Starting phenix.real_space_refine (version: dev) on Fri Apr 8 03:37:59 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oib_12924/04_2022/7oib_12924.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oib_12924/04_2022/7oib_12924.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oib_12924/04_2022/7oib_12924.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oib_12924/04_2022/7oib_12924.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oib_12924/04_2022/7oib_12924.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oib_12924/04_2022/7oib_12924.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "D PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 86": "OD1" <-> "OD2" Residue "D GLU 116": "OE1" <-> "OE2" Residue "D GLU 155": "OE1" <-> "OE2" Residue "D GLU 199": "OE1" <-> "OE2" Residue "D ASP 251": "OD1" <-> "OD2" Residue "E ASP 50": "OD1" <-> "OD2" Residue "E ASP 126": "OD1" <-> "OD2" Residue "E TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 301": "OD1" <-> "OD2" Residue "E ASP 331": "OD1" <-> "OD2" Residue "E TYR 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 334": "OD1" <-> "OD2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "F ASP 85": "OD1" <-> "OD2" Residue "F GLU 194": "OE1" <-> "OE2" Residue "F GLU 205": "OE1" <-> "OE2" Residue "F GLU 224": "OE1" <-> "OE2" Residue "F GLU 225": "OE1" <-> "OE2" Residue "F ASP 277": "OD1" <-> "OD2" Residue "F ASP 292": "OD1" <-> "OD2" Residue "H GLU 92": "OE1" <-> "OE2" Residue "I GLU 136": "OE1" <-> "OE2" Residue "K ASP 52": "OD1" <-> "OD2" Residue "K PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 37": "OE1" <-> "OE2" Residue "M GLU 68": "OE1" <-> "OE2" Residue "M TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 85": "OE1" <-> "OE2" Residue "M PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 142": "OE1" <-> "OE2" Residue "M GLU 161": "OE1" <-> "OE2" Residue "M ASP 216": "OD1" <-> "OD2" Residue "M GLU 231": "OE1" <-> "OE2" Residue "M ASP 250": "OD1" <-> "OD2" Residue "M ASP 261": "OD1" <-> "OD2" Residue "M ASP 287": "OD1" <-> "OD2" Residue "M GLU 288": "OE1" <-> "OE2" Residue "M TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 54": "OE1" <-> "OE2" Residue "N PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 84": "OE1" <-> "OE2" Residue "N ASP 148": "OD1" <-> "OD2" Residue "N TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 196": "OE1" <-> "OE2" Residue "N GLU 204": "OE1" <-> "OE2" Residue "N TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 23": "OE1" <-> "OE2" Residue "O GLU 40": "OE1" <-> "OE2" Residue "O GLU 57": "OE1" <-> "OE2" Residue "O ASP 67": "OD1" <-> "OD2" Residue "O ASP 84": "OD1" <-> "OD2" Residue "O TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 47": "OE1" <-> "OE2" Residue "P PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 126": "OE1" <-> "OE2" Residue "P GLU 138": "OE1" <-> "OE2" Residue "Q GLU 165": "OE1" <-> "OE2" Residue "Q GLU 219": "OE1" <-> "OE2" Residue "Q GLU 234": "OE1" <-> "OE2" Residue "Q PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 251": "OE1" <-> "OE2" Residue "Q ASP 268": "OD1" <-> "OD2" Residue "Q GLU 272": "OE1" <-> "OE2" Residue "Q TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 279": "OE1" <-> "OE2" Residue "Q GLU 287": "OE1" <-> "OE2" Residue "R GLU 126": "OE1" <-> "OE2" Residue "R PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 78": "OE1" <-> "OE2" Residue "S GLU 85": "OE1" <-> "OE2" Residue "S PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 111": "OE1" <-> "OE2" Residue "S GLU 126": "OE1" <-> "OE2" Residue "S ASP 139": "OD1" <-> "OD2" Residue "T GLU 72": "OE1" <-> "OE2" Residue "T TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 107": "OE1" <-> "OE2" Residue "T ASP 110": "OD1" <-> "OD2" Residue "T GLU 119": "OE1" <-> "OE2" Residue "T GLU 144": "OE1" <-> "OE2" Residue "T GLU 168": "OE1" <-> "OE2" Residue "T TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 180": "OE1" <-> "OE2" Residue "T GLU 198": "OE1" <-> "OE2" Residue "U PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 47": "OE1" <-> "OE2" Residue "U ASP 52": "OD1" <-> "OD2" Residue "U PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 52": "OE1" <-> "OE2" Residue "V PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 66": "OE1" <-> "OE2" Residue "V ASP 127": "OD1" <-> "OD2" Residue "V ASP 181": "OD1" <-> "OD2" Residue "V GLU 196": "OE1" <-> "OE2" Residue "V GLU 197": "OE1" <-> "OE2" Residue "V GLU 200": "OE1" <-> "OE2" Residue "V GLU 206": "OE1" <-> "OE2" Residue "W PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 34": "OE1" <-> "OE2" Residue "X PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 60": "OE1" <-> "OE2" Residue "X GLU 63": "OE1" <-> "OE2" Residue "X GLU 83": "OE1" <-> "OE2" Residue "X PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 111": "OE1" <-> "OE2" Residue "X GLU 117": "OE1" <-> "OE2" Residue "X ASP 136": "OD1" <-> "OD2" Residue "X TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 151": "OE1" <-> "OE2" Residue "X ASP 173": "OD1" <-> "OD2" Residue "X ASP 180": "OD1" <-> "OD2" Residue "X TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 189": "OD1" <-> "OD2" Residue "X GLU 202": "OE1" <-> "OE2" Residue "X GLU 219": "OE1" <-> "OE2" Residue "X GLU 233": "OE1" <-> "OE2" Residue "Y GLU 65": "OE1" <-> "OE2" Residue "Y PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 108": "OE1" <-> "OE2" Residue "Y GLU 116": "OE1" <-> "OE2" Residue "Y GLU 148": "OE1" <-> "OE2" Residue "Y GLU 150": "OE1" <-> "OE2" Residue "Y GLU 161": "OE1" <-> "OE2" Residue "Y GLU 224": "OE1" <-> "OE2" Residue "Y GLU 227": "OE1" <-> "OE2" Residue "Z TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 131": "OE1" <-> "OE2" Residue "0 GLU 88": "OE1" <-> "OE2" Residue "0 GLU 112": "OE1" <-> "OE2" Residue "0 PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 GLU 163": "OE1" <-> "OE2" Residue "1 GLU 39": "OE1" <-> "OE2" Residue "1 PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 146": "OE1" <-> "OE2" Residue "3 TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 47": "OD1" <-> "OD2" Residue "5 GLU 95": "OE1" <-> "OE2" Residue "5 TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 115": "OE1" <-> "OE2" Residue "5 ASP 141": "OD1" <-> "OD2" Residue "5 ASP 151": "OD1" <-> "OD2" Residue "5 GLU 169": "OE1" <-> "OE2" Residue "5 TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 216": "OE1" <-> "OE2" Residue "5 GLU 267": "OE1" <-> "OE2" Residue "5 TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 281": "OE1" <-> "OE2" Residue "5 TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 348": "OD1" <-> "OD2" Residue "5 ASP 377": "OD1" <-> "OD2" Residue "5 ASP 379": "OD1" <-> "OD2" Residue "5 PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 399": "OE1" <-> "OE2" Residue "6 TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 55": "OD1" <-> "OD2" Residue "6 GLU 76": "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 GLU 181": "OE1" <-> "OE2" Residue "6 GLU 197": "OE1" <-> "OE2" Residue "6 ASP 229": "OD1" <-> "OD2" Residue "6 TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 309": "OE1" <-> "OE2" Residue "6 GLU 343": "OE1" <-> "OE2" Residue "6 TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 367": "OD1" <-> "OD2" Residue "6 ASP 371": "OD1" <-> "OD2" Residue "6 TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 155": "OE1" <-> "OE2" Residue "7 PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 161": "OE1" <-> "OE2" Residue "7 TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 222": "OE1" <-> "OE2" Residue "7 GLU 242": "OE1" <-> "OE2" Residue "7 GLU 249": "OE1" <-> "OE2" Residue "7 ASP 262": "OD1" <-> "OD2" Residue "7 GLU 318": "OE1" <-> "OE2" Residue "8 GLU 128": "OE1" <-> "OE2" Residue "8 GLU 132": "OE1" <-> "OE2" Residue "8 GLU 141": "OE1" <-> "OE2" Residue "9 GLU 55": "OE1" <-> "OE2" Residue "9 ASP 64": "OD1" <-> "OD2" Residue "9 GLU 101": "OE1" <-> "OE2" Residue "9 PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 48": "OE1" <-> "OE2" Residue "b GLU 86": "OE1" <-> "OE2" Residue "b PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 46": "OE1" <-> "OE2" Residue "c GLU 62": "OE1" <-> "OE2" Residue "c GLU 101": "OE1" <-> "OE2" Residue "c GLU 124": "OE1" <-> "OE2" Residue "c ASP 143": "OD1" <-> "OD2" Residue "c GLU 151": "OE1" <-> "OE2" Residue "c GLU 163": "OE1" <-> "OE2" Residue "c GLU 183": "OE1" <-> "OE2" Residue "c PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 217": "OD1" <-> "OD2" Residue "c GLU 230": "OE1" <-> "OE2" Residue "c GLU 243": "OE1" <-> "OE2" Residue "c TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 283": "OE1" <-> "OE2" Residue "c PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 309": "OE1" <-> "OE2" Residue "d ASP 143": "OD1" <-> "OD2" Residue "d TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 226": "OD1" <-> "OD2" Residue "d GLU 244": "OE1" <-> "OE2" Residue "d TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 78": "OE1" <-> "OE2" Residue "e PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 87": "OE1" <-> "OE2" Residue "f TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 104": "OE1" <-> "OE2" Residue "f GLU 123": "OE1" <-> "OE2" Residue "f GLU 180": "OE1" <-> "OE2" Residue "g ASP 59": "OD1" <-> "OD2" Residue "g ASP 77": "OD1" <-> "OD2" Residue "g TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 71": "OE1" <-> "OE2" Residue "h TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 93": "OD1" <-> "OD2" Residue "i TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 83": "OE1" <-> "OE2" Residue "m GLU 70": "OE1" <-> "OE2" Residue "o GLU 69": "OE1" <-> "OE2" Residue "o GLU 72": "OE1" <-> "OE2" Residue "p GLU 109": "OE1" <-> "OE2" Residue "p GLU 113": "OE1" <-> "OE2" Residue "p ASP 149": "OD1" <-> "OD2" Residue "q GLU 43": "OE1" <-> "OE2" Residue "q TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 80": "OE1" <-> "OE2" Residue "q GLU 89": "OE1" <-> "OE2" Residue "q GLU 101": "OE1" <-> "OE2" Residue "q GLU 110": "OE1" <-> "OE2" Residue "q GLU 118": "OE1" <-> "OE2" Residue "q GLU 144": "OE1" <-> "OE2" Residue "r GLU 59": "OE1" <-> "OE2" Residue "r TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ASP 85": "OD1" <-> "OD2" Residue "r GLU 111": "OE1" <-> "OE2" Residue "r ASP 183": "OD1" <-> "OD2" Residue "r TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 64": "OE1" <-> "OE2" Residue "s GLU 78": "OE1" <-> "OE2" Residue "s ASP 103": "OD1" <-> "OD2" Residue "s TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 170": "OE1" <-> "OE2" Residue "s GLU 215": "OE1" <-> "OE2" Residue "s ASP 227": "OD1" <-> "OD2" Residue "s TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 254": "OD1" <-> "OD2" Residue "s GLU 260": "OE1" <-> "OE2" Residue "s TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 304": "OD1" <-> "OD2" Residue "s GLU 348": "OE1" <-> "OE2" Residue "s PHE 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 88360 Number of models: 1 Model: "" Number of chains: 56 Chain: "D" Number of atoms: 1706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1706 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 11, 'TRANS': 208} Chain breaks: 1 Chain: "E" Number of atoms: 2258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2258 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 22, 'TRANS': 262} Chain breaks: 1 Chain: "F" Number of atoms: 2013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 2013 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 21, 'TRANS': 228} Chain: "H" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 784 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "I" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1283 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 11, 'TRANS': 146} Chain breaks: 1 Chain: "J" Number of atoms: 1061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1061 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 9, 'TRANS': 130} Chain: "K" Number of atoms: 1451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1451 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 15, 'TRANS': 161} Chain: "L" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 889 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "M" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2305 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 26, 'TRANS': 260} Chain: "N" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1654 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 14, 'TRANS': 190} Chain: "O" Number of atoms: 1245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1245 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 9, 'TRANS': 142} Chain: "P" Number of atoms: 1148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1148 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 134, 'PCIS': 1} Chain: "Q" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1805 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 14, 'TRANS': 202} Chain: "R" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1153 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "S" Number of atoms: 1251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1251 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 9, 'TRANS': 145, 'PCIS': 1} Chain: "T" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1305 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 12, 'TRANS': 146} Chain breaks: 1 Chain: "U" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1154 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 11, 'TRANS': 127} Chain breaks: 1 Chain: "V" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1575 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 16, 'TRANS': 175} Chain breaks: 1 Chain: "W" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 859 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "X" Number of atoms: 2035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 2035 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 18, 'TRANS': 224} Chain: "Y" Number of atoms: 1517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1517 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 7, 'TRANS': 168} Chain: "Z" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 978 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 11, 'TRANS': 108} Chain: "0" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 880 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "1" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 433 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 1, 'TRANS': 50} Chain: "2" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Chain: "3" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 831 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "5" Number of atoms: 3156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3156 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 31, 'TRANS': 354, 'PCIS': 1} Chain breaks: 1 Chain: "6" Number of atoms: 2640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2640 Classifications: {'peptide': 324} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 28, 'TRANS': 295} Chain breaks: 3 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 5, 'ARG:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 59 Chain: "7" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2334 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 17, 'TRANS': 269} Chain: "8" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 836 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 9, 'TRANS': 89} Chain: "9" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 8, 'TRANS': 107, 'PCIS': 1} Chain breaks: 1 Chain: "a" Number of atoms: 686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 686 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 10, 'TRANS': 71} Chain breaks: 1 Chain: "b" Number of atoms: 1178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1178 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 9, 'TRANS': 138} Chain: "c" Number of atoms: 2217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2217 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 15, 'TRANS': 258, 'PCIS': 1} Chain breaks: 1 Chain: "d" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1741 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 17, 'TRANS': 193} Chain breaks: 3 Chain: "e" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1762 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 9, 'TRANS': 207} Chain breaks: 2 Chain: "f" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 915 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "g" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1067 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 13, 'TRANS': 113, 'PCIS': 2} Chain: "h" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 827 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 7, 'TRANS': 92} Chain breaks: 1 Chain: "i" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 827 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 5, 'TRANS': 91} Chain: "j" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 684 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 6, 'TRANS': 78} Chain: "k" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 627 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain breaks: 1 Chain: "l" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 221 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "m" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 372 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 3, 'TRANS': 41} Chain: "o" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 665 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "p" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1058 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain breaks: 3 Chain: "q" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1011 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 14, 'TRANS': 105} 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: {'rna3p_pyr': 423, 'rna2p_pur': 118, 'rna3p_pur': 463, 'rna2p_pyr': 88} Link IDs: {'rna3p': 886, 'rna2p': 205} Chain breaks: 22 Chain: "B" Number of atoms: 1191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1191 Classifications: {'RNA': 56} Modifications used: {'rna3p_pyr': 26, 'rna2p_pur': 1, 'rna3p_pur': 29} Link IDs: {'rna3p': 54, 'rna2p': 1} Chain breaks: 4 Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "0" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "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 0 110 165.646 88.819 174.254 1.00 53.49 S ATOM 31715 SG CYS 0 113 163.022 86.831 176.240 1.00 57.61 S ATOM 31795 SG CYS 0 123 161.959 89.812 174.638 1.00 35.55 S ATOM 31818 SG CYS 0 126 164.422 90.094 177.649 1.00 44.59 S ATOM 7048 SG CYS I 64 140.894 100.811 61.396 1.00 95.02 S ATOM 59930 SG CYS r 70 145.301 101.736 61.921 1.00 83.16 S ATOM 60245 SG CYS r 108 143.184 103.468 61.780 1.00 86.02 S Time building chain proxies: 37.16, per 1000 atoms: 0.42 Number of scatterers: 88360 At special positions: 0 Unit cell: (222.22, 188.616, 254.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 266 16.00 P 1148 15.00 Mg 49 11.99 O 19066 8.00 N 16087 7.00 C 51742 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: 29.81 Conformation dependent library (CDL) restraints added in 7.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN 0 200 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 113 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 123 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 126 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 110 " pdb=" ZN r 301 " pdb="ZN ZN r 301 " - pdb=" SG CYS r 70 " pdb="ZN ZN r 301 " - pdb=" SG CYS I 64 " pdb="ZN ZN r 301 " - pdb=" SG CYS r 108 " Number of angles added : 6 15368 Ramachandran restraints generated. 7684 Oldfield, 0 Emsley, 7684 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14792 Finding SS restraints... Secondary structure from input PDB file: 254 helices and 83 sheets defined 36.6% alpha, 14.1% beta 308 base pairs and 614 stacking pairs defined. Time for finding SS restraints: 22.85 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: 3.786A pdb=" N ASN D 263 " --> pdb=" O LYS D 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 76 removed outlier: 3.958A pdb=" N PHE E 60 " --> pdb=" O GLU E 56 " (cutoff:3.500A) 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 removed outlier: 3.657A pdb=" N PHE E 198 " --> pdb=" O ALA E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 217 through 222 Processing helix chain 'E' and resid 304 through 308 removed outlier: 4.218A pdb=" N LYS E 308 " --> pdb=" O PRO E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 320 through 324 removed outlier: 3.526A pdb=" N GLY E 323 " --> pdb=" O PHE E 320 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 88 Processing helix chain 'F' and resid 92 through 106 Processing helix chain 'F' and resid 166 through 184 Processing helix chain 'F' and resid 199 through 210 removed outlier: 3.585A pdb=" N LEU F 203 " --> pdb=" O ASP F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 235 Processing helix chain 'F' and resid 250 through 256 Processing helix chain 'F' and resid 263 through 274 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 133 through 146 removed outlier: 3.597A pdb=" N LYS H 137 " --> pdb=" O SER H 133 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS H 138 " --> pdb=" O PRO H 134 " (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 117 Processing helix chain 'I' and resid 130 through 138 Processing helix chain 'I' and resid 160 through 170 removed outlier: 4.052A pdb=" N MET I 164 " --> pdb=" O LYS I 160 " (cutoff:3.500A) Processing helix chain 'I' and resid 187 through 196 Processing helix chain 'J' and resid 45 through 59 Processing helix chain 'J' and resid 87 through 95 removed outlier: 3.507A pdb=" N LEU J 91 " --> pdb=" O VAL J 87 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 122 Processing helix chain 'J' and resid 136 through 150 removed outlier: 4.511A pdb=" N VAL J 140 " --> pdb=" O PRO J 136 " (cutoff:3.500A) removed outlier: 3.517A 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 62 through 64 No H-bonds generated for 'chain 'K' and resid 62 through 64' 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 123 removed outlier: 3.581A pdb=" N GLU K 123 " --> pdb=" O ARG K 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 134 through 139 Processing helix chain 'K' and resid 159 through 166 removed outlier: 3.527A pdb=" N PHE K 166 " --> pdb=" O GLU K 162 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 49 removed outlier: 3.673A pdb=" N SER L 49 " --> pdb=" O ALA L 45 " (cutoff:3.500A) Processing helix chain 'L' and resid 136 through 140 removed outlier: 3.884A pdb=" N ALA L 139 " --> pdb=" O LYS L 136 " (cutoff:3.500A) removed outlier: 3.537A 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 98 through 107 Processing helix chain 'M' and resid 117 through 125 removed outlier: 3.628A pdb=" N LEU M 121 " --> pdb=" O ASP M 117 " (cutoff:3.500A) Processing helix chain 'M' and resid 160 through 170 removed outlier: 3.815A pdb=" N ASN M 170 " --> pdb=" O ALA M 166 " (cutoff:3.500A) Processing helix chain 'M' and resid 180 through 189 removed outlier: 3.520A 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 240 removed outlier: 3.557A pdb=" N TYR M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) Processing helix chain 'M' and resid 252 through 258 removed outlier: 3.696A pdb=" N THR M 258 " --> pdb=" O LYS M 254 " (cutoff:3.500A) 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: 4.114A pdb=" N SER N 112 " --> pdb=" O THR N 108 " (cutoff:3.500A) Processing helix chain 'N' and resid 168 through 183 removed outlier: 3.856A pdb=" N VAL N 172 " --> pdb=" O GLU N 168 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N GLY N 174 " --> pdb=" O GLU N 170 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N PHE N 175 " --> pdb=" O GLU N 171 " (cutoff:3.500A) Processing helix chain 'N' and resid 192 through 209 removed outlier: 3.700A 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: 4.022A 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 Processing helix chain 'O' and resid 69 through 80 Processing helix chain 'O' and resid 84 through 92 removed outlier: 3.970A pdb=" N LYS O 88 " --> pdb=" O ASP O 84 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE O 90 " --> pdb=" O ILE O 86 " (cutoff:3.500A) Processing helix chain 'O' and resid 92 through 97 removed outlier: 3.561A pdb=" N TYR O 97 " --> pdb=" O LEU O 93 " (cutoff:3.500A) Processing helix chain 'O' and resid 143 through 158 Processing helix chain 'P' and resid 54 through 59 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: 3.889A 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 77 through 81 Processing helix chain 'Q' and resid 88 through 106 removed outlier: 4.056A 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 244 through 249 removed outlier: 3.869A pdb=" N CYS Q 248 " --> pdb=" O ARG Q 244 " (cutoff:3.500A) Processing helix chain 'Q' and resid 250 through 260 removed outlier: 4.294A pdb=" N TRP Q 260 " --> pdb=" O GLU Q 256 " (cutoff:3.500A) Processing helix chain 'Q' and resid 264 through 268 removed outlier: 3.712A pdb=" N ASP Q 268 " --> pdb=" O LEU Q 265 " (cutoff:3.500A) Processing helix chain 'Q' and resid 276 through 289 removed outlier: 3.783A pdb=" N ALA Q 280 " --> pdb=" O SER Q 276 " (cutoff:3.500A) removed outlier: 3.853A 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 36 removed outlier: 3.872A pdb=" N LYS R 35 " --> pdb=" O ARG R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 38 through 79 removed outlier: 4.408A pdb=" N TYR R 58 " --> pdb=" O THR R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 91 Processing helix chain 'R' and resid 98 through 109 Processing helix chain 'R' and resid 109 through 131 Processing helix chain 'S' and resid 68 through 90 Processing helix chain 'T' and resid 49 through 54 removed outlier: 3.908A pdb=" N LYS T 53 " --> pdb=" O ARG T 49 " (cutoff:3.500A) removed outlier: 3.521A 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: 4.891A pdb=" N TYR T 89 " --> pdb=" O ASP T 85 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU T 90 " --> pdb=" O LYS T 86 " (cutoff:3.500A) Processing helix chain 'T' and resid 98 through 108 removed outlier: 3.919A pdb=" N PHE T 108 " --> pdb=" O ALA T 104 " (cutoff:3.500A) Processing helix chain 'T' and resid 111 through 132 removed outlier: 3.663A pdb=" N LYS T 115 " --> pdb=" O LYS T 111 " (cutoff:3.500A) Processing helix chain 'T' and resid 191 through 206 removed outlier: 3.524A pdb=" N SER T 205 " --> pdb=" O GLN T 201 " (cutoff:3.500A) removed outlier: 3.515A 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: 3.649A pdb=" N GLN U 135 " --> pdb=" O GLU U 131 " (cutoff:3.500A) Processing helix chain 'U' and resid 141 through 145 removed outlier: 3.556A 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 removed outlier: 3.864A pdb=" N LEU V 183 " --> pdb=" O VAL V 179 " (cutoff:3.500A) Processing helix chain 'V' and resid 193 through 203 Processing helix chain 'W' and resid 110 through 119 removed outlier: 3.532A pdb=" N ARG W 119 " --> pdb=" O ASP W 115 " (cutoff:3.500A) Processing helix chain 'X' and resid 7 through 9 No H-bonds generated for 'chain 'X' and resid 7 through 9' Processing helix chain 'X' and resid 10 through 16 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 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 138 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 171 Processing helix chain 'X' and resid 180 through 191 removed outlier: 3.578A pdb=" N ARG X 184 " --> pdb=" O ASP X 180 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR X 191 " --> pdb=" O ILE X 187 " (cutoff:3.500A) Processing helix chain 'X' and resid 192 through 195 removed outlier: 3.693A pdb=" N ALA X 195 " --> pdb=" O LYS X 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 192 through 195' Processing helix chain 'X' and resid 197 through 202 removed outlier: 3.506A pdb=" N GLU X 202 " --> pdb=" O GLU X 198 " (cutoff:3.500A) Processing helix chain 'X' and resid 207 through 219 Processing helix chain 'X' and resid 225 through 243 removed outlier: 3.621A pdb=" N ILE X 229 " --> pdb=" O PRO X 225 " (cutoff:3.500A) Processing helix chain 'Y' and resid 63 through 68 removed outlier: 3.642A pdb=" N GLU Y 66 " --> pdb=" O GLY Y 63 " (cutoff:3.500A) Processing helix chain 'Y' and resid 70 through 74 Processing helix chain 'Y' and resid 86 through 91 removed outlier: 3.656A pdb=" N LEU Y 90 " --> pdb=" O THR Y 86 " (cutoff:3.500A) Processing helix chain 'Y' and resid 94 through 123 Processing helix chain 'Y' and resid 129 through 158 removed outlier: 3.672A pdb=" N ASP Y 133 " --> pdb=" O PRO Y 129 " (cutoff:3.500A) Processing helix chain 'Y' and resid 187 through 191 removed outlier: 3.625A 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 49 through 56 Processing helix chain 'Z' and resid 79 through 90 Processing helix chain 'Z' and resid 103 through 113 removed outlier: 3.507A pdb=" N VAL Z 113 " --> pdb=" O LYS Z 109 " (cutoff:3.500A) 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: 3.947A 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: 3.621A pdb=" N ILE 3 111 " --> pdb=" O VAL 3 107 " (cutoff:3.500A) Processing helix chain '3' and resid 132 through 136 removed outlier: 3.660A pdb=" N LYS 3 135 " --> pdb=" O LYS 3 132 " (cutoff:3.500A) Processing helix chain '3' and resid 137 through 145 Processing helix chain '3' and resid 151 through 161 removed outlier: 3.587A pdb=" N MET 3 161 " --> pdb=" O LEU 3 157 " (cutoff:3.500A) Processing helix chain '3' and resid 163 through 168 removed outlier: 3.724A pdb=" N ARG 3 168 " --> pdb=" O PHE 3 165 " (cutoff:3.500A) Processing helix chain '3' and resid 177 through 181 removed outlier: 3.706A pdb=" N HIS 3 181 " --> pdb=" O GLN 3 178 " (cutoff:3.500A) Processing helix chain '5' and resid 84 through 88 removed outlier: 3.926A pdb=" N TYR 5 88 " --> pdb=" O PRO 5 85 " (cutoff:3.500A) Processing helix chain '5' and resid 116 through 125 removed outlier: 3.952A pdb=" N ALA 5 120 " --> pdb=" O GLY 5 116 " (cutoff:3.500A) 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 removed outlier: 3.578A pdb=" N LEU 5 198 " --> pdb=" O HIS 5 195 " (cutoff:3.500A) Processing helix chain '5' and resid 241 through 248 Processing helix chain '5' and resid 305 through 330 Processing helix chain '5' and resid 408 through 419 Processing helix chain '6' and resid 54 through 66 Processing helix chain '6' and resid 73 through 79 removed outlier: 3.897A 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 142 removed outlier: 4.070A pdb=" N VAL 6 135 " --> pdb=" O PRO 6 131 " (cutoff:3.500A) Processing helix chain '6' and resid 143 through 155 removed outlier: 3.526A pdb=" N HIS 6 147 " --> pdb=" O CYS 6 143 " (cutoff:3.500A) Processing helix chain '6' and resid 156 through 162 Processing helix chain '6' and resid 299 through 306 Processing helix chain '6' and resid 324 through 333 removed outlier: 3.582A pdb=" N THR 6 328 " --> pdb=" O ASP 6 324 " (cutoff:3.500A) Processing helix chain '6' and resid 364 through 369 removed outlier: 4.328A pdb=" N TYR 6 369 " --> pdb=" O TYR 6 365 " (cutoff:3.500A) Processing helix chain '7' and resid 37 through 58 removed outlier: 3.915A pdb=" N LEU 7 58 " --> pdb=" O ARG 7 54 " (cutoff:3.500A) Processing helix chain '7' and resid 87 through 96 Processing helix chain '7' and resid 97 through 102 removed outlier: 3.697A pdb=" N LYS 7 102 " --> pdb=" O TRP 7 98 " (cutoff:3.500A) Processing helix chain '7' and resid 135 through 156 Processing helix chain '7' and resid 173 through 177 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 153 Processing helix chain '8' and resid 156 through 161 removed outlier: 4.134A pdb=" N GLU 8 160 " --> pdb=" O LYS 8 156 " (cutoff:3.500A) Processing helix chain '9' and resid 27 through 34 Processing helix chain '9' and resid 87 through 105 removed outlier: 3.529A pdb=" N LEU 9 91 " --> pdb=" O THR 9 87 " (cutoff:3.500A) Proline residue: 9 98 - end of helix removed outlier: 4.000A pdb=" N LYS 9 105 " --> pdb=" O GLU 9 101 " (cutoff:3.500A) Processing helix chain '9' and resid 113 through 118 removed outlier: 3.987A pdb=" N LYS 9 116 " --> pdb=" O ASN 9 113 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY 9 118 " --> pdb=" O GLU 9 115 " (cutoff:3.500A) Processing helix chain 'a' and resid 68 through 72 removed outlier: 3.501A pdb=" N HIS a 71 " --> pdb=" O PRO a 68 " (cutoff:3.500A) Processing helix chain 'a' and resid 105 through 117 Processing helix chain 'a' and resid 127 through 133 Processing helix chain 'b' and resid 37 through 39 No H-bonds generated for 'chain 'b' and resid 37 through 39' Processing helix chain 'b' and resid 40 through 58 removed outlier: 5.039A pdb=" N VAL b 51 " --> pdb=" O VAL b 47 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE b 52 " --> pdb=" O GLU b 48 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ASP b 53 " --> pdb=" O ARG b 49 " (cutoff:3.500A) Processing helix chain 'b' and resid 93 through 107 Processing helix chain 'b' and resid 139 through 143 removed outlier: 3.502A pdb=" N GLY b 142 " --> pdb=" O THR b 139 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU b 143 " --> pdb=" O PHE b 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 139 through 143' Processing helix chain 'c' and resid 35 through 53 Processing helix chain 'c' and resid 67 through 79 removed outlier: 3.827A pdb=" N LEU c 79 " --> pdb=" O PHE c 75 " (cutoff:3.500A) Processing helix chain 'c' and resid 84 through 92 Processing helix chain 'c' and resid 94 through 105 removed outlier: 3.903A pdb=" N ILE c 98 " --> pdb=" O ASN c 94 " (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 171 Processing helix chain 'c' and resid 174 through 179 removed outlier: 3.703A 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: 3.713A pdb=" N THR c 224 " --> pdb=" O THR c 221 " (cutoff:3.500A) Processing helix chain 'c' and resid 227 through 231 Processing helix chain 'c' and resid 236 through 248 removed outlier: 3.942A 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: 3.552A pdb=" N ILE d 122 " --> pdb=" O SER d 118 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP d 127 " --> pdb=" O ARG d 123 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N TYR d 128 " --> pdb=" O ARG d 124 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP d 129 " --> pdb=" O ILE d 125 " (cutoff:3.500A) Processing helix chain 'd' and resid 136 through 152 removed outlier: 3.731A pdb=" N LYS d 140 " --> pdb=" O ASP d 136 " (cutoff:3.500A) Processing helix chain 'd' and resid 156 through 164 removed outlier: 3.764A pdb=" N LEU d 160 " --> pdb=" O ASP d 156 " (cutoff:3.500A) Processing helix chain 'd' and resid 168 through 174 removed outlier: 3.583A pdb=" N TRP d 174 " --> pdb=" O PRO d 170 " (cutoff:3.500A) Processing helix chain 'e' and resid 64 through 81 removed outlier: 3.675A pdb=" N GLU e 68 " --> pdb=" O THR e 64 " (cutoff:3.500A) Processing helix chain 'e' and resid 85 through 104 removed outlier: 3.668A pdb=" N LEU e 89 " --> pdb=" O SER e 85 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP e 93 " --> pdb=" O LEU e 89 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLU e 94 " --> pdb=" O ARG e 90 " (cutoff:3.500A) Processing helix chain 'e' and resid 117 through 131 removed outlier: 4.221A pdb=" N PHE e 131 " --> pdb=" O LYS e 127 " (cutoff:3.500A) Processing helix chain 'e' and resid 183 through 196 removed outlier: 4.120A pdb=" N SER e 196 " --> pdb=" O LEU e 192 " (cutoff:3.500A) Processing helix chain 'e' and resid 259 through 264 Processing helix chain 'e' and resid 271 through 275 removed outlier: 3.776A pdb=" N ARG e 274 " --> pdb=" O GLN e 271 " (cutoff:3.500A) Processing helix chain 'f' and resid 100 through 116 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: 3.866A pdb=" N LEU g 120 " --> pdb=" O ASP g 116 " (cutoff:3.500A) removed outlier: 3.587A 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 Processing helix chain 'h' and resid 93 through 109 Processing helix chain 'h' and resid 122 through 130 Processing helix chain 'h' and resid 138 through 144 Processing helix chain 'i' and resid 48 through 53 removed outlier: 3.695A pdb=" N MET i 53 " --> pdb=" O GLU i 49 " (cutoff:3.500A) Processing helix chain 'i' and resid 69 through 73 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 Processing helix chain 'j' and resid 25 through 31 Processing helix chain 'j' and resid 60 through 105 Processing helix chain 'k' and resid 27 through 37 removed outlier: 4.027A pdb=" N ARG k 31 " --> pdb=" O VAL k 27 " (cutoff:3.500A) Processing helix chain 'k' and resid 39 through 44 Processing helix chain 'k' and resid 82 through 96 Processing helix chain 'l' and resid 115 through 132 Processing helix chain 'o' and resid 28 through 49 removed outlier: 3.522A pdb=" N LYS o 32 " --> pdb=" O SER o 28 " (cutoff:3.500A) Processing helix chain 'o' and resid 63 through 79 Processing helix chain 'o' and resid 87 through 96 removed outlier: 3.923A 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 removed outlier: 3.651A pdb=" N TYR p 49 " --> pdb=" O LEU p 45 " (cutoff:3.500A) 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 removed outlier: 3.565A pdb=" N ILE p 127 " --> pdb=" O LYS p 124 " (cutoff:3.500A) No H-bonds generated for '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 48 through 53 removed outlier: 4.244A pdb=" N LEU q 52 " --> pdb=" O PRO q 48 " (cutoff:3.500A) Processing helix chain 'q' and resid 53 through 65 removed outlier: 3.729A 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: 3.786A pdb=" N SER q 74 " --> pdb=" O VAL q 71 " (cutoff:3.500A) removed outlier: 3.814A 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 144 Proline residue: q 129 - end of helix removed outlier: 3.525A pdb=" N GLU q 144 " --> pdb=" O ARG q 140 " (cutoff:3.500A) Processing helix chain 'r' and resid 70 through 75 Processing helix chain 'r' and resid 85 through 91 removed outlier: 4.172A pdb=" N LEU r 89 " --> pdb=" O ASP r 85 " (cutoff:3.500A) Processing helix chain 'r' and resid 101 through 106 Processing helix chain 'r' and resid 108 through 124 removed outlier: 3.656A pdb=" N ARG r 124 " --> pdb=" O LYS r 120 " (cutoff:3.500A) Processing helix chain 'r' and resid 155 through 159 removed outlier: 4.217A pdb=" N VAL r 159 " --> pdb=" O PRO r 156 " (cutoff:3.500A) Processing helix chain 'r' and resid 178 through 182 removed outlier: 3.579A pdb=" N ARG r 182 " --> pdb=" O PRO r 179 " (cutoff:3.500A) Processing helix chain 's' and resid 55 through 72 removed outlier: 3.772A 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: 3.678A 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 removed outlier: 3.540A pdb=" N VAL s 171 " --> pdb=" O GLU s 167 " (cutoff:3.500A) Processing helix chain 's' and resid 172 through 189 Processing helix chain 's' and resid 192 through 197 Processing helix chain 's' and resid 307 through 314 Processing helix chain 's' and resid 316 through 318 No H-bonds generated for 'chain 's' and resid 316 through 318' Processing helix chain 's' and resid 319 through 342 Processing helix chain 's' and resid 415 through 426 Processing sheet with id=AA1, first strand: chain 'D' and resid 76 through 78 Processing sheet with id=AA2, first strand: chain 'D' and resid 147 through 152 removed outlier: 5.477A pdb=" N ILE D 139 " --> pdb=" O VAL D 129 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU D 141 " --> pdb=" O ILE D 127 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 181 through 183 removed outlier: 5.856A pdb=" N LEU D 216 " --> pdb=" O GLN D 227 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLN D 227 " --> pdb=" O LEU D 216 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 331 through 332 removed outlier: 5.272A pdb=" N LYS E 272 " --> pdb=" O ASN E 286 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N TYR E 284 " --> pdb=" O TRP E 274 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ILE E 276 " --> pdb=" O ILE E 282 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE E 282 " --> pdb=" O ILE E 276 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LEU E 296 " --> pdb=" O LYS E 209 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N LYS E 209 " --> pdb=" O LEU E 296 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL E 206 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N TYR E 269 " --> pdb=" O VAL E 206 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ALA E 208 " --> pdb=" O THR E 267 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N THR E 267 " --> pdb=" O ALA E 208 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 109 through 110 Processing sheet with id=AA6, first strand: chain 'E' and resid 175 through 181 removed outlier: 6.182A pdb=" N GLY E 148 " --> pdb=" O VAL E 129 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N VAL E 129 " --> pdb=" O GLY E 148 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N CYS E 127 " --> pdb=" O LEU E 193 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 214 through 216 Processing sheet with id=AA8, first strand: chain 'F' and resid 79 through 82 removed outlier: 10.066A pdb=" N LEU F 187 " --> pdb=" O GLN F 63 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N TRP F 65 " --> pdb=" O LEU F 187 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ILE F 189 " --> pdb=" O TRP F 65 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU F 217 " --> pdb=" O VAL F 260 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N THR F 262 " --> pdb=" O LEU F 217 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N VAL F 219 " --> pdb=" O THR F 262 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL F 216 " --> pdb=" O ASN F 241 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ILE F 243 " --> pdb=" O VAL F 216 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LEU F 218 " --> pdb=" O ILE F 243 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 109 through 110 Processing sheet with id=AB1, first strand: chain 'H' and resid 54 through 58 removed outlier: 6.943A pdb=" N ILE H 55 " --> pdb=" O VAL H 83 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 111 through 114 Processing sheet with id=AB3, first strand: chain 'I' and resid 122 through 124 removed outlier: 4.163A pdb=" N VAL I 98 " --> pdb=" O LEU I 177 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 179 through 181 Processing sheet with id=AB5, first strand: chain 'J' and resid 110 through 113 Processing sheet with id=AB6, first strand: chain 'K' and resid 125 through 128 removed outlier: 6.417A pdb=" N VAL K 57 " --> pdb=" O HIS K 126 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N PHE K 128 " --> pdb=" O VAL K 57 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE K 59 " --> pdb=" O PHE K 128 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N TRP K 18 " --> pdb=" O LEU K 141 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU K 143 " --> pdb=" O TRP K 18 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 66 through 67 removed outlier: 3.726A pdb=" N PHE K 67 " --> pdb=" O ASN r 148 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'K' and resid 76 through 80 Processing sheet with id=AB9, first strand: chain 'L' and resid 39 through 40 removed outlier: 6.614A pdb=" N ARG L 39 " --> pdb=" O VAL L 105 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N LEU L 107 " --> pdb=" O ARG L 39 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N GLN L 72 " --> pdb=" O VAL L 60 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N VAL L 60 " --> pdb=" O GLN L 72 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU L 74 " --> pdb=" O ILE L 58 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG L 56 " --> pdb=" O ALA L 76 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 99 through 100 removed outlier: 6.906A pdb=" N ILE Q 150 " --> pdb=" O ILE Q 138 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL Q 154 " --> pdb=" O LEU Q 134 " (cutoff:3.500A) removed outlier: 9.821A pdb=" N LEU Q 134 " --> pdb=" O VAL Q 154 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE Q 116 " --> pdb=" O VAL Q 176 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N VAL Q 176 " --> pdb=" O ILE Q 116 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ARG Q 118 " --> pdb=" O ILE Q 174 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ILE Q 174 " --> pdb=" O ARG Q 118 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N THR Q 120 " --> pdb=" O GLN Q 172 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'M' and resid 92 through 97 removed outlier: 6.684A pdb=" N GLN M 92 " --> pdb=" O TYR M 136 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N VAL M 138 " --> pdb=" O GLN M 92 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LYS M 94 " --> pdb=" O VAL M 138 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N LEU M 140 " --> pdb=" O LYS M 94 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N LEU M 96 " --> pdb=" O LEU M 140 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'M' and resid 153 through 156 removed outlier: 3.875A pdb=" N THR M 175 " --> pdb=" O ILE M 154 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL M 156 " --> pdb=" O THR M 175 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'M' and resid 274 through 276 removed outlier: 3.839A pdb=" N ILE M 282 " --> pdb=" O VAL g 42 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'N' and resid 118 through 122 removed outlier: 6.641A pdb=" N LEU N 159 " --> pdb=" O ALA N 91 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ALA N 91 " --> pdb=" O LEU N 159 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N VAL N 161 " --> pdb=" O ILE N 89 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE N 89 " --> pdb=" O VAL N 161 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'N' and resid 95 through 97 Processing sheet with id=AC7, first strand: chain 'N' and resid 241 through 242 removed outlier: 3.648A pdb=" N TRP N 242 " --> pdb=" O PHE N 245 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'O' and resid 41 through 45 Processing sheet with id=AC9, first strand: chain 'P' and resid 47 through 48 removed outlier: 3.774A pdb=" N PHE W 142 " --> pdb=" O PHE P 48 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N VAL 6 341 " --> pdb=" O VAL W 145 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'P' and resid 80 through 85 Processing sheet with id=AD2, first strand: chain 'S' and resid 104 through 109 removed outlier: 6.424A pdb=" N PHE S 96 " --> pdb=" O VAL S 136 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL S 136 " --> pdb=" O PHE S 96 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N VAL S 98 " --> pdb=" O LEU S 134 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N LEU S 134 " --> pdb=" O GLY S 145 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY S 145 " --> pdb=" O LEU S 134 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'b' and resid 119 through 120 removed outlier: 6.507A pdb=" N GLN S 190 " --> pdb=" O LYS S 163 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LYS S 163 " --> pdb=" O GLN S 190 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL S 192 " --> pdb=" O ILE S 161 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLU S 157 " --> pdb=" O ASN S 196 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ILE S 198 " --> pdb=" O ARG S 155 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ARG S 155 " --> pdb=" O ILE S 198 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N VAL S 156 " --> pdb=" O LEU S 130 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'S' and resid 169 through 175 Processing sheet with id=AD5, first strand: chain 'T' and resid 72 through 80 removed outlier: 7.148A pdb=" N GLU T 72 " --> pdb=" O GLU T 180 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N GLU T 180 " --> pdb=" O GLU T 72 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N TYR T 74 " --> pdb=" O LEU T 178 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LEU T 178 " --> pdb=" O TYR T 74 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N CYS T 76 " --> pdb=" O VAL T 176 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL T 176 " --> pdb=" O CYS T 76 " (cutoff:3.500A) removed outlier: 5.580A 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: 6.510A pdb=" N VAL T 179 " --> pdb=" O ILE T 142 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ILE T 142 " --> pdb=" O VAL T 179 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'T' and resid 153 through 155 Processing sheet with id=AD7, first strand: chain 'U' and resid 18 through 19 Processing sheet with id=AD8, first strand: chain 'U' and resid 28 through 29 removed outlier: 4.564A pdb=" N GLN U 41 " --> pdb=" O VAL U 29 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'V' and resid 88 through 89 removed outlier: 6.398A pdb=" N THR V 61 " --> pdb=" O VAL V 123 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU V 122 " --> pdb=" O THR V 131 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR V 131 " --> pdb=" O LEU V 122 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'V' and resid 85 through 86 Processing sheet with id=AE2, first strand: chain 'V' and resid 93 through 98 Processing sheet with id=AE3, first strand: chain 'V' and resid 133 through 136 Processing sheet with id=AE4, first strand: chain 'V' and resid 176 through 177 Processing sheet with id=AE5, first strand: chain 'V' and resid 214 through 216 Processing sheet with id=AE6, first strand: chain 'W' and resid 52 through 53 removed outlier: 6.451A pdb=" N ILE W 66 " --> pdb=" O ALA W 91 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ALA W 91 " --> pdb=" O ILE W 66 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'W' and resid 60 through 61 Processing sheet with id=AE8, first strand: chain 'X' and resid 50 through 52 Processing sheet with id=AE9, first strand: chain 'X' and resid 86 through 91 Processing sheet with id=AF1, first strand: chain 'X' and resid 110 through 116 Processing sheet with id=AF2, first strand: chain 'Y' and resid 166 through 170 Processing sheet with id=AF3, first strand: chain 'Z' and resid 97 through 101 Processing sheet with id=AF4, first strand: chain 'Z' and resid 138 through 139 Processing sheet with id=AF5, first strand: chain '0' and resid 107 through 109 Processing sheet with id=AF6, first strand: chain '0' and resid 156 through 159 Processing sheet with id=AF7, first strand: chain '1' and resid 29 through 35 removed outlier: 7.653A pdb=" N ASN 1 15 " --> pdb=" O ARG 1 63 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ARG 1 63 " --> pdb=" O ASN 1 15 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LEU 1 17 " --> pdb=" O LYS 1 61 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N LYS 1 61 " --> pdb=" O LEU 1 17 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N ARG 1 19 " --> pdb=" O LYS 1 59 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LYS 1 59 " --> pdb=" O ARG 1 19 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain '3' and resid 115 through 116 Processing sheet with id=AF9, first strand: chain '5' and resid 207 through 215 Processing sheet with id=AG1, first strand: chain '5' and resid 126 through 130 removed outlier: 5.927A pdb=" N LYS 5 127 " --> pdb=" O ALA 5 374 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N VAL 5 376 " --> pdb=" O LYS 5 127 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE 5 129 " --> pdb=" O VAL 5 376 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N SER 5 378 " --> pdb=" O ILE 5 129 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ASN 5 372 " --> pdb=" O ASN 5 360 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ASN 5 360 " --> pdb=" O ASN 5 372 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ALA 5 374 " --> pdb=" O GLN 5 358 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N GLN 5 358 " --> pdb=" O ALA 5 374 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N VAL 5 376 " --> pdb=" O VAL 5 356 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL 5 356 " --> pdb=" O VAL 5 376 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N SER 5 378 " --> pdb=" O PHE 5 354 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N PHE 5 354 " --> pdb=" O SER 5 378 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N THR 5 361 " --> pdb=" O GLN 5 338 " (cutoff:3.500A) removed outlier: 10.179A pdb=" N GLN 5 338 " --> pdb=" O THR 5 361 " (cutoff:3.500A) removed outlier: 12.586A pdb=" N TYR 5 287 " --> pdb=" O PRO 5 339 " (cutoff:3.500A) removed outlier: 9.784A pdb=" N VAL 5 341 " --> pdb=" O TYR 5 287 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N HIS 5 289 " --> pdb=" O VAL 5 341 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU 5 230 " --> pdb=" O HIS 5 289 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain '5' and resid 385 through 387 Processing sheet with id=AG3, first strand: chain '6' and resid 183 through 187 Processing sheet with id=AG4, first strand: chain '6' and resid 191 through 192 removed outlier: 6.871A pdb=" N ASN 6 191 " --> pdb=" O GLN 6 320 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N LEU 6 272 " --> pdb=" O ALA 6 314 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU 6 316 " --> pdb=" O PHE 6 270 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N PHE 6 270 " --> pdb=" O LEU 6 316 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N PHE 6 318 " --> pdb=" O LEU 6 268 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU 6 268 " --> pdb=" O PHE 6 318 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLN 6 320 " --> pdb=" O HIS 6 266 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N HIS 6 266 " --> pdb=" O GLN 6 320 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N TRP 6 214 " --> pdb=" O THR 6 238 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N THR 6 238 " --> pdb=" O TRP 6 214 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N LEU 6 216 " --> pdb=" O LEU 6 236 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU 6 218 " --> pdb=" O HIS 6 234 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain '6' and resid 191 through 192 removed outlier: 6.871A pdb=" N ASN 6 191 " --> pdb=" O GLN 6 320 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N LEU 6 272 " --> pdb=" O ALA 6 314 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU 6 316 " --> pdb=" O PHE 6 270 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N PHE 6 270 " --> pdb=" O LEU 6 316 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N PHE 6 318 " --> pdb=" O LEU 6 268 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU 6 268 " --> pdb=" O PHE 6 318 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLN 6 320 " --> pdb=" O HIS 6 266 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N HIS 6 266 " --> pdb=" O GLN 6 320 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N TRP 6 214 " --> pdb=" O THR 6 238 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N THR 6 238 " --> pdb=" O TRP 6 214 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N LEU 6 216 " --> pdb=" O LEU 6 236 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU 6 218 " --> pdb=" O HIS 6 234 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain '7' and resid 64 through 69 Processing sheet with id=AG7, first strand: chain '7' and resid 106 through 108 Processing sheet with id=AG8, first strand: chain '7' and resid 164 through 168 removed outlier: 7.045A pdb=" N ASP 7 182 " --> pdb=" O VAL 7 167 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL 7 300 " --> pdb=" O VAL 7 280 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N VAL 7 280 " --> pdb=" O VAL 7 300 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N LEU 7 302 " --> pdb=" O TYR 7 278 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N TYR 7 278 " --> pdb=" O LEU 7 302 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain '7' and resid 217 through 222 Processing sheet with id=AH1, first strand: chain '9' and resid 42 through 45 Processing sheet with id=AH2, first strand: chain 'b' and resid 8 through 9 Processing sheet with id=AH3, first strand: chain 'b' and resid 84 through 88 removed outlier: 5.961A pdb=" N ARG b 74 " --> pdb=" O PHE b 31 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N VAL b 76 " --> pdb=" O LEU b 29 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLU b 78 " --> pdb=" O GLN b 27 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N GLN b 27 " --> pdb=" O VAL b 62 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N TYR b 64 " --> pdb=" O GLN b 27 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU b 29 " --> pdb=" O TYR b 64 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE b 63 " --> pdb=" O LYS h 153 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'c' and resid 254 through 259 removed outlier: 6.463A pdb=" N PHE c 271 " --> pdb=" O THR c 258 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N TYR c 270 " --> pdb=" O PRO c 285 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL c 272 " --> pdb=" O GLU c 283 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLU c 283 " --> pdb=" O VAL c 272 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU c 274 " --> pdb=" O ILE c 281 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'd' and resid 184 through 196 removed outlier: 4.758A pdb=" N SER d 188 " --> pdb=" O HIS d 217 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N HIS d 217 " --> pdb=" O SER d 188 " (cutoff:3.500A) removed outlier: 8.546A pdb=" N GLU d 190 " --> pdb=" O ARG d 215 " (cutoff:3.500A) removed outlier: 9.000A pdb=" N ARG d 215 " --> pdb=" O GLU d 190 " (cutoff:3.500A) removed outlier: 10.291A pdb=" N SER d 192 " --> pdb=" O THR d 213 " (cutoff:3.500A) removed outlier: 11.006A pdb=" N THR d 213 " --> pdb=" O SER d 192 " (cutoff:3.500A) removed outlier: 10.385A pdb=" N VAL d 194 " --> pdb=" O GLN d 211 " (cutoff:3.500A) removed outlier: 12.746A pdb=" N GLN d 211 " --> pdb=" O VAL d 194 " (cutoff:3.500A) removed outlier: 11.957A pdb=" N GLN d 196 " --> pdb=" O TYR d 209 " (cutoff:3.500A) removed outlier: 12.470A pdb=" N TYR d 209 " --> pdb=" O GLN d 196 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N GLU d 249 " --> pdb=" O MET d 261 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N MET d 261 " --> pdb=" O GLU d 249 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'e' and resid 175 through 177 removed outlier: 3.531A pdb=" N PHE e 232 " --> pdb=" O LEU e 48 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'e' and resid 54 through 55 removed outlier: 3.947A pdb=" N LEU e 157 " --> pdb=" O ARG e 55 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'e' and resid 161 through 164 Processing sheet with id=AH9, first strand: chain 'e' and resid 199 through 202 Processing sheet with id=AI1, first strand: chain 'f' and resid 126 through 130 removed outlier: 4.319A pdb=" N GLU f 154 " --> pdb=" O MET f 127 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N THR f 129 " --> pdb=" O THR f 152 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N THR f 152 " --> pdb=" O THR f 129 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'g' and resid 84 through 86 Processing sheet with id=AI3, first strand: chain 'g' and resid 96 through 101 Processing sheet with id=AI4, first strand: chain 'k' and resid 50 through 55 removed outlier: 3.642A pdb=" N ILE r 49 " --> pdb=" O ILE k 75 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLY r 51 " --> pdb=" O ARG k 77 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'm' and resid 52 through 57 Processing sheet with id=AI6, first strand: chain 'p' and resid 77 through 80 Processing sheet with id=AI7, first strand: chain 's' and resid 206 through 211 removed outlier: 4.147A pdb=" N ASP s 234 " --> pdb=" O VAL s 93 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 's' and resid 112 through 116 removed outlier: 6.378A pdb=" N VAL s 113 " --> pdb=" O CYS s 393 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N GLY s 395 " --> pdb=" O VAL s 113 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU s 115 " --> pdb=" O GLY s 395 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL s 360 " --> pdb=" O GLN s 298 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N HIS s 300 " --> pdb=" O VAL s 360 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 's' and resid 112 through 116 removed outlier: 6.378A pdb=" N VAL s 113 " --> pdb=" O CYS s 393 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N GLY s 395 " --> pdb=" O VAL s 113 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU s 115 " --> pdb=" O GLY s 395 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 's' and resid 215 through 216 Processing sheet with id=AJ2, first strand: chain 's' and resid 404 through 405 2397 hydrogen bonds defined for protein. 6723 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 747 hydrogen bonds 1288 hydrogen bond angles 0 basepair planarities 308 basepair parallelities 614 stacking parallelities Total time for adding SS restraints: 44.95 Time building geometry restraints manager: 32.70 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: 21043 1.33 - 1.46: 25900 1.46 - 1.58: 43096 1.58 - 1.70: 2270 1.70 - 1.82: 422 Bond restraints: 92731 Sorted by residual: bond pdb=" C VAL N 151 " pdb=" N THR N 152 " ideal model delta sigma weight residual 1.331 1.458 -0.127 2.07e-02 2.33e+03 3.79e+01 bond pdb=" CB TRP 8 121 " pdb=" CG TRP 8 121 " ideal model delta sigma weight residual 1.498 1.601 -0.103 3.10e-02 1.04e+03 1.10e+01 bond pdb=" C ARG P 173 " pdb=" N GLU P 174 " ideal model delta sigma weight residual 1.327 1.268 0.059 2.31e-02 1.87e+03 6.56e+00 bond pdb=" N3 U A 340 " pdb=" C4 U A 340 " ideal model delta sigma weight residual 1.380 1.335 0.045 2.00e-02 2.50e+03 4.97e+00 bond pdb=" C PHE 8 169 " pdb=" N PRO 8 170 " ideal model delta sigma weight residual 1.340 1.400 -0.060 2.76e-02 1.31e+03 4.78e+00 ... (remaining 92726 not shown) Histogram of bond angle deviations from ideal: 92.41 - 101.68: 858 101.68 - 110.95: 40246 110.95 - 120.21: 52543 120.21 - 129.48: 35939 129.48 - 138.75: 1227 Bond angle restraints: 130813 Sorted by residual: angle pdb=" CB ARG I 83 " pdb=" CG ARG I 83 " pdb=" CD ARG I 83 " ideal model delta sigma weight residual 111.30 130.61 -19.31 2.30e+00 1.89e-01 7.05e+01 angle pdb=" C ARG X 36 " pdb=" N THR X 37 " pdb=" CA THR X 37 " ideal model delta sigma weight residual 120.67 130.37 -9.70 1.34e+00 5.57e-01 5.23e+01 angle pdb=" CG1 ILE e 172 " pdb=" CB ILE e 172 " pdb=" CG2 ILE e 172 " ideal model delta sigma weight residual 110.70 92.41 18.29 3.00e+00 1.11e-01 3.72e+01 angle pdb=" C LEU P 137 " pdb=" N GLU P 138 " pdb=" CA GLU P 138 " ideal model delta sigma weight residual 120.29 128.39 -8.10 1.42e+00 4.96e-01 3.25e+01 angle pdb=" CA GLU m 70 " pdb=" CB GLU m 70 " pdb=" CG GLU m 70 " ideal model delta sigma weight residual 114.10 125.43 -11.33 2.00e+00 2.50e-01 3.21e+01 ... (remaining 130808 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.83: 52273 35.83 - 71.67: 1301 71.67 - 107.50: 129 107.50 - 143.34: 9 143.34 - 179.17: 30 Dihedral angle restraints: 53742 sinusoidal: 30911 harmonic: 22831 Sorted by residual: 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 200.00 21.66 178.34 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C A 143 " pdb=" C1' C A 143 " pdb=" N1 C A 143 " pdb=" C2 C A 143 " ideal model delta sinusoidal sigma weight residual 200.00 26.86 173.14 1 1.50e+01 4.44e-03 8.50e+01 dihedral pdb=" O4' C A 396 " pdb=" C1' C A 396 " pdb=" N1 C A 396 " pdb=" C2 C A 396 " ideal model delta sinusoidal sigma weight residual 200.00 34.66 165.34 1 1.50e+01 4.44e-03 8.39e+01 ... (remaining 53739 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 13646 0.075 - 0.149: 1437 0.149 - 0.224: 91 0.224 - 0.299: 21 0.299 - 0.374: 5 Chirality restraints: 15200 Sorted by residual: chirality pdb=" CB ILE V 154 " pdb=" CA ILE V 154 " pdb=" CG1 ILE V 154 " pdb=" CG2 ILE V 154 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.49e+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 2.09 0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" C3' A A 573 " pdb=" C4' A A 573 " pdb=" O3' A A 573 " pdb=" C2' A A 573 " both_signs ideal model delta sigma weight residual False -2.74 -2.43 -0.32 2.00e-01 2.50e+01 2.55e+00 ... (remaining 15197 not shown) Planarity restraints: 12556 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL U 63 " -0.094 5.00e-02 4.00e+02 1.42e-01 3.25e+01 pdb=" N PRO U 64 " 0.246 5.00e-02 4.00e+02 pdb=" CA PRO U 64 " -0.079 5.00e-02 4.00e+02 pdb=" CD PRO U 64 " -0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE K 151 " -0.087 5.00e-02 4.00e+02 1.28e-01 2.63e+01 pdb=" N PRO K 152 " 0.221 5.00e-02 4.00e+02 pdb=" CA PRO K 152 " -0.068 5.00e-02 4.00e+02 pdb=" CD PRO K 152 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER 8 154 " -0.061 5.00e-02 4.00e+02 9.26e-02 1.37e+01 pdb=" N PRO 8 155 " 0.160 5.00e-02 4.00e+02 pdb=" CA PRO 8 155 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO 8 155 " -0.050 5.00e-02 4.00e+02 ... (remaining 12553 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 969 2.59 - 3.17: 66239 3.17 - 3.75: 153499 3.75 - 4.32: 205788 4.32 - 4.90: 315365 Nonbonded interactions: 741860 Sorted by model distance: nonbonded pdb=" CA MET E 106 " pdb=" O VAL E 119 " model vdw 2.019 3.470 nonbonded pdb=" OP2 G A 248 " pdb="MG MG A1607 " model vdw 2.105 2.170 nonbonded pdb=" OP2 A A 357 " pdb="MG MG A1609 " model vdw 2.116 2.170 nonbonded pdb=" O6 G A 106 " pdb="MG MG A1606 " model vdw 2.130 2.170 nonbonded pdb=" OP2 G A 106 " pdb="MG MG A1604 " model vdw 2.133 2.170 ... (remaining 741855 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 1148 5.49 5 Mg 49 5.21 5 S 266 5.16 5 C 51742 2.51 5 N 16087 2.21 5 O 19066 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.990 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: 16.670 Check model and map are aligned: 1.170 Convert atoms to be neutral: 0.600 Process input model: 221.660 Find NCS groups from input model: 2.790 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Set scattering table: 0.030 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 247.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 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 0.127 92731 Z= 0.241 Angle : 0.858 19.314 130813 Z= 0.450 Chirality : 0.046 0.374 15200 Planarity : 0.007 0.142 12556 Dihedral : 15.288 179.171 38950 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.76 % Favored : 96.23 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.09), residues: 7684 helix: -0.48 (0.10), residues: 2531 sheet: -0.74 (0.16), residues: 933 loop : -1.09 (0.09), residues: 4220 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15368 Ramachandran restraints generated. 7684 Oldfield, 0 Emsley, 7684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15368 Ramachandran restraints generated. 7684 Oldfield, 0 Emsley, 7684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1619 residues out of total 6926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1617 time to evaluate : 6.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 1617 average time/residue: 0.8237 time to fit residues: 2247.8384 Evaluate side-chains 1264 residues out of total 6926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1264 time to evaluate : 6.612 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.5115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 875 random chunks: chunk 738 optimal weight: 4.9990 chunk 663 optimal weight: 8.9990 chunk 368 optimal weight: 0.9990 chunk 226 optimal weight: 8.9990 chunk 447 optimal weight: 8.9990 chunk 354 optimal weight: 6.9990 chunk 685 optimal weight: 0.0570 chunk 265 optimal weight: 1.9990 chunk 417 optimal weight: 0.5980 chunk 510 optimal weight: 3.9990 chunk 794 optimal weight: 7.9990 overall best weight: 1.5304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 205 GLN ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 GLN E 137 ASN E 184 ASN F 98 GLN L 59 HIS L 89 HIS M 26 ASN M 198 GLN N 110 ASN N 222 ASN ** P 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 139 GLN R 12 ASN R 94 GLN ** S 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 139 ASN Y 92 ASN Y 110 ASN Y 183 GLN 3 178 GLN ** 5 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 49 ASN ** a 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 107 GLN b 129 GLN ** b 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 65 ASN d 149 HIS ** d 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 211 GLN d 217 HIS ** d 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 122 ASN ** k 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 58 GLN o 91 GLN p 96 ASN s 152 GLN ** s 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.102 92731 Z= 0.229 Angle : 0.601 13.563 130813 Z= 0.305 Chirality : 0.039 0.271 15200 Planarity : 0.005 0.097 12556 Dihedral : 14.177 178.741 22420 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.45 % Favored : 96.53 % Rotamer Outliers : 1.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.09), residues: 7684 helix: 0.34 (0.10), residues: 2580 sheet: -0.79 (0.16), residues: 1020 loop : -0.79 (0.10), residues: 4084 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15368 Ramachandran restraints generated. 7684 Oldfield, 0 Emsley, 7684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15368 Ramachandran restraints generated. 7684 Oldfield, 0 Emsley, 7684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1467 residues out of total 6926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 1336 time to evaluate : 6.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 131 outliers final: 88 residues processed: 1396 average time/residue: 0.7944 time to fit residues: 1890.1952 Evaluate side-chains 1260 residues out of total 6926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 1172 time to evaluate : 6.649 Switching outliers to nearest non-outliers outliers start: 88 outliers final: 0 residues processed: 88 average time/residue: 0.6035 time to fit residues: 110.7511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 875 random chunks: chunk 441 optimal weight: 4.9990 chunk 246 optimal weight: 2.9990 chunk 661 optimal weight: 4.9990 chunk 541 optimal weight: 2.9990 chunk 219 optimal weight: 7.9990 chunk 796 optimal weight: 5.9990 chunk 859 optimal weight: 8.9990 chunk 708 optimal weight: 8.9990 chunk 789 optimal weight: 4.9990 chunk 271 optimal weight: 0.0770 chunk 638 optimal weight: 0.6980 overall best weight: 2.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 205 GLN D 233 GLN J 133 GLN K 160 GLN ** L 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 178 GLN P 115 HIS ** Q 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 94 GLN ** S 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 139 ASN T 195 HIS T 202 GLN X 237 GLN Z 150 HIS 2 77 GLN 5 109 HIS ** 5 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 333 GLN 6 361 GLN 7 49 ASN ** a 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 129 GLN ** b 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 65 ASN c 222 GLN d 167 HIS d 211 GLN ** d 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 262 HIS ** g 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 82 GLN ** k 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 96 ASN q 81 GLN ** s 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.090 92731 Z= 0.296 Angle : 0.614 18.108 130813 Z= 0.309 Chirality : 0.041 0.308 15200 Planarity : 0.005 0.137 12556 Dihedral : 14.152 179.868 22420 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.88 % Favored : 96.10 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.10), residues: 7684 helix: 0.68 (0.10), residues: 2580 sheet: -0.80 (0.16), residues: 1027 loop : -0.69 (0.10), residues: 4077 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15368 Ramachandran restraints generated. 7684 Oldfield, 0 Emsley, 7684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15368 Ramachandran restraints generated. 7684 Oldfield, 0 Emsley, 7684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1417 residues out of total 6926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 1298 time to evaluate : 6.719 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 outliers start: 119 outliers final: 65 residues processed: 1350 average time/residue: 0.8095 time to fit residues: 1861.8741 Evaluate side-chains 1273 residues out of total 6926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 1208 time to evaluate : 6.687 Switching outliers to nearest non-outliers outliers start: 65 outliers final: 0 residues processed: 65 average time/residue: 0.6301 time to fit residues: 85.9014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 875 random chunks: chunk 786 optimal weight: 6.9990 chunk 598 optimal weight: 50.0000 chunk 413 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 chunk 379 optimal weight: 1.9990 chunk 534 optimal weight: 4.9990 chunk 798 optimal weight: 10.0000 chunk 845 optimal weight: 10.0000 chunk 417 optimal weight: 0.5980 chunk 757 optimal weight: 5.9990 chunk 227 optimal weight: 5.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 102 GLN ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 HIS H 104 ASN J 133 GLN K 94 GLN K 160 GLN L 33 GLN L 89 HIS ** P 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 196 ASN T 139 ASN ** U 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 237 GLN Y 99 HIS 2 77 GLN 3 178 GLN ** 5 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 214 ASN ** 5 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 320 GLN 6 359 HIS ** a 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 66 ASN ** b 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 65 ASN ** d 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 217 HIS d 235 GLN d 251 GLN ** g 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 96 ASN r 96 HIS s 152 GLN s 179 GLN s 240 GLN ** s 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.097 92731 Z= 0.323 Angle : 0.625 10.724 130813 Z= 0.314 Chirality : 0.041 0.425 15200 Planarity : 0.005 0.102 12556 Dihedral : 14.201 179.818 22420 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.02 % Favored : 95.95 % Rotamer Outliers : 2.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.10), residues: 7684 helix: 0.83 (0.10), residues: 2574 sheet: -0.70 (0.16), residues: 1019 loop : -0.65 (0.10), residues: 4091 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15368 Ramachandran restraints generated. 7684 Oldfield, 0 Emsley, 7684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15368 Ramachandran restraints generated. 7684 Oldfield, 0 Emsley, 7684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1401 residues out of total 6926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 1261 time to evaluate : 7.745 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 outliers start: 140 outliers final: 70 residues processed: 1338 average time/residue: 0.8816 time to fit residues: 2019.0160 Evaluate side-chains 1268 residues out of total 6926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 1198 time to evaluate : 6.667 Switching outliers to nearest non-outliers outliers start: 70 outliers final: 0 residues processed: 70 average time/residue: 0.6674 time to fit residues: 95.1544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 875 random chunks: chunk 704 optimal weight: 0.9980 chunk 480 optimal weight: 6.9990 chunk 12 optimal weight: 0.2980 chunk 629 optimal weight: 0.7980 chunk 348 optimal weight: 5.9990 chunk 721 optimal weight: 0.3980 chunk 584 optimal weight: 30.0000 chunk 0 optimal weight: 7.9990 chunk 431 optimal weight: 0.5980 chunk 759 optimal weight: 10.0000 chunk 213 optimal weight: 9.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 233 GLN E 52 HIS ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 160 GLN ** P 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 139 ASN X 237 GLN 2 77 GLN ** 5 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 174 HIS 6 320 GLN 9 113 ASN ** a 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 66 ASN b 129 GLN ** b 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 65 ASN ** d 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 112 ASN ** g 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 125 ASN s 152 GLN s 179 GLN ** s 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.062 92731 Z= 0.156 Angle : 0.560 10.410 130813 Z= 0.281 Chirality : 0.038 0.300 15200 Planarity : 0.005 0.099 12556 Dihedral : 14.132 179.619 22420 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.46 % Favored : 96.51 % Rotamer Outliers : 1.40 % 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: -0.06 (0.10), residues: 7684 helix: 1.08 (0.11), residues: 2580 sheet: -0.64 (0.16), residues: 1001 loop : -0.55 (0.10), residues: 4103 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15368 Ramachandran restraints generated. 7684 Oldfield, 0 Emsley, 7684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15368 Ramachandran restraints generated. 7684 Oldfield, 0 Emsley, 7684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1374 residues out of total 6926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 1277 time to evaluate : 7.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 97 outliers final: 41 residues processed: 1326 average time/residue: 0.8257 time to fit residues: 1866.9823 Evaluate side-chains 1252 residues out of total 6926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 1211 time to evaluate : 6.685 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.6426 time to fit residues: 57.8966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 875 random chunks: chunk 284 optimal weight: 0.9980 chunk 761 optimal weight: 5.9990 chunk 167 optimal weight: 7.9990 chunk 496 optimal weight: 7.9990 chunk 208 optimal weight: 8.9990 chunk 846 optimal weight: 9.9990 chunk 702 optimal weight: 6.9990 chunk 391 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 280 optimal weight: 1.9990 chunk 444 optimal weight: 6.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 52 HIS P 41 ASN ** Q 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 94 GLN ** S 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 237 GLN Y 183 GLN Z 53 HIS 2 77 GLN ** 5 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 275 ASN ** 5 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 113 ASN b 107 GLN b 129 GLN c 48 GLN ** d 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 75 GLN e 76 GLN ** e 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 271 GLN ** g 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 82 GLN ** k 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 125 ASN p 143 GLN r 76 ASN r 96 HIS s 96 GLN s 152 GLN s 179 GLN ** s 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.098 92731 Z= 0.328 Angle : 0.628 11.221 130813 Z= 0.315 Chirality : 0.041 0.400 15200 Planarity : 0.006 0.110 12556 Dihedral : 14.151 179.169 22420 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.02 % Favored : 95.95 % Rotamer Outliers : 1.88 % 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: -0.09 (0.10), residues: 7684 helix: 1.07 (0.10), residues: 2566 sheet: -0.71 (0.16), residues: 1040 loop : -0.57 (0.10), residues: 4078 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15368 Ramachandran restraints generated. 7684 Oldfield, 0 Emsley, 7684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15368 Ramachandran restraints generated. 7684 Oldfield, 0 Emsley, 7684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1358 residues out of total 6926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 1228 time to evaluate : 6.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 130 outliers final: 91 residues processed: 1289 average time/residue: 0.8242 time to fit residues: 1809.0997 Evaluate side-chains 1268 residues out of total 6926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 1177 time to evaluate : 6.579 Switching outliers to nearest non-outliers outliers start: 91 outliers final: 0 residues processed: 91 average time/residue: 0.6280 time to fit residues: 117.1436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 875 random chunks: chunk 816 optimal weight: 3.9990 chunk 95 optimal weight: 40.0000 chunk 482 optimal weight: 0.7980 chunk 618 optimal weight: 30.0000 chunk 479 optimal weight: 3.9990 chunk 712 optimal weight: 10.0000 chunk 472 optimal weight: 5.9990 chunk 843 optimal weight: 8.9990 chunk 527 optimal weight: 1.9990 chunk 514 optimal weight: 1.9990 chunk 389 optimal weight: 0.3980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 52 HIS L 59 HIS P 147 GLN ** Q 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 94 GLN ** S 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 139 ASN ** V 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 237 GLN Y 122 GLN 2 77 GLN 5 150 GLN ** 5 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 174 HIS ** 6 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 320 GLN 7 84 ASN 8 151 GLN 8 158 HIS ** a 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 128 GLN c 204 GLN ** d 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 130 GLN ** e 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 112 ASN ** g 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 125 ASN p 143 GLN s 152 GLN s 179 GLN s 343 GLN ** s 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.088 92731 Z= 0.247 Angle : 0.600 21.082 130813 Z= 0.298 Chirality : 0.040 0.376 15200 Planarity : 0.005 0.102 12556 Dihedral : 14.134 179.713 22420 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.84 % Favored : 96.13 % Rotamer Outliers : 1.00 % 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: -0.02 (0.10), residues: 7684 helix: 1.14 (0.11), residues: 2562 sheet: -0.69 (0.16), residues: 1049 loop : -0.52 (0.10), residues: 4073 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15368 Ramachandran restraints generated. 7684 Oldfield, 0 Emsley, 7684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15368 Ramachandran restraints generated. 7684 Oldfield, 0 Emsley, 7684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1276 residues out of total 6926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 1207 time to evaluate : 6.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 69 outliers final: 34 residues processed: 1240 average time/residue: 0.8476 time to fit residues: 1791.6974 Evaluate side-chains 1199 residues out of total 6926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 1165 time to evaluate : 6.671 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.6676 time to fit residues: 50.5142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 875 random chunks: chunk 521 optimal weight: 5.9990 chunk 336 optimal weight: 1.9990 chunk 503 optimal weight: 5.9990 chunk 254 optimal weight: 8.9990 chunk 165 optimal weight: 9.9990 chunk 163 optimal weight: 1.9990 chunk 536 optimal weight: 2.9990 chunk 574 optimal weight: 5.9990 chunk 416 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 662 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 52 HIS ** J 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 HIS M 102 GLN P 41 ASN P 147 GLN ** Q 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 94 GLN ** S 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 139 ASN V 92 ASN X 237 GLN 2 77 GLN ** 5 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 320 GLN 7 298 GLN ** 8 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 107 GLN ** d 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 125 ASN p 143 GLN r 96 HIS ** s 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.103 92731 Z= 0.283 Angle : 0.611 11.676 130813 Z= 0.305 Chirality : 0.040 0.306 15200 Planarity : 0.005 0.108 12556 Dihedral : 14.130 179.373 22420 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.26 % Favored : 95.72 % Rotamer Outliers : 1.06 % 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: -0.01 (0.10), residues: 7684 helix: 1.15 (0.10), residues: 2561 sheet: -0.71 (0.16), residues: 1061 loop : -0.51 (0.10), residues: 4062 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15368 Ramachandran restraints generated. 7684 Oldfield, 0 Emsley, 7684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15368 Ramachandran restraints generated. 7684 Oldfield, 0 Emsley, 7684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1265 residues out of total 6926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 1192 time to evaluate : 6.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 73 outliers final: 44 residues processed: 1222 average time/residue: 0.8737 time to fit residues: 1824.5660 Evaluate side-chains 1202 residues out of total 6926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 1158 time to evaluate : 6.787 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.6760 time to fit residues: 65.2883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 875 random chunks: chunk 767 optimal weight: 4.9990 chunk 807 optimal weight: 60.0000 chunk 737 optimal weight: 5.9990 chunk 785 optimal weight: 8.9990 chunk 473 optimal weight: 0.0970 chunk 342 optimal weight: 10.0000 chunk 617 optimal weight: 9.9990 chunk 241 optimal weight: 2.9990 chunk 710 optimal weight: 4.9990 chunk 743 optimal weight: 5.9990 chunk 783 optimal weight: 4.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 252 HIS ** J 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 79 HIS P 147 GLN ** Q 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 94 GLN ** S 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 139 ASN U 62 ASN X 237 GLN 2 77 GLN ** 5 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 307 HIS 6 320 GLN 7 298 GLN ** 8 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 30 GLN j 31 GLN ** k 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 96 ASN p 125 ASN ** s 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.106 92731 Z= 0.419 Angle : 0.690 12.530 130813 Z= 0.345 Chirality : 0.044 0.330 15200 Planarity : 0.006 0.113 12556 Dihedral : 14.237 178.284 22420 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.45 % Favored : 95.52 % Rotamer Outliers : 0.70 % 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: -0.19 (0.10), residues: 7684 helix: 0.96 (0.10), residues: 2576 sheet: -0.81 (0.15), residues: 1065 loop : -0.60 (0.10), residues: 4043 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15368 Ramachandran restraints generated. 7684 Oldfield, 0 Emsley, 7684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15368 Ramachandran restraints generated. 7684 Oldfield, 0 Emsley, 7684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1243 residues out of total 6926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 1195 time to evaluate : 6.917 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 outliers start: 48 outliers final: 31 residues processed: 1209 average time/residue: 0.8691 time to fit residues: 1794.4436 Evaluate side-chains 1208 residues out of total 6926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 1177 time to evaluate : 6.939 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.6829 time to fit residues: 48.0937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 875 random chunks: chunk 516 optimal weight: 3.9990 chunk 831 optimal weight: 10.0000 chunk 507 optimal weight: 5.9990 chunk 394 optimal weight: 0.8980 chunk 577 optimal weight: 20.0000 chunk 871 optimal weight: 20.0000 chunk 802 optimal weight: 3.9990 chunk 694 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 536 optimal weight: 0.9980 chunk 425 optimal weight: 5.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 147 GLN ** Q 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 94 GLN ** S 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 139 ASN X 237 GLN 2 51 ASN 2 77 GLN ** 5 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 298 GLN ** 8 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 107 GLN ** d 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 130 GLN ** e 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 112 ASN ** g 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 131 ASN ** k 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 96 ASN p 125 ASN ** s 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.113 92731 Z= 0.235 Angle : 0.610 11.963 130813 Z= 0.305 Chirality : 0.040 0.280 15200 Planarity : 0.005 0.116 12556 Dihedral : 14.166 179.344 22420 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.07 % Favored : 95.90 % Rotamer Outliers : 0.35 % 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: -0.05 (0.10), residues: 7684 helix: 1.11 (0.10), residues: 2558 sheet: -0.76 (0.16), residues: 1053 loop : -0.53 (0.10), residues: 4073 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15368 Ramachandran restraints generated. 7684 Oldfield, 0 Emsley, 7684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15368 Ramachandran restraints generated. 7684 Oldfield, 0 Emsley, 7684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1231 residues out of total 6926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1207 time to evaluate : 6.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 14 residues processed: 1216 average time/residue: 0.8685 time to fit residues: 1807.9053 Evaluate side-chains 1180 residues out of total 6926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 1166 time to evaluate : 6.705 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.6727 time to fit residues: 26.5399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 875 random chunks: chunk 551 optimal weight: 0.9980 chunk 739 optimal weight: 4.9990 chunk 212 optimal weight: 5.9990 chunk 640 optimal weight: 6.9990 chunk 102 optimal weight: 50.0000 chunk 192 optimal weight: 0.5980 chunk 695 optimal weight: 0.4980 chunk 290 optimal weight: 1.9990 chunk 713 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 72 GLN E 137 ASN ** J 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 147 GLN ** Q 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 94 GLN ** S 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 237 GLN 2 77 GLN ** 5 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 174 HIS ** 6 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 298 GLN 8 127 GLN ** 8 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 75 GLN e 76 GLN e 118 GLN ** g 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 96 ASN p 125 ASN p 143 GLN s 240 GLN ** s 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.166450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.121894 restraints weight = 122689.634| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.59 r_work: 0.3289 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 1.52 restraints_weight: 0.2500 r_work: 0.3240 rms_B_bonded: 1.79 restraints_weight: 0.1250 r_work: 0.3206 rms_B_bonded: 2.25 restraints_weight: 0.0625 r_work: 0.3154 rms_B_bonded: 3.04 restraints_weight: 0.0312 r_work: 0.3070 rms_B_bonded: 4.46 restraints_weight: 0.0156 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.095 92731 Z= 0.206 Angle : 0.598 11.822 130813 Z= 0.298 Chirality : 0.039 0.343 15200 Planarity : 0.005 0.124 12556 Dihedral : 14.110 179.816 22420 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.80 % Favored : 96.17 % Rotamer Outliers : 0.45 % 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: 0.02 (0.10), residues: 7684 helix: 1.19 (0.10), residues: 2566 sheet: -0.78 (0.16), residues: 1041 loop : -0.47 (0.10), residues: 4077 =============================================================================== Job complete usr+sys time: 24878.03 seconds wall clock time: 434 minutes 57.22 seconds (26097.22 seconds total)