28, 'TRANS': 295} Chain breaks: 3 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 5, 'ARG:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 59 Chain: "7" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2334 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 17, 'TRANS': 269} Chain: "8" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 836 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 9, 'TRANS': 89} Chain: "9" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 8, 'TRANS': 107, 'PCIS': 1} Chain breaks: 1 Chain: "a" Number of atoms: 686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 686 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 10, 'TRANS': 71} Chain breaks: 1 Chain: "b" Number of atoms: 1178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1178 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 9, 'TRANS': 138} Chain: "c" Number of atoms: 2217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2217 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 15, 'TRANS': 258, 'PCIS': 1} Chain breaks: 1 Chain: "d" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1741 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 17, 'TRANS': 193} Chain breaks: 3 Chain: "e" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1762 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 9, 'TRANS': 207} Chain breaks: 2 Chain: "f" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 915 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "g" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1067 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 13, 'TRANS': 113, 'PCIS': 2} Chain: "h" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 827 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 7, 'TRANS': 92} Chain breaks: 1 Chain: "i" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 827 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 5, 'TRANS': 91} Chain: "j" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 684 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 6, 'TRANS': 78} Chain: "k" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 627 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain breaks: 1 Chain: "l" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 221 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "m" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 372 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 3, 'TRANS': 41} Chain: "o" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 665 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "p" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1058 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain breaks: 3 Chain: "q" Number of atoms: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1076 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 14, 'TRANS': 113} Chain: "r" Number of atoms: 1203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1203 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 16, 'TRANS': 129} Chain breaks: 2 Chain: "s" Number of atoms: 3036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 3036 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 21, 'TRANS': 348} Chain breaks: 1 Chain: "u" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 927 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "v" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 588 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "w" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 638 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "A" Number of atoms: 23184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1092, 23184 Classifications: {'RNA': 1092} Modifications used: {'rna3p_pyr': 423, 'rna2p_pur': 119, 'rna3p_pur': 462, 'rna2p_pyr': 88} Link IDs: {'rna3p': 885, 'rna2p': 206} Chain breaks: 22 Chain: "B" Number of atoms: 1191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1191 Classifications: {'RNA': 56} Modifications used: {'rna3p_pyr': 26, 'rna2p_pur': 1, 'rna3p_pur': 29} Link IDs: {'rna3p': 54, 'rna2p': 1} Chain breaks: 4 Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "0" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "v" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'PNS': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Unusual residues: {' MG': 47} Classifications: {'undetermined': 47} Link IDs: {None: 46} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 31693 SG CYS 0 110 164.986 84.658 173.779 1.00 33.03 S ATOM 31715 SG CYS 0 113 161.874 83.967 174.865 1.00 40.65 S ATOM 31795 SG CYS 0 123 162.638 87.148 172.909 1.00 20.89 S ATOM 31818 SG CYS 0 126 163.184 86.778 176.866 1.00 29.39 S ATOM 7048 SG CYS I 64 140.741 101.045 61.013 1.00 54.65 S ATOM 59995 SG CYS r 70 145.114 100.705 61.402 1.00 49.79 S ATOM 60310 SG CYS r 108 142.891 102.952 61.357 1.00 44.91 S Time building chain proxies: 37.67, per 1000 atoms: 0.42 Number of scatterers: 90599 At special positions: 0 Unit cell: (220.052, 223.304, 254.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 282 16.00 P 1149 15.00 Mg 49 11.99 O 19480 8.00 N 16469 7.00 C 53168 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 31.31 Conformation dependent library (CDL) restraints added in 7.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN 0 200 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 113 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 110 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 123 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 126 " pdb=" ZN r 301 " pdb="ZN ZN r 301 " - pdb=" SG CYS I 64 " pdb="ZN ZN r 301 " - pdb=" SG CYS r 70 " pdb="ZN ZN r 301 " - pdb=" SG CYS r 108 " Number of angles added : 6 15890 Ramachandran restraints generated. 7945 Oldfield, 0 Emsley, 7945 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15306 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 268 helices and 78 sheets defined 32.1% alpha, 11.2% beta 308 base pairs and 601 stacking pairs defined. Time for finding SS restraints: 24.55 Creating SS restraints... Processing helix chain 'D' and resid 184 through 186 No H-bonds generated for 'chain 'D' and resid 184 through 186' Processing helix chain 'D' and resid 260 through 265 Processing helix chain 'E' and resid 57 through 75 Processing helix chain 'E' and resid 135 through 138 No H-bonds generated for 'chain 'E' and resid 135 through 138' Processing helix chain 'E' and resid 154 through 156 No H-bonds generated for 'chain 'E' and resid 154 through 156' Processing helix chain 'E' and resid 159 through 168 Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 218 through 221 No H-bonds generated for 'chain 'E' and resid 218 through 221' Processing helix chain 'E' and resid 305 through 307 No H-bonds generated for 'chain 'E' and resid 305 through 307' Processing helix chain 'E' and resid 321 through 323 No H-bonds generated for 'chain 'E' and resid 321 through 323' Processing helix chain 'F' and resid 84 through 87 No H-bonds generated for 'chain 'F' and resid 84 through 87' Processing helix chain 'F' and resid 93 through 105 Processing helix chain 'F' and resid 167 through 183 Processing helix chain 'F' and resid 200 through 209 Processing helix chain 'F' and resid 228 through 236 removed outlier: 4.425A pdb=" N ARG F 236 " --> pdb=" O GLU F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 247 No H-bonds generated for 'chain 'F' and resid 245 through 247' Processing helix chain 'F' and resid 250 through 255 Processing helix chain 'F' and resid 263 through 275 Processing helix chain 'H' and resid 86 through 88 No H-bonds generated for 'chain 'H' and resid 86 through 88' Processing helix chain 'H' and resid 116 through 121 Processing helix chain 'H' and resid 123 through 126 No H-bonds generated for 'chain 'H' and resid 123 through 126' Processing helix chain 'H' and resid 134 through 145 removed outlier: 4.356A pdb=" N LYS H 138 " --> pdb=" O PRO H 134 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU H 139 " --> pdb=" O GLU H 135 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 50 Processing helix chain 'I' and resid 62 through 64 No H-bonds generated for 'chain 'I' and resid 62 through 64' Processing helix chain 'I' and resid 78 through 92 Processing helix chain 'I' and resid 106 through 115 Processing helix chain 'I' and resid 128 through 137 Proline residue: I 133 - end of helix Processing helix chain 'I' and resid 144 through 146 No H-bonds generated for 'chain 'I' and resid 144 through 146' Processing helix chain 'I' and resid 162 through 170 Processing helix chain 'I' and resid 188 through 195 Processing helix chain 'J' and resid 46 through 58 Processing helix chain 'J' and resid 88 through 94 Processing helix chain 'J' and resid 114 through 121 Processing helix chain 'J' and resid 137 through 149 Processing helix chain 'K' and resid 6 through 14 Processing helix chain 'K' and resid 28 through 39 Processing helix chain 'K' and resid 62 through 64 No H-bonds generated for 'chain 'K' and resid 62 through 64' Processing helix chain 'K' and resid 70 through 73 Processing helix chain 'K' and resid 92 through 98 Processing helix chain 'K' and resid 102 through 111 Processing helix chain 'K' and resid 117 through 124 removed outlier: 3.771A pdb=" N ARG K 124 " --> pdb=" O THR K 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 138 No H-bonds generated for 'chain 'K' and resid 135 through 138' Processing helix chain 'K' and resid 160 through 165 Processing helix chain 'L' and resid 45 through 48 No H-bonds generated for 'chain 'L' and resid 45 through 48' Processing helix chain 'L' and resid 135 through 138 No H-bonds generated for 'chain 'L' and resid 135 through 138' Processing helix chain 'M' and resid 11 through 17 Processing helix chain 'M' and resid 82 through 84 No H-bonds generated for 'chain 'M' and resid 82 through 84' Processing helix chain 'M' and resid 98 through 106 Processing helix chain 'M' and resid 118 through 123 Processing helix chain 'M' and resid 161 through 170 removed outlier: 3.976A pdb=" N ASN M 170 " --> pdb=" O ALA M 166 " (cutoff:3.500A) Processing helix chain 'M' and resid 181 through 188 Processing helix chain 'M' and resid 190 through 194 Processing helix chain 'M' and resid 211 through 214 No H-bonds generated for 'chain 'M' and resid 211 through 214' Processing helix chain 'M' and resid 229 through 239 Processing helix chain 'M' and resid 251 through 257 removed outlier: 4.543A pdb=" N LYS M 254 " --> pdb=" O GLU M 251 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N CYS M 257 " --> pdb=" O LYS M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 288 through 294 Processing helix chain 'N' and resid 69 through 71 No H-bonds generated for 'chain 'N' and resid 69 through 71' Processing helix chain 'N' and resid 99 through 111 Processing helix chain 'N' and resid 169 through 182 removed outlier: 4.291A pdb=" N GLY N 174 " --> pdb=" O GLU N 170 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N PHE N 175 " --> pdb=" O GLU N 171 " (cutoff:3.500A) Processing helix chain 'N' and resid 192 through 208 Processing helix chain 'N' and resid 215 through 221 Processing helix chain 'N' and resid 226 through 228 No H-bonds generated for 'chain 'N' and resid 226 through 228' Processing helix chain 'N' and resid 232 through 237 removed outlier: 3.562A pdb=" N LEU N 235 " --> pdb=" O PRO N 232 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N HIS N 237 " --> pdb=" O ASP N 234 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 39 Processing helix chain 'O' and resid 46 through 65 removed outlier: 4.366A pdb=" N LEU O 65 " --> pdb=" O ASP O 61 " (cutoff:3.500A) Processing helix chain 'O' and resid 70 through 79 Processing helix chain 'O' and resid 83 through 91 Proline residue: O 87 - end of helix Processing helix chain 'O' and resid 93 through 96 No H-bonds generated for 'chain 'O' and resid 93 through 96' Processing helix chain 'O' and resid 144 through 157 Processing helix chain 'P' and resid 55 through 58 No H-bonds generated for 'chain 'P' and resid 55 through 58' Processing helix chain 'P' and resid 110 through 113 No H-bonds generated for 'chain 'P' and resid 110 through 113' Processing helix chain 'P' and resid 122 through 138 Processing helix chain 'P' and resid 150 through 153 No H-bonds generated for 'chain 'P' and resid 150 through 153' Processing helix chain 'P' and resid 156 through 168 Processing helix chain 'Q' and resid 89 through 105 Processing helix chain 'Q' and resid 144 through 146 No H-bonds generated for 'chain 'Q' and resid 144 through 146' Processing helix chain 'Q' and resid 188 through 191 Processing helix chain 'Q' and resid 195 through 198 Processing helix chain 'Q' and resid 251 through 258 Processing helix chain 'Q' and resid 264 through 267 No H-bonds generated for 'chain 'Q' and resid 264 through 267' Processing helix chain 'Q' and resid 277 through 289 removed outlier: 3.645A pdb=" N SER Q 289 " --> pdb=" O GLU Q 285 " (cutoff:3.500A) Processing helix chain 'R' and resid 18 through 27 removed outlier: 4.450A pdb=" N HIS R 27 " --> pdb=" O GLU R 23 " (cutoff:3.500A) Processing helix chain 'R' and resid 33 through 36 Processing helix chain 'R' and resid 39 through 78 removed outlier: 4.451A pdb=" N TYR R 58 " --> pdb=" O THR R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 83 through 91 Processing helix chain 'R' and resid 99 through 108 Processing helix chain 'R' and resid 110 through 132 Processing helix chain 'S' and resid 69 through 89 Processing helix chain 'T' and resid 50 through 55 removed outlier: 3.528A pdb=" N LYS T 54 " --> pdb=" O LYS T 50 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASN T 55 " --> pdb=" O TRP T 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 50 through 55' Processing helix chain 'T' and resid 87 through 93 Processing helix chain 'T' and resid 99 through 107 Processing helix chain 'T' and resid 112 through 131 Processing helix chain 'T' and resid 192 through 204 Processing helix chain 'U' and resid 50 through 60 Processing helix chain 'U' and resid 127 through 134 removed outlier: 3.728A pdb=" N GLU U 133 " --> pdb=" O MET U 129 " (cutoff:3.500A) Processing helix chain 'U' and resid 142 through 144 No H-bonds generated for 'chain 'U' and resid 142 through 144' Processing helix chain 'V' and resid 29 through 34 Processing helix chain 'V' and resid 179 through 182 No H-bonds generated for 'chain 'V' and resid 179 through 182' Processing helix chain 'V' and resid 194 through 201 Processing helix chain 'W' and resid 111 through 119 Processing helix chain 'X' and resid 8 through 17 removed outlier: 5.126A pdb=" N LYS X 12 " --> pdb=" O TRP X 9 " (cutoff:3.500A) Processing helix chain 'X' and resid 20 through 23 Processing helix chain 'X' and resid 26 through 33 Processing helix chain 'X' and resid 73 through 77 Processing helix chain 'X' and resid 129 through 138 Processing helix chain 'X' and resid 141 through 147 Processing helix chain 'X' and resid 150 through 153 No H-bonds generated for 'chain 'X' and resid 150 through 153' Processing helix chain 'X' and resid 156 through 170 Processing helix chain 'X' and resid 181 through 190 Processing helix chain 'X' and resid 192 through 194 No H-bonds generated for 'chain 'X' and resid 192 through 194' Processing helix chain 'X' and resid 198 through 203 removed outlier: 5.313A pdb=" N TRP X 203 " --> pdb=" O GLU X 199 " (cutoff:3.500A) Processing helix chain 'X' and resid 208 through 219 Processing helix chain 'X' and resid 226 through 242 Processing helix chain 'Y' and resid 64 through 67 Processing helix chain 'Y' and resid 71 through 73 No H-bonds generated for 'chain 'Y' and resid 71 through 73' Processing helix chain 'Y' and resid 87 through 91 Processing helix chain 'Y' and resid 95 through 122 Processing helix chain 'Y' and resid 130 through 157 Processing helix chain 'Y' and resid 188 through 190 No H-bonds generated for 'chain 'Y' and resid 188 through 190' Processing helix chain 'Y' and resid 192 through 196 Processing helix chain 'Y' and resid 206 through 237 Processing helix chain 'Z' and resid 43 through 46 Processing helix chain 'Z' and resid 50 through 55 Processing helix chain 'Z' and resid 80 through 89 Processing helix chain 'Z' and resid 104 through 112 Processing helix chain '0' and resid 87 through 94 Processing helix chain '0' and resid 124 through 145 Processing helix chain '2' and resid 57 through 64 Processing helix chain '2' and resid 66 through 71 Processing helix chain '2' and resid 73 through 85 Processing helix chain '3' and resid 108 through 113 Processing helix chain '3' and resid 133 through 135 No H-bonds generated for 'chain '3' and resid 133 through 135' Processing helix chain '3' and resid 138 through 144 Processing helix chain '3' and resid 152 through 160 Processing helix chain '3' and resid 176 through 178 No H-bonds generated for 'chain '3' and resid 176 through 178' Processing helix chain '5' and resid 48 through 51 Processing helix chain '5' and resid 85 through 87 No H-bonds generated for 'chain '5' and resid 85 through 87' Processing helix chain '5' and resid 117 through 123 Processing helix chain '5' and resid 134 through 139 removed outlier: 4.313A pdb=" N LEU 5 139 " --> pdb=" O LYS 5 135 " (cutoff:3.500A) Processing helix chain '5' and resid 150 through 162 Processing helix chain '5' and resid 173 through 193 Proline residue: 5 178 - end of helix removed outlier: 4.541A pdb=" N ILE 5 192 " --> pdb=" O CYS 5 188 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N LEU 5 193 " --> pdb=" O LYS 5 189 " (cutoff:3.500A) Processing helix chain '5' and resid 196 through 199 Processing helix chain '5' and resid 242 through 249 removed outlier: 4.110A pdb=" N LYS 5 249 " --> pdb=" O ILE 5 245 " (cutoff:3.500A) Processing helix chain '5' and resid 306 through 329 Processing helix chain '5' and resid 409 through 418 Processing helix chain '6' and resid 55 through 66 Processing helix chain '6' and resid 74 through 78 Processing helix chain '6' and resid 100 through 114 Processing helix chain '6' and resid 117 through 124 Processing helix chain '6' and resid 132 through 141 Processing helix chain '6' and resid 144 through 154 Processing helix chain '6' and resid 158 through 161 No H-bonds generated for 'chain '6' and resid 158 through 161' Processing helix chain '6' and resid 300 through 306 Processing helix chain '6' and resid 325 through 332 Processing helix chain '6' and resid 363 through 368 Processing helix chain '7' and resid 37 through 57 Processing helix chain '7' and resid 88 through 95 Processing helix chain '7' and resid 97 through 101 removed outlier: 4.183A pdb=" N ARG 7 101 " --> pdb=" O TRP 7 98 " (cutoff:3.500A) Processing helix chain '7' and resid 108 through 110 No H-bonds generated for 'chain '7' and resid 108 through 110' Processing helix chain '7' and resid 136 through 155 Processing helix chain '7' and resid 174 through 176 No H-bonds generated for 'chain '7' and resid 174 through 176' Processing helix chain '7' and resid 187 through 189 No H-bonds generated for 'chain '7' and resid 187 through 189' Processing helix chain '7' and resid 196 through 212 Processing helix chain '7' and resid 223 through 229 Processing helix chain '7' and resid 234 through 244 Processing helix chain '7' and resid 272 through 274 No H-bonds generated for 'chain '7' and resid 272 through 274' Processing helix chain '7' and resid 310 through 319 Processing helix chain '8' and resid 108 through 153 Processing helix chain '8' and resid 158 through 161 No H-bonds generated for 'chain '8' and resid 158 through 161' Processing helix chain '8' and resid 166 through 168 No H-bonds generated for 'chain '8' and resid 166 through 168' Processing helix chain '9' and resid 28 through 33 Processing helix chain '9' and resid 88 through 104 Proline residue: 9 98 - end of helix Processing helix chain '9' and resid 115 through 117 No H-bonds generated for 'chain '9' and resid 115 through 117' Processing helix chain 'a' and resid 105 through 116 Processing helix chain 'a' and resid 128 through 132 Processing helix chain 'b' and resid 41 through 49 Processing helix chain 'b' and resid 51 through 57 Processing helix chain 'b' and resid 94 through 106 Processing helix chain 'b' and resid 140 through 142 No H-bonds generated for 'chain 'b' and resid 140 through 142' Processing helix chain 'c' and resid 36 through 52 Processing helix chain 'c' and resid 60 through 62 No H-bonds generated for 'chain 'c' and resid 60 through 62' Processing helix chain 'c' and resid 68 through 78 Processing helix chain 'c' and resid 85 through 91 Processing helix chain 'c' and resid 95 through 106 removed outlier: 4.138A pdb=" N GLN c 106 " --> pdb=" O GLU c 102 " (cutoff:3.500A) Processing helix chain 'c' and resid 123 through 144 Processing helix chain 'c' and resid 150 through 160 Processing helix chain 'c' and resid 163 through 170 Processing helix chain 'c' and resid 188 through 218 Proline residue: c 208 - end of helix Processing helix chain 'c' and resid 220 through 223 Processing helix chain 'c' and resid 228 through 231 No H-bonds generated for 'chain 'c' and resid 228 through 231' Processing helix chain 'c' and resid 237 through 247 Processing helix chain 'c' and resid 289 through 305 Processing helix chain 'd' and resid 53 through 63 Processing helix chain 'd' and resid 120 through 126 Processing helix chain 'd' and resid 137 through 153 Processing helix chain 'd' and resid 157 through 163 Processing helix chain 'd' and resid 169 through 173 Processing helix chain 'e' and resid 65 through 80 Processing helix chain 'e' and resid 86 through 89 No H-bonds generated for 'chain 'e' and resid 86 through 89' Processing helix chain 'e' and resid 92 through 103 Processing helix chain 'e' and resid 117 through 130 Processing helix chain 'e' and resid 184 through 194 Processing helix chain 'e' and resid 258 through 263 removed outlier: 3.568A pdb=" N ASP e 262 " --> pdb=" O ASP e 258 " (cutoff:3.500A) Processing helix chain 'e' and resid 272 through 274 No H-bonds generated for 'chain 'e' and resid 272 through 274' Processing helix chain 'f' and resid 60 through 62 No H-bonds generated for 'chain 'f' and resid 60 through 62' Processing helix chain 'f' and resid 100 through 115 Processing helix chain 'f' and resid 164 through 176 Processing helix chain 'g' and resid 45 through 49 Processing helix chain 'g' and resid 117 through 127 Processing helix chain 'g' and resid 154 through 164 Processing helix chain 'h' and resid 66 through 77 Processing helix chain 'h' and resid 86 through 88 No H-bonds generated for 'chain 'h' and resid 86 through 88' Processing helix chain 'h' and resid 94 through 108 Processing helix chain 'h' and resid 123 through 130 Processing helix chain 'h' and resid 139 through 143 removed outlier: 4.542A pdb=" N LEU h 143 " --> pdb=" O PHE h 140 " (cutoff:3.500A) Processing helix chain 'i' and resid 49 through 52 No H-bonds generated for 'chain 'i' and resid 49 through 52' Processing helix chain 'i' and resid 70 through 72 No H-bonds generated for 'chain 'i' and resid 70 through 72' Processing helix chain 'i' and resid 78 through 80 No H-bonds generated for 'chain 'i' and resid 78 through 80' Processing helix chain 'i' and resid 87 through 101 removed outlier: 6.527A pdb=" N SER i 100 " --> pdb=" O LYS i 96 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ARG i 101 " --> pdb=" O MET i 97 " (cutoff:3.500A) Processing helix chain 'i' and resid 104 through 121 Processing helix chain 'j' and resid 27 through 30 No H-bonds generated for 'chain 'j' and resid 27 through 30' Processing helix chain 'j' and resid 42 through 45 No H-bonds generated for 'chain 'j' and resid 42 through 45' Processing helix chain 'j' and resid 61 through 104 Processing helix chain 'k' and resid 28 through 36 Processing helix chain 'k' and resid 40 through 43 No H-bonds generated for 'chain 'k' and resid 40 through 43' Processing helix chain 'k' and resid 83 through 95 Processing helix chain 'l' and resid 115 through 132 Processing helix chain 'o' and resid 29 through 48 Processing helix chain 'o' and resid 64 through 80 removed outlier: 3.594A pdb=" N SER o 80 " --> pdb=" O ALA o 76 " (cutoff:3.500A) Processing helix chain 'o' and resid 88 through 98 removed outlier: 4.372A pdb=" N VAL o 97 " --> pdb=" O ASP o 93 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N THR o 98 " --> pdb=" O HIS o 94 " (cutoff:3.500A) Processing helix chain 'p' and resid 45 through 48 No H-bonds generated for 'chain 'p' and resid 45 through 48' Processing helix chain 'p' and resid 56 through 58 No H-bonds generated for 'chain 'p' and resid 56 through 58' Processing helix chain 'p' and resid 113 through 122 Processing helix chain 'p' and resid 124 through 126 No H-bonds generated for 'chain 'p' and resid 124 through 126' Processing helix chain 'p' and resid 143 through 162 Processing helix chain 'p' and resid 175 through 188 Processing helix chain 'q' and resid 54 through 68 removed outlier: 7.558A pdb=" N ALA q 66 " --> pdb=" O ALA q 62 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N ALA q 67 " --> pdb=" O ARG q 63 " (cutoff:3.500A) Processing helix chain 'q' and resid 72 through 74 No H-bonds generated for 'chain 'q' and resid 72 through 74' Processing helix chain 'q' and resid 79 through 92 Processing helix chain 'q' and resid 96 through 149 Proline residue: q 129 - end of helix Processing helix chain 'r' and resid 71 through 75 Processing helix chain 'r' and resid 86 through 92 removed outlier: 4.098A pdb=" N PHE r 92 " --> pdb=" O LEU r 88 " (cutoff:3.500A) Processing helix chain 'r' and resid 102 through 105 No H-bonds generated for 'chain 'r' and resid 102 through 105' Processing helix chain 'r' and resid 109 through 123 Processing helix chain 'r' and resid 156 through 158 No H-bonds generated for 'chain 'r' and resid 156 through 158' Processing helix chain 'r' and resid 179 through 181 No H-bonds generated for 'chain 'r' and resid 179 through 181' Processing helix chain 's' and resid 56 through 71 Processing helix chain 's' and resid 76 through 84 Processing helix chain 's' and resid 102 through 110 Processing helix chain 's' and resid 141 through 154 Processing helix chain 's' and resid 168 through 171 No H-bonds generated for 'chain 's' and resid 168 through 171' Processing helix chain 's' and resid 173 through 188 Processing helix chain 's' and resid 193 through 196 No H-bonds generated for 'chain 's' and resid 193 through 196' Processing helix chain 's' and resid 304 through 306 No H-bonds generated for 'chain 's' and resid 304 through 306' Processing helix chain 's' and resid 308 through 313 Processing helix chain 's' and resid 318 through 343 removed outlier: 3.988A pdb=" N GLU s 321 " --> pdb=" O ASP s 318 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE s 324 " --> pdb=" O GLU s 321 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN s 327 " --> pdb=" O PHE s 324 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA s 330 " --> pdb=" O ASN s 327 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER s 331 " --> pdb=" O ALA s 328 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU s 332 " --> pdb=" O ILE s 329 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR s 336 " --> pdb=" O PHE s 333 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET s 341 " --> pdb=" O ALA s 338 " (cutoff:3.500A) Processing helix chain 's' and resid 416 through 425 Processing helix chain 'u' and resid 94 through 103 Processing helix chain 'u' and resid 132 through 149 Processing helix chain 'u' and resid 182 through 188 Processing helix chain 'u' and resid 190 through 193 No H-bonds generated for 'chain 'u' and resid 190 through 193' Processing helix chain 'v' and resid 6 through 21 removed outlier: 4.449A pdb=" N LEU v 10 " --> pdb=" O ARG v 6 " (cutoff:3.500A) Processing helix chain 'v' and resid 28 through 39 Processing helix chain 'v' and resid 48 through 63 Processing helix chain 'w' and resid 76 through 89 Processing helix chain 'w' and resid 112 through 123 Processing helix chain 'w' and resid 132 through 135 No H-bonds generated for 'chain 'w' and resid 132 through 135' Processing helix chain 'w' and resid 141 through 151 Processing sheet with id= A, first strand: chain 'D' and resid 122 through 125 Processing sheet with id= B, first strand: chain 'D' and resid 139 through 144 Processing sheet with id= C, first strand: chain 'D' and resid 181 through 183 Processing sheet with id= D, first strand: chain 'D' and resid 233 through 236 removed outlier: 6.388A pdb=" N GLN D 227 " --> pdb=" O LEU D 216 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N LEU D 216 " --> pdb=" O GLN D 227 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 265 through 268 removed outlier: 5.316A pdb=" N LYS E 209 " --> pdb=" O LEU E 296 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LEU E 296 " --> pdb=" O LYS E 209 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU E 121 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ASN E 286 " --> pdb=" O VAL E 273 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL E 273 " --> pdb=" O ASN E 286 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 175 through 181 removed outlier: 6.191A pdb=" N GLY E 148 " --> pdb=" O VAL E 129 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N VAL E 129 " --> pdb=" O GLY E 148 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 214 through 216 Processing sheet with id= H, first strand: chain 'F' and resid 62 through 65 Processing sheet with id= I, first strand: chain 'F' and resid 187 through 190 removed outlier: 6.537A pdb=" N LEU F 259 " --> pdb=" O HIS F 188 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N MET F 190 " --> pdb=" O LEU F 259 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU F 261 " --> pdb=" O MET F 190 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'H' and resid 111 through 114 Processing sheet with id= K, first strand: chain 'H' and resid 54 through 58 removed outlier: 6.406A pdb=" N GLU H 57 " --> pdb=" O LEU H 82 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N LEU H 82 " --> pdb=" O GLU H 57 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'I' and resid 122 through 124 Processing sheet with id= M, first strand: chain 'I' and resid 179 through 181 Processing sheet with id= N, first strand: chain 'J' and resid 110 through 113 Processing sheet with id= O, first strand: chain 'K' and resid 125 through 127 removed outlier: 6.638A pdb=" N VAL K 57 " --> pdb=" O HIS K 126 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N TYR K 19 " --> pdb=" O VAL K 58 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N MET K 60 " --> pdb=" O TYR K 19 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU K 21 " --> pdb=" O MET K 60 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N LEU K 20 " --> pdb=" O VAL K 142 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N GLU K 144 " --> pdb=" O LEU K 20 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ASP K 22 " --> pdb=" O GLU K 144 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'K' and resid 76 through 80 Processing sheet with id= Q, first strand: chain 'L' and resid 72 through 77 Processing sheet with id= R, first strand: chain 'M' and resid 94 through 97 Processing sheet with id= S, first strand: chain 'M' and resid 153 through 156 removed outlier: 6.267A pdb=" N VAL M 173 " --> pdb=" O ILE M 154 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N VAL M 156 " --> pdb=" O VAL M 173 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N THR M 175 " --> pdb=" O VAL M 156 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'M' and resid 274 through 276 Processing sheet with id= U, first strand: chain 'N' and resid 87 through 91 Processing sheet with id= V, first strand: chain 'N' and resid 95 through 97 Processing sheet with id= W, first strand: chain 'N' and resid 118 through 122 Processing sheet with id= X, first strand: chain 'N' and resid 129 through 132 Processing sheet with id= Y, first strand: chain 'O' and resid 41 through 45 removed outlier: 4.396A pdb=" N MET O 120 " --> pdb=" O ILE O 110 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'P' and resid 80 through 85 Processing sheet with id= AA, first strand: chain 'Q' and resid 173 through 178 removed outlier: 6.867A pdb=" N ILE Q 116 " --> pdb=" O VAL Q 177 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N LEU Q 134 " --> pdb=" O VAL Q 154 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL Q 154 " --> pdb=" O LEU Q 134 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE Q 150 " --> pdb=" O ILE Q 138 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'S' and resid 106 through 109 Processing sheet with id= AC, first strand: chain 'S' and resid 112 through 116 Processing sheet with id= AD, first strand: chain 'S' and resid 127 through 129 removed outlier: 6.591A pdb=" N THR S 159 " --> pdb=" O ILE S 195 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ILE S 195 " --> pdb=" O THR S 159 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'S' and resid 169 through 175 Processing sheet with id= AF, first strand: chain 'T' and resid 72 through 77 removed outlier: 6.475A pdb=" N VAL T 179 " --> pdb=" O ILE T 142 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N ILE T 142 " --> pdb=" O VAL T 179 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'T' and resid 153 through 155 Processing sheet with id= AH, first strand: chain 'U' and resid 39 through 44 Processing sheet with id= AI, first strand: chain 'V' and resid 120 through 122 removed outlier: 6.894A pdb=" N VAL V 87 " --> pdb=" O VAL V 77 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N VAL V 79 " --> pdb=" O TRP V 85 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TRP V 85 " --> pdb=" O VAL V 79 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'V' and resid 96 through 98 Processing sheet with id= AK, first strand: chain 'V' and resid 133 through 136 removed outlier: 3.632A pdb=" N ARG V 136 " --> pdb=" O VAL V 144 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL V 144 " --> pdb=" O ARG V 136 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'W' and resid 95 through 103 Processing sheet with id= AM, first strand: chain 'X' and resid 50 through 52 Processing sheet with id= AN, first strand: chain 'X' and resid 86 through 91 Processing sheet with id= AO, first strand: chain 'X' and resid 110 through 116 Processing sheet with id= AP, first strand: chain 'Y' and resid 166 through 170 Processing sheet with id= AQ, first strand: chain 'Z' and resid 98 through 101 Processing sheet with id= AR, first strand: chain '0' and resid 107 through 109 Processing sheet with id= AS, first strand: chain '0' and resid 156 through 158 removed outlier: 5.981A pdb=" N ARG 0 173 " --> pdb=" O VAL 0 157 " (cutoff:3.500A) No H-bonds generated for sheet with id= AS Processing sheet with id= AT, first strand: chain '1' and resid 29 through 35 removed outlier: 5.502A pdb=" N ARG 1 19 " --> pdb=" O LYS 1 61 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LYS 1 61 " --> pdb=" O ARG 1 19 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain '1' and resid 42 through 47 Processing sheet with id= AV, first strand: chain '5' and resid 266 through 268 removed outlier: 7.042A pdb=" N LEU 5 219 " --> pdb=" O TYR 5 105 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N PHE 5 107 " --> pdb=" O LEU 5 219 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N GLN 5 221 " --> pdb=" O PHE 5 107 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain '5' and resid 126 through 130 removed outlier: 7.423A pdb=" N ASN 5 372 " --> pdb=" O LYS 5 127 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N ILE 5 129 " --> pdb=" O ASN 5 372 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ALA 5 374 " --> pdb=" O ILE 5 129 " (cutoff:3.500A) removed outlier: 10.239A pdb=" N VAL 5 341 " --> pdb=" O TYR 5 287 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N HIS 5 289 " --> pdb=" O VAL 5 341 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU 5 230 " --> pdb=" O HIS 5 289 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain '5' and resid 385 through 387 Processing sheet with id= AY, first strand: chain '6' and resid 203 through 206 Processing sheet with id= AZ, first strand: chain '6' and resid 214 through 220 removed outlier: 5.574A pdb=" N LYS 6 274 " --> pdb=" O PRO 6 313 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain '6' and resid 236 through 238 removed outlier: 4.350A pdb=" N LEU 6 236 " --> pdb=" O CYS 6 252 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N CYS 6 252 " --> pdb=" O LEU 6 236 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THR 6 238 " --> pdb=" O VAL 6 250 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N VAL 6 250 " --> pdb=" O THR 6 238 " (cutoff:3.500A) No H-bonds generated for sheet with id= BA Processing sheet with id= BB, first strand: chain '7' and resid 64 through 69 Processing sheet with id= BC, first strand: chain '7' and resid 106 through 108 Processing sheet with id= BD, first strand: chain '7' and resid 282 through 285 removed outlier: 6.414A pdb=" N VAL 7 184 " --> pdb=" O LEU 7 166 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N LEU 7 166 " --> pdb=" O VAL 7 184 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain '7' and resid 217 through 222 Processing sheet with id= BF, first strand: chain '7' and resid 275 through 280 removed outlier: 6.565A pdb=" N LEU 7 302 " --> pdb=" O PHE 7 276 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N TYR 7 278 " --> pdb=" O VAL 7 300 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N VAL 7 300 " --> pdb=" O TYR 7 278 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain '9' and resid 42 through 45 Processing sheet with id= BH, first strand: chain 'a' and resid 45 through 51 Processing sheet with id= BI, first strand: chain 'b' and resid 28 through 31 removed outlier: 6.717A pdb=" N VAL b 62 " --> pdb=" O LEU b 29 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N PHE b 31 " --> pdb=" O VAL b 62 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N TYR b 64 " --> pdb=" O PHE b 31 " (cutoff:3.500A) No H-bonds generated for sheet with id= BI Processing sheet with id= BJ, first strand: chain 'b' and resid 74 through 78 Processing sheet with id= BK, first strand: chain 'c' and resid 254 through 259 removed outlier: 6.459A pdb=" N PHE c 271 " --> pdb=" O THR c 258 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N CYS c 276 " --> pdb=" O LEU c 280 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N LEU c 280 " --> pdb=" O CYS c 276 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'd' and resid 184 through 186 removed outlier: 5.573A pdb=" N GLU d 249 " --> pdb=" O MET d 261 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N MET d 261 " --> pdb=" O GLU d 249 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'd' and resid 193 through 196 removed outlier: 6.496A pdb=" N THR d 213 " --> pdb=" O VAL d 195 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'e' and resid 175 through 177 removed outlier: 7.291A pdb=" N GLY e 228 " --> pdb=" O ARG e 46 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N LEU e 48 " --> pdb=" O GLY e 228 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N LYS e 230 " --> pdb=" O LEU e 48 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ALA e 50 " --> pdb=" O LYS e 230 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N PHE e 232 " --> pdb=" O ALA e 50 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'e' and resid 161 through 164 Processing sheet with id= BP, first strand: chain 'e' and resid 199 through 203 removed outlier: 5.723A pdb=" N LYS e 203 " --> pdb=" O LEU e 238 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LEU e 238 " --> pdb=" O LYS e 203 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'f' and resid 93 through 97 Processing sheet with id= BR, first strand: chain 'g' and resid 84 through 86 Processing sheet with id= BS, first strand: chain 'g' and resid 96 through 101 Processing sheet with id= BT, first strand: chain 'k' and resid 50 through 55 Processing sheet with id= BU, first strand: chain 'm' and resid 64 through 68 Processing sheet with id= BV, first strand: chain 'p' and resid 77 through 80 Processing sheet with id= BW, first strand: chain 'r' and resid 36 through 41 Processing sheet with id= BX, first strand: chain 's' and resid 274 through 276 removed outlier: 4.702A pdb=" N PHE s 274 " --> pdb=" O MET s 92 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ASP s 234 " --> pdb=" O VAL s 93 " (cutoff:3.500A) Processing sheet with id= BY, first strand: chain 's' and resid 112 through 116 removed outlier: 6.769A pdb=" N ASN s 391 " --> pdb=" O VAL s 113 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N LEU s 115 " --> pdb=" O ASN s 391 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N CYS s 393 " --> pdb=" O LEU s 115 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLN s 298 " --> pdb=" O VAL s 360 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N THR s 362 " --> pdb=" O GLN s 298 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N HIS s 300 " --> pdb=" O THR s 362 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 'u' and resid 108 through 113 2088 hydrogen bonds defined for protein. 5871 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 747 hydrogen bonds 1288 hydrogen bond angles 0 basepair planarities 308 basepair parallelities 601 stacking parallelities Total time for adding SS restraints: 48.08 Time building geometry restraints manager: 34.23 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: 12179 1.32 - 1.44: 32275 1.44 - 1.57: 47834 1.57 - 1.70: 2272 1.70 - 1.83: 449 Bond restraints: 95009 Sorted by residual: bond pdb=" C VAL N 151 " pdb=" N THR N 152 " ideal model delta sigma weight residual 1.331 1.490 -0.159 2.07e-02 2.33e+03 5.91e+01 bond pdb=" CA THR M 149 " pdb=" CB THR M 149 " ideal model delta sigma weight residual 1.527 1.629 -0.102 2.48e-02 1.63e+03 1.69e+01 bond pdb=" CG PRO Q 228 " pdb=" CD PRO Q 228 " ideal model delta sigma weight residual 1.503 1.369 0.134 3.40e-02 8.65e+02 1.55e+01 bond pdb=" CB PRO Q 228 " pdb=" CG PRO Q 228 " ideal model delta sigma weight residual 1.492 1.657 -0.165 5.00e-02 4.00e+02 1.09e+01 bond pdb=" C GLU D 199 " pdb=" N PRO D 200 " ideal model delta sigma weight residual 1.331 1.364 -0.033 1.20e-02 6.94e+03 7.56e+00 ... (remaining 95004 not shown) Histogram of bond angle deviations from ideal: 92.61 - 102.16: 1320 102.16 - 111.71: 49169 111.71 - 121.25: 57738 121.25 - 130.80: 24769 130.80 - 140.35: 876 Bond angle restraints: 133872 Sorted by residual: angle pdb=" C MET Q 204 " pdb=" N LYS Q 205 " pdb=" CA LYS Q 205 " ideal model delta sigma weight residual 120.65 140.35 -19.70 1.36e+00 5.41e-01 2.10e+02 angle pdb=" CA PRO Q 228 " pdb=" N PRO Q 228 " pdb=" CD PRO Q 228 " ideal model delta sigma weight residual 112.00 97.13 14.87 1.40e+00 5.10e-01 1.13e+02 angle pdb=" CA PRO 6 169 " pdb=" N PRO 6 169 " pdb=" CD PRO 6 169 " ideal model delta sigma weight residual 112.00 99.15 12.85 1.40e+00 5.10e-01 8.43e+01 angle pdb=" C ARG X 36 " pdb=" N THR X 37 " pdb=" CA THR X 37 " ideal model delta sigma weight residual 120.49 130.69 -10.20 1.42e+00 4.96e-01 5.16e+01 angle pdb=" N PRO Q 228 " pdb=" CD PRO Q 228 " pdb=" CG PRO Q 228 " ideal model delta sigma weight residual 103.20 92.61 10.59 1.50e+00 4.44e-01 4.98e+01 ... (remaining 133867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 53639 35.94 - 71.88: 1366 71.88 - 107.81: 96 107.81 - 143.75: 10 143.75 - 179.69: 30 Dihedral angle restraints: 55141 sinusoidal: 31520 harmonic: 23621 Sorted by residual: dihedral pdb=" C4' A A 135 " pdb=" C3' A A 135 " pdb=" C2' A A 135 " pdb=" C1' A A 135 " ideal model delta sinusoidal sigma weight residual -35.00 33.78 -68.78 1 8.00e+00 1.56e-02 9.57e+01 dihedral pdb=" C5' A A 135 " pdb=" C4' A A 135 " pdb=" C3' A A 135 " pdb=" O3' A A 135 " ideal model delta sinusoidal sigma weight residual 147.00 78.49 68.51 1 8.00e+00 1.56e-02 9.50e+01 dihedral pdb=" O4' C A 396 " pdb=" C1' C A 396 " pdb=" N1 C A 396 " pdb=" C2 C A 396 " ideal model delta sinusoidal sigma weight residual 200.00 25.44 174.56 1 1.50e+01 4.44e-03 8.51e+01 ... (remaining 55138 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 13988 0.078 - 0.156: 1428 0.156 - 0.233: 93 0.233 - 0.311: 13 0.311 - 0.389: 9 Chirality restraints: 15531 Sorted by residual: chirality pdb=" C3' U A 110 " pdb=" C4' U A 110 " pdb=" O3' U A 110 " pdb=" C2' U A 110 " both_signs ideal model delta sigma weight residual False -2.74 -2.36 -0.39 2.00e-01 2.50e+01 3.78e+00 chirality pdb=" CB ILE u 126 " pdb=" CA ILE u 126 " pdb=" CG1 ILE u 126 " pdb=" CG2 ILE u 126 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.52e+00 chirality pdb=" C3' A A 573 " pdb=" C4' A A 573 " pdb=" O3' A A 573 " pdb=" C2' A A 573 " both_signs ideal model delta sigma weight residual False -2.74 -2.38 -0.36 2.00e-01 2.50e+01 3.28e+00 ... (remaining 15528 not shown) Planarity restraints: 12945 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL 6 168 " -0.125 5.00e-02 4.00e+02 1.79e-01 5.12e+01 pdb=" N PRO 6 169 " 0.309 5.00e-02 4.00e+02 pdb=" CA PRO 6 169 " -0.099 5.00e-02 4.00e+02 pdb=" CD PRO 6 169 " -0.085 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP X 180 " 0.101 5.00e-02 4.00e+02 1.48e-01 3.50e+01 pdb=" N PRO X 181 " -0.256 5.00e-02 4.00e+02 pdb=" CA PRO X 181 " 0.078 5.00e-02 4.00e+02 pdb=" CD PRO X 181 " 0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU s 174 " 0.088 5.00e-02 4.00e+02 1.28e-01 2.60e+01 pdb=" N PRO s 175 " -0.220 5.00e-02 4.00e+02 pdb=" CA PRO s 175 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO s 175 " 0.068 5.00e-02 4.00e+02 ... (remaining 12942 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.24: 37 2.24 - 2.90: 32653 2.90 - 3.57: 128679 3.57 - 4.23: 237032 4.23 - 4.90: 361539 Nonbonded interactions: 759940 Sorted by model distance: nonbonded pdb=" OG SER w 112 " pdb=" O26 PNS v 101 " model vdw 1.574 2.432 nonbonded pdb=" N4 C A 662 " pdb=" O4 U A 772 " model vdw 1.999 2.520 nonbonded pdb=" CA MET E 106 " pdb=" O VAL E 119 " model vdw 1.999 3.470 nonbonded pdb=" OP2 G A 106 " pdb="MG MG A1604 " model vdw 2.085 2.170 nonbonded pdb=" OP1 C A1245 " pdb="MG MG A1634 " model vdw 2.090 2.170 ... (remaining 759935 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 Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 1149 5.49 5 Mg 49 5.21 5 S 282 5.16 5 C 53168 2.51 5 N 16469 2.21 5 O 19480 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.720 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: 15.760 Check model and map are aligned: 1.040 Convert atoms to be neutral: 0.620 Process input model: 226.560 Find NCS groups from input model: 2.760 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Set scattering table: 0.050 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 253.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.165 95009 Z= 0.257 Angle : 0.873 19.698 133872 Z= 0.460 Chirality : 0.047 0.389 15531 Planarity : 0.007 0.179 12945 Dihedral : 15.158 179.688 39835 Min Nonbonded Distance : 1.574 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.93 % Favored : 96.05 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.09), residues: 7945 helix: -0.56 (0.09), residues: 2685 sheet: -0.94 (0.16), residues: 1008 loop : -1.07 (0.09), residues: 4252 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15890 Ramachandran restraints generated. 7945 Oldfield, 0 Emsley, 7945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15890 Ramachandran restraints generated. 7945 Oldfield, 0 Emsley, 7945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1385 residues out of total 7169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1381 time to evaluate : 6.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 1383 average time/residue: 0.8508 time to fit residues: 1972.9966 Evaluate side-chains 1078 residues out of total 7169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1078 time to evaluate : 6.884 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.9383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 899 random chunks: chunk 759 optimal weight: 0.9980 chunk 681 optimal weight: 1.9990 chunk 378 optimal weight: 5.9990 chunk 232 optimal weight: 0.0770 chunk 459 optimal weight: 8.9990 chunk 364 optimal weight: 2.9990 chunk 704 optimal weight: 2.9990 chunk 272 optimal weight: 2.9990 chunk 428 optimal weight: 7.9990 chunk 524 optimal weight: 6.9990 chunk 816 optimal weight: 5.9990 overall best weight: 1.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 ASN D 205 GLN D 252 HIS F 257 GLN N 222 ASN O 91 GLN ** O 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 175 GLN ** S 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 195 HIS U 23 ASN U 103 GLN W 41 ASN X 89 GLN ** Z 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 353 HIS 6 359 HIS 7 55 GLN 7 84 ASN 7 232 HIS c 155 ASN c 193 GLN c 249 ASN d 161 HIS ** e 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 155 GLN ** r 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 358 GLN s 397 GLN ** v 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.084 95009 Z= 0.249 Angle : 0.624 16.151 133872 Z= 0.312 Chirality : 0.040 0.333 15531 Planarity : 0.006 0.130 12945 Dihedral : 14.241 179.834 22724 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.41 % Favored : 96.56 % Rotamer Outliers : 1.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.09), residues: 7945 helix: 0.19 (0.10), residues: 2700 sheet: -0.88 (0.15), residues: 1059 loop : -0.85 (0.09), residues: 4186 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15890 Ramachandran restraints generated. 7945 Oldfield, 0 Emsley, 7945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15890 Ramachandran restraints generated. 7945 Oldfield, 0 Emsley, 7945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1230 residues out of total 7169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 1124 time to evaluate : 6.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 106 outliers final: 71 residues processed: 1174 average time/residue: 0.8434 time to fit residues: 1670.8703 Evaluate side-chains 1087 residues out of total 7169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 1016 time to evaluate : 6.659 Switching outliers to nearest non-outliers outliers start: 71 outliers final: 0 residues processed: 71 average time/residue: 0.6492 time to fit residues: 95.1288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 899 random chunks: chunk 453 optimal weight: 10.0000 chunk 253 optimal weight: 10.0000 chunk 679 optimal weight: 5.9990 chunk 555 optimal weight: 1.9990 chunk 225 optimal weight: 7.9990 chunk 817 optimal weight: 5.9990 chunk 883 optimal weight: 10.0000 chunk 728 optimal weight: 5.9990 chunk 811 optimal weight: 10.0000 chunk 278 optimal weight: 0.0970 chunk 656 optimal weight: 2.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 HIS H 88 HIS M 170 ASN O 91 GLN ** O 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 146 ASN P 79 HIS Q 175 GLN ** S 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 74 HIS U 101 HIS ** Y 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 384 GLN 7 84 ASN a 71 HIS d 149 HIS ** e 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 65 HIS k 19 GLN ** p 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 240 GLN v 19 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.096 95009 Z= 0.393 Angle : 0.703 19.470 133872 Z= 0.351 Chirality : 0.044 0.356 15531 Planarity : 0.006 0.124 12945 Dihedral : 14.339 179.096 22724 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.88 % Favored : 96.10 % Rotamer Outliers : 1.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.09), residues: 7945 helix: 0.31 (0.10), residues: 2705 sheet: -0.81 (0.16), residues: 1036 loop : -0.78 (0.09), residues: 4204 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15890 Ramachandran restraints generated. 7945 Oldfield, 0 Emsley, 7945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15890 Ramachandran restraints generated. 7945 Oldfield, 0 Emsley, 7945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1199 residues out of total 7169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 1077 time to evaluate : 6.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 122 outliers final: 64 residues processed: 1152 average time/residue: 0.8515 time to fit residues: 1657.3151 Evaluate side-chains 1055 residues out of total 7169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 991 time to evaluate : 6.688 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 0 residues processed: 64 average time/residue: 0.6653 time to fit residues: 88.0630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 899 random chunks: chunk 808 optimal weight: 10.0000 chunk 614 optimal weight: 20.0000 chunk 424 optimal weight: 6.9990 chunk 90 optimal weight: 20.0000 chunk 390 optimal weight: 7.9990 chunk 549 optimal weight: 1.9990 chunk 820 optimal weight: 4.9990 chunk 868 optimal weight: 20.0000 chunk 428 optimal weight: 7.9990 chunk 777 optimal weight: 50.0000 chunk 234 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 GLN D 252 HIS ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 184 ASN K 160 GLN L 59 HIS ** L 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 99 ASN S 75 HIS ** S 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 133 ASN U 41 GLN Y 99 HIS Y 110 ASN ** Z 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 126 GLN 5 96 HIS ** 5 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 295 GLN 6 354 GLN 7 84 ASN 7 232 HIS ** 9 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 137 ASN b 24 GLN d 161 HIS ** e 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 59 ASN ** p 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 60 GLN q 134 ASN s 314 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.186 95009 Z= 0.643 Angle : 0.841 19.705 133872 Z= 0.416 Chirality : 0.050 0.354 15531 Planarity : 0.007 0.131 12945 Dihedral : 14.619 179.651 22724 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.61 % Favored : 95.37 % Rotamer Outliers : 2.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.09), residues: 7945 helix: 0.17 (0.10), residues: 2699 sheet: -0.80 (0.16), residues: 1058 loop : -0.92 (0.10), residues: 4188 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15890 Ramachandran restraints generated. 7945 Oldfield, 0 Emsley, 7945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15890 Ramachandran restraints generated. 7945 Oldfield, 0 Emsley, 7945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1280 residues out of total 7169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 1067 time to evaluate : 9.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 213 outliers final: 113 residues processed: 1198 average time/residue: 0.8590 time to fit residues: 1740.9111 Evaluate side-chains 1108 residues out of total 7169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 995 time to evaluate : 6.704 Switching outliers to nearest non-outliers outliers start: 113 outliers final: 0 residues processed: 113 average time/residue: 0.6594 time to fit residues: 149.0090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 899 random chunks: chunk 723 optimal weight: 0.7980 chunk 493 optimal weight: 5.9990 chunk 12 optimal weight: 50.0000 chunk 647 optimal weight: 10.0000 chunk 358 optimal weight: 1.9990 chunk 741 optimal weight: 0.8980 chunk 600 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 443 optimal weight: 2.9990 chunk 779 optimal weight: 50.0000 chunk 219 optimal weight: 6.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 59 HIS ** L 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 139 GLN Q 175 GLN ** S 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 103 GLN Y 110 ASN ** Z 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 156 ASN ** 5 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 354 GLN ** 9 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 137 ASN b 120 HIS b 129 GLN c 249 ASN ** e 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 58 GLN ** p 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.083 95009 Z= 0.304 Angle : 0.656 16.251 133872 Z= 0.326 Chirality : 0.042 0.322 15531 Planarity : 0.005 0.125 12945 Dihedral : 14.353 178.232 22724 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.70 % Favored : 96.27 % Rotamer Outliers : 1.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.09), residues: 7945 helix: 0.45 (0.10), residues: 2693 sheet: -0.63 (0.16), residues: 1052 loop : -0.77 (0.10), residues: 4200 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15890 Ramachandran restraints generated. 7945 Oldfield, 0 Emsley, 7945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15890 Ramachandran restraints generated. 7945 Oldfield, 0 Emsley, 7945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1196 residues out of total 7169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 1054 time to evaluate : 6.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 142 outliers final: 61 residues processed: 1139 average time/residue: 0.8506 time to fit residues: 1635.4020 Evaluate side-chains 1064 residues out of total 7169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 1003 time to evaluate : 6.676 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 0 residues processed: 61 average time/residue: 0.7165 time to fit residues: 88.1870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 899 random chunks: chunk 292 optimal weight: 0.9980 chunk 782 optimal weight: 7.9990 chunk 171 optimal weight: 7.9990 chunk 510 optimal weight: 50.0000 chunk 214 optimal weight: 0.8980 chunk 869 optimal weight: 20.0000 chunk 722 optimal weight: 3.9990 chunk 402 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 287 optimal weight: 0.5980 chunk 456 optimal weight: 10.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 HIS F 74 GLN L 59 HIS ** L 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 87 GLN Q 107 HIS Q 139 GLN ** S 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 103 GLN X 108 GLN Y 110 ASN ** Z 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 137 ASN c 172 ASN ** e 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 152 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.099 95009 Z= 0.183 Angle : 0.598 13.298 133872 Z= 0.296 Chirality : 0.039 0.322 15531 Planarity : 0.005 0.135 12945 Dihedral : 14.154 178.556 22724 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.65 % Favored : 96.32 % Rotamer Outliers : 1.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.09), residues: 7945 helix: 0.71 (0.10), residues: 2685 sheet: -0.60 (0.16), residues: 1059 loop : -0.63 (0.10), residues: 4201 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15890 Ramachandran restraints generated. 7945 Oldfield, 0 Emsley, 7945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15890 Ramachandran restraints generated. 7945 Oldfield, 0 Emsley, 7945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1203 residues out of total 7169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 1096 time to evaluate : 6.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 107 outliers final: 52 residues processed: 1147 average time/residue: 0.8853 time to fit residues: 1718.1336 Evaluate side-chains 1077 residues out of total 7169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 1025 time to evaluate : 6.689 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 0 residues processed: 52 average time/residue: 0.6448 time to fit residues: 72.4319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 899 random chunks: chunk 838 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 495 optimal weight: 1.9990 chunk 635 optimal weight: 0.5980 chunk 492 optimal weight: 4.9990 chunk 732 optimal weight: 6.9990 chunk 485 optimal weight: 4.9990 chunk 866 optimal weight: 10.0000 chunk 542 optimal weight: 4.9990 chunk 528 optimal weight: 1.9990 chunk 400 optimal weight: 3.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 115 HIS ** S 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 110 ASN ** Z 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 137 ASN c 193 GLN e 54 GLN ** e 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 60 GLN s 240 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.107 95009 Z= 0.271 Angle : 0.628 15.629 133872 Z= 0.311 Chirality : 0.041 0.354 15531 Planarity : 0.005 0.135 12945 Dihedral : 14.119 178.305 22724 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.80 % Favored : 96.16 % Rotamer Outliers : 1.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.09), residues: 7945 helix: 0.74 (0.10), residues: 2698 sheet: -0.65 (0.16), residues: 1077 loop : -0.61 (0.10), residues: 4170 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15890 Ramachandran restraints generated. 7945 Oldfield, 0 Emsley, 7945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15890 Ramachandran restraints generated. 7945 Oldfield, 0 Emsley, 7945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1140 residues out of total 7169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 1049 time to evaluate : 6.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 91 outliers final: 51 residues processed: 1105 average time/residue: 0.8632 time to fit residues: 1611.1191 Evaluate side-chains 1066 residues out of total 7169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 1015 time to evaluate : 6.807 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 0 residues processed: 51 average time/residue: 0.6541 time to fit residues: 71.6379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 899 random chunks: chunk 536 optimal weight: 4.9990 chunk 346 optimal weight: 5.9990 chunk 517 optimal weight: 0.8980 chunk 261 optimal weight: 0.7980 chunk 170 optimal weight: 0.0370 chunk 167 optimal weight: 3.9990 chunk 550 optimal weight: 0.9980 chunk 590 optimal weight: 8.9990 chunk 428 optimal weight: 9.9990 chunk 80 optimal weight: 0.8980 chunk 681 optimal weight: 0.7980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 101 ASN ** L 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 210 GLN ** O 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 139 GLN ** S 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 133 ASN ** U 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 110 ASN ** Z 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 137 ASN e 54 GLN e 245 GLN e 248 ASN ** p 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 134 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.121 95009 Z= 0.165 Angle : 0.594 13.909 133872 Z= 0.293 Chirality : 0.038 0.356 15531 Planarity : 0.005 0.124 12945 Dihedral : 14.022 179.962 22724 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.73 % Favored : 96.25 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.10), residues: 7945 helix: 0.89 (0.10), residues: 2679 sheet: -0.61 (0.16), residues: 1069 loop : -0.53 (0.10), residues: 4197 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15890 Ramachandran restraints generated. 7945 Oldfield, 0 Emsley, 7945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15890 Ramachandran restraints generated. 7945 Oldfield, 0 Emsley, 7945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1137 residues out of total 7169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 1089 time to evaluate : 6.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 26 residues processed: 1115 average time/residue: 0.8658 time to fit residues: 1632.2484 Evaluate side-chains 1044 residues out of total 7169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 1018 time to evaluate : 6.690 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.6767 time to fit residues: 41.4816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 899 random chunks: chunk 788 optimal weight: 7.9990 chunk 830 optimal weight: 60.0000 chunk 757 optimal weight: 4.9990 chunk 807 optimal weight: 5.9990 chunk 829 optimal weight: 50.0000 chunk 485 optimal weight: 4.9990 chunk 351 optimal weight: 6.9990 chunk 634 optimal weight: 4.9990 chunk 247 optimal weight: 1.9990 chunk 729 optimal weight: 0.5980 chunk 763 optimal weight: 2.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 139 GLN ** S 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 133 ASN U 4 ASN ** U 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 110 ASN ** Z 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 123 GLN a 137 ASN c 80 GLN e 54 GLN ** e 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 240 GLN s 296 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.404 95009 Z= 0.360 Angle : 0.697 50.667 133872 Z= 0.343 Chirality : 0.042 0.379 15531 Planarity : 0.006 0.149 12945 Dihedral : 14.036 178.708 22724 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.91 % Favored : 96.06 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.10), residues: 7945 helix: 0.78 (0.10), residues: 2696 sheet: -0.62 (0.16), residues: 1074 loop : -0.56 (0.10), residues: 4175 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15890 Ramachandran restraints generated. 7945 Oldfield, 0 Emsley, 7945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15890 Ramachandran restraints generated. 7945 Oldfield, 0 Emsley, 7945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1077 residues out of total 7169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 1033 time to evaluate : 6.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 28 residues processed: 1051 average time/residue: 0.8911 time to fit residues: 1591.2648 Evaluate side-chains 1025 residues out of total 7169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 997 time to evaluate : 6.785 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.6571 time to fit residues: 43.5199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 899 random chunks: chunk 804 optimal weight: 0.5980 chunk 530 optimal weight: 4.9990 chunk 853 optimal weight: 6.9990 chunk 521 optimal weight: 5.9990 chunk 405 optimal weight: 2.9990 chunk 593 optimal weight: 8.9990 chunk 895 optimal weight: 30.0000 chunk 824 optimal weight: 6.9990 chunk 713 optimal weight: 5.9990 chunk 74 optimal weight: 0.0970 chunk 550 optimal weight: 0.8980 overall best weight: 1.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 137 ASN e 54 GLN ** e 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 240 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.337 95009 Z= 0.264 Angle : 0.655 26.251 133872 Z= 0.324 Chirality : 0.040 0.385 15531 Planarity : 0.005 0.147 12945 Dihedral : 14.025 179.476 22724 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.85 % Favored : 96.12 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.10), residues: 7945 helix: 0.84 (0.10), residues: 2677 sheet: -0.59 (0.16), residues: 1062 loop : -0.53 (0.10), residues: 4206 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15890 Ramachandran restraints generated. 7945 Oldfield, 0 Emsley, 7945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15890 Ramachandran restraints generated. 7945 Oldfield, 0 Emsley, 7945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1040 residues out of total 7169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 1021 time to evaluate : 7.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 12 residues processed: 1027 average time/residue: 0.8925 time to fit residues: 1548.9965 Evaluate side-chains 1022 residues out of total 7169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 1010 time to evaluate : 6.708 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.6929 time to fit residues: 24.2488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 899 random chunks: chunk 437 optimal weight: 20.0000 chunk 566 optimal weight: 0.1980 chunk 759 optimal weight: 9.9990 chunk 218 optimal weight: 0.9980 chunk 657 optimal weight: 0.2980 chunk 105 optimal weight: 30.0000 chunk 198 optimal weight: 0.9990 chunk 714 optimal weight: 6.9990 chunk 298 optimal weight: 0.0980 chunk 733 optimal weight: 10.0000 chunk 90 optimal weight: 50.0000 overall best weight: 0.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 ASN ** E 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 113 ASN ** L 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 137 ASN e 54 GLN ** e 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.196956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.166068 restraints weight = 122323.628| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 1.39 r_work: 0.3850 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.3820 rms_B_bonded: 1.67 restraints_weight: 0.2500 r_work: 0.3788 rms_B_bonded: 2.11 restraints_weight: 0.1250 r_work: 0.3747 rms_B_bonded: 2.74 restraints_weight: 0.0625 r_work: 0.3685 rms_B_bonded: 3.73 restraints_weight: 0.0312 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.258 95009 Z= 0.174 Angle : 0.618 23.144 133872 Z= 0.308 Chirality : 0.038 0.376 15531 Planarity : 0.005 0.162 12945 Dihedral : 13.942 179.835 22724 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.78 % Favored : 96.21 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.10), residues: 7945 helix: 0.99 (0.10), residues: 2668 sheet: -0.57 (0.16), residues: 1040 loop : -0.47 (0.10), residues: 4237 =============================================================================== Job complete usr+sys time: 22939.40 seconds wall clock time: 402 minutes 47.30 seconds (24167.30 seconds total)