Starting phenix.real_space_refine on Tue Feb 20 20:55:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oia_12923/02_2024/7oia_12923.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oia_12923/02_2024/7oia_12923.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oia_12923/02_2024/7oia_12923.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oia_12923/02_2024/7oia_12923.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oia_12923/02_2024/7oia_12923.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oia_12923/02_2024/7oia_12923.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 1220 5.49 5 Mg 49 5.21 5 S 266 5.16 5 C 52663 2.51 5 N 16440 2.21 5 O 19635 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 161": "OD1" <-> "OD2" Residue "D ASP 180": "OD1" <-> "OD2" Residue "D GLU 197": "OE1" <-> "OE2" Residue "D TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 50": "OD1" <-> "OD2" Residue "E GLU 56": "OE1" <-> "OE2" Residue "E ASP 67": "OD1" <-> "OD2" Residue "E GLU 68": "OE1" <-> "OE2" Residue "E ASP 69": "OD1" <-> "OD2" Residue "E GLU 91": "OE1" <-> "OE2" Residue "E ASP 126": "OD1" <-> "OD2" Residue "E ASP 183": "OD1" <-> "OD2" Residue "E PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 268": "OE1" <-> "OE2" Residue "E ASP 309": "OD1" <-> "OD2" Residue "E GLU 325": "OE1" <-> "OE2" Residue "E GLU 335": "OE1" <-> "OE2" Residue "F GLU 75": "OE1" <-> "OE2" Residue "F PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 119": "OE1" <-> "OE2" Residue "F GLU 205": "OE1" <-> "OE2" Residue "F ASP 271": "OD1" <-> "OD2" Residue "F ASP 292": "OD1" <-> "OD2" Residue "H GLU 67": "OE1" <-> "OE2" Residue "H GLU 95": "OE1" <-> "OE2" Residue "H GLU 103": "OE1" <-> "OE2" Residue "H TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 143": "OE1" <-> "OE2" Residue "I GLU 157": "OE1" <-> "OE2" Residue "K GLU 73": "OE1" <-> "OE2" Residue "K PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 135": "OE1" <-> "OE2" Residue "K PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 109": "OE1" <-> "OE2" Residue "M GLU 37": "OE1" <-> "OE2" Residue "M PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 143": "OE1" <-> "OE2" Residue "M GLU 168": "OE1" <-> "OE2" Residue "M GLU 209": "OE1" <-> "OE2" Residue "M TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 235": "OE1" <-> "OE2" Residue "M TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 65": "OE1" <-> "OE2" Residue "N GLU 84": "OE1" <-> "OE2" Residue "N TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 162": "OE1" <-> "OE2" Residue "N GLU 216": "OE1" <-> "OE2" Residue "N TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 43": "OE1" <-> "OE2" Residue "O ASP 67": "OD1" <-> "OD2" Residue "O PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 124": "OE1" <-> "OE2" Residue "P GLU 76": "OE1" <-> "OE2" Residue "P GLU 138": "OE1" <-> "OE2" Residue "P TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 174": "OE1" <-> "OE2" Residue "Q GLU 79": "OE1" <-> "OE2" Residue "Q PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 95": "OE1" <-> "OE2" Residue "Q GLU 196": "OE1" <-> "OE2" Residue "Q TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 234": "OE1" <-> "OE2" Residue "Q PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 266": "OE1" <-> "OE2" Residue "Q PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 272": "OE1" <-> "OE2" Residue "Q TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 274": "OD1" <-> "OD2" Residue "Q GLU 285": "OE1" <-> "OE2" Residue "R TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 126": "OE1" <-> "OE2" Residue "S GLU 78": "OE1" <-> "OE2" Residue "S PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 139": "OD1" <-> "OD2" Residue "S GLU 157": "OE1" <-> "OE2" Residue "S GLU 165": "OE1" <-> "OE2" Residue "T GLU 52": "OE1" <-> "OE2" Residue "T GLU 107": "OE1" <-> "OE2" Residue "T ASP 126": "OD1" <-> "OD2" Residue "T GLU 168": "OE1" <-> "OE2" Residue "T TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 180": "OE1" <-> "OE2" Residue "T GLU 187": "OE1" <-> "OE2" Residue "U PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 58": "OE1" <-> "OE2" Residue "U ASP 109": "OD1" <-> "OD2" Residue "V TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 47": "OE1" <-> "OE2" Residue "V ASP 51": "OD1" <-> "OD2" Residue "V ASP 53": "OD1" <-> "OD2" Residue "V GLU 112": "OE1" <-> "OE2" Residue "V GLU 132": "OE1" <-> "OE2" Residue "V GLU 134": "OE1" <-> "OE2" Residue "V ASP 172": "OD1" <-> "OD2" Residue "V GLU 184": "OE1" <-> "OE2" Residue "V TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 196": "OE1" <-> "OE2" Residue "X TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 18": "OE1" <-> "OE2" Residue "X GLU 34": "OE1" <-> "OE2" Residue "X GLU 35": "OE1" <-> "OE2" Residue "X TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 111": "OE1" <-> "OE2" Residue "X GLU 113": "OE1" <-> "OE2" Residue "X PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 117": "OE1" <-> "OE2" Residue "X ASP 173": "OD1" <-> "OD2" Residue "X PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 202": "OE1" <-> "OE2" Residue "X GLU 209": "OE1" <-> "OE2" Residue "X GLU 210": "OE1" <-> "OE2" Residue "X GLU 213": "OE1" <-> "OE2" Residue "X GLU 220": "OE1" <-> "OE2" Residue "X GLU 233": "OE1" <-> "OE2" Residue "Y GLU 96": "OE1" <-> "OE2" Residue "Y TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 108": "OE1" <-> "OE2" Residue "Y GLU 116": "OE1" <-> "OE2" Residue "Y GLU 118": "OE1" <-> "OE2" Residue "Y GLU 150": "OE1" <-> "OE2" Residue "Y GLU 161": "OE1" <-> "OE2" Residue "Y GLU 227": "OE1" <-> "OE2" Residue "Y PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 82": "OE1" <-> "OE2" Residue "0 TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 52": "OE1" <-> "OE2" Residue "3 GLU 146": "OE1" <-> "OE2" Residue "3 PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 51": "OE1" <-> "OE2" Residue "5 PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 115": "OE1" <-> "OE2" Residue "5 GLU 134": "OE1" <-> "OE2" Residue "5 GLU 168": "OE1" <-> "OE2" Residue "5 GLU 174": "OE1" <-> "OE2" Residue "5 PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 254": "OE1" <-> "OE2" Residue "5 PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 267": "OE1" <-> "OE2" Residue "5 TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 307": "OD1" <-> "OD2" Residue "5 TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 409": "OE1" <-> "OE2" Residue "5 PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 62": "OE1" <-> "OE2" Residue "6 GLU 64": "OE1" <-> "OE2" Residue "6 PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 182": "OD1" <-> "OD2" Residue "6 GLU 227": "OE1" <-> "OE2" Residue "6 ASP 229": "OD1" <-> "OD2" Residue "6 TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 63": "OE1" <-> "OE2" Residue "7 GLU 97": "OE1" <-> "OE2" Residue "7 TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 155": "OE1" <-> "OE2" Residue "7 GLU 171": "OE1" <-> "OE2" Residue "7 PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 191": "OE1" <-> "OE2" Residue "7 GLU 197": "OE1" <-> "OE2" Residue "7 PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 217": "OE1" <-> "OE2" Residue "7 GLU 220": "OE1" <-> "OE2" Residue "7 PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 314": "OD1" <-> "OD2" Residue "8 PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 109": "OE1" <-> "OE2" Residue "8 TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 149": "OE1" <-> "OE2" Residue "9 PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 94": "OE1" <-> "OE2" Residue "9 GLU 120": "OE1" <-> "OE2" Residue "9 PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 48": "OE1" <-> "OE2" Residue "a TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 70": "OE1" <-> "OE2" Residue "b PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 44": "OE1" <-> "OE2" Residue "c GLU 46": "OE1" <-> "OE2" Residue "c GLU 101": "OE1" <-> "OE2" Residue "c ASP 143": "OD1" <-> "OD2" Residue "c ASP 147": "OD1" <-> "OD2" Residue "c GLU 183": "OE1" <-> "OE2" Residue "c GLU 254": "OE1" <-> "OE2" Residue "c TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 293": "OE1" <-> "OE2" Residue "c GLU 309": "OE1" <-> "OE2" Residue "d ASP 171": "OD1" <-> "OD2" Residue "d ASP 237": "OD1" <-> "OD2" Residue "d GLU 249": "OE1" <-> "OE2" Residue "d TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 123": "OE1" <-> "OE2" Residue "g GLU 44": "OE1" <-> "OE2" Residue "g TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 163": "OE1" <-> "OE2" Residue "h TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 88": "OD1" <-> "OD2" Residue "h GLU 92": "OE1" <-> "OE2" Residue "h ASP 93": "OD1" <-> "OD2" Residue "h ASP 141": "OD1" <-> "OD2" Residue "i TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 72": "OE1" <-> "OE2" Residue "i TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 48": "OD1" <-> "OD2" Residue "j GLU 71": "OE1" <-> "OE2" Residue "m GLU 70": "OE1" <-> "OE2" Residue "o GLU 40": "OE1" <-> "OE2" Residue "o TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 38": "OE1" <-> "OE2" Residue "p ASP 74": "OD1" <-> "OD2" Residue "p GLU 132": "OE1" <-> "OE2" Residue "p GLU 160": "OE1" <-> "OE2" Residue "q GLU 88": "OE1" <-> "OE2" Residue "q GLU 89": "OE1" <-> "OE2" Residue "q GLU 91": "OE1" <-> "OE2" Residue "q TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 110": "OE1" <-> "OE2" Residue "q GLU 111": "OE1" <-> "OE2" Residue "q GLU 144": "OE1" <-> "OE2" Residue "r GLU 59": "OE1" <-> "OE2" Residue "r PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 234": "OD1" <-> "OD2" Residue "s ASP 235": "OD1" <-> "OD2" Residue "s GLU 249": "OE1" <-> "OE2" Residue "s GLU 260": "OE1" <-> "OE2" Residue "s ASP 269": "OD1" <-> "OD2" Residue "s ASP 290": "OD1" <-> "OD2" Residue "s PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 321": "OE1" <-> "OE2" Residue "s PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 350": "OD1" <-> "OD2" Residue "s ASP 363": "OD1" <-> "OD2" Residue "s TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 406": "OE1" <-> "OE2" Residue "s ASP 409": "OD1" <-> "OD2" Residue "s PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 90275 Number of models: 1 Model: "" Number of chains: 57 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: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 134} 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: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 145} 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: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 354} 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: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 107} 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: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 258} 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: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 113} 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: 1379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1379 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 15, 'TRANS': 148} 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: "A" Number of atoms: 23184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1092, 23184 Classifications: {'RNA': 1092} Modifications used: {'rna2p_pur': 118, 'rna2p_pyr': 88, 'rna3p_pur': 463, 'rna3p_pyr': 423} Link IDs: {'rna2p': 205, 'rna3p': 886} 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: {'rna2p_pur': 1, 'rna3p_pur': 29, 'rna3p_pyr': 26} Link IDs: {'rna2p': 1, 'rna3p': 54} Chain breaks: 4 Chain: "z" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1547 Inner-chain residues flagged as termini: ['pdbres=" G z 1 "'] Classifications: {'RNA': 73} Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 9, 'rna3p_pur': 31, 'rna3p_pyr': 25} Link IDs: {'rna2p': 16, 'rna3p': 56} Chain breaks: 1 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: "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 0 110 165.386 86.240 174.251 1.00 21.29 S ATOM 31715 SG CYS 0 113 162.637 84.169 176.022 1.00 20.63 S ATOM 31795 SG CYS 0 123 161.696 87.275 174.622 1.00 13.13 S ATOM 31818 SG CYS 0 126 164.144 87.393 177.612 1.00 17.55 S ATOM 7048 SG CYS I 64 140.860 99.479 61.702 1.00 31.96 S ATOM 60298 SG CYS r 70 145.389 99.324 61.789 1.00 30.10 S ATOM 60613 SG CYS r 108 143.554 101.299 61.582 1.00 28.20 S Time building chain proxies: 35.54, per 1000 atoms: 0.39 Number of scatterers: 90275 At special positions: 0 Unit cell: (220.052, 205.96, 255.824, 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 266 16.00 P 1220 15.00 Mg 49 11.99 O 19635 8.00 N 16440 7.00 C 52663 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 33.10 Conformation dependent library (CDL) restraints added in 10.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 0 200 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 123 " 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 0 126 " 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 15456 Ramachandran restraints generated. 7728 Oldfield, 0 Emsley, 7728 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14878 Finding SS restraints... Secondary structure from input PDB file: 261 helices and 81 sheets defined 37.4% alpha, 14.1% beta 323 base pairs and 640 stacking pairs defined. Time for finding SS restraints: 24.44 Creating SS restraints... Processing helix chain 'D' and resid 185 through 187 No H-bonds generated for 'chain 'D' and resid 185 through 187' Processing helix chain 'D' and resid 259 through 266 removed outlier: 3.844A pdb=" N ASN D 263 " --> pdb=" O LYS D 259 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU D 266 " --> pdb=" O ARG D 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 76 Processing helix chain 'E' and resid 134 through 139 Processing helix chain 'E' and resid 158 through 169 Processing helix chain 'E' and resid 194 through 198 Processing helix chain 'E' and resid 217 through 222 Processing helix chain 'E' and resid 304 through 308 removed outlier: 3.905A pdb=" N LYS E 308 " --> pdb=" O PRO E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 320 through 324 Processing helix chain 'F' and resid 83 through 88 Processing helix chain 'F' and resid 92 through 107 removed outlier: 4.592A pdb=" N LYS F 107 " --> pdb=" O GLN F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 184 Processing helix chain 'F' and resid 199 through 211 Processing helix chain 'F' and resid 227 through 235 Processing helix chain 'F' and resid 246 through 248 No H-bonds generated for 'chain 'F' and resid 246 through 248' Processing helix chain 'F' and resid 249 through 256 Processing helix chain 'F' and resid 263 through 277 removed outlier: 4.003A pdb=" N GLN F 276 " --> pdb=" O LYS F 272 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASP F 277 " --> pdb=" O LEU F 273 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 78 Processing helix chain 'H' and resid 87 through 89 No H-bonds generated for 'chain 'H' and resid 87 through 89' Processing helix chain 'H' and resid 115 through 122 Processing helix chain 'H' and resid 135 through 146 removed outlier: 3.917A pdb=" N LEU H 139 " --> pdb=" O GLU H 135 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 51 Processing helix chain 'I' and resid 61 through 65 Processing helix chain 'I' and resid 78 through 93 Processing helix chain 'I' and resid 105 through 116 Processing helix chain 'I' and resid 127 through 138 Proline residue: I 133 - end of helix Processing helix chain 'I' and resid 143 through 147 removed outlier: 4.083A pdb=" N PHE I 147 " --> pdb=" O LEU I 144 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 171 removed outlier: 3.637A pdb=" N VAL I 171 " --> pdb=" O ILE I 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 187 through 197 removed outlier: 3.549A pdb=" N LEU I 197 " --> pdb=" O ASN I 193 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 59 removed outlier: 3.630A pdb=" N PHE J 49 " --> pdb=" O SER J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 95 Processing helix chain 'J' and resid 114 through 122 Processing helix chain 'J' and resid 136 through 150 removed outlier: 4.679A pdb=" N VAL J 140 " --> pdb=" O PRO J 136 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER J 150 " --> pdb=" O GLY J 146 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 15 Processing helix chain 'K' and resid 27 through 40 Processing helix chain 'K' and resid 70 through 75 Processing helix chain 'K' and resid 92 through 99 Processing helix chain 'K' and resid 101 through 112 Processing helix chain 'K' and resid 117 through 124 removed outlier: 3.531A pdb=" N GLU K 123 " --> pdb=" O ARG K 119 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG K 124 " --> pdb=" O THR K 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 134 through 139 Processing helix chain 'K' and resid 159 through 166 removed outlier: 3.745A pdb=" N PHE K 166 " --> pdb=" O GLU K 162 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 49 removed outlier: 3.804A pdb=" N SER L 49 " --> pdb=" O ALA L 45 " (cutoff:3.500A) Processing helix chain 'L' and resid 124 through 129 removed outlier: 4.051A pdb=" N LEU L 127 " --> pdb=" O PRO L 124 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG L 128 " --> pdb=" O THR L 125 " (cutoff:3.500A) Processing helix chain 'L' and resid 136 through 140 removed outlier: 3.739A pdb=" N ALA L 139 " --> pdb=" O LYS L 136 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE L 140 " --> pdb=" O VAL L 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 136 through 140' Processing helix chain 'M' and resid 11 through 18 Processing helix chain 'M' and resid 73 through 78 removed outlier: 3.859A pdb=" N ILE M 78 " --> pdb=" O PHE M 74 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 107 Processing helix chain 'M' and resid 117 through 124 Processing helix chain 'M' and resid 160 through 170 removed outlier: 3.998A pdb=" N ASN M 170 " --> pdb=" O ALA M 166 " (cutoff:3.500A) Processing helix chain 'M' and resid 180 through 189 removed outlier: 3.848A pdb=" N LYS M 189 " --> pdb=" O ASP M 185 " (cutoff:3.500A) Processing helix chain 'M' and resid 190 through 195 Processing helix chain 'M' and resid 210 through 215 Processing helix chain 'M' and resid 228 through 241 Processing helix chain 'M' and resid 252 through 258 Processing helix chain 'M' and resid 287 through 295 Processing helix chain 'N' and resid 68 through 72 Processing helix chain 'N' and resid 98 through 112 removed outlier: 3.845A pdb=" N SER N 112 " --> pdb=" O THR N 108 " (cutoff:3.500A) Processing helix chain 'N' and resid 169 through 182 removed outlier: 4.313A pdb=" N GLY N 174 " --> pdb=" O GLU N 170 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N PHE N 175 " --> pdb=" O GLU N 171 " (cutoff:3.500A) Processing helix chain 'N' and resid 192 through 209 removed outlier: 3.619A pdb=" N ASN N 209 " --> pdb=" O ARG N 205 " (cutoff:3.500A) Processing helix chain 'N' and resid 214 through 222 Processing helix chain 'N' and resid 225 through 229 removed outlier: 3.737A pdb=" N LYS N 228 " --> pdb=" O GLY N 225 " (cutoff:3.500A) Processing helix chain 'N' and resid 233 through 238 Processing helix chain 'O' and resid 21 through 40 Processing helix chain 'O' and resid 46 through 64 removed outlier: 3.630A pdb=" N LYS O 64 " --> pdb=" O ILE O 60 " (cutoff:3.500A) Processing helix chain 'O' and resid 69 through 80 Processing helix chain 'O' and resid 84 through 92 removed outlier: 4.352A pdb=" N LYS O 88 " --> pdb=" O ASP O 84 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE O 90 " --> pdb=" O ILE O 86 " (cutoff:3.500A) Processing helix chain 'O' and resid 92 through 97 removed outlier: 3.547A pdb=" N ARG O 96 " --> pdb=" O VAL O 92 " (cutoff:3.500A) Processing helix chain 'O' and resid 143 through 158 Processing helix chain 'P' and resid 109 through 114 Processing helix chain 'P' and resid 121 through 139 Processing helix chain 'P' and resid 149 through 154 removed outlier: 3.812A pdb=" N ALA P 154 " --> pdb=" O PRO P 150 " (cutoff:3.500A) Processing helix chain 'P' and resid 155 through 169 Processing helix chain 'Q' and resid 88 through 106 removed outlier: 3.897A pdb=" N PHE Q 92 " --> pdb=" O ASP Q 88 " (cutoff:3.500A) Processing helix chain 'Q' and resid 187 through 192 Processing helix chain 'Q' and resid 194 through 198 Processing helix chain 'Q' and resid 250 through 259 Processing helix chain 'Q' and resid 276 through 289 removed outlier: 3.579A pdb=" N SER Q 289 " --> pdb=" O GLU Q 285 " (cutoff:3.500A) Processing helix chain 'R' and resid 17 through 26 Processing helix chain 'R' and resid 32 through 37 removed outlier: 3.737A pdb=" N LYS R 35 " --> pdb=" O ARG R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 38 through 79 removed outlier: 4.562A pdb=" N TYR R 58 " --> pdb=" O THR R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 92 Processing helix chain 'R' and resid 98 through 109 Processing helix chain 'R' and resid 109 through 133 Processing helix chain 'S' and resid 68 through 90 Processing helix chain 'T' and resid 49 through 54 removed outlier: 4.043A pdb=" N LYS T 53 " --> pdb=" O ARG T 49 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS T 54 " --> pdb=" O LYS T 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 49 through 54' Processing helix chain 'T' and resid 55 through 57 No H-bonds generated for 'chain 'T' and resid 55 through 57' Processing helix chain 'T' and resid 83 through 94 removed outlier: 4.133A pdb=" N TYR T 89 " --> pdb=" O ASP T 85 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU T 90 " --> pdb=" O LYS T 86 " (cutoff:3.500A) Processing helix chain 'T' and resid 98 through 107 Processing helix chain 'T' and resid 111 through 132 removed outlier: 3.829A pdb=" N LYS T 115 " --> pdb=" O LYS T 111 " (cutoff:3.500A) Processing helix chain 'T' and resid 191 through 206 removed outlier: 3.552A pdb=" N ARG T 206 " --> pdb=" O GLN T 202 " (cutoff:3.500A) Processing helix chain 'U' and resid 49 through 61 Processing helix chain 'U' and resid 127 through 135 removed outlier: 3.567A pdb=" N GLN U 135 " --> pdb=" O GLU U 131 " (cutoff:3.500A) Processing helix chain 'U' and resid 141 through 145 removed outlier: 3.606A pdb=" N GLY U 145 " --> pdb=" O PRO U 142 " (cutoff:3.500A) Processing helix chain 'V' and resid 28 through 35 Processing helix chain 'V' and resid 178 through 183 Processing helix chain 'V' and resid 193 through 203 Processing helix chain 'W' and resid 110 through 119 removed outlier: 3.729A pdb=" N ARG W 119 " --> pdb=" O ASP W 115 " (cutoff:3.500A) Processing helix chain 'X' and resid 7 through 16 removed outlier: 3.517A pdb=" N TRP X 11 " --> pdb=" O PRO X 7 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LYS X 12 " --> pdb=" O VAL X 8 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N ARG X 13 " --> pdb=" O TRP X 9 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU X 16 " --> pdb=" O LYS X 12 " (cutoff:3.500A) Processing helix chain 'X' and resid 17 through 18 No H-bonds generated for 'chain 'X' and resid 17 through 18' Processing helix chain 'X' and resid 19 through 24 removed outlier: 3.660A pdb=" N LEU X 24 " --> pdb=" O CYS X 21 " (cutoff:3.500A) Processing helix chain 'X' and resid 25 through 34 Processing helix chain 'X' and resid 72 through 77 Processing helix chain 'X' and resid 128 through 139 Processing helix chain 'X' and resid 140 through 148 Processing helix chain 'X' and resid 149 through 154 Processing helix chain 'X' and resid 155 through 172 removed outlier: 3.641A pdb=" N GLN X 172 " --> pdb=" O ARG X 168 " (cutoff:3.500A) Processing helix chain 'X' and resid 180 through 191 removed outlier: 3.796A pdb=" N ARG X 184 " --> pdb=" O ASP X 180 " (cutoff:3.500A) Processing helix chain 'X' and resid 192 through 195 Processing helix chain 'X' and resid 197 through 202 Processing helix chain 'X' and resid 207 through 220 Processing helix chain 'X' and resid 225 through 243 removed outlier: 3.753A pdb=" N ILE X 229 " --> pdb=" O PRO X 225 " (cutoff:3.500A) Processing helix chain 'Y' and resid 63 through 68 removed outlier: 4.012A pdb=" N GLU Y 66 " --> pdb=" O GLY Y 63 " (cutoff:3.500A) Processing helix chain 'Y' and resid 70 through 74 removed outlier: 3.500A pdb=" N TRP Y 74 " --> pdb=" O PRO Y 71 " (cutoff:3.500A) Processing helix chain 'Y' and resid 86 through 91 Processing helix chain 'Y' and resid 94 through 122 Processing helix chain 'Y' and resid 129 through 158 removed outlier: 3.920A pdb=" N ASP Y 133 " --> pdb=" O PRO Y 129 " (cutoff:3.500A) Processing helix chain 'Y' and resid 187 through 191 removed outlier: 3.679A pdb=" N LEU Y 190 " --> pdb=" O PRO Y 187 " (cutoff:3.500A) Processing helix chain 'Y' and resid 193 through 197 Processing helix chain 'Y' and resid 205 through 238 Processing helix chain 'Z' and resid 42 through 47 removed outlier: 3.794A pdb=" N GLN Z 47 " --> pdb=" O LYS Z 44 " (cutoff:3.500A) Processing helix chain 'Z' and resid 49 through 56 Processing helix chain 'Z' and resid 79 through 90 Processing helix chain 'Z' and resid 103 through 113 Processing helix chain '0' and resid 86 through 95 Processing helix chain '0' and resid 123 through 146 Processing helix chain '2' and resid 56 through 65 Processing helix chain '2' and resid 65 through 72 removed outlier: 3.849A pdb=" N THR 2 72 " --> pdb=" O ARG 2 68 " (cutoff:3.500A) Processing helix chain '2' and resid 72 through 86 Processing helix chain '3' and resid 107 through 114 removed outlier: 3.741A pdb=" N ILE 3 111 " --> pdb=" O VAL 3 107 " (cutoff:3.500A) Processing helix chain '3' and resid 132 through 136 removed outlier: 3.501A pdb=" N LYS 3 135 " --> pdb=" O LYS 3 132 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS 3 136 " --> pdb=" O LEU 3 133 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 132 through 136' Processing helix chain '3' and resid 137 through 145 Processing helix chain '3' and resid 151 through 161 Processing helix chain '3' and resid 163 through 168 removed outlier: 3.788A pdb=" N ARG 3 168 " --> pdb=" O PHE 3 165 " (cutoff:3.500A) Processing helix chain '3' and resid 177 through 181 removed outlier: 3.816A pdb=" N HIS 3 181 " --> pdb=" O GLN 3 178 " (cutoff:3.500A) Processing helix chain '5' and resid 47 through 51 Processing helix chain '5' and resid 84 through 88 removed outlier: 3.693A pdb=" N PHE 5 87 " --> pdb=" O ASP 5 84 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR 5 88 " --> pdb=" O PRO 5 85 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 84 through 88' Processing helix chain '5' and resid 116 through 125 Processing helix chain '5' and resid 133 through 138 Processing helix chain '5' and resid 149 through 163 Processing helix chain '5' and resid 172 through 191 Proline residue: 5 178 - end of helix Processing helix chain '5' and resid 195 through 199 Processing helix chain '5' and resid 241 through 248 Processing helix chain '5' and resid 249 through 251 No H-bonds generated for 'chain '5' and resid 249 through 251' Processing helix chain '5' and resid 305 through 330 Processing helix chain '5' and resid 407 through 419 removed outlier: 4.493A pdb=" N PHE 5 411 " --> pdb=" O LYS 5 407 " (cutoff:3.500A) Processing helix chain '6' and resid 54 through 67 Processing helix chain '6' and resid 73 through 79 removed outlier: 3.999A pdb=" N TYR 6 77 " --> pdb=" O THR 6 73 " (cutoff:3.500A) Processing helix chain '6' and resid 100 through 115 Processing helix chain '6' and resid 116 through 125 Processing helix chain '6' and resid 131 through 143 removed outlier: 3.829A pdb=" N VAL 6 135 " --> pdb=" O PRO 6 131 " (cutoff:3.500A) Processing helix chain '6' and resid 143 through 155 removed outlier: 3.556A pdb=" N HIS 6 147 " --> pdb=" O CYS 6 143 " (cutoff:3.500A) Processing helix chain '6' and resid 156 through 162 removed outlier: 4.007A pdb=" N ASP 6 160 " --> pdb=" O GLY 6 156 " (cutoff:3.500A) Processing helix chain '6' and resid 196 through 200 removed outlier: 3.837A pdb=" N ALA 6 199 " --> pdb=" O THR 6 196 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLN 6 200 " --> pdb=" O GLU 6 197 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 196 through 200' Processing helix chain '6' and resid 299 through 307 removed outlier: 3.868A pdb=" N HIS 6 307 " --> pdb=" O PHE 6 303 " (cutoff:3.500A) Processing helix chain '6' and resid 325 through 334 Processing helix chain '6' and resid 364 through 369 removed outlier: 4.282A pdb=" N TYR 6 369 " --> pdb=" O TYR 6 365 " (cutoff:3.500A) Processing helix chain '7' and resid 37 through 58 Processing helix chain '7' and resid 87 through 96 removed outlier: 3.530A pdb=" N CYS 7 91 " --> pdb=" O THR 7 87 " (cutoff:3.500A) Processing helix chain '7' and resid 96 through 103 removed outlier: 3.639A pdb=" N CYS 7 100 " --> pdb=" O SER 7 96 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS 7 102 " --> pdb=" O TRP 7 98 " (cutoff:3.500A) Processing helix chain '7' and resid 135 through 156 removed outlier: 3.917A pdb=" N ASN 7 139 " --> pdb=" O PRO 7 135 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG 7 156 " --> pdb=" O CYS 7 152 " (cutoff:3.500A) Processing helix chain '7' and resid 173 through 177 removed outlier: 3.783A pdb=" N GLY 7 177 " --> pdb=" O VAL 7 174 " (cutoff:3.500A) Processing helix chain '7' and resid 186 through 190 Processing helix chain '7' and resid 195 through 212 Processing helix chain '7' and resid 223 through 230 Processing helix chain '7' and resid 233 through 245 Processing helix chain '7' and resid 271 through 273 No H-bonds generated for 'chain '7' and resid 271 through 273' Processing helix chain '7' and resid 309 through 320 Processing helix chain '8' and resid 107 through 154 Processing helix chain '8' and resid 157 through 162 removed outlier: 4.047A pdb=" N ILE 8 162 " --> pdb=" O HIS 8 158 " (cutoff:3.500A) Processing helix chain '9' and resid 27 through 34 Processing helix chain '9' and resid 87 through 105 Proline residue: 9 98 - end of helix removed outlier: 3.756A pdb=" N LYS 9 105 " --> pdb=" O GLU 9 101 " (cutoff:3.500A) Processing helix chain '9' and resid 113 through 118 removed outlier: 3.622A pdb=" N LYS 9 116 " --> pdb=" O ASN 9 113 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY 9 118 " --> pdb=" O GLU 9 115 " (cutoff:3.500A) Processing helix chain 'a' and resid 68 through 72 Processing helix chain 'a' and resid 105 through 117 Processing helix chain 'a' and resid 119 through 123 removed outlier: 3.963A pdb=" N ARG a 122 " --> pdb=" O THR a 119 " (cutoff:3.500A) Processing helix chain 'a' and resid 127 through 134 Processing helix chain 'b' and resid 40 through 50 Processing helix chain 'b' and resid 50 through 58 Processing helix chain 'b' and resid 93 through 107 Processing helix chain 'b' and resid 139 through 143 Processing helix chain 'c' and resid 35 through 53 Processing helix chain 'c' and resid 59 through 63 Processing helix chain 'c' and resid 67 through 79 removed outlier: 3.732A pdb=" N LEU c 79 " --> pdb=" O PHE c 75 " (cutoff:3.500A) Processing helix chain 'c' and resid 84 through 93 Processing helix chain 'c' and resid 95 through 106 removed outlier: 3.672A pdb=" N GLN c 106 " --> pdb=" O GLU c 102 " (cutoff:3.500A) Processing helix chain 'c' and resid 122 through 145 Processing helix chain 'c' and resid 149 through 161 Processing helix chain 'c' and resid 162 through 172 removed outlier: 3.795A pdb=" N ASN c 172 " --> pdb=" O HIS c 168 " (cutoff:3.500A) Processing helix chain 'c' and resid 174 through 179 removed outlier: 3.894A pdb=" N LEU c 178 " --> pdb=" O ALA c 174 " (cutoff:3.500A) Processing helix chain 'c' and resid 187 through 219 Proline residue: c 208 - end of helix Processing helix chain 'c' and resid 220 through 224 removed outlier: 3.643A pdb=" N THR c 224 " --> pdb=" O THR c 221 " (cutoff:3.500A) Processing helix chain 'c' and resid 236 through 248 removed outlier: 3.686A pdb=" N LEU c 240 " --> pdb=" O ASN c 236 " (cutoff:3.500A) Processing helix chain 'c' and resid 288 through 306 Processing helix chain 'd' and resid 52 through 64 Processing helix chain 'd' and resid 118 through 130 removed outlier: 4.950A pdb=" N TYR d 128 " --> pdb=" O ARG d 124 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASP d 129 " --> pdb=" O ILE d 125 " (cutoff:3.500A) Processing helix chain 'd' and resid 136 through 153 removed outlier: 3.650A pdb=" N LYS d 140 " --> pdb=" O ASP d 136 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN d 153 " --> pdb=" O HIS d 149 " (cutoff:3.500A) Processing helix chain 'd' and resid 156 through 164 removed outlier: 3.769A pdb=" N LEU d 160 " --> pdb=" O ASP d 156 " (cutoff:3.500A) Processing helix chain 'd' and resid 168 through 174 Processing helix chain 'e' and resid 64 through 81 Processing helix chain 'e' and resid 85 through 90 Processing helix chain 'e' and resid 91 through 104 removed outlier: 3.537A pdb=" N ASN e 95 " --> pdb=" O ALA e 91 " (cutoff:3.500A) Processing helix chain 'e' and resid 117 through 131 Processing helix chain 'e' and resid 183 through 195 Processing helix chain 'e' and resid 259 through 264 Processing helix chain 'e' and resid 271 through 275 removed outlier: 3.713A pdb=" N ARG e 274 " --> pdb=" O GLN e 271 " (cutoff:3.500A) Processing helix chain 'f' and resid 59 through 63 removed outlier: 3.658A pdb=" N ILE f 63 " --> pdb=" O LYS f 60 " (cutoff:3.500A) Processing helix chain 'f' and resid 100 through 117 Processing helix chain 'f' and resid 163 through 177 Processing helix chain 'g' and resid 45 through 50 Processing helix chain 'g' and resid 116 through 129 removed outlier: 3.688A pdb=" N LEU g 120 " --> pdb=" O ASP g 116 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER g 129 " --> pdb=" O GLU g 125 " (cutoff:3.500A) Processing helix chain 'g' and resid 153 through 165 Processing helix chain 'h' and resid 65 through 78 Processing helix chain 'h' and resid 85 through 89 removed outlier: 3.666A pdb=" N ILE h 89 " --> pdb=" O TRP h 86 " (cutoff:3.500A) Processing helix chain 'h' and resid 93 through 109 Processing helix chain 'h' and resid 122 through 131 removed outlier: 3.631A pdb=" N VAL h 126 " --> pdb=" O ARG h 122 " (cutoff:3.500A) Processing helix chain 'h' and resid 138 through 144 Processing helix chain 'i' and resid 48 through 53 removed outlier: 3.536A pdb=" N MET i 53 " --> pdb=" O GLU i 49 " (cutoff:3.500A) Processing helix chain 'i' and resid 69 through 74 removed outlier: 3.869A pdb=" N ILE i 74 " --> pdb=" O LYS i 71 " (cutoff:3.500A) Processing helix chain 'i' and resid 77 through 81 removed outlier: 3.990A pdb=" N ARG i 81 " --> pdb=" O ILE i 78 " (cutoff:3.500A) Processing helix chain 'i' and resid 86 through 99 Processing helix chain 'i' and resid 100 through 102 No H-bonds generated for 'chain 'i' and resid 100 through 102' Processing helix chain 'i' and resid 103 through 124 removed outlier: 3.505A pdb=" N ARG i 123 " --> pdb=" O LYS i 119 " (cutoff:3.500A) Processing helix chain 'j' and resid 25 through 31 Processing helix chain 'j' and resid 41 through 46 removed outlier: 3.711A pdb=" N LEU j 46 " --> pdb=" O PRO j 42 " (cutoff:3.500A) Processing helix chain 'j' and resid 60 through 105 Processing helix chain 'k' and resid 27 through 37 removed outlier: 3.835A pdb=" N ARG k 31 " --> pdb=" O VAL k 27 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL k 37 " --> pdb=" O PHE k 33 " (cutoff:3.500A) Processing helix chain 'k' and resid 39 through 44 Processing helix chain 'k' and resid 82 through 96 removed outlier: 3.606A pdb=" N MET k 86 " --> pdb=" O THR k 82 " (cutoff:3.500A) Processing helix chain 'l' and resid 115 through 133 Processing helix chain 'o' and resid 28 through 49 Processing helix chain 'o' and resid 63 through 80 Processing helix chain 'o' and resid 87 through 96 removed outlier: 4.115A pdb=" N GLN o 91 " --> pdb=" O PHE o 87 " (cutoff:3.500A) Processing helix chain 'o' and resid 97 through 99 No H-bonds generated for 'chain 'o' and resid 97 through 99' Processing helix chain 'p' and resid 44 through 49 Processing helix chain 'p' and resid 55 through 59 Processing helix chain 'p' and resid 112 through 123 Processing helix chain 'p' and resid 124 through 127 Processing helix chain 'p' and resid 142 through 163 Processing helix chain 'p' and resid 175 through 189 Processing helix chain 'q' and resid 53 through 65 removed outlier: 3.709A pdb=" N ALA q 57 " --> pdb=" O GLY q 53 " (cutoff:3.500A) Processing helix chain 'q' and resid 66 through 69 Processing helix chain 'q' and resid 71 through 75 removed outlier: 3.510A pdb=" N SER q 74 " --> pdb=" O VAL q 71 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU q 75 " --> pdb=" O PRO q 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 71 through 75' Processing helix chain 'q' and resid 78 through 93 Processing helix chain 'q' and resid 95 through 155 Proline residue: q 129 - end of helix Processing helix chain 'q' and resid 169 through 188 removed outlier: 4.060A pdb=" N ALA q 173 " --> pdb=" O ASP q 169 " (cutoff:3.500A) Processing helix chain 'r' and resid 70 through 75 Processing helix chain 'r' and resid 86 through 91 Processing helix chain 'r' and resid 101 through 106 removed outlier: 3.601A pdb=" N THR r 105 " --> pdb=" O PRO r 101 " (cutoff:3.500A) Processing helix chain 'r' and resid 108 through 125 removed outlier: 3.509A pdb=" N ARG r 124 " --> pdb=" O LYS r 120 " (cutoff:3.500A) Processing helix chain 'r' and resid 155 through 159 removed outlier: 3.550A pdb=" N SER r 158 " --> pdb=" O ALA r 155 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL r 159 " --> pdb=" O PRO r 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 155 through 159' Processing helix chain 'r' and resid 178 through 182 removed outlier: 3.610A pdb=" N ARG r 182 " --> pdb=" O PRO r 179 " (cutoff:3.500A) Processing helix chain 's' and resid 55 through 72 removed outlier: 3.611A pdb=" N ARG s 59 " --> pdb=" O SER s 55 " (cutoff:3.500A) Processing helix chain 's' and resid 75 through 84 Processing helix chain 's' and resid 101 through 111 removed outlier: 3.949A pdb=" N TRP s 105 " --> pdb=" O ASN s 101 " (cutoff:3.500A) Processing helix chain 's' and resid 141 through 155 Processing helix chain 's' and resid 167 through 172 Processing helix chain 's' and resid 172 through 189 Processing helix chain 's' and resid 192 through 198 removed outlier: 3.624A pdb=" N ALA s 198 " --> pdb=" O LEU s 195 " (cutoff:3.500A) Processing helix chain 's' and resid 307 through 314 Processing helix chain 's' and resid 319 through 342 Processing helix chain 's' and resid 415 through 425 Processing sheet with id=AA1, first strand: chain 'D' and resid 77 through 78 Processing sheet with id=AA2, first strand: chain 'D' and resid 147 through 152 removed outlier: 3.780A pdb=" N GLN D 128 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ALA D 143 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N VAL D 126 " --> pdb=" O ALA D 143 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 181 through 183 removed outlier: 5.851A pdb=" N LEU D 216 " --> pdb=" O GLN D 227 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLN D 227 " --> pdb=" O LEU D 216 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 331 through 333 removed outlier: 6.841A pdb=" N VAL E 273 " --> pdb=" O ASN E 286 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASN E 286 " --> pdb=" O VAL E 273 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLY E 105 " --> pdb=" O LEU E 121 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N GLN E 123 " --> pdb=" O LYS E 103 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N LYS E 103 " --> pdb=" O GLN E 123 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N LEU E 296 " --> pdb=" O LYS E 209 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N LYS E 209 " --> pdb=" O LEU E 296 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N VAL E 204 " --> pdb=" O GLY E 270 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY E 270 " --> pdb=" O VAL E 204 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 173 through 181 removed outlier: 6.423A pdb=" N LYS E 173 " --> pdb=" O THR E 151 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N THR E 151 " --> pdb=" O LYS E 173 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N GLY E 148 " --> pdb=" O VAL E 129 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N VAL E 129 " --> pdb=" O GLY E 148 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR E 191 " --> pdb=" O VAL E 129 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 214 through 216 Processing sheet with id=AA7, first strand: chain 'F' and resid 79 through 82 removed outlier: 9.978A pdb=" N LEU F 187 " --> pdb=" O GLN F 63 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N TRP F 65 " --> pdb=" O LEU F 187 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE F 189 " --> pdb=" O TRP F 65 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU F 217 " --> pdb=" O VAL F 260 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N THR F 262 " --> pdb=" O LEU F 217 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N VAL F 219 " --> pdb=" O THR F 262 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL F 216 " --> pdb=" O ASN F 241 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ILE F 243 " --> pdb=" O VAL F 216 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU F 218 " --> pdb=" O ILE F 243 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 109 through 110 Processing sheet with id=AA9, first strand: chain 'H' and resid 54 through 58 removed outlier: 6.971A pdb=" N ILE H 55 " --> pdb=" O VAL H 83 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 111 through 114 Processing sheet with id=AB2, first strand: chain 'I' and resid 122 through 125 removed outlier: 3.824A pdb=" N MET I 152 " --> pdb=" O CYS I 99 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA I 97 " --> pdb=" O LEU I 154 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N VAL I 98 " --> pdb=" O GLY I 178 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLY I 178 " --> pdb=" O VAL I 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 110 through 113 removed outlier: 6.848A pdb=" N GLY J 110 " --> pdb=" O ARG J 154 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL J 156 " --> pdb=" O GLY J 110 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL J 112 " --> pdb=" O VAL J 156 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'K' and resid 125 through 127 removed outlier: 6.323A pdb=" N VAL K 57 " --> pdb=" O HIS K 126 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU K 143 " --> pdb=" O TRP K 18 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 66 through 67 removed outlier: 4.006A pdb=" N PHE K 67 " --> pdb=" O ASN r 148 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'K' and resid 76 through 80 Processing sheet with id=AB7, first strand: chain 'L' and resid 39 through 40 removed outlier: 6.729A pdb=" N ARG L 39 " --> pdb=" O VAL L 105 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N LEU L 107 " --> pdb=" O ARG L 39 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN L 104 " --> pdb=" O VAL L 87 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N GLN L 72 " --> pdb=" O VAL L 60 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N VAL L 60 " --> pdb=" O GLN L 72 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU L 74 " --> pdb=" O ILE L 58 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 99 through 100 removed outlier: 6.654A pdb=" N VAL Q 154 " --> pdb=" O LEU Q 134 " (cutoff:3.500A) removed outlier: 9.841A pdb=" N LEU Q 134 " --> pdb=" O VAL Q 154 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE Q 116 " --> pdb=" O VAL Q 177 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ALA Q 122 " --> pdb=" O VAL Q 171 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N VAL Q 171 " --> pdb=" O ALA Q 122 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 92 through 97 removed outlier: 6.912A pdb=" N GLN M 92 " --> pdb=" O TYR M 136 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N VAL M 138 " --> pdb=" O GLN M 92 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N LYS M 94 " --> pdb=" O VAL M 138 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N LEU M 140 " --> pdb=" O LYS M 94 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N LEU M 96 " --> pdb=" O LEU M 140 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 153 through 155 Processing sheet with id=AC2, first strand: chain 'M' and resid 274 through 276 removed outlier: 3.645A pdb=" N ILE M 282 " --> pdb=" O VAL g 42 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 118 through 122 removed outlier: 6.611A pdb=" N LEU N 159 " --> pdb=" O ALA N 91 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ALA N 91 " --> pdb=" O LEU N 159 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N VAL N 161 " --> pdb=" O ILE N 89 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE N 89 " --> pdb=" O VAL N 161 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE N 87 " --> pdb=" O MET N 163 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 95 through 97 Processing sheet with id=AC5, first strand: chain 'N' and resid 241 through 242 Processing sheet with id=AC6, first strand: chain 'O' and resid 41 through 45 Processing sheet with id=AC7, first strand: chain 'P' and resid 47 through 48 removed outlier: 4.234A pdb=" N PHE W 142 " --> pdb=" O PHE P 48 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N PHE W 142 " --> pdb=" O VAL 6 345 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL 6 345 " --> pdb=" O PHE W 142 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N LEU W 144 " --> pdb=" O GLU 6 343 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N GLU 6 343 " --> pdb=" O LEU W 144 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA W 146 " --> pdb=" O VAL 6 341 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'P' and resid 79 through 85 removed outlier: 7.066A pdb=" N VAL P 90 " --> pdb=" O SER P 106 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N SER P 106 " --> pdb=" O VAL P 90 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ALA P 92 " --> pdb=" O SER P 104 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N SER P 104 " --> pdb=" O ALA P 92 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL P 94 " --> pdb=" O VAL P 102 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'S' and resid 104 through 109 removed outlier: 6.638A pdb=" N PHE S 96 " --> pdb=" O VAL S 136 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL S 136 " --> pdb=" O PHE S 96 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL S 98 " --> pdb=" O LEU S 134 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N LEU S 134 " --> pdb=" O GLY S 145 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'b' and resid 119 through 120 removed outlier: 6.281A pdb=" N GLU S 165 " --> pdb=" O PRO S 189 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N THR S 191 " --> pdb=" O LYS S 163 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LYS S 163 " --> pdb=" O THR S 191 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N LEU S 193 " --> pdb=" O ILE S 161 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N ILE S 161 " --> pdb=" O LEU S 193 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ILE S 195 " --> pdb=" O THR S 159 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N THR S 159 " --> pdb=" O ILE S 195 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N VAL S 156 " --> pdb=" O LEU S 130 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'S' and resid 169 through 175 Processing sheet with id=AD3, first strand: chain 'T' and resid 72 through 80 removed outlier: 7.015A pdb=" N GLU T 72 " --> pdb=" O GLU T 180 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N GLU T 180 " --> pdb=" O GLU T 72 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N TYR T 74 " --> pdb=" O LEU T 178 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N LEU T 178 " --> pdb=" O TYR T 74 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N CYS T 76 " --> pdb=" O VAL T 176 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N VAL T 176 " --> pdb=" O CYS T 76 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ARG T 78 " --> pdb=" O TYR T 174 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N TYR T 174 " --> pdb=" O ARG T 78 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL T 179 " --> pdb=" O ILE T 142 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N ILE T 142 " --> pdb=" O VAL T 179 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'T' and resid 153 through 155 Processing sheet with id=AD5, first strand: chain 'U' and resid 18 through 19 Processing sheet with id=AD6, first strand: chain 'U' and resid 28 through 29 removed outlier: 4.460A pdb=" N GLN U 41 " --> pdb=" O VAL U 29 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'V' and resid 115 through 116 removed outlier: 3.573A pdb=" N GLN V 78 " --> pdb=" O VAL V 87 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N GLY V 89 " --> pdb=" O VAL V 76 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N VAL V 76 " --> pdb=" O GLY V 89 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'V' and resid 93 through 98 Processing sheet with id=AD9, first strand: chain 'V' and resid 133 through 136 removed outlier: 3.674A pdb=" N ARG V 136 " --> pdb=" O VAL V 144 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL V 144 " --> pdb=" O ARG V 136 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ARG V 145 " --> pdb=" O ILE V 154 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'V' and resid 176 through 177 Processing sheet with id=AE2, first strand: chain 'V' and resid 214 through 216 Processing sheet with id=AE3, first strand: chain 'W' and resid 52 through 53 removed outlier: 6.612A pdb=" N LEU W 89 " --> pdb=" O ILE W 67 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'W' and resid 60 through 61 Processing sheet with id=AE5, first strand: chain 'X' and resid 50 through 52 Processing sheet with id=AE6, first strand: chain 'X' and resid 86 through 91 Processing sheet with id=AE7, first strand: chain 'X' and resid 110 through 116 Processing sheet with id=AE8, first strand: chain 'Y' and resid 166 through 170 Processing sheet with id=AE9, first strand: chain 'Z' and resid 98 through 101 Processing sheet with id=AF1, first strand: chain 'Z' and resid 138 through 139 Processing sheet with id=AF2, first strand: chain '0' and resid 107 through 109 Processing sheet with id=AF3, first strand: chain '0' and resid 156 through 159 Processing sheet with id=AF4, first strand: chain '1' and resid 29 through 35 removed outlier: 5.930A pdb=" N ARG 1 19 " --> pdb=" O LYS 1 61 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N LYS 1 61 " --> pdb=" O ARG 1 19 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N VAL 1 21 " --> pdb=" O LYS 1 59 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N LYS 1 59 " --> pdb=" O VAL 1 21 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain '3' and resid 115 through 116 Processing sheet with id=AF6, first strand: chain '5' and resid 207 through 215 Processing sheet with id=AF7, first strand: chain '5' and resid 126 through 130 removed outlier: 6.143A pdb=" N LYS 5 127 " --> pdb=" O ALA 5 374 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N VAL 5 376 " --> pdb=" O LYS 5 127 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE 5 129 " --> pdb=" O VAL 5 376 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N SER 5 378 " --> pdb=" O ILE 5 129 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASP 5 379 " --> pdb=" O PHE 5 352 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N PHE 5 352 " --> pdb=" O ASP 5 379 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N THR 5 361 " --> pdb=" O GLN 5 338 " (cutoff:3.500A) removed outlier: 10.220A pdb=" N GLN 5 338 " --> pdb=" O THR 5 361 " (cutoff:3.500A) removed outlier: 9.253A pdb=" N TYR 5 287 " --> pdb=" O VAL 5 341 " (cutoff:3.500A) removed outlier: 9.147A pdb=" N GLN 5 343 " --> pdb=" O TYR 5 287 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N HIS 5 289 " --> pdb=" O GLN 5 343 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N VAL 5 345 " --> pdb=" O HIS 5 289 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU 5 291 " --> pdb=" O VAL 5 345 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N THR 5 347 " --> pdb=" O LEU 5 291 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU 5 293 " --> pdb=" O THR 5 347 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU 5 230 " --> pdb=" O HIS 5 289 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain '5' and resid 385 through 387 Processing sheet with id=AF9, first strand: chain '6' and resid 183 through 187 Processing sheet with id=AG1, first strand: chain '6' and resid 191 through 192 removed outlier: 6.334A pdb=" N ASN 6 191 " --> pdb=" O GLN 6 320 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU 6 272 " --> pdb=" O ALA 6 314 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU 6 316 " --> pdb=" O PHE 6 270 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N PHE 6 270 " --> pdb=" O LEU 6 316 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N PHE 6 318 " --> pdb=" O LEU 6 268 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU 6 268 " --> pdb=" O PHE 6 318 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLN 6 320 " --> pdb=" O HIS 6 266 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N HIS 6 266 " --> pdb=" O GLN 6 320 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N TRP 6 214 " --> pdb=" O THR 6 238 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N THR 6 238 " --> pdb=" O TRP 6 214 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N LEU 6 216 " --> pdb=" O LEU 6 236 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU 6 218 " --> pdb=" O HIS 6 234 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain '6' and resid 191 through 192 removed outlier: 6.334A pdb=" N ASN 6 191 " --> pdb=" O GLN 6 320 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU 6 272 " --> pdb=" O ALA 6 314 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU 6 316 " --> pdb=" O PHE 6 270 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N PHE 6 270 " --> pdb=" O LEU 6 316 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N PHE 6 318 " --> pdb=" O LEU 6 268 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU 6 268 " --> pdb=" O PHE 6 318 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLN 6 320 " --> pdb=" O HIS 6 266 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N HIS 6 266 " --> pdb=" O GLN 6 320 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N TRP 6 214 " --> pdb=" O THR 6 238 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N THR 6 238 " --> pdb=" O TRP 6 214 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N LEU 6 216 " --> pdb=" O LEU 6 236 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU 6 218 " --> pdb=" O HIS 6 234 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain '7' and resid 124 through 125 removed outlier: 8.073A pdb=" N ILE 7 125 " --> pdb=" O GLU 7 66 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LYS 7 68 " --> pdb=" O ILE 7 125 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain '7' and resid 106 through 108 Processing sheet with id=AG5, first strand: chain '7' and resid 165 through 168 removed outlier: 6.947A pdb=" N ASP 7 182 " --> pdb=" O VAL 7 167 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL 7 300 " --> pdb=" O VAL 7 280 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N VAL 7 280 " --> pdb=" O VAL 7 300 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N LEU 7 302 " --> pdb=" O TYR 7 278 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N TYR 7 278 " --> pdb=" O LEU 7 302 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain '7' and resid 217 through 222 Processing sheet with id=AG7, first strand: chain '9' and resid 42 through 45 Processing sheet with id=AG8, first strand: chain 'a' and resid 73 through 74 removed outlier: 5.642A pdb=" N SER c 255 " --> pdb=" O TYR c 275 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TYR c 275 " --> pdb=" O SER c 255 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N LEU c 257 " --> pdb=" O GLY c 273 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N GLY c 273 " --> pdb=" O LEU c 257 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N TYR c 270 " --> pdb=" O PRO c 285 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL c 272 " --> pdb=" O GLU c 283 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLU c 283 " --> pdb=" O VAL c 272 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU c 274 " --> pdb=" O ILE c 281 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'b' and resid 8 through 9 Processing sheet with id=AH1, first strand: chain 'b' and resid 84 through 88 removed outlier: 6.049A pdb=" N ARG b 74 " --> pdb=" O PHE b 31 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N VAL b 76 " --> pdb=" O LEU b 29 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLU b 78 " --> pdb=" O GLN b 27 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLN b 27 " --> pdb=" O VAL b 62 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N TYR b 64 " --> pdb=" O GLN b 27 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU b 29 " --> pdb=" O TYR b 64 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE b 63 " --> pdb=" O LYS h 153 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'd' and resid 184 through 196 removed outlier: 11.238A pdb=" N GLU d 187 " --> pdb=" O THR d 221 " (cutoff:3.500A) removed outlier: 9.869A pdb=" N THR d 221 " --> pdb=" O GLU d 187 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N LEU d 189 " --> pdb=" O ARG d 219 " (cutoff:3.500A) removed outlier: 9.214A pdb=" N ARG d 219 " --> pdb=" O LEU d 189 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N HIS d 217 " --> pdb=" O PRO d 191 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR d 213 " --> pdb=" O VAL d 195 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLU d 249 " --> pdb=" O MET d 261 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N MET d 261 " --> pdb=" O GLU d 249 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'e' and resid 175 through 177 Processing sheet with id=AH4, first strand: chain 'e' and resid 54 through 55 removed outlier: 3.694A pdb=" N LEU e 157 " --> pdb=" O ARG e 55 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'e' and resid 161 through 164 Processing sheet with id=AH6, first strand: chain 'e' and resid 199 through 202 Processing sheet with id=AH7, first strand: chain 'f' and resid 80 through 81 Processing sheet with id=AH8, first strand: chain 'f' and resid 90 through 97 removed outlier: 3.870A pdb=" N ILE f 93 " --> pdb=" O VAL f 157 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL f 157 " --> pdb=" O ILE f 93 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'g' and resid 84 through 86 Processing sheet with id=AI1, first strand: chain 'g' and resid 96 through 101 Processing sheet with id=AI2, first strand: chain 'k' and resid 50 through 55 removed outlier: 4.454A pdb=" N GLY r 51 " --> pdb=" O ARG k 77 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'm' and resid 52 through 56 Processing sheet with id=AI4, first strand: chain 'p' and resid 77 through 80 Processing sheet with id=AI5, first strand: chain 's' and resid 206 through 211 removed outlier: 4.077A pdb=" N ASP s 234 " --> pdb=" O VAL s 93 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N PHE s 274 " --> pdb=" O MET s 92 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 's' and resid 112 through 116 Processing sheet with id=AI7, first strand: chain 's' and resid 112 through 116 Processing sheet with id=AI8, first strand: chain 's' and resid 215 through 216 Processing sheet with id=AI9, first strand: chain 's' and resid 404 through 405 removed outlier: 3.566A pdb=" N THR s 404 " --> pdb=" O LYS s 411 " (cutoff:3.500A) 2465 hydrogen bonds defined for protein. 6900 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 780 hydrogen bonds 1330 hydrogen bond angles 0 basepair planarities 323 basepair parallelities 640 stacking parallelities Total time for adding SS restraints: 49.20 Time building geometry restraints manager: 35.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 20852 1.33 - 1.46: 28515 1.46 - 1.58: 42630 1.58 - 1.70: 2412 1.70 - 1.83: 422 Bond restraints: 94831 Sorted by residual: bond pdb=" C VAL N 151 " pdb=" N THR N 152 " ideal model delta sigma weight residual 1.331 1.471 -0.140 2.07e-02 2.33e+03 4.59e+01 bond pdb=" C GLN 7 290 " pdb=" N PRO 7 291 " ideal model delta sigma weight residual 1.336 1.379 -0.043 1.20e-02 6.94e+03 1.30e+01 bond pdb=" C LYS i 68 " pdb=" N HIS i 69 " ideal model delta sigma weight residual 1.331 1.267 0.064 2.07e-02 2.33e+03 9.54e+00 bond pdb=" CB PRO D 114 " pdb=" CG PRO D 114 " ideal model delta sigma weight residual 1.492 1.646 -0.154 5.00e-02 4.00e+02 9.48e+00 bond pdb=" C PHE 8 169 " pdb=" N PRO 8 170 " ideal model delta sigma weight residual 1.334 1.398 -0.064 2.34e-02 1.83e+03 7.53e+00 ... (remaining 94826 not shown) Histogram of bond angle deviations from ideal: 96.45 - 105.46: 7482 105.46 - 114.47: 58423 114.47 - 123.48: 59762 123.48 - 132.49: 8050 132.49 - 141.51: 274 Bond angle restraints: 133991 Sorted by residual: angle pdb=" CA PRO D 114 " pdb=" N PRO D 114 " pdb=" CD PRO D 114 " ideal model delta sigma weight residual 112.00 98.62 13.38 1.40e+00 5.10e-01 9.14e+01 angle pdb=" C MET Q 204 " pdb=" N LYS Q 205 " pdb=" CA LYS Q 205 " ideal model delta sigma weight residual 120.68 131.42 -10.74 1.52e+00 4.33e-01 4.99e+01 angle pdb=" CA PRO E 89 " pdb=" N PRO E 89 " pdb=" CD PRO E 89 " ideal model delta sigma weight residual 112.00 103.98 8.02 1.40e+00 5.10e-01 3.28e+01 angle pdb=" N ILE N 72 " pdb=" CA ILE N 72 " pdb=" C ILE N 72 " ideal model delta sigma weight residual 111.90 107.28 4.62 8.10e-01 1.52e+00 3.26e+01 angle pdb=" N VAL 5 140 " pdb=" CA VAL 5 140 " pdb=" C VAL 5 140 " ideal model delta sigma weight residual 113.43 107.28 6.15 1.09e+00 8.42e-01 3.18e+01 ... (remaining 133986 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 54999 35.97 - 71.93: 2919 71.93 - 107.90: 409 107.90 - 143.86: 7 143.86 - 179.83: 30 Dihedral angle restraints: 58364 sinusoidal: 35402 harmonic: 22962 Sorted by residual: dihedral pdb=" O4' U A1228 " pdb=" C1' U A1228 " pdb=" N1 U A1228 " pdb=" C2 U A1228 " ideal model delta sinusoidal sigma weight residual -160.00 13.58 -173.58 1 1.50e+01 4.44e-03 8.51e+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 26.97 173.03 1 1.50e+01 4.44e-03 8.50e+01 dihedral pdb=" O4' C A 709 " pdb=" C1' C A 709 " pdb=" N1 C A 709 " pdb=" C2 C A 709 " ideal model delta sinusoidal sigma weight residual -160.00 10.71 -170.71 1 1.50e+01 4.44e-03 8.48e+01 ... (remaining 58361 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 14161 0.080 - 0.160: 1351 0.160 - 0.240: 79 0.240 - 0.320: 17 0.320 - 0.400: 6 Chirality restraints: 15614 Sorted by residual: chirality pdb=" CB VAL i 98 " pdb=" CA VAL i 98 " pdb=" CG1 VAL i 98 " pdb=" CG2 VAL i 98 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 3.99e+00 chirality pdb=" C1' A A 141 " pdb=" O4' A A 141 " pdb=" C2' A A 141 " pdb=" N9 A A 141 " both_signs ideal model delta sigma weight residual False 2.46 2.08 0.38 2.00e-01 2.50e+01 3.59e+00 chirality pdb=" CB ILE 5 270 " pdb=" CA ILE 5 270 " pdb=" CG1 ILE 5 270 " pdb=" CG2 ILE 5 270 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.57e+00 ... (remaining 15611 not shown) Planarity restraints: 12697 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 113 " 0.117 5.00e-02 4.00e+02 1.65e-01 4.35e+01 pdb=" N PRO D 114 " -0.285 5.00e-02 4.00e+02 pdb=" CA PRO D 114 " 0.086 5.00e-02 4.00e+02 pdb=" CD PRO D 114 " 0.081 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER S 58 " 0.093 5.00e-02 4.00e+02 1.39e-01 3.08e+01 pdb=" N PRO S 59 " -0.240 5.00e-02 4.00e+02 pdb=" CA PRO S 59 " 0.075 5.00e-02 4.00e+02 pdb=" CD PRO S 59 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG M 45 " 0.414 9.50e-02 1.11e+02 1.86e-01 2.19e+01 pdb=" NE ARG M 45 " -0.030 2.00e-02 2.50e+03 pdb=" CZ ARG M 45 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG M 45 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG M 45 " 0.009 2.00e-02 2.50e+03 ... (remaining 12694 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 1347 2.63 - 3.19: 71185 3.19 - 3.76: 156877 3.76 - 4.33: 211956 4.33 - 4.90: 320939 Nonbonded interactions: 762304 Sorted by model distance: nonbonded pdb=" OP1 C A1245 " pdb="MG MG A1634 " model vdw 2.057 2.170 nonbonded pdb=" OP2 A A 357 " pdb="MG MG A1609 " model vdw 2.090 2.170 nonbonded pdb=" OP2 G A 248 " pdb="MG MG A1607 " model vdw 2.102 2.170 nonbonded pdb=" OP2 A A 703 " pdb="MG MG A1644 " model vdw 2.104 2.170 nonbonded pdb=" OP2 A A 580 " pdb="MG MG A1647 " model vdw 2.109 2.170 ... (remaining 762299 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 2.110 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: 13.350 Check model and map are aligned: 1.020 Set scattering table: 0.620 Process input model: 231.330 Find NCS groups from input model: 2.600 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 254.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 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 0.154 94831 Z= 0.272 Angle : 0.868 21.207 133991 Z= 0.455 Chirality : 0.047 0.400 15614 Planarity : 0.008 0.186 12697 Dihedral : 19.235 179.831 43486 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.67 % Favored : 96.29 % Rotamer: Outliers : 0.03 % Allowed : 0.32 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.18 (0.09), residues: 7728 helix: -0.37 (0.10), residues: 2556 sheet: -0.75 (0.16), residues: 973 loop : -1.00 (0.09), residues: 4199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP 6 235 HIS 0.012 0.001 HIS o 94 PHE 0.046 0.002 PHE I 90 TYR 0.041 0.002 TYR V 95 ARG 0.017 0.001 ARG d 215 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15456 Ramachandran restraints generated. 7728 Oldfield, 0 Emsley, 7728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15456 Ramachandran restraints generated. 7728 Oldfield, 0 Emsley, 7728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1355 residues out of total 6963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1353 time to evaluate : 6.434 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: K 24 LYS cc_start: 0.8265 (tttm) cc_final: 0.8047 (ttmm) REVERT: N 131 ILE cc_start: 0.8726 (mm) cc_final: 0.8485 (mt) REVERT: N 206 GLU cc_start: 0.7295 (pt0) cc_final: 0.7089 (pt0) REVERT: O 73 MET cc_start: 0.7943 (tpp) cc_final: 0.7678 (mmm) REVERT: P 87 GLN cc_start: 0.7599 (tt0) cc_final: 0.7288 (tt0) REVERT: R 98 ASN cc_start: 0.8700 (p0) cc_final: 0.8468 (p0) REVERT: S 54 THR cc_start: 0.8133 (m) cc_final: 0.7892 (m) REVERT: S 179 ASN cc_start: 0.8088 (t0) cc_final: 0.7767 (t0) REVERT: U 26 ILE cc_start: 0.8335 (tt) cc_final: 0.8069 (tt) REVERT: U 58 GLU cc_start: 0.7505 (tt0) cc_final: 0.7257 (tt0) REVERT: V 199 MET cc_start: 0.7587 (mmm) cc_final: 0.7361 (mtp) REVERT: X 95 ASP cc_start: 0.8282 (p0) cc_final: 0.8010 (p0) REVERT: Z 40 ARG cc_start: 0.8020 (mtp85) cc_final: 0.7796 (mtp85) REVERT: 1 51 LYS cc_start: 0.8006 (mttm) cc_final: 0.7744 (mtmm) REVERT: c 163 GLU cc_start: 0.6529 (mt-10) cc_final: 0.5968 (mt-10) REVERT: c 243 GLU cc_start: 0.6921 (tm-30) cc_final: 0.6607 (tm-30) REVERT: d 242 VAL cc_start: 0.7860 (t) cc_final: 0.7611 (m) REVERT: h 116 ARG cc_start: 0.7904 (mtm-85) cc_final: 0.7630 (mtm-85) outliers start: 2 outliers final: 0 residues processed: 1355 average time/residue: 0.8733 time to fit residues: 1985.1819 Evaluate side-chains 1123 residues out of total 6963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1123 time to evaluate : 6.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 886 random chunks: chunk 748 optimal weight: 1.9990 chunk 671 optimal weight: 4.9990 chunk 372 optimal weight: 3.9990 chunk 229 optimal weight: 5.9990 chunk 452 optimal weight: 10.0000 chunk 358 optimal weight: 8.9990 chunk 694 optimal weight: 8.9990 chunk 268 optimal weight: 5.9990 chunk 422 optimal weight: 5.9990 chunk 516 optimal weight: 4.9990 chunk 804 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 205 GLN E 115 GLN E 184 ASN ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 33 GLN L 104 ASN ** M 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 120 GLN Q 107 HIS Q 158 GLN R 63 ASN R 77 GLN S 118 ASN T 202 GLN ** T 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 18 HIS ** W 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 76 HIS X 172 GLN Y 225 ASN 0 96 ASN 1 52 GLN 2 54 GLN 5 146 HIS ** 5 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 302 HIS 6 163 HIS ** 6 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 84 ASN a 126 HIS ** b 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 155 ASN d 161 HIS ** e 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 94 HIS f 108 GLN h 87 GLN ** k 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 60 GLN q 120 HIS s 87 GLN ** s 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 281 HIS s 296 HIS s 382 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.111 94831 Z= 0.500 Angle : 0.753 18.217 133991 Z= 0.378 Chirality : 0.047 0.386 15614 Planarity : 0.007 0.147 12697 Dihedral : 20.476 179.719 26849 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.11 % Favored : 95.86 % Rotamer: Outliers : 2.09 % Allowed : 8.79 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: -0.73 (0.09), residues: 7728 helix: 0.27 (0.10), residues: 2610 sheet: -0.86 (0.16), residues: 1010 loop : -0.83 (0.10), residues: 4108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP 6 235 HIS 0.011 0.002 HIS 6 307 PHE 0.041 0.002 PHE U 24 TYR 0.033 0.002 TYR T 82 ARG 0.014 0.001 ARG 8 114 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15456 Ramachandran restraints generated. 7728 Oldfield, 0 Emsley, 7728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15456 Ramachandran restraints generated. 7728 Oldfield, 0 Emsley, 7728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1283 residues out of total 6963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 1138 time to evaluate : 6.249 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: I 95 MET cc_start: 0.2986 (ppp) cc_final: 0.2515 (ptt) REVERT: K 52 ASP cc_start: 0.8285 (t0) cc_final: 0.7930 (t0) REVERT: M 130 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.8023 (pt0) REVERT: N 206 GLU cc_start: 0.7352 (pt0) cc_final: 0.7142 (pt0) REVERT: P 87 GLN cc_start: 0.8072 (tt0) cc_final: 0.7759 (tt0) REVERT: P 147 GLN cc_start: 0.9047 (OUTLIER) cc_final: 0.8791 (pt0) REVERT: R 109 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7477 (mt-10) REVERT: S 56 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8532 (tp) REVERT: S 121 ASP cc_start: 0.6986 (m-30) cc_final: 0.6515 (m-30) REVERT: W 45 LYS cc_start: 0.8712 (mtmm) cc_final: 0.8504 (mttm) REVERT: X 95 ASP cc_start: 0.8471 (p0) cc_final: 0.8156 (p0) REVERT: Y 109 ARG cc_start: 0.7199 (ttp-170) cc_final: 0.6906 (ttp-170) REVERT: 3 112 ASP cc_start: 0.8037 (m-30) cc_final: 0.7749 (m-30) REVERT: 6 170 ARG cc_start: 0.4447 (mtt180) cc_final: 0.3429 (mtt180) REVERT: 7 81 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.7471 (mtp) REVERT: 7 153 VAL cc_start: 0.8309 (OUTLIER) cc_final: 0.8085 (p) REVERT: o 35 MET cc_start: 0.8649 (ttt) cc_final: 0.8432 (ttm) REVERT: r 85 ASP cc_start: 0.7219 (p0) cc_final: 0.6784 (p0) outliers start: 145 outliers final: 104 residues processed: 1211 average time/residue: 0.9067 time to fit residues: 1847.0837 Evaluate side-chains 1153 residues out of total 6963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 1044 time to evaluate : 6.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 331 ASP Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 253 MET Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain K residue 68 SER Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain M residue 130 GLN Chi-restraints excluded: chain M residue 146 ASP Chi-restraints excluded: chain M residue 167 ILE Chi-restraints excluded: chain M residue 243 ILE Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain M residue 279 ASP Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain N residue 214 THR Chi-restraints excluded: chain N residue 220 THR Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 123 ILE Chi-restraints excluded: chain P residue 147 GLN Chi-restraints excluded: chain P residue 157 SER Chi-restraints excluded: chain Q residue 150 ILE Chi-restraints excluded: chain R residue 16 ASP Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain S residue 56 LEU Chi-restraints excluded: chain S residue 103 SER Chi-restraints excluded: chain S residue 164 THR Chi-restraints excluded: chain S residue 185 ILE Chi-restraints excluded: chain S residue 186 VAL Chi-restraints excluded: chain T residue 138 SER Chi-restraints excluded: chain T residue 209 VAL Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 24 PHE Chi-restraints excluded: chain V residue 191 LEU Chi-restraints excluded: chain W residue 46 SER Chi-restraints excluded: chain W residue 61 VAL Chi-restraints excluded: chain W residue 83 VAL Chi-restraints excluded: chain X residue 22 SER Chi-restraints excluded: chain X residue 65 VAL Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 137 GLU Chi-restraints excluded: chain X residue 199 GLU Chi-restraints excluded: chain Y residue 81 SER Chi-restraints excluded: chain Y residue 176 ILE Chi-restraints excluded: chain Z residue 135 SER Chi-restraints excluded: chain Z residue 146 VAL Chi-restraints excluded: chain 0 residue 96 ASN Chi-restraints excluded: chain 0 residue 105 ASN Chi-restraints excluded: chain 0 residue 157 VAL Chi-restraints excluded: chain 0 residue 186 THR Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 1 residue 33 LYS Chi-restraints excluded: chain 2 residue 56 SER Chi-restraints excluded: chain 3 residue 94 LEU Chi-restraints excluded: chain 3 residue 156 LYS Chi-restraints excluded: chain 5 residue 98 LEU Chi-restraints excluded: chain 5 residue 208 THR Chi-restraints excluded: chain 5 residue 238 THR Chi-restraints excluded: chain 5 residue 262 ILE Chi-restraints excluded: chain 5 residue 347 THR Chi-restraints excluded: chain 5 residue 365 ASP Chi-restraints excluded: chain 6 residue 132 LEU Chi-restraints excluded: chain 6 residue 166 THR Chi-restraints excluded: chain 6 residue 194 THR Chi-restraints excluded: chain 6 residue 275 GLN Chi-restraints excluded: chain 6 residue 325 ASP Chi-restraints excluded: chain 6 residue 328 THR Chi-restraints excluded: chain 7 residue 70 VAL Chi-restraints excluded: chain 7 residue 78 VAL Chi-restraints excluded: chain 7 residue 81 MET Chi-restraints excluded: chain 7 residue 153 VAL Chi-restraints excluded: chain 8 residue 140 LEU Chi-restraints excluded: chain 9 residue 46 SER Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain b residue 75 VAL Chi-restraints excluded: chain b residue 138 THR Chi-restraints excluded: chain c residue 274 LEU Chi-restraints excluded: chain d residue 180 THR Chi-restraints excluded: chain e residue 93 ASP Chi-restraints excluded: chain f residue 113 LEU Chi-restraints excluded: chain g residue 68 THR Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain o residue 51 MET Chi-restraints excluded: chain p residue 61 VAL Chi-restraints excluded: chain p residue 136 THR Chi-restraints excluded: chain p residue 140 SER Chi-restraints excluded: chain q residue 68 SER Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 69 THR Chi-restraints excluded: chain s residue 86 MET Chi-restraints excluded: chain s residue 152 GLN Chi-restraints excluded: chain s residue 171 VAL Chi-restraints excluded: chain s residue 200 LEU Chi-restraints excluded: chain s residue 241 ILE Chi-restraints excluded: chain s residue 259 ILE Chi-restraints excluded: chain s residue 322 VAL Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain s residue 416 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 886 random chunks: chunk 447 optimal weight: 4.9990 chunk 249 optimal weight: 0.9980 chunk 669 optimal weight: 8.9990 chunk 547 optimal weight: 2.9990 chunk 221 optimal weight: 0.0570 chunk 806 optimal weight: 0.9990 chunk 870 optimal weight: 20.0000 chunk 717 optimal weight: 1.9990 chunk 799 optimal weight: 4.9990 chunk 274 optimal weight: 0.6980 chunk 646 optimal weight: 8.9990 overall best weight: 0.9502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 184 ASN H 121 ASN I 43 GLN I 101 ASN L 33 GLN Q 107 HIS S 118 ASN S 179 ASN ** W 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 175 GLN ** Y 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 67 HIS Z 136 ASN 0 96 ASN ** 1 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 146 HIS ** 5 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 307 HIS a 126 HIS ** b 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 129 GLN d 149 HIS d 161 HIS d 220 GLN ** e 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 146 ASN r 79 HIS ** s 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 315 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 94831 Z= 0.172 Angle : 0.574 17.298 133991 Z= 0.289 Chirality : 0.039 0.263 15614 Planarity : 0.005 0.084 12697 Dihedral : 20.335 179.855 26849 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.35 % Favored : 96.62 % Rotamer: Outliers : 1.83 % Allowed : 11.90 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: -0.28 (0.10), residues: 7728 helix: 0.83 (0.10), residues: 2623 sheet: -0.80 (0.16), residues: 988 loop : -0.64 (0.10), residues: 4117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP 6 235 HIS 0.010 0.001 HIS 6 307 PHE 0.021 0.001 PHE N 175 TYR 0.022 0.001 TYR 5 176 ARG 0.009 0.000 ARG b 141 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15456 Ramachandran restraints generated. 7728 Oldfield, 0 Emsley, 7728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15456 Ramachandran restraints generated. 7728 Oldfield, 0 Emsley, 7728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1269 residues out of total 6963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 1142 time to evaluate : 6.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 78 LYS cc_start: 0.8394 (ttpp) cc_final: 0.8150 (ttpp) REVERT: F 190 MET cc_start: 0.7315 (mmt) cc_final: 0.7104 (mmt) REVERT: I 95 MET cc_start: 0.2797 (ppp) cc_final: 0.2523 (ptt) REVERT: L 106 VAL cc_start: 0.7321 (t) cc_final: 0.7095 (m) REVERT: P 87 GLN cc_start: 0.8014 (tt0) cc_final: 0.7743 (tt0) REVERT: Q 136 ILE cc_start: 0.7815 (OUTLIER) cc_final: 0.7364 (tp) REVERT: Q 167 TYR cc_start: 0.8444 (m-80) cc_final: 0.8214 (m-80) REVERT: Q 259 LYS cc_start: 0.7675 (tppt) cc_final: 0.7397 (ptpp) REVERT: Y 109 ARG cc_start: 0.6939 (ttp-170) cc_final: 0.6714 (ttp-170) REVERT: 6 170 ARG cc_start: 0.4366 (mtt180) cc_final: 0.3469 (mtt180) REVERT: 7 148 MET cc_start: 0.7122 (tmm) cc_final: 0.6786 (ttt) REVERT: 7 153 VAL cc_start: 0.8085 (OUTLIER) cc_final: 0.7875 (p) REVERT: 9 16 ASP cc_start: 0.6788 (m-30) cc_final: 0.6580 (m-30) REVERT: c 243 GLU cc_start: 0.7124 (tm-30) cc_final: 0.6892 (tm-30) REVERT: i 128 ARG cc_start: 0.6597 (OUTLIER) cc_final: 0.3742 (ptp90) REVERT: o 35 MET cc_start: 0.8568 (ttt) cc_final: 0.8146 (ttt) REVERT: r 85 ASP cc_start: 0.6916 (p0) cc_final: 0.6700 (p0) REVERT: s 239 ASN cc_start: 0.8445 (p0) cc_final: 0.8169 (p0) REVERT: s 411 LYS cc_start: 0.6675 (mmtt) cc_final: 0.6397 (mtpp) outliers start: 127 outliers final: 80 residues processed: 1209 average time/residue: 0.8667 time to fit residues: 1755.3568 Evaluate side-chains 1121 residues out of total 6963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 1038 time to evaluate : 6.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain M residue 146 ASP Chi-restraints excluded: chain M residue 167 ILE Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain N residue 70 SER Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain N residue 176 LEU Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain P residue 44 VAL Chi-restraints excluded: chain P residue 102 VAL Chi-restraints excluded: chain Q residue 136 ILE Chi-restraints excluded: chain S residue 86 MET Chi-restraints excluded: chain S residue 118 ASN Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 159 THR Chi-restraints excluded: chain S residue 164 THR Chi-restraints excluded: chain S residue 185 ILE Chi-restraints excluded: chain T residue 209 VAL Chi-restraints excluded: chain U residue 51 VAL Chi-restraints excluded: chain V residue 69 ASP Chi-restraints excluded: chain V residue 193 THR Chi-restraints excluded: chain W residue 46 SER Chi-restraints excluded: chain W residue 83 VAL Chi-restraints excluded: chain W residue 105 VAL Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain X residue 137 GLU Chi-restraints excluded: chain Z residue 135 SER Chi-restraints excluded: chain Z residue 136 ASN Chi-restraints excluded: chain 0 residue 105 ASN Chi-restraints excluded: chain 0 residue 186 THR Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 1 residue 33 LYS Chi-restraints excluded: chain 1 residue 52 GLN Chi-restraints excluded: chain 2 residue 56 SER Chi-restraints excluded: chain 3 residue 94 LEU Chi-restraints excluded: chain 3 residue 156 LYS Chi-restraints excluded: chain 5 residue 98 LEU Chi-restraints excluded: chain 5 residue 262 ILE Chi-restraints excluded: chain 5 residue 295 ASP Chi-restraints excluded: chain 5 residue 365 ASP Chi-restraints excluded: chain 6 residue 125 LEU Chi-restraints excluded: chain 6 residue 132 LEU Chi-restraints excluded: chain 6 residue 166 THR Chi-restraints excluded: chain 6 residue 174 HIS Chi-restraints excluded: chain 6 residue 184 LEU Chi-restraints excluded: chain 6 residue 275 GLN Chi-restraints excluded: chain 6 residue 328 THR Chi-restraints excluded: chain 7 residue 70 VAL Chi-restraints excluded: chain 7 residue 78 VAL Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 153 VAL Chi-restraints excluded: chain 9 residue 46 SER Chi-restraints excluded: chain 9 residue 130 LEU Chi-restraints excluded: chain a residue 47 VAL Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain b residue 75 VAL Chi-restraints excluded: chain e residue 92 LEU Chi-restraints excluded: chain e residue 93 ASP Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain i residue 32 ILE Chi-restraints excluded: chain i residue 128 ARG Chi-restraints excluded: chain k residue 54 ASP Chi-restraints excluded: chain k residue 55 VAL Chi-restraints excluded: chain o residue 58 GLN Chi-restraints excluded: chain p residue 111 ILE Chi-restraints excluded: chain p residue 136 THR Chi-restraints excluded: chain q residue 52 LEU Chi-restraints excluded: chain s residue 69 THR Chi-restraints excluded: chain s residue 83 LEU Chi-restraints excluded: chain s residue 152 GLN Chi-restraints excluded: chain s residue 200 LEU Chi-restraints excluded: chain s residue 241 ILE Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain s residue 396 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 886 random chunks: chunk 796 optimal weight: 4.9990 chunk 606 optimal weight: 0.4980 chunk 418 optimal weight: 0.8980 chunk 89 optimal weight: 10.0000 chunk 384 optimal weight: 5.9990 chunk 541 optimal weight: 3.9990 chunk 808 optimal weight: 50.0000 chunk 856 optimal weight: 5.9990 chunk 422 optimal weight: 5.9990 chunk 766 optimal weight: 4.9990 chunk 230 optimal weight: 8.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 72 GLN H 121 ASN ** K 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 104 ASN O 91 GLN Q 107 HIS Q 158 GLN R 63 ASN ** R 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 118 ASN S 179 ASN T 202 GLN T 210 HIS ** U 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 18 HIS Z 67 HIS Z 136 ASN 1 52 GLN 5 146 HIS ** 5 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 126 HIS ** b 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 129 GLN d 161 HIS ** e 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 382 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 94831 Z= 0.367 Angle : 0.642 16.411 133991 Z= 0.322 Chirality : 0.043 0.350 15614 Planarity : 0.006 0.104 12697 Dihedral : 20.280 179.726 26849 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.27 % Favored : 95.72 % Rotamer: Outliers : 2.81 % Allowed : 13.24 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: -0.25 (0.10), residues: 7728 helix: 0.90 (0.10), residues: 2618 sheet: -0.81 (0.16), residues: 1027 loop : -0.65 (0.10), residues: 4083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP Q 264 HIS 0.009 0.001 HIS I 41 PHE 0.031 0.002 PHE U 24 TYR 0.022 0.002 TYR S 92 ARG 0.008 0.001 ARG F 170 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15456 Ramachandran restraints generated. 7728 Oldfield, 0 Emsley, 7728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15456 Ramachandran restraints generated. 7728 Oldfield, 0 Emsley, 7728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1282 residues out of total 6963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 1087 time to evaluate : 6.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 82 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8703 (mt) REVERT: M 130 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.7959 (pt0) REVERT: N 195 LEU cc_start: 0.8383 (tp) cc_final: 0.8176 (tp) REVERT: P 87 GLN cc_start: 0.8121 (tt0) cc_final: 0.7821 (tt0) REVERT: P 147 GLN cc_start: 0.8953 (OUTLIER) cc_final: 0.8601 (pt0) REVERT: Q 136 ILE cc_start: 0.7925 (OUTLIER) cc_final: 0.7549 (tp) REVERT: S 104 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7588 (mtt-85) REVERT: 6 170 ARG cc_start: 0.4516 (mtt180) cc_final: 0.3665 (mtt180) REVERT: 7 81 MET cc_start: 0.7685 (OUTLIER) cc_final: 0.7316 (mtp) REVERT: 7 148 MET cc_start: 0.7120 (tmm) cc_final: 0.6819 (ttt) REVERT: 7 153 VAL cc_start: 0.8214 (OUTLIER) cc_final: 0.7993 (p) REVERT: 7 227 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7463 (tt) REVERT: c 243 GLU cc_start: 0.7201 (tm-30) cc_final: 0.6990 (tm-30) REVERT: i 128 ARG cc_start: 0.6763 (OUTLIER) cc_final: 0.3750 (ptp90) REVERT: o 35 MET cc_start: 0.8640 (ttt) cc_final: 0.8333 (ttt) REVERT: r 85 ASP cc_start: 0.7050 (p0) cc_final: 0.6811 (p0) outliers start: 195 outliers final: 141 residues processed: 1194 average time/residue: 0.8792 time to fit residues: 1761.3117 Evaluate side-chains 1176 residues out of total 6963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 1026 time to evaluate : 6.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 331 ASP Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 84 ARG Chi-restraints excluded: chain I residue 166 ARG Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain L residue 89 HIS Chi-restraints excluded: chain M residue 130 GLN Chi-restraints excluded: chain M residue 146 ASP Chi-restraints excluded: chain M residue 152 VAL Chi-restraints excluded: chain M residue 154 ILE Chi-restraints excluded: chain M residue 167 ILE Chi-restraints excluded: chain M residue 234 LEU Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain M residue 279 ASP Chi-restraints excluded: chain N residue 70 SER Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain N residue 176 LEU Chi-restraints excluded: chain N residue 214 THR Chi-restraints excluded: chain N residue 220 THR Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 84 ASP Chi-restraints excluded: chain P residue 44 VAL Chi-restraints excluded: chain P residue 102 VAL Chi-restraints excluded: chain P residue 147 GLN Chi-restraints excluded: chain P residue 157 SER Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 136 ILE Chi-restraints excluded: chain Q residue 150 ILE Chi-restraints excluded: chain Q residue 154 VAL Chi-restraints excluded: chain R residue 16 ASP Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain S residue 86 MET Chi-restraints excluded: chain S residue 104 ARG Chi-restraints excluded: chain S residue 114 ILE Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 164 THR Chi-restraints excluded: chain S residue 185 ILE Chi-restraints excluded: chain T residue 138 SER Chi-restraints excluded: chain T residue 209 VAL Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 24 PHE Chi-restraints excluded: chain U residue 51 VAL Chi-restraints excluded: chain V residue 69 ASP Chi-restraints excluded: chain V residue 191 LEU Chi-restraints excluded: chain V residue 193 THR Chi-restraints excluded: chain W residue 46 SER Chi-restraints excluded: chain W residue 83 VAL Chi-restraints excluded: chain W residue 105 VAL Chi-restraints excluded: chain X residue 22 SER Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain X residue 137 GLU Chi-restraints excluded: chain X residue 142 ASP Chi-restraints excluded: chain X residue 222 ASP Chi-restraints excluded: chain Y residue 81 SER Chi-restraints excluded: chain Y residue 172 ILE Chi-restraints excluded: chain Y residue 176 ILE Chi-restraints excluded: chain Z residue 92 GLU Chi-restraints excluded: chain Z residue 105 SER Chi-restraints excluded: chain Z residue 146 VAL Chi-restraints excluded: chain 0 residue 96 ASN Chi-restraints excluded: chain 0 residue 102 LYS Chi-restraints excluded: chain 0 residue 105 ASN Chi-restraints excluded: chain 0 residue 186 THR Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 1 residue 33 LYS Chi-restraints excluded: chain 2 residue 56 SER Chi-restraints excluded: chain 3 residue 94 LEU Chi-restraints excluded: chain 3 residue 156 LYS Chi-restraints excluded: chain 5 residue 98 LEU Chi-restraints excluded: chain 5 residue 208 THR Chi-restraints excluded: chain 5 residue 262 ILE Chi-restraints excluded: chain 5 residue 295 ASP Chi-restraints excluded: chain 5 residue 365 ASP Chi-restraints excluded: chain 5 residue 391 VAL Chi-restraints excluded: chain 6 residue 45 LEU Chi-restraints excluded: chain 6 residue 132 LEU Chi-restraints excluded: chain 6 residue 166 THR Chi-restraints excluded: chain 6 residue 174 HIS Chi-restraints excluded: chain 6 residue 184 LEU Chi-restraints excluded: chain 6 residue 222 ASP Chi-restraints excluded: chain 6 residue 328 THR Chi-restraints excluded: chain 7 residue 70 VAL Chi-restraints excluded: chain 7 residue 78 VAL Chi-restraints excluded: chain 7 residue 81 MET Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 153 VAL Chi-restraints excluded: chain 7 residue 227 LEU Chi-restraints excluded: chain 7 residue 314 ASP Chi-restraints excluded: chain 8 residue 140 LEU Chi-restraints excluded: chain 8 residue 141 GLU Chi-restraints excluded: chain 9 residue 46 SER Chi-restraints excluded: chain 9 residue 130 LEU Chi-restraints excluded: chain a residue 47 VAL Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain b residue 75 VAL Chi-restraints excluded: chain b residue 138 THR Chi-restraints excluded: chain c residue 274 LEU Chi-restraints excluded: chain d residue 160 LEU Chi-restraints excluded: chain d residue 180 THR Chi-restraints excluded: chain d residue 243 LEU Chi-restraints excluded: chain e residue 93 ASP Chi-restraints excluded: chain f residue 53 THR Chi-restraints excluded: chain g residue 68 THR Chi-restraints excluded: chain g residue 108 THR Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain h residue 120 MET Chi-restraints excluded: chain i residue 128 ARG Chi-restraints excluded: chain k residue 54 ASP Chi-restraints excluded: chain k residue 55 VAL Chi-restraints excluded: chain m residue 54 VAL Chi-restraints excluded: chain o residue 44 GLU Chi-restraints excluded: chain o residue 51 MET Chi-restraints excluded: chain o residue 58 GLN Chi-restraints excluded: chain p residue 111 ILE Chi-restraints excluded: chain p residue 135 LEU Chi-restraints excluded: chain p residue 136 THR Chi-restraints excluded: chain q residue 52 LEU Chi-restraints excluded: chain q residue 68 SER Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 69 THR Chi-restraints excluded: chain s residue 83 LEU Chi-restraints excluded: chain s residue 86 MET Chi-restraints excluded: chain s residue 152 GLN Chi-restraints excluded: chain s residue 200 LEU Chi-restraints excluded: chain s residue 229 LEU Chi-restraints excluded: chain s residue 241 ILE Chi-restraints excluded: chain s residue 259 ILE Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain s residue 374 LEU Chi-restraints excluded: chain s residue 396 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 886 random chunks: chunk 713 optimal weight: 30.0000 chunk 486 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 637 optimal weight: 0.6980 chunk 353 optimal weight: 0.8980 chunk 730 optimal weight: 5.9990 chunk 591 optimal weight: 20.0000 chunk 1 optimal weight: 2.9990 chunk 437 optimal weight: 0.5980 chunk 768 optimal weight: 5.9990 chunk 216 optimal weight: 10.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 72 GLN H 121 ASN ** K 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 104 ASN Q 107 HIS R 63 ASN ** R 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 23 ASN ** Z 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 67 HIS 5 146 HIS ** 5 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 163 HIS 6 239 ASN 6 307 HIS ** b 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 127 GLN b 129 GLN d 161 HIS ** e 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 281 HIS s 358 GLN s 382 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 94831 Z= 0.155 Angle : 0.550 16.120 133991 Z= 0.276 Chirality : 0.038 0.302 15614 Planarity : 0.004 0.062 12697 Dihedral : 20.202 179.730 26849 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.31 % Favored : 96.67 % Rotamer: Outliers : 2.42 % Allowed : 14.81 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: 7728 helix: 1.22 (0.10), residues: 2622 sheet: -0.72 (0.16), residues: 997 loop : -0.52 (0.10), residues: 4109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP d 183 HIS 0.008 0.001 HIS o 94 PHE 0.041 0.001 PHE e 128 TYR 0.021 0.001 TYR S 92 ARG 0.007 0.000 ARG K 154 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15456 Ramachandran restraints generated. 7728 Oldfield, 0 Emsley, 7728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15456 Ramachandran restraints generated. 7728 Oldfield, 0 Emsley, 7728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1263 residues out of total 6963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 1095 time to evaluate : 6.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 184 LEU cc_start: 0.6155 (OUTLIER) cc_final: 0.5772 (mm) REVERT: F 82 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8521 (mt) REVERT: I 152 MET cc_start: 0.4416 (OUTLIER) cc_final: 0.3831 (pmm) REVERT: M 130 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.7962 (pt0) REVERT: P 87 GLN cc_start: 0.8049 (tt0) cc_final: 0.7642 (tt0) REVERT: Q 136 ILE cc_start: 0.7801 (OUTLIER) cc_final: 0.7449 (tp) REVERT: R 59 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.7689 (mm) REVERT: S 170 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8634 (mm) REVERT: X 64 ASP cc_start: 0.8066 (OUTLIER) cc_final: 0.7767 (p0) REVERT: 6 170 ARG cc_start: 0.4551 (mtt180) cc_final: 0.3881 (mtt180) REVERT: 7 81 MET cc_start: 0.7552 (OUTLIER) cc_final: 0.7328 (mtp) REVERT: i 42 LYS cc_start: 0.7383 (ttpp) cc_final: 0.7123 (tptt) REVERT: i 128 ARG cc_start: 0.6607 (OUTLIER) cc_final: 0.3682 (ptp90) REVERT: o 35 MET cc_start: 0.8534 (ttt) cc_final: 0.8272 (ttt) outliers start: 168 outliers final: 107 residues processed: 1201 average time/residue: 0.8729 time to fit residues: 1758.7300 Evaluate side-chains 1153 residues out of total 6963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 1036 time to evaluate : 6.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 331 ASP Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 84 ARG Chi-restraints excluded: chain I residue 94 ARG Chi-restraints excluded: chain I residue 152 MET Chi-restraints excluded: chain I residue 166 ARG Chi-restraints excluded: chain I residue 174 LEU Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain M residue 130 GLN Chi-restraints excluded: chain M residue 146 ASP Chi-restraints excluded: chain M residue 167 ILE Chi-restraints excluded: chain M residue 234 LEU Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain M residue 279 ASP Chi-restraints excluded: chain N residue 70 SER Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain N residue 176 LEU Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain P residue 44 VAL Chi-restraints excluded: chain P residue 102 VAL Chi-restraints excluded: chain P residue 147 GLN Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 136 ILE Chi-restraints excluded: chain Q residue 154 VAL Chi-restraints excluded: chain Q residue 278 ILE Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain S residue 86 MET Chi-restraints excluded: chain S residue 114 ILE Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 164 THR Chi-restraints excluded: chain S residue 170 ILE Chi-restraints excluded: chain S residue 185 ILE Chi-restraints excluded: chain S residue 186 VAL Chi-restraints excluded: chain V residue 69 ASP Chi-restraints excluded: chain V residue 191 LEU Chi-restraints excluded: chain V residue 193 THR Chi-restraints excluded: chain W residue 46 SER Chi-restraints excluded: chain W residue 83 VAL Chi-restraints excluded: chain X residue 22 SER Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain X residue 128 THR Chi-restraints excluded: chain X residue 137 GLU Chi-restraints excluded: chain X residue 142 ASP Chi-restraints excluded: chain 0 residue 102 LYS Chi-restraints excluded: chain 0 residue 105 ASN Chi-restraints excluded: chain 0 residue 186 THR Chi-restraints excluded: chain 1 residue 33 LYS Chi-restraints excluded: chain 2 residue 56 SER Chi-restraints excluded: chain 3 residue 94 LEU Chi-restraints excluded: chain 3 residue 186 LEU Chi-restraints excluded: chain 5 residue 67 VAL Chi-restraints excluded: chain 5 residue 365 ASP Chi-restraints excluded: chain 6 residue 45 LEU Chi-restraints excluded: chain 6 residue 132 LEU Chi-restraints excluded: chain 6 residue 166 THR Chi-restraints excluded: chain 6 residue 174 HIS Chi-restraints excluded: chain 6 residue 184 LEU Chi-restraints excluded: chain 6 residue 325 ASP Chi-restraints excluded: chain 6 residue 328 THR Chi-restraints excluded: chain 7 residue 59 THR Chi-restraints excluded: chain 7 residue 70 VAL Chi-restraints excluded: chain 7 residue 78 VAL Chi-restraints excluded: chain 7 residue 81 MET Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 314 ASP Chi-restraints excluded: chain 8 residue 132 GLU Chi-restraints excluded: chain 8 residue 141 GLU Chi-restraints excluded: chain 8 residue 165 ASP Chi-restraints excluded: chain 9 residue 46 SER Chi-restraints excluded: chain 9 residue 130 LEU Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain b residue 32 SER Chi-restraints excluded: chain b residue 138 THR Chi-restraints excluded: chain c residue 274 LEU Chi-restraints excluded: chain c residue 307 PHE Chi-restraints excluded: chain d residue 160 LEU Chi-restraints excluded: chain d residue 193 HIS Chi-restraints excluded: chain d residue 243 LEU Chi-restraints excluded: chain e residue 93 ASP Chi-restraints excluded: chain e residue 275 PHE Chi-restraints excluded: chain g residue 68 THR Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain h residue 120 MET Chi-restraints excluded: chain i residue 128 ARG Chi-restraints excluded: chain k residue 54 ASP Chi-restraints excluded: chain k residue 55 VAL Chi-restraints excluded: chain m residue 54 VAL Chi-restraints excluded: chain o residue 58 GLN Chi-restraints excluded: chain p residue 111 ILE Chi-restraints excluded: chain p residue 136 THR Chi-restraints excluded: chain q residue 52 LEU Chi-restraints excluded: chain q residue 68 SER Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 83 LEU Chi-restraints excluded: chain s residue 118 LEU Chi-restraints excluded: chain s residue 152 GLN Chi-restraints excluded: chain s residue 200 LEU Chi-restraints excluded: chain s residue 241 ILE Chi-restraints excluded: chain s residue 301 LEU Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain s residue 374 LEU Chi-restraints excluded: chain s residue 396 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 886 random chunks: chunk 288 optimal weight: 1.9990 chunk 771 optimal weight: 4.9990 chunk 169 optimal weight: 20.0000 chunk 502 optimal weight: 9.9990 chunk 211 optimal weight: 10.0000 chunk 857 optimal weight: 4.9990 chunk 711 optimal weight: 0.0980 chunk 396 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 283 optimal weight: 3.9990 chunk 450 optimal weight: 9.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 87 HIS E 72 GLN H 121 ASN K 26 GLN M 102 GLN O 91 GLN ** R 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 179 ASN T 133 ASN U 23 ASN V 18 HIS X 175 GLN ** Z 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 67 HIS Z 136 ASN 5 146 HIS ** 5 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 163 HIS ** 6 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 128 GLN c 204 GLN d 161 HIS ** e 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 124 GLN ** s 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 382 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 94831 Z= 0.234 Angle : 0.573 15.689 133991 Z= 0.286 Chirality : 0.039 0.338 15614 Planarity : 0.005 0.081 12697 Dihedral : 20.141 179.901 26849 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.78 % Favored : 96.21 % Rotamer: Outliers : 2.87 % Allowed : 15.03 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: 0.10 (0.10), residues: 7728 helix: 1.29 (0.10), residues: 2622 sheet: -0.69 (0.16), residues: 1013 loop : -0.49 (0.10), residues: 4093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP Q 264 HIS 0.008 0.001 HIS o 94 PHE 0.047 0.001 PHE e 128 TYR 0.020 0.001 TYR 5 176 ARG 0.008 0.000 ARG r 189 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15456 Ramachandran restraints generated. 7728 Oldfield, 0 Emsley, 7728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15456 Ramachandran restraints generated. 7728 Oldfield, 0 Emsley, 7728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1246 residues out of total 6963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 1047 time to evaluate : 6.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 184 LEU cc_start: 0.6255 (OUTLIER) cc_final: 0.5864 (mm) REVERT: F 82 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8540 (mt) REVERT: I 152 MET cc_start: 0.4493 (OUTLIER) cc_final: 0.3918 (pmm) REVERT: M 130 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.7922 (pt0) REVERT: P 87 GLN cc_start: 0.8094 (tt0) cc_final: 0.7715 (tt0) REVERT: Q 136 ILE cc_start: 0.7823 (OUTLIER) cc_final: 0.7439 (tp) REVERT: R 59 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.7729 (mm) REVERT: S 170 ILE cc_start: 0.8899 (OUTLIER) cc_final: 0.8656 (mm) REVERT: T 133 ASN cc_start: 0.7867 (t0) cc_final: 0.7606 (t0) REVERT: X 192 LYS cc_start: 0.7946 (mttp) cc_final: 0.7738 (mttp) REVERT: 5 165 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7325 (tm-30) REVERT: 5 358 GLN cc_start: 0.7293 (OUTLIER) cc_final: 0.6893 (tm-30) REVERT: 6 37 ASN cc_start: 0.8000 (m-40) cc_final: 0.7798 (m110) REVERT: 6 170 ARG cc_start: 0.4690 (mtt180) cc_final: 0.3926 (mtt180) REVERT: 7 81 MET cc_start: 0.7643 (OUTLIER) cc_final: 0.7335 (mtp) REVERT: i 42 LYS cc_start: 0.7419 (ttpp) cc_final: 0.7152 (tptt) REVERT: i 128 ARG cc_start: 0.6705 (OUTLIER) cc_final: 0.3539 (ptp90) REVERT: o 35 MET cc_start: 0.8590 (ttt) cc_final: 0.8321 (ttt) REVERT: q 125 MET cc_start: 0.7260 (mmm) cc_final: 0.6628 (mmp) outliers start: 199 outliers final: 152 residues processed: 1165 average time/residue: 0.8795 time to fit residues: 1718.8188 Evaluate side-chains 1162 residues out of total 6963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 999 time to evaluate : 6.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain E residue 107 MET Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 331 ASP Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 84 ARG Chi-restraints excluded: chain I residue 94 ARG Chi-restraints excluded: chain I residue 152 MET Chi-restraints excluded: chain I residue 166 ARG Chi-restraints excluded: chain I residue 168 LEU Chi-restraints excluded: chain I residue 174 LEU Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain M residue 130 GLN Chi-restraints excluded: chain M residue 146 ASP Chi-restraints excluded: chain M residue 149 THR Chi-restraints excluded: chain M residue 167 ILE Chi-restraints excluded: chain M residue 234 LEU Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain M residue 279 ASP Chi-restraints excluded: chain N residue 70 SER Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain N residue 176 LEU Chi-restraints excluded: chain N residue 214 THR Chi-restraints excluded: chain O residue 18 MET Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain P residue 44 VAL Chi-restraints excluded: chain P residue 102 VAL Chi-restraints excluded: chain P residue 147 GLN Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 136 ILE Chi-restraints excluded: chain Q residue 154 VAL Chi-restraints excluded: chain Q residue 278 ILE Chi-restraints excluded: chain R residue 16 ASP Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain S residue 86 MET Chi-restraints excluded: chain S residue 114 ILE Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 164 THR Chi-restraints excluded: chain S residue 170 ILE Chi-restraints excluded: chain S residue 185 ILE Chi-restraints excluded: chain S residue 186 VAL Chi-restraints excluded: chain T residue 138 SER Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 24 PHE Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 51 VAL Chi-restraints excluded: chain V residue 69 ASP Chi-restraints excluded: chain V residue 191 LEU Chi-restraints excluded: chain V residue 193 THR Chi-restraints excluded: chain W residue 46 SER Chi-restraints excluded: chain W residue 61 VAL Chi-restraints excluded: chain W residue 83 VAL Chi-restraints excluded: chain W residue 105 VAL Chi-restraints excluded: chain X residue 22 SER Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain X residue 101 LEU Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain X residue 128 THR Chi-restraints excluded: chain X residue 137 GLU Chi-restraints excluded: chain X residue 142 ASP Chi-restraints excluded: chain Y residue 172 ILE Chi-restraints excluded: chain Y residue 176 ILE Chi-restraints excluded: chain Z residue 92 GLU Chi-restraints excluded: chain Z residue 135 SER Chi-restraints excluded: chain Z residue 136 ASN Chi-restraints excluded: chain 0 residue 105 ASN Chi-restraints excluded: chain 0 residue 186 THR Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 1 residue 33 LYS Chi-restraints excluded: chain 2 residue 56 SER Chi-restraints excluded: chain 3 residue 94 LEU Chi-restraints excluded: chain 3 residue 156 LYS Chi-restraints excluded: chain 3 residue 186 LEU Chi-restraints excluded: chain 5 residue 67 VAL Chi-restraints excluded: chain 5 residue 165 GLN Chi-restraints excluded: chain 5 residue 167 THR Chi-restraints excluded: chain 5 residue 295 ASP Chi-restraints excluded: chain 5 residue 358 GLN Chi-restraints excluded: chain 5 residue 365 ASP Chi-restraints excluded: chain 5 residue 391 VAL Chi-restraints excluded: chain 6 residue 45 LEU Chi-restraints excluded: chain 6 residue 125 LEU Chi-restraints excluded: chain 6 residue 132 LEU Chi-restraints excluded: chain 6 residue 166 THR Chi-restraints excluded: chain 6 residue 174 HIS Chi-restraints excluded: chain 6 residue 184 LEU Chi-restraints excluded: chain 6 residue 222 ASP Chi-restraints excluded: chain 6 residue 325 ASP Chi-restraints excluded: chain 6 residue 327 VAL Chi-restraints excluded: chain 6 residue 328 THR Chi-restraints excluded: chain 7 residue 59 THR Chi-restraints excluded: chain 7 residue 70 VAL Chi-restraints excluded: chain 7 residue 78 VAL Chi-restraints excluded: chain 7 residue 81 MET Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 314 ASP Chi-restraints excluded: chain 8 residue 132 GLU Chi-restraints excluded: chain 8 residue 141 GLU Chi-restraints excluded: chain 8 residue 165 ASP Chi-restraints excluded: chain 9 residue 46 SER Chi-restraints excluded: chain 9 residue 130 LEU Chi-restraints excluded: chain a residue 54 ASP Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 126 HIS Chi-restraints excluded: chain b residue 32 SER Chi-restraints excluded: chain b residue 138 THR Chi-restraints excluded: chain c residue 274 LEU Chi-restraints excluded: chain c residue 280 LEU Chi-restraints excluded: chain d residue 160 LEU Chi-restraints excluded: chain d residue 193 HIS Chi-restraints excluded: chain d residue 243 LEU Chi-restraints excluded: chain e residue 93 ASP Chi-restraints excluded: chain e residue 275 PHE Chi-restraints excluded: chain f residue 90 VAL Chi-restraints excluded: chain g residue 68 THR Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain h residue 120 MET Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain i residue 128 ARG Chi-restraints excluded: chain k residue 54 ASP Chi-restraints excluded: chain k residue 55 VAL Chi-restraints excluded: chain m residue 54 VAL Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 44 GLU Chi-restraints excluded: chain o residue 51 MET Chi-restraints excluded: chain o residue 58 GLN Chi-restraints excluded: chain p residue 111 ILE Chi-restraints excluded: chain p residue 136 THR Chi-restraints excluded: chain q residue 52 LEU Chi-restraints excluded: chain q residue 68 SER Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 83 LEU Chi-restraints excluded: chain s residue 86 MET Chi-restraints excluded: chain s residue 118 LEU Chi-restraints excluded: chain s residue 152 GLN Chi-restraints excluded: chain s residue 171 VAL Chi-restraints excluded: chain s residue 200 LEU Chi-restraints excluded: chain s residue 229 LEU Chi-restraints excluded: chain s residue 241 ILE Chi-restraints excluded: chain s residue 301 LEU Chi-restraints excluded: chain s residue 318 ASP Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain s residue 374 LEU Chi-restraints excluded: chain s residue 396 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 886 random chunks: chunk 826 optimal weight: 6.9990 chunk 96 optimal weight: 0.7980 chunk 488 optimal weight: 8.9990 chunk 626 optimal weight: 0.9990 chunk 485 optimal weight: 1.9990 chunk 721 optimal weight: 9.9990 chunk 478 optimal weight: 5.9990 chunk 853 optimal weight: 6.9990 chunk 534 optimal weight: 4.9990 chunk 520 optimal weight: 7.9990 chunk 394 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 121 ASN ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 33 GLN O 91 GLN ** P 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 107 HIS ** R 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 74 HIS V 18 HIS ** Z 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 146 HIS ** 5 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 163 HIS ** 6 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 165 ASN c 204 GLN d 161 HIS ** e 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 51 GLN ** s 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 382 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 94831 Z= 0.290 Angle : 0.600 15.155 133991 Z= 0.299 Chirality : 0.041 0.314 15614 Planarity : 0.005 0.087 12697 Dihedral : 20.149 179.283 26849 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.83 % Favored : 96.16 % Rotamer: Outliers : 3.13 % Allowed : 15.23 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: 0.11 (0.10), residues: 7728 helix: 1.30 (0.10), residues: 2620 sheet: -0.69 (0.16), residues: 1023 loop : -0.49 (0.10), residues: 4085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP Q 264 HIS 0.008 0.001 HIS o 94 PHE 0.051 0.002 PHE e 128 TYR 0.024 0.001 TYR S 92 ARG 0.009 0.000 ARG s 428 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15456 Ramachandran restraints generated. 7728 Oldfield, 0 Emsley, 7728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15456 Ramachandran restraints generated. 7728 Oldfield, 0 Emsley, 7728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1257 residues out of total 6963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 1040 time to evaluate : 6.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 184 LEU cc_start: 0.6380 (OUTLIER) cc_final: 0.6145 (mm) REVERT: F 82 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8595 (mt) REVERT: I 152 MET cc_start: 0.4273 (OUTLIER) cc_final: 0.3720 (pmm) REVERT: K 73 GLU cc_start: 0.8039 (mp0) cc_final: 0.7756 (mp0) REVERT: M 130 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.7928 (pt0) REVERT: P 87 GLN cc_start: 0.8152 (tt0) cc_final: 0.7862 (tt0) REVERT: Q 136 ILE cc_start: 0.7860 (OUTLIER) cc_final: 0.7445 (tp) REVERT: R 59 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.7788 (mm) REVERT: S 170 ILE cc_start: 0.8915 (OUTLIER) cc_final: 0.8661 (mm) REVERT: T 133 ASN cc_start: 0.7946 (t0) cc_final: 0.7688 (t0) REVERT: 5 165 GLN cc_start: 0.7899 (OUTLIER) cc_final: 0.7333 (tm-30) REVERT: 5 358 GLN cc_start: 0.7284 (OUTLIER) cc_final: 0.6894 (tm-30) REVERT: 6 170 ARG cc_start: 0.4754 (mtt180) cc_final: 0.3981 (mtt180) REVERT: 7 81 MET cc_start: 0.7701 (OUTLIER) cc_final: 0.7397 (mtp) REVERT: a 132 CYS cc_start: 0.6507 (m) cc_final: 0.6270 (m) REVERT: e 257 LYS cc_start: 0.4354 (tptt) cc_final: 0.3902 (tptp) REVERT: i 42 LYS cc_start: 0.7438 (ttpp) cc_final: 0.7101 (tptt) REVERT: i 128 ARG cc_start: 0.6703 (OUTLIER) cc_final: 0.3559 (ptp90) REVERT: o 35 MET cc_start: 0.8609 (ttt) cc_final: 0.8332 (ttt) REVERT: o 58 GLN cc_start: 0.9001 (OUTLIER) cc_final: 0.8462 (mt0) REVERT: q 125 MET cc_start: 0.7336 (mmm) cc_final: 0.6841 (mmp) REVERT: s 373 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.6965 (tm-30) outliers start: 217 outliers final: 175 residues processed: 1168 average time/residue: 0.8979 time to fit residues: 1755.0129 Evaluate side-chains 1196 residues out of total 6963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 1008 time to evaluate : 6.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain E residue 107 MET Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 331 ASP Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 124 LEU Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 84 ARG Chi-restraints excluded: chain I residue 94 ARG Chi-restraints excluded: chain I residue 152 MET Chi-restraints excluded: chain I residue 166 ARG Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain M residue 130 GLN Chi-restraints excluded: chain M residue 146 ASP Chi-restraints excluded: chain M residue 149 THR Chi-restraints excluded: chain M residue 167 ILE Chi-restraints excluded: chain M residue 234 LEU Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain M residue 279 ASP Chi-restraints excluded: chain N residue 70 SER Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain N residue 132 THR Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain N residue 176 LEU Chi-restraints excluded: chain N residue 214 THR Chi-restraints excluded: chain N residue 220 THR Chi-restraints excluded: chain O residue 18 MET Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 84 ASP Chi-restraints excluded: chain O residue 110 ILE Chi-restraints excluded: chain P residue 44 VAL Chi-restraints excluded: chain P residue 102 VAL Chi-restraints excluded: chain P residue 147 GLN Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 136 ILE Chi-restraints excluded: chain Q residue 150 ILE Chi-restraints excluded: chain Q residue 154 VAL Chi-restraints excluded: chain R residue 16 ASP Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain S residue 86 MET Chi-restraints excluded: chain S residue 114 ILE Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 164 THR Chi-restraints excluded: chain S residue 170 ILE Chi-restraints excluded: chain S residue 185 ILE Chi-restraints excluded: chain S residue 186 VAL Chi-restraints excluded: chain T residue 138 SER Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 24 PHE Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 51 VAL Chi-restraints excluded: chain V residue 69 ASP Chi-restraints excluded: chain V residue 191 LEU Chi-restraints excluded: chain V residue 193 THR Chi-restraints excluded: chain W residue 46 SER Chi-restraints excluded: chain W residue 61 VAL Chi-restraints excluded: chain W residue 83 VAL Chi-restraints excluded: chain W residue 105 VAL Chi-restraints excluded: chain X residue 22 SER Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain X residue 101 LEU Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain X residue 128 THR Chi-restraints excluded: chain X residue 137 GLU Chi-restraints excluded: chain X residue 142 ASP Chi-restraints excluded: chain Y residue 172 ILE Chi-restraints excluded: chain Y residue 176 ILE Chi-restraints excluded: chain Z residue 92 GLU Chi-restraints excluded: chain Z residue 105 SER Chi-restraints excluded: chain Z residue 146 VAL Chi-restraints excluded: chain 0 residue 96 ASN Chi-restraints excluded: chain 0 residue 102 LYS Chi-restraints excluded: chain 0 residue 105 ASN Chi-restraints excluded: chain 0 residue 186 THR Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 1 residue 33 LYS Chi-restraints excluded: chain 2 residue 56 SER Chi-restraints excluded: chain 3 residue 94 LEU Chi-restraints excluded: chain 3 residue 156 LYS Chi-restraints excluded: chain 3 residue 186 LEU Chi-restraints excluded: chain 5 residue 74 ILE Chi-restraints excluded: chain 5 residue 106 ILE Chi-restraints excluded: chain 5 residue 165 GLN Chi-restraints excluded: chain 5 residue 167 THR Chi-restraints excluded: chain 5 residue 193 LEU Chi-restraints excluded: chain 5 residue 208 THR Chi-restraints excluded: chain 5 residue 295 ASP Chi-restraints excluded: chain 5 residue 358 GLN Chi-restraints excluded: chain 5 residue 359 LEU Chi-restraints excluded: chain 5 residue 365 ASP Chi-restraints excluded: chain 5 residue 391 VAL Chi-restraints excluded: chain 6 residue 125 LEU Chi-restraints excluded: chain 6 residue 132 LEU Chi-restraints excluded: chain 6 residue 166 THR Chi-restraints excluded: chain 6 residue 174 HIS Chi-restraints excluded: chain 6 residue 184 LEU Chi-restraints excluded: chain 6 residue 222 ASP Chi-restraints excluded: chain 6 residue 325 ASP Chi-restraints excluded: chain 6 residue 327 VAL Chi-restraints excluded: chain 6 residue 328 THR Chi-restraints excluded: chain 7 residue 59 THR Chi-restraints excluded: chain 7 residue 70 VAL Chi-restraints excluded: chain 7 residue 78 VAL Chi-restraints excluded: chain 7 residue 81 MET Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 314 ASP Chi-restraints excluded: chain 8 residue 132 GLU Chi-restraints excluded: chain 8 residue 141 GLU Chi-restraints excluded: chain 8 residue 165 ASP Chi-restraints excluded: chain 9 residue 46 SER Chi-restraints excluded: chain 9 residue 130 LEU Chi-restraints excluded: chain a residue 54 ASP Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 126 HIS Chi-restraints excluded: chain b residue 32 SER Chi-restraints excluded: chain b residue 75 VAL Chi-restraints excluded: chain b residue 122 ASP Chi-restraints excluded: chain b residue 138 THR Chi-restraints excluded: chain c residue 142 GLU Chi-restraints excluded: chain c residue 274 LEU Chi-restraints excluded: chain c residue 280 LEU Chi-restraints excluded: chain d residue 160 LEU Chi-restraints excluded: chain d residue 180 THR Chi-restraints excluded: chain d residue 193 HIS Chi-restraints excluded: chain d residue 243 LEU Chi-restraints excluded: chain e residue 93 ASP Chi-restraints excluded: chain e residue 131 PHE Chi-restraints excluded: chain e residue 275 PHE Chi-restraints excluded: chain f residue 90 VAL Chi-restraints excluded: chain g residue 68 THR Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain h residue 120 MET Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain i residue 110 LEU Chi-restraints excluded: chain i residue 128 ARG Chi-restraints excluded: chain k residue 54 ASP Chi-restraints excluded: chain k residue 55 VAL Chi-restraints excluded: chain m residue 54 VAL Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 44 GLU Chi-restraints excluded: chain o residue 51 MET Chi-restraints excluded: chain o residue 58 GLN Chi-restraints excluded: chain p residue 61 VAL Chi-restraints excluded: chain p residue 111 ILE Chi-restraints excluded: chain p residue 135 LEU Chi-restraints excluded: chain p residue 136 THR Chi-restraints excluded: chain q residue 52 LEU Chi-restraints excluded: chain q residue 68 SER Chi-restraints excluded: chain r residue 183 ASP Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 69 THR Chi-restraints excluded: chain s residue 83 LEU Chi-restraints excluded: chain s residue 86 MET Chi-restraints excluded: chain s residue 152 GLN Chi-restraints excluded: chain s residue 171 VAL Chi-restraints excluded: chain s residue 200 LEU Chi-restraints excluded: chain s residue 229 LEU Chi-restraints excluded: chain s residue 241 ILE Chi-restraints excluded: chain s residue 301 LEU Chi-restraints excluded: chain s residue 318 ASP Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain s residue 373 GLN Chi-restraints excluded: chain s residue 374 LEU Chi-restraints excluded: chain s residue 396 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 886 random chunks: chunk 528 optimal weight: 0.7980 chunk 341 optimal weight: 2.9990 chunk 510 optimal weight: 5.9990 chunk 257 optimal weight: 1.9990 chunk 167 optimal weight: 0.9980 chunk 165 optimal weight: 0.0980 chunk 542 optimal weight: 4.9990 chunk 581 optimal weight: 9.9990 chunk 422 optimal weight: 0.0570 chunk 79 optimal weight: 10.0000 chunk 671 optimal weight: 50.0000 overall best weight: 0.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 121 ASN I 101 ASN L 33 GLN O 91 GLN ** P 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 18 HIS V 73 GLN Z 67 HIS Z 136 ASN 5 146 HIS ** 5 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 37 ASN 6 163 HIS ** 6 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 128 GLN c 204 GLN d 161 HIS ** e 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 72 HIS ** s 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 382 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 94831 Z= 0.153 Angle : 0.545 14.830 133991 Z= 0.271 Chirality : 0.037 0.298 15614 Planarity : 0.004 0.060 12697 Dihedral : 20.096 179.859 26849 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.42 % Favored : 96.57 % Rotamer: Outliers : 2.51 % Allowed : 16.18 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: 0.31 (0.10), residues: 7728 helix: 1.49 (0.10), residues: 2617 sheet: -0.56 (0.16), residues: 1009 loop : -0.39 (0.10), residues: 4102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP Q 264 HIS 0.008 0.001 HIS o 94 PHE 0.054 0.001 PHE e 128 TYR 0.022 0.001 TYR e 84 ARG 0.011 0.000 ARG Q 244 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15456 Ramachandran restraints generated. 7728 Oldfield, 0 Emsley, 7728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15456 Ramachandran restraints generated. 7728 Oldfield, 0 Emsley, 7728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1244 residues out of total 6963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 1070 time to evaluate : 6.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 82 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8501 (mt) REVERT: I 152 MET cc_start: 0.4073 (OUTLIER) cc_final: 0.3571 (pmm) REVERT: P 87 GLN cc_start: 0.8116 (tt0) cc_final: 0.7836 (tt0) REVERT: Q 136 ILE cc_start: 0.7878 (OUTLIER) cc_final: 0.7460 (tp) REVERT: R 59 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.7686 (mm) REVERT: S 170 ILE cc_start: 0.8851 (OUTLIER) cc_final: 0.8640 (mm) REVERT: T 133 ASN cc_start: 0.7941 (t0) cc_final: 0.7685 (t0) REVERT: W 93 GLU cc_start: 0.7457 (mm-30) cc_final: 0.7202 (mm-30) REVERT: X 64 ASP cc_start: 0.8023 (OUTLIER) cc_final: 0.7694 (p0) REVERT: Y 224 GLU cc_start: 0.7513 (mt-10) cc_final: 0.7268 (mt-10) REVERT: 5 165 GLN cc_start: 0.7849 (OUTLIER) cc_final: 0.7256 (tm-30) REVERT: 5 358 GLN cc_start: 0.7286 (OUTLIER) cc_final: 0.6907 (tm-30) REVERT: 6 170 ARG cc_start: 0.4559 (mtt180) cc_final: 0.3974 (mtt180) REVERT: e 257 LYS cc_start: 0.4155 (tptt) cc_final: 0.3656 (tptp) REVERT: i 42 LYS cc_start: 0.7405 (ttpp) cc_final: 0.7148 (tptt) REVERT: i 128 ARG cc_start: 0.6631 (OUTLIER) cc_final: 0.3700 (ptp90) REVERT: o 35 MET cc_start: 0.8538 (ttt) cc_final: 0.8302 (ttt) REVERT: o 52 PRO cc_start: 0.8598 (Cg_endo) cc_final: 0.8346 (Cg_exo) REVERT: q 125 MET cc_start: 0.7466 (mmm) cc_final: 0.6907 (mmp) REVERT: s 373 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.6915 (tm-30) outliers start: 174 outliers final: 133 residues processed: 1177 average time/residue: 0.8741 time to fit residues: 1725.8926 Evaluate side-chains 1167 residues out of total 6963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 1024 time to evaluate : 6.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 207 ILE Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain E residue 107 MET Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 331 ASP Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 84 ARG Chi-restraints excluded: chain I residue 94 ARG Chi-restraints excluded: chain I residue 152 MET Chi-restraints excluded: chain I residue 166 ARG Chi-restraints excluded: chain I residue 174 LEU Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 146 ASP Chi-restraints excluded: chain M residue 234 LEU Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain M residue 279 ASP Chi-restraints excluded: chain N residue 70 SER Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain O residue 18 MET Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 23 GLU Chi-restraints excluded: chain O residue 110 ILE Chi-restraints excluded: chain P residue 44 VAL Chi-restraints excluded: chain P residue 98 ASN Chi-restraints excluded: chain P residue 102 VAL Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 136 ILE Chi-restraints excluded: chain Q residue 150 ILE Chi-restraints excluded: chain Q residue 154 VAL Chi-restraints excluded: chain R residue 16 ASP Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain S residue 114 ILE Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 164 THR Chi-restraints excluded: chain S residue 170 ILE Chi-restraints excluded: chain S residue 185 ILE Chi-restraints excluded: chain S residue 186 VAL Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain V residue 69 ASP Chi-restraints excluded: chain V residue 191 LEU Chi-restraints excluded: chain V residue 193 THR Chi-restraints excluded: chain W residue 46 SER Chi-restraints excluded: chain W residue 61 VAL Chi-restraints excluded: chain W residue 83 VAL Chi-restraints excluded: chain X residue 22 SER Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain X residue 101 LEU Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain X residue 128 THR Chi-restraints excluded: chain X residue 137 GLU Chi-restraints excluded: chain X residue 142 ASP Chi-restraints excluded: chain Z residue 92 GLU Chi-restraints excluded: chain 0 residue 102 LYS Chi-restraints excluded: chain 0 residue 105 ASN Chi-restraints excluded: chain 2 residue 56 SER Chi-restraints excluded: chain 3 residue 94 LEU Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 3 residue 186 LEU Chi-restraints excluded: chain 5 residue 67 VAL Chi-restraints excluded: chain 5 residue 74 ILE Chi-restraints excluded: chain 5 residue 165 GLN Chi-restraints excluded: chain 5 residue 167 THR Chi-restraints excluded: chain 5 residue 193 LEU Chi-restraints excluded: chain 5 residue 358 GLN Chi-restraints excluded: chain 5 residue 359 LEU Chi-restraints excluded: chain 5 residue 365 ASP Chi-restraints excluded: chain 6 residue 45 LEU Chi-restraints excluded: chain 6 residue 125 LEU Chi-restraints excluded: chain 6 residue 132 LEU Chi-restraints excluded: chain 6 residue 166 THR Chi-restraints excluded: chain 6 residue 174 HIS Chi-restraints excluded: chain 6 residue 184 LEU Chi-restraints excluded: chain 6 residue 222 ASP Chi-restraints excluded: chain 6 residue 325 ASP Chi-restraints excluded: chain 6 residue 327 VAL Chi-restraints excluded: chain 6 residue 328 THR Chi-restraints excluded: chain 7 residue 59 THR Chi-restraints excluded: chain 7 residue 70 VAL Chi-restraints excluded: chain 7 residue 78 VAL Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 314 ASP Chi-restraints excluded: chain 8 residue 132 GLU Chi-restraints excluded: chain 8 residue 141 GLU Chi-restraints excluded: chain 8 residue 165 ASP Chi-restraints excluded: chain 9 residue 46 SER Chi-restraints excluded: chain 9 residue 130 LEU Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 126 HIS Chi-restraints excluded: chain b residue 32 SER Chi-restraints excluded: chain b residue 75 VAL Chi-restraints excluded: chain b residue 138 THR Chi-restraints excluded: chain c residue 274 LEU Chi-restraints excluded: chain d residue 193 HIS Chi-restraints excluded: chain d residue 243 LEU Chi-restraints excluded: chain e residue 93 ASP Chi-restraints excluded: chain e residue 131 PHE Chi-restraints excluded: chain e residue 275 PHE Chi-restraints excluded: chain f residue 90 VAL Chi-restraints excluded: chain g residue 68 THR Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain h residue 120 MET Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain i residue 128 ARG Chi-restraints excluded: chain k residue 54 ASP Chi-restraints excluded: chain k residue 55 VAL Chi-restraints excluded: chain m residue 54 VAL Chi-restraints excluded: chain o residue 58 GLN Chi-restraints excluded: chain p residue 111 ILE Chi-restraints excluded: chain q residue 52 LEU Chi-restraints excluded: chain q residue 68 SER Chi-restraints excluded: chain s residue 83 LEU Chi-restraints excluded: chain s residue 86 MET Chi-restraints excluded: chain s residue 118 LEU Chi-restraints excluded: chain s residue 152 GLN Chi-restraints excluded: chain s residue 200 LEU Chi-restraints excluded: chain s residue 229 LEU Chi-restraints excluded: chain s residue 241 ILE Chi-restraints excluded: chain s residue 301 LEU Chi-restraints excluded: chain s residue 318 ASP Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain s residue 373 GLN Chi-restraints excluded: chain s residue 374 LEU Chi-restraints excluded: chain s residue 396 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 886 random chunks: chunk 776 optimal weight: 6.9990 chunk 818 optimal weight: 6.9990 chunk 746 optimal weight: 7.9990 chunk 795 optimal weight: 4.9990 chunk 817 optimal weight: 4.9990 chunk 478 optimal weight: 3.9990 chunk 346 optimal weight: 3.9990 chunk 624 optimal weight: 7.9990 chunk 244 optimal weight: 2.9990 chunk 719 optimal weight: 9.9990 chunk 752 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 91 GLN Q 107 HIS ** R 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 179 ASN V 18 HIS Z 67 HIS Z 136 ASN 1 52 GLN 5 146 HIS ** 5 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 163 HIS 6 307 HIS c 128 GLN c 204 GLN d 161 HIS ** e 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 31 GLN ** k 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 123 HIS ** s 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 382 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.100 94831 Z= 0.491 Angle : 0.704 14.146 133991 Z= 0.349 Chirality : 0.046 0.392 15614 Planarity : 0.006 0.122 12697 Dihedral : 20.189 179.970 26849 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.45 % Favored : 95.54 % Rotamer: Outliers : 2.87 % Allowed : 16.21 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: 0.04 (0.10), residues: 7728 helix: 1.21 (0.10), residues: 2613 sheet: -0.67 (0.16), residues: 1044 loop : -0.51 (0.10), residues: 4071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP Q 264 HIS 0.012 0.001 HIS I 41 PHE 0.055 0.002 PHE e 128 TYR 0.025 0.002 TYR S 92 ARG 0.013 0.001 ARG 2 87 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15456 Ramachandran restraints generated. 7728 Oldfield, 0 Emsley, 7728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15456 Ramachandran restraints generated. 7728 Oldfield, 0 Emsley, 7728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1245 residues out of total 6963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 1046 time to evaluate : 6.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 82 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8723 (mt) REVERT: F 170 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.6736 (mtp85) REVERT: I 152 MET cc_start: 0.4291 (OUTLIER) cc_final: 0.3691 (pmm) REVERT: K 73 GLU cc_start: 0.8094 (mp0) cc_final: 0.7780 (mp0) REVERT: M 130 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.8229 (pt0) REVERT: R 59 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.7905 (mm) REVERT: S 170 ILE cc_start: 0.8962 (OUTLIER) cc_final: 0.8700 (mm) REVERT: T 133 ASN cc_start: 0.7920 (t0) cc_final: 0.7684 (t0) REVERT: Y 238 PHE cc_start: 0.6756 (m-10) cc_final: 0.6444 (m-10) REVERT: 3 112 ASP cc_start: 0.8019 (m-30) cc_final: 0.7741 (m-30) REVERT: 3 156 LYS cc_start: 0.7658 (OUTLIER) cc_final: 0.7228 (mtmm) REVERT: 5 165 GLN cc_start: 0.7971 (OUTLIER) cc_final: 0.7441 (tm-30) REVERT: 5 264 ASP cc_start: 0.7442 (m-30) cc_final: 0.7141 (m-30) REVERT: 5 358 GLN cc_start: 0.7347 (OUTLIER) cc_final: 0.6947 (tm-30) REVERT: 6 170 ARG cc_start: 0.4697 (mtt180) cc_final: 0.3987 (mtt180) REVERT: e 257 LYS cc_start: 0.4186 (tptt) cc_final: 0.3800 (tptt) REVERT: i 42 LYS cc_start: 0.7389 (ttpp) cc_final: 0.7088 (tptt) REVERT: i 128 ARG cc_start: 0.6869 (OUTLIER) cc_final: 0.3953 (ptp90) REVERT: s 255 TYR cc_start: 0.7915 (t80) cc_final: 0.7658 (t80) REVERT: s 373 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.7193 (tm-30) outliers start: 199 outliers final: 170 residues processed: 1157 average time/residue: 0.8824 time to fit residues: 1707.5545 Evaluate side-chains 1185 residues out of total 6963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 1004 time to evaluate : 6.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 207 ILE Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain E residue 107 MET Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 331 ASP Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 170 ARG Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 124 LEU Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 84 ARG Chi-restraints excluded: chain I residue 94 ARG Chi-restraints excluded: chain I residue 152 MET Chi-restraints excluded: chain I residue 166 ARG Chi-restraints excluded: chain I residue 174 LEU Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain M residue 130 GLN Chi-restraints excluded: chain M residue 146 ASP Chi-restraints excluded: chain M residue 234 LEU Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain M residue 279 ASP Chi-restraints excluded: chain N residue 70 SER Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain N residue 132 THR Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain N residue 214 THR Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 23 GLU Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 84 ASP Chi-restraints excluded: chain O residue 110 ILE Chi-restraints excluded: chain P residue 44 VAL Chi-restraints excluded: chain P residue 102 VAL Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 150 ILE Chi-restraints excluded: chain Q residue 154 VAL Chi-restraints excluded: chain R residue 16 ASP Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain S residue 114 ILE Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 164 THR Chi-restraints excluded: chain S residue 170 ILE Chi-restraints excluded: chain S residue 185 ILE Chi-restraints excluded: chain S residue 186 VAL Chi-restraints excluded: chain T residue 138 SER Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 24 PHE Chi-restraints excluded: chain U residue 26 ILE Chi-restraints excluded: chain V residue 69 ASP Chi-restraints excluded: chain V residue 191 LEU Chi-restraints excluded: chain V residue 193 THR Chi-restraints excluded: chain W residue 46 SER Chi-restraints excluded: chain W residue 61 VAL Chi-restraints excluded: chain W residue 83 VAL Chi-restraints excluded: chain X residue 22 SER Chi-restraints excluded: chain X residue 36 ARG Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain X residue 101 LEU Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain X residue 137 GLU Chi-restraints excluded: chain X residue 222 ASP Chi-restraints excluded: chain Y residue 172 ILE Chi-restraints excluded: chain Y residue 176 ILE Chi-restraints excluded: chain Z residue 92 GLU Chi-restraints excluded: chain Z residue 105 SER Chi-restraints excluded: chain Z residue 136 ASN Chi-restraints excluded: chain 0 residue 96 ASN Chi-restraints excluded: chain 0 residue 102 LYS Chi-restraints excluded: chain 0 residue 105 ASN Chi-restraints excluded: chain 0 residue 157 VAL Chi-restraints excluded: chain 0 residue 186 THR Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 2 residue 56 SER Chi-restraints excluded: chain 3 residue 94 LEU Chi-restraints excluded: chain 3 residue 156 LYS Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 3 residue 186 LEU Chi-restraints excluded: chain 5 residue 74 ILE Chi-restraints excluded: chain 5 residue 165 GLN Chi-restraints excluded: chain 5 residue 167 THR Chi-restraints excluded: chain 5 residue 193 LEU Chi-restraints excluded: chain 5 residue 208 THR Chi-restraints excluded: chain 5 residue 358 GLN Chi-restraints excluded: chain 5 residue 359 LEU Chi-restraints excluded: chain 5 residue 365 ASP Chi-restraints excluded: chain 5 residue 391 VAL Chi-restraints excluded: chain 6 residue 125 LEU Chi-restraints excluded: chain 6 residue 132 LEU Chi-restraints excluded: chain 6 residue 166 THR Chi-restraints excluded: chain 6 residue 174 HIS Chi-restraints excluded: chain 6 residue 184 LEU Chi-restraints excluded: chain 6 residue 222 ASP Chi-restraints excluded: chain 6 residue 325 ASP Chi-restraints excluded: chain 6 residue 327 VAL Chi-restraints excluded: chain 6 residue 328 THR Chi-restraints excluded: chain 7 residue 59 THR Chi-restraints excluded: chain 7 residue 70 VAL Chi-restraints excluded: chain 7 residue 78 VAL Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 314 ASP Chi-restraints excluded: chain 8 residue 132 GLU Chi-restraints excluded: chain 8 residue 141 GLU Chi-restraints excluded: chain 8 residue 165 ASP Chi-restraints excluded: chain 9 residue 46 SER Chi-restraints excluded: chain 9 residue 130 LEU Chi-restraints excluded: chain a residue 54 ASP Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 126 HIS Chi-restraints excluded: chain b residue 32 SER Chi-restraints excluded: chain b residue 75 VAL Chi-restraints excluded: chain b residue 134 THR Chi-restraints excluded: chain b residue 138 THR Chi-restraints excluded: chain c residue 142 GLU Chi-restraints excluded: chain c residue 246 LYS Chi-restraints excluded: chain c residue 274 LEU Chi-restraints excluded: chain d residue 160 LEU Chi-restraints excluded: chain d residue 175 ASP Chi-restraints excluded: chain d residue 180 THR Chi-restraints excluded: chain d residue 193 HIS Chi-restraints excluded: chain d residue 243 LEU Chi-restraints excluded: chain e residue 93 ASP Chi-restraints excluded: chain e residue 131 PHE Chi-restraints excluded: chain e residue 275 PHE Chi-restraints excluded: chain f residue 53 THR Chi-restraints excluded: chain f residue 90 VAL Chi-restraints excluded: chain g residue 68 THR Chi-restraints excluded: chain g residue 108 THR Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain h residue 120 MET Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain i residue 110 LEU Chi-restraints excluded: chain i residue 128 ARG Chi-restraints excluded: chain k residue 54 ASP Chi-restraints excluded: chain k residue 55 VAL Chi-restraints excluded: chain m residue 54 VAL Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 58 GLN Chi-restraints excluded: chain p residue 61 VAL Chi-restraints excluded: chain p residue 111 ILE Chi-restraints excluded: chain p residue 135 LEU Chi-restraints excluded: chain p residue 183 MET Chi-restraints excluded: chain q residue 52 LEU Chi-restraints excluded: chain q residue 68 SER Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 69 THR Chi-restraints excluded: chain s residue 83 LEU Chi-restraints excluded: chain s residue 86 MET Chi-restraints excluded: chain s residue 152 GLN Chi-restraints excluded: chain s residue 171 VAL Chi-restraints excluded: chain s residue 200 LEU Chi-restraints excluded: chain s residue 229 LEU Chi-restraints excluded: chain s residue 241 ILE Chi-restraints excluded: chain s residue 301 LEU Chi-restraints excluded: chain s residue 318 ASP Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain s residue 373 GLN Chi-restraints excluded: chain s residue 374 LEU Chi-restraints excluded: chain s residue 396 THR Chi-restraints excluded: chain s residue 415 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 886 random chunks: chunk 793 optimal weight: 0.6980 chunk 522 optimal weight: 10.0000 chunk 841 optimal weight: 3.9990 chunk 513 optimal weight: 0.8980 chunk 399 optimal weight: 0.9980 chunk 584 optimal weight: 20.0000 chunk 882 optimal weight: 80.0000 chunk 812 optimal weight: 80.0000 chunk 702 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 542 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 121 ASN L 33 GLN P 88 HIS ** P 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 107 HIS ** T 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 67 HIS 5 146 HIS ** 5 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 163 HIS 6 307 HIS b 127 GLN c 128 GLN c 204 GLN d 161 HIS ** e 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 382 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 94831 Z= 0.172 Angle : 0.573 13.809 133991 Z= 0.285 Chirality : 0.038 0.316 15614 Planarity : 0.004 0.068 12697 Dihedral : 20.136 179.990 26849 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.30 % Favored : 96.69 % Rotamer: Outliers : 2.07 % Allowed : 17.04 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: 0.28 (0.10), residues: 7728 helix: 1.45 (0.10), residues: 2617 sheet: -0.59 (0.16), residues: 1006 loop : -0.39 (0.10), residues: 4105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP Q 264 HIS 0.009 0.001 HIS d 217 PHE 0.052 0.001 PHE e 128 TYR 0.022 0.001 TYR e 84 ARG 0.013 0.000 ARG Q 244 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15456 Ramachandran restraints generated. 7728 Oldfield, 0 Emsley, 7728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15456 Ramachandran restraints generated. 7728 Oldfield, 0 Emsley, 7728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1187 residues out of total 6963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 1043 time to evaluate : 6.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 82 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8545 (mt) REVERT: I 152 MET cc_start: 0.4187 (OUTLIER) cc_final: 0.3694 (pmm) REVERT: K 73 GLU cc_start: 0.7916 (mp0) cc_final: 0.7642 (mp0) REVERT: M 130 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.7827 (pt0) REVERT: O 73 MET cc_start: 0.8145 (tpp) cc_final: 0.7830 (mmm) REVERT: Q 167 TYR cc_start: 0.8244 (m-80) cc_final: 0.7915 (m-80) REVERT: Q 244 ARG cc_start: 0.6309 (mmm160) cc_final: 0.6060 (mmm160) REVERT: R 59 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.7702 (mm) REVERT: T 133 ASN cc_start: 0.7909 (t0) cc_final: 0.7646 (t0) REVERT: W 93 GLU cc_start: 0.7391 (mm-30) cc_final: 0.7151 (mm-30) REVERT: X 64 ASP cc_start: 0.8052 (OUTLIER) cc_final: 0.7705 (p0) REVERT: Y 238 PHE cc_start: 0.6737 (m-10) cc_final: 0.6417 (m-10) REVERT: 5 165 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.7311 (tm-30) REVERT: 5 358 GLN cc_start: 0.7322 (OUTLIER) cc_final: 0.6960 (tm-30) REVERT: 6 170 ARG cc_start: 0.4626 (mtt180) cc_final: 0.4101 (mtt180) REVERT: e 257 LYS cc_start: 0.4192 (tptt) cc_final: 0.3858 (tptt) REVERT: h 120 MET cc_start: 0.6944 (OUTLIER) cc_final: 0.6705 (mpp) REVERT: i 42 LYS cc_start: 0.7367 (ttpp) cc_final: 0.7076 (tptt) REVERT: i 128 ARG cc_start: 0.6710 (OUTLIER) cc_final: 0.3584 (ptp90) REVERT: o 35 MET cc_start: 0.8576 (ttt) cc_final: 0.8323 (ttt) REVERT: o 52 PRO cc_start: 0.8669 (Cg_endo) cc_final: 0.8434 (Cg_exo) REVERT: s 373 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.7056 (tm-30) outliers start: 144 outliers final: 119 residues processed: 1130 average time/residue: 0.8686 time to fit residues: 1654.8351 Evaluate side-chains 1164 residues out of total 6963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 1035 time to evaluate : 6.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 207 ILE Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain E residue 107 MET Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 331 ASP Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 84 ARG Chi-restraints excluded: chain I residue 94 ARG Chi-restraints excluded: chain I residue 152 MET Chi-restraints excluded: chain I residue 166 ARG Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain M residue 130 GLN Chi-restraints excluded: chain M residue 146 ASP Chi-restraints excluded: chain M residue 234 LEU Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain M residue 279 ASP Chi-restraints excluded: chain N residue 70 SER Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain N residue 214 THR Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 23 GLU Chi-restraints excluded: chain O residue 110 ILE Chi-restraints excluded: chain P residue 44 VAL Chi-restraints excluded: chain P residue 102 VAL Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 154 VAL Chi-restraints excluded: chain R residue 16 ASP Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain S residue 114 ILE Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 164 THR Chi-restraints excluded: chain S residue 185 ILE Chi-restraints excluded: chain S residue 186 VAL Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain V residue 69 ASP Chi-restraints excluded: chain V residue 191 LEU Chi-restraints excluded: chain V residue 193 THR Chi-restraints excluded: chain W residue 46 SER Chi-restraints excluded: chain W residue 83 VAL Chi-restraints excluded: chain X residue 22 SER Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain X residue 101 LEU Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain X residue 137 GLU Chi-restraints excluded: chain Z residue 92 GLU Chi-restraints excluded: chain Z residue 135 SER Chi-restraints excluded: chain 0 residue 102 LYS Chi-restraints excluded: chain 0 residue 105 ASN Chi-restraints excluded: chain 2 residue 56 SER Chi-restraints excluded: chain 3 residue 94 LEU Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 3 residue 186 LEU Chi-restraints excluded: chain 5 residue 74 ILE Chi-restraints excluded: chain 5 residue 165 GLN Chi-restraints excluded: chain 5 residue 167 THR Chi-restraints excluded: chain 5 residue 358 GLN Chi-restraints excluded: chain 5 residue 359 LEU Chi-restraints excluded: chain 5 residue 365 ASP Chi-restraints excluded: chain 6 residue 132 LEU Chi-restraints excluded: chain 6 residue 166 THR Chi-restraints excluded: chain 6 residue 174 HIS Chi-restraints excluded: chain 6 residue 222 ASP Chi-restraints excluded: chain 6 residue 325 ASP Chi-restraints excluded: chain 6 residue 327 VAL Chi-restraints excluded: chain 6 residue 328 THR Chi-restraints excluded: chain 7 residue 59 THR Chi-restraints excluded: chain 7 residue 70 VAL Chi-restraints excluded: chain 7 residue 78 VAL Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 314 ASP Chi-restraints excluded: chain 8 residue 132 GLU Chi-restraints excluded: chain 8 residue 165 ASP Chi-restraints excluded: chain 9 residue 46 SER Chi-restraints excluded: chain 9 residue 130 LEU Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 126 HIS Chi-restraints excluded: chain b residue 32 SER Chi-restraints excluded: chain b residue 138 THR Chi-restraints excluded: chain c residue 274 LEU Chi-restraints excluded: chain d residue 193 HIS Chi-restraints excluded: chain d residue 243 LEU Chi-restraints excluded: chain e residue 93 ASP Chi-restraints excluded: chain e residue 131 PHE Chi-restraints excluded: chain e residue 184 LEU Chi-restraints excluded: chain e residue 275 PHE Chi-restraints excluded: chain f residue 90 VAL Chi-restraints excluded: chain g residue 68 THR Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain h residue 120 MET Chi-restraints excluded: chain i residue 128 ARG Chi-restraints excluded: chain k residue 54 ASP Chi-restraints excluded: chain k residue 55 VAL Chi-restraints excluded: chain m residue 54 VAL Chi-restraints excluded: chain o residue 58 GLN Chi-restraints excluded: chain p residue 61 VAL Chi-restraints excluded: chain p residue 111 ILE Chi-restraints excluded: chain p residue 183 MET Chi-restraints excluded: chain q residue 52 LEU Chi-restraints excluded: chain s residue 69 THR Chi-restraints excluded: chain s residue 83 LEU Chi-restraints excluded: chain s residue 86 MET Chi-restraints excluded: chain s residue 152 GLN Chi-restraints excluded: chain s residue 200 LEU Chi-restraints excluded: chain s residue 301 LEU Chi-restraints excluded: chain s residue 318 ASP Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain s residue 373 GLN Chi-restraints excluded: chain s residue 374 LEU Chi-restraints excluded: chain s residue 396 THR Chi-restraints excluded: chain s residue 415 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 886 random chunks: chunk 430 optimal weight: 0.8980 chunk 558 optimal weight: 0.9990 chunk 748 optimal weight: 0.9990 chunk 215 optimal weight: 0.9980 chunk 648 optimal weight: 0.0670 chunk 103 optimal weight: 40.0000 chunk 195 optimal weight: 10.0000 chunk 704 optimal weight: 0.7980 chunk 294 optimal weight: 9.9990 chunk 722 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 121 ASN K 56 HIS L 33 GLN ** P 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 107 HIS ** S 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 18 HIS Z 67 HIS 5 146 HIS ** 5 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 163 HIS 6 307 HIS c 204 GLN d 161 HIS e 130 GLN ** e 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 382 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.180246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.156142 restraints weight = 106871.002| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 0.81 r_work: 0.3368 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 94831 Z= 0.161 Angle : 0.556 14.721 133991 Z= 0.276 Chirality : 0.037 0.284 15614 Planarity : 0.004 0.059 12697 Dihedral : 20.008 179.852 26849 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.55 % Favored : 96.44 % Rotamer: Outliers : 1.99 % Allowed : 17.20 % Favored : 80.81 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 1.32 % 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: 0.44 (0.10), residues: 7728 helix: 1.59 (0.10), residues: 2621 sheet: -0.51 (0.16), residues: 996 loop : -0.30 (0.10), residues: 4111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP Q 264 HIS 0.009 0.001 HIS d 217 PHE 0.046 0.001 PHE I 173 TYR 0.021 0.001 TYR e 84 ARG 0.012 0.000 ARG Q 244 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25185.58 seconds wall clock time: 441 minutes 4.23 seconds (26464.23 seconds total)