Starting phenix.real_space_refine (version: dev) on Tue Feb 21 17:04:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdn_4824/02_2023/6rdn_4824_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdn_4824/02_2023/6rdn_4824.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdn_4824/02_2023/6rdn_4824.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdn_4824/02_2023/6rdn_4824.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdn_4824/02_2023/6rdn_4824_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdn_4824/02_2023/6rdn_4824_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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 Process input model Symmetric amino acids flipped Residue "1 TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 28": "NH1" <-> "NH2" Residue "1 PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 33": "OE1" <-> "OE2" Residue "1 GLU 49": "OE1" <-> "OE2" Residue "1 ASP 96": "OD1" <-> "OD2" Residue "1 ARG 150": "NH1" <-> "NH2" Residue "1 ASP 172": "OD1" <-> "OD2" Residue "1 ARG 182": "NH1" <-> "NH2" Residue "1 GLU 229": "OE1" <-> "OE2" Residue "1 ARG 259": "NH1" <-> "NH2" Residue "1 PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 329": "OE1" <-> "OE2" Residue "1 GLU 350": "OE1" <-> "OE2" Residue "1 ASP 353": "OD1" <-> "OD2" Residue "1 ARG 359": "NH1" <-> "NH2" Residue "1 GLU 385": "OE1" <-> "OE2" Residue "1 ARG 387": "NH1" <-> "NH2" Residue "1 GLU 409": "OE1" <-> "OE2" Residue "1 TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 422": "OD1" <-> "OD2" Residue "1 ASP 425": "OD1" <-> "OD2" Residue "1 ARG 434": "NH1" <-> "NH2" Residue "1 GLU 496": "OE1" <-> "OE2" Residue "1 ASP 504": "OD1" <-> "OD2" Residue "1 ASP 601": "OD1" <-> "OD2" Residue "1 ARG 609": "NH1" <-> "NH2" Residue "2 TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 45": "NH1" <-> "NH2" Residue "2 ASP 60": "OD1" <-> "OD2" Residue "2 TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 86": "OE1" <-> "OE2" Residue "2 ARG 173": "NH1" <-> "NH2" Residue "2 ASP 189": "OD1" <-> "OD2" Residue "2 ASP 194": "OD1" <-> "OD2" Residue "2 PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 258": "OD1" <-> "OD2" Residue "2 PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 278": "OD1" <-> "OD2" Residue "2 PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 346": "NH1" <-> "NH2" Residue "2 GLU 348": "OE1" <-> "OE2" Residue "2 TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 420": "OE1" <-> "OE2" Residue "2 GLU 422": "OE1" <-> "OE2" Residue "2 TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 149": "NH1" <-> "NH2" Residue "3 ASP 154": "OD1" <-> "OD2" Residue "3 PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 213": "NH1" <-> "NH2" Residue "3 TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 233": "NH1" <-> "NH2" Residue "3 ARG 242": "NH1" <-> "NH2" Residue "3 ARG 257": "NH1" <-> "NH2" Residue "3 ASP 259": "OD1" <-> "OD2" Residue "3 PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 291": "OE1" <-> "OE2" Residue "3 TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 295": "OE1" <-> "OE2" Residue "3 GLU 301": "OE1" <-> "OE2" Residue "3 PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 320": "OE1" <-> "OE2" Residue "4 TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 84": "NH1" <-> "NH2" Residue "4 TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 156": "OD1" <-> "OD2" Residue "4 GLU 160": "OE1" <-> "OE2" Residue "4 ARG 176": "NH1" <-> "NH2" Residue "4 TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 193": "OE1" <-> "OE2" Residue "4 GLU 202": "OE1" <-> "OE2" Residue "4 TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 225": "OE1" <-> "OE2" Residue "4 ASP 231": "OD1" <-> "OD2" Residue "4 ARG 232": "NH1" <-> "NH2" Residue "4 ARG 255": "NH1" <-> "NH2" Residue "4 TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 36": "NH1" <-> "NH2" Residue "5 GLU 37": "OE1" <-> "OE2" Residue "5 ARG 50": "NH1" <-> "NH2" Residue "5 GLU 93": "OE1" <-> "OE2" Residue "5 ARG 112": "NH1" <-> "NH2" Residue "6 PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 25": "OD1" <-> "OD2" Residue "7 ARG 81": "NH1" <-> "NH2" Residue "7 TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 109": "OD1" <-> "OD2" Residue "7 PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 164": "NH1" <-> "NH2" Residue "7 ARG 165": "NH1" <-> "NH2" Residue "7 ARG 166": "NH1" <-> "NH2" Residue "7 PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ARG 13": "NH1" <-> "NH2" Residue "8 ARG 65": "NH1" <-> "NH2" Residue "8 TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 12": "OE1" <-> "OE2" Residue "9 PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ARG 28": "NH1" <-> "NH2" Residue "9 ARG 40": "NH1" <-> "NH2" Residue "9 PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 111": "OE1" <-> "OE2" Residue "C PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 111": "OE1" <-> "OE2" Residue "I GLU 111": "OE1" <-> "OE2" Residue "M ARG 115": "NH1" <-> "NH2" Residue "M ASP 128": "OD1" <-> "OD2" Residue "M ASP 140": "OD1" <-> "OD2" Residue "M ARG 145": "NH1" <-> "NH2" Residue "M PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 232": "NH1" <-> "NH2" Residue "M ARG 239": "NH1" <-> "NH2" Residue "M PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 127": "OD1" <-> "OD2" Residue "P GLU 136": "OE1" <-> "OE2" Residue "P GLU 142": "OE1" <-> "OE2" Residue "P TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 206": "NH1" <-> "NH2" Residue "P GLU 216": "OE1" <-> "OE2" Residue "P PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 25": "OD1" <-> "OD2" Residue "Q PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 42": "NH1" <-> "NH2" Residue "Q ARG 48": "NH1" <-> "NH2" Residue "R PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 95": "OD1" <-> "OD2" Residue "R GLU 117": "OE1" <-> "OE2" Residue "R ASP 156": "OD1" <-> "OD2" Residue "R ASP 174": "OD1" <-> "OD2" Residue "R PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 46": "NH1" <-> "NH2" Residue "S ASP 91": "OD1" <-> "OD2" Residue "S GLU 131": "OE1" <-> "OE2" Residue "S GLU 133": "OE1" <-> "OE2" Residue "S ASP 136": "OD1" <-> "OD2" Residue "S ARG 147": "NH1" <-> "NH2" Residue "S ARG 152": "NH1" <-> "NH2" Residue "S ARG 157": "NH1" <-> "NH2" Residue "S TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 180": "OE1" <-> "OE2" Residue "S TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 214": "OD1" <-> "OD2" Residue "S ASP 232": "OD1" <-> "OD2" Residue "S GLU 238": "OE1" <-> "OE2" Residue "S ARG 244": "NH1" <-> "NH2" Residue "S TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 303": "OE1" <-> "OE2" Residue "S GLU 306": "OE1" <-> "OE2" Residue "T GLU 47": "OE1" <-> "OE2" Residue "T ARG 49": "NH1" <-> "NH2" Residue "T ARG 86": "NH1" <-> "NH2" Residue "T ASP 135": "OD1" <-> "OD2" Residue "T ASP 142": "OD1" <-> "OD2" Residue "T ARG 162": "NH1" <-> "NH2" Residue "T ASP 165": "OD1" <-> "OD2" Residue "T ASP 172": "OD1" <-> "OD2" Residue "T ARG 195": "NH1" <-> "NH2" Residue "T ARG 199": "NH1" <-> "NH2" Residue "T PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 283": "NH1" <-> "NH2" Residue "T TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 294": "OD1" <-> "OD2" Residue "T TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 325": "OD1" <-> "OD2" Residue "T ASP 353": "OD1" <-> "OD2" Residue "T ASP 403": "OD1" <-> "OD2" Residue "T GLU 409": "OE1" <-> "OE2" Residue "T GLU 411": "OE1" <-> "OE2" Residue "T PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 429": "NH1" <-> "NH2" Residue "T PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 454": "NH1" <-> "NH2" Residue "T GLU 482": "OE1" <-> "OE2" Residue "T PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 547": "OD1" <-> "OD2" Residue "T ARG 555": "NH1" <-> "NH2" Residue "U ARG 49": "NH1" <-> "NH2" Residue "U PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 74": "OE1" <-> "OE2" Residue "U ARG 96": "NH1" <-> "NH2" Residue "U TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 112": "OD1" <-> "OD2" Residue "U TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 146": "NH1" <-> "NH2" Residue "U ARG 162": "NH1" <-> "NH2" Residue "U ASP 165": "OD1" <-> "OD2" Residue "U ARG 181": "NH1" <-> "NH2" Residue "U ARG 199": "NH1" <-> "NH2" Residue "U PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 221": "OE1" <-> "OE2" Residue "U ARG 227": "NH1" <-> "NH2" Residue "U ASP 237": "OD1" <-> "OD2" Residue "U ARG 254": "NH1" <-> "NH2" Residue "U TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 283": "NH1" <-> "NH2" Residue "U TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 311": "OE1" <-> "OE2" Residue "U PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 314": "NH1" <-> "NH2" Residue "U ASP 325": "OD1" <-> "OD2" Residue "U ARG 342": "NH1" <-> "NH2" Residue "U ARG 343": "NH1" <-> "NH2" Residue "U ARG 364": "NH1" <-> "NH2" Residue "U PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 409": "OE1" <-> "OE2" Residue "U PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 449": "OE1" <-> "OE2" Residue "U ARG 454": "NH1" <-> "NH2" Residue "U GLU 455": "OE1" <-> "OE2" Residue "U PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 479": "NH1" <-> "NH2" Residue "U ARG 496": "NH1" <-> "NH2" Residue "U TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 513": "NH1" <-> "NH2" Residue "U PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 547": "OD1" <-> "OD2" Residue "V ARG 49": "NH1" <-> "NH2" Residue "V PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 72": "OE1" <-> "OE2" Residue "V PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 142": "OD1" <-> "OD2" Residue "V ARG 181": "NH1" <-> "NH2" Residue "V ASP 210": "OD1" <-> "OD2" Residue "V ARG 217": "NH1" <-> "NH2" Residue "V ARG 220": "NH1" <-> "NH2" Residue "V TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 266": "NH1" <-> "NH2" Residue "V PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 314": "NH1" <-> "NH2" Residue "V ARG 335": "NH1" <-> "NH2" Residue "V ARG 342": "NH1" <-> "NH2" Residue "V ARG 343": "NH1" <-> "NH2" Residue "V ARG 347": "NH1" <-> "NH2" Residue "V ARG 360": "NH1" <-> "NH2" Residue "V PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 403": "OD1" <-> "OD2" Residue "V PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 429": "NH1" <-> "NH2" Residue "V ARG 454": "NH1" <-> "NH2" Residue "V GLU 455": "OE1" <-> "OE2" Residue "V PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 465": "OD1" <-> "OD2" Residue "V ARG 476": "NH1" <-> "NH2" Residue "V PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 496": "NH1" <-> "NH2" Residue "V ARG 513": "NH1" <-> "NH2" Residue "V GLU 521": "OE1" <-> "OE2" Residue "V ASP 547": "OD1" <-> "OD2" Residue "V GLU 553": "OE1" <-> "OE2" Residue "V ARG 555": "NH1" <-> "NH2" Residue "X ARG 51": "NH1" <-> "NH2" Residue "X GLU 55": "OE1" <-> "OE2" Residue "X ASP 82": "OD1" <-> "OD2" Residue "X GLU 146": "OE1" <-> "OE2" Residue "X PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 152": "OE1" <-> "OE2" Residue "X GLU 156": "OE1" <-> "OE2" Residue "X PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 215": "OE1" <-> "OE2" Residue "X ARG 218": "NH1" <-> "NH2" Residue "X GLU 219": "OE1" <-> "OE2" Residue "X ARG 225": "NH1" <-> "NH2" Residue "X GLU 226": "OE1" <-> "OE2" Residue "X GLU 238": "OE1" <-> "OE2" Residue "X ARG 239": "NH1" <-> "NH2" Residue "X TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 253": "OE1" <-> "OE2" Residue "X PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 285": "OD1" <-> "OD2" Residue "X GLU 296": "OE1" <-> "OE2" Residue "X TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 378": "OD1" <-> "OD2" Residue "X ARG 385": "NH1" <-> "NH2" Residue "X TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 401": "NH1" <-> "NH2" Residue "X ASP 415": "OD1" <-> "OD2" Residue "X ASP 429": "OD1" <-> "OD2" Residue "X GLU 451": "OE1" <-> "OE2" Residue "X PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 494": "OE1" <-> "OE2" Residue "X ASP 505": "OD1" <-> "OD2" Residue "X ARG 509": "NH1" <-> "NH2" Residue "X GLU 511": "OE1" <-> "OE2" Residue "X GLU 520": "OE1" <-> "OE2" Residue "X ASP 528": "OD1" <-> "OD2" Residue "X GLU 533": "OE1" <-> "OE2" Residue "X ASP 548": "OD1" <-> "OD2" Residue "Y TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 71": "NH1" <-> "NH2" Residue "Y ARG 86": "NH1" <-> "NH2" Residue "Y ASP 94": "OD1" <-> "OD2" Residue "Y ASP 104": "OD1" <-> "OD2" Residue "Y ARG 115": "NH1" <-> "NH2" Residue "Y ARG 120": "NH1" <-> "NH2" Residue "Y ASP 139": "OD1" <-> "OD2" Residue "Y ARG 145": "NH1" <-> "NH2" Residue "Y PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 215": "OE1" <-> "OE2" Residue "Y ARG 258": "NH1" <-> "NH2" Residue "Y GLU 270": "OE1" <-> "OE2" Residue "Y TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 348": "OD1" <-> "OD2" Residue "Y ASP 359": "OD1" <-> "OD2" Residue "Y ARG 366": "NH1" <-> "NH2" Residue "Y TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 385": "NH1" <-> "NH2" Residue "Y ASP 423": "OD1" <-> "OD2" Residue "Y PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 479": "OD1" <-> "OD2" Residue "Y PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 528": "OD1" <-> "OD2" Residue "Y PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 552": "OE1" <-> "OE2" Residue "Z TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 51": "NH1" <-> "NH2" Residue "Z GLU 66": "OE1" <-> "OE2" Residue "Z ARG 71": "NH1" <-> "NH2" Residue "Z ASP 82": "OD1" <-> "OD2" Residue "Z ARG 86": "NH1" <-> "NH2" Residue "Z ARG 98": "NH1" <-> "NH2" Residue "Z ARG 120": "NH1" <-> "NH2" Residue "Z ASP 130": "OD1" <-> "OD2" Residue "Z GLU 156": "OE1" <-> "OE2" Residue "Z PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 216": "NH1" <-> "NH2" Residue "Z ARG 258": "NH1" <-> "NH2" Residue "Z GLU 270": "OE1" <-> "OE2" Residue "Z ARG 289": "NH1" <-> "NH2" Residue "Z GLU 323": "OE1" <-> "OE2" Residue "Z PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 378": "OD1" <-> "OD2" Residue "Z ASP 381": "OD1" <-> "OD2" Residue "Z ARG 385": "NH1" <-> "NH2" Residue "Z ARG 401": "NH1" <-> "NH2" Residue "Z ASP 409": "OD1" <-> "OD2" Residue "Z TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 435": "NH1" <-> "NH2" Residue "Z ARG 437": "NH1" <-> "NH2" Residue "Z TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 480": "OD1" <-> "OD2" Residue "Z GLU 483": "OE1" <-> "OE2" Residue "Z ASP 500": "OD1" <-> "OD2" Residue "Z ARG 509": "NH1" <-> "NH2" Residue "Z ASP 513": "OD1" <-> "OD2" Residue "Z PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 552": "OE1" <-> "OE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 53748 Number of models: 1 Model: "" Number of chains: 37 Chain: "0" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 607 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 8, 'TRANS': 72} Chain: "1" Number of atoms: 4661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4661 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 31, 'TRANS': 563} Chain: "2" Number of atoms: 3163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3163 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 17, 'TRANS': 423} Chain: "3" Number of atoms: 1874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1874 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 239} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 7 Chain: "4" Number of atoms: 2177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2177 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 9, 'TRANS': 280} Chain: "5" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 986 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "6" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 926 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "7" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1347 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 5, 'TRANS': 170} Chain: "8" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 692 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 7, 'TRANS': 80} Chain: "9" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 776 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 5, 'TRANS': 91} Chain: "A" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "B" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "C" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain breaks: 1 Chain: "D" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "E" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "F" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "G" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "H" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "I" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "J" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "M" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1640 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "P" Number of atoms: 1532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1532 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 5, 'TRANS': 187} Chain: "Q" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 561 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 5, 'TRANS': 66} Chain: "R" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1303 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 13, 'TRANS': 163} Chain: "S" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2130 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 271} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 3979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3979 Classifications: {'peptide': 523} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Chain: "U" Number of atoms: 3980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3980 Classifications: {'peptide': 523} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Chain: "V" Number of atoms: 3962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3962 Classifications: {'peptide': 520} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 494} Chain: "X" Number of atoms: 4115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4115 Classifications: {'peptide': 542} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 517} Chain: "Y" Number of atoms: 3957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3957 Classifications: {'peptide': 521} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 498} Chain: "Z" Number of atoms: 4087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4087 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 513} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 22.27, per 1000 atoms: 0.41 Number of scatterers: 53748 At special positions: 0 Unit cell: (209.547, 134.784, 260.091, 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 1 29.99 S 149 16.00 P 13 15.00 Mg 5 11.99 O 10171 8.00 N 9112 7.00 C 34297 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: 16.60 Conformation dependent library (CDL) restraints added in 6.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN M 600 " pdb="ZN ZN M 600 " - pdb=" NE2 HIS M 248 " pdb="ZN ZN M 600 " - pdb=" NE2 HIS M 252 " 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13086 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 282 helices and 30 sheets defined 51.1% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.74 Creating SS restraints... Processing helix chain '0' and resid 4 through 7 No H-bonds generated for 'chain '0' and resid 4 through 7' Processing helix chain '0' and resid 18 through 30 Processing helix chain '0' and resid 44 through 49 Processing helix chain '0' and resid 52 through 55 No H-bonds generated for 'chain '0' and resid 52 through 55' Processing helix chain '1' and resid 46 through 71 Processing helix chain '1' and resid 78 through 80 No H-bonds generated for 'chain '1' and resid 78 through 80' Processing helix chain '1' and resid 97 through 99 No H-bonds generated for 'chain '1' and resid 97 through 99' Processing helix chain '1' and resid 107 through 141 removed outlier: 3.807A pdb=" N ALA 1 140 " --> pdb=" O GLU 1 136 " (cutoff:3.500A) Processing helix chain '1' and resid 164 through 175 removed outlier: 4.432A pdb=" N THR 1 169 " --> pdb=" O GLU 1 165 " (cutoff:3.500A) Processing helix chain '1' and resid 191 through 203 removed outlier: 3.521A pdb=" N ALA 1 196 " --> pdb=" O GLY 1 192 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N PHE 1 200 " --> pdb=" O ALA 1 196 " (cutoff:3.500A) Processing helix chain '1' and resid 210 through 223 Processing helix chain '1' and resid 242 through 270 Processing helix chain '1' and resid 272 through 276 removed outlier: 3.788A pdb=" N ALA 1 275 " --> pdb=" O PRO 1 272 " (cutoff:3.500A) Processing helix chain '1' and resid 279 through 281 No H-bonds generated for 'chain '1' and resid 279 through 281' Processing helix chain '1' and resid 290 through 292 No H-bonds generated for 'chain '1' and resid 290 through 292' Processing helix chain '1' and resid 298 through 304 Processing helix chain '1' and resid 311 through 316 Processing helix chain '1' and resid 324 through 326 No H-bonds generated for 'chain '1' and resid 324 through 326' Processing helix chain '1' and resid 331 through 333 No H-bonds generated for 'chain '1' and resid 331 through 333' Processing helix chain '1' and resid 339 through 350 Processing helix chain '1' and resid 354 through 361 Processing helix chain '1' and resid 363 through 366 Processing helix chain '1' and resid 376 through 387 removed outlier: 3.769A pdb=" N VAL 1 382 " --> pdb=" O GLU 1 378 " (cutoff:3.500A) Processing helix chain '1' and resid 393 through 420 removed outlier: 4.655A pdb=" N VAL 1 418 " --> pdb=" O GLU 1 414 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N ILE 1 419 " --> pdb=" O GLU 1 415 " (cutoff:3.500A) Processing helix chain '1' and resid 426 through 431 Processing helix chain '1' and resid 436 through 443 Processing helix chain '1' and resid 447 through 458 Processing helix chain '1' and resid 464 through 477 Processing helix chain '1' and resid 480 through 482 No H-bonds generated for 'chain '1' and resid 480 through 482' Processing helix chain '1' and resid 486 through 489 No H-bonds generated for 'chain '1' and resid 486 through 489' Processing helix chain '1' and resid 491 through 515 removed outlier: 3.980A pdb=" N GLU 1 501 " --> pdb=" O LEU 1 497 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP 1 504 " --> pdb=" O LEU 1 500 " (cutoff:3.500A) Processing helix chain '1' and resid 519 through 535 Processing helix chain '1' and resid 542 through 548 Processing helix chain '1' and resid 550 through 561 Processing helix chain '1' and resid 567 through 573 Processing helix chain '1' and resid 577 through 587 Processing helix chain '1' and resid 589 through 591 No H-bonds generated for 'chain '1' and resid 589 through 591' Processing helix chain '1' and resid 593 through 605 Processing helix chain '2' and resid 8 through 16 Processing helix chain '2' and resid 26 through 39 Processing helix chain '2' and resid 45 through 57 Processing helix chain '2' and resid 63 through 76 Processing helix chain '2' and resid 81 through 94 removed outlier: 3.992A pdb=" N ALA 2 88 " --> pdb=" O VAL 2 84 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N GLY 2 89 " --> pdb=" O ALA 2 85 " (cutoff:3.500A) Proline residue: 2 90 - end of helix Processing helix chain '2' and resid 100 through 112 Processing helix chain '2' and resid 118 through 130 removed outlier: 3.885A pdb=" N VAL 2 127 " --> pdb=" O LYS 2 123 " (cutoff:3.500A) Processing helix chain '2' and resid 137 through 149 Processing helix chain '2' and resid 155 through 167 removed outlier: 3.658A pdb=" N VAL 2 164 " --> pdb=" O ALA 2 160 " (cutoff:3.500A) Processing helix chain '2' and resid 172 through 185 Processing helix chain '2' and resid 190 through 199 removed outlier: 4.289A pdb=" N ALA 2 195 " --> pdb=" O ALA 2 191 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS 2 198 " --> pdb=" O ASP 2 194 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N SER 2 199 " --> pdb=" O ALA 2 195 " (cutoff:3.500A) Processing helix chain '2' and resid 207 through 219 Processing helix chain '2' and resid 229 through 234 Processing helix chain '2' and resid 241 through 252 removed outlier: 3.819A pdb=" N GLU 2 246 " --> pdb=" O ALA 2 242 " (cutoff:3.500A) Processing helix chain '2' and resid 259 through 275 removed outlier: 3.733A pdb=" N VAL 2 268 " --> pdb=" O ALA 2 264 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL 2 269 " --> pdb=" O LEU 2 265 " (cutoff:3.500A) Proline residue: 2 271 - end of helix Processing helix chain '2' and resid 282 through 294 Processing helix chain '2' and resid 301 through 320 removed outlier: 4.109A pdb=" N SER 2 305 " --> pdb=" O ALA 2 301 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE 2 306 " --> pdb=" O ALA 2 302 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY 2 312 " --> pdb=" O ALA 2 308 " (cutoff:3.500A) Processing helix chain '2' and resid 326 through 340 Processing helix chain '2' and resid 346 through 353 Processing helix chain '2' and resid 397 through 409 removed outlier: 3.824A pdb=" N GLN 2 409 " --> pdb=" O VAL 2 405 " (cutoff:3.500A) Processing helix chain '2' and resid 418 through 421 No H-bonds generated for 'chain '2' and resid 418 through 421' Processing helix chain '2' and resid 427 through 439 Processing helix chain '3' and resid 78 through 85 Processing helix chain '3' and resid 103 through 112 Processing helix chain '3' and resid 118 through 127 removed outlier: 4.386A pdb=" N LYS 3 123 " --> pdb=" O ASP 3 119 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU 3 126 " --> pdb=" O VAL 3 122 " (cutoff:3.500A) Processing helix chain '3' and resid 132 through 134 No H-bonds generated for 'chain '3' and resid 132 through 134' Processing helix chain '3' and resid 137 through 149 Processing helix chain '3' and resid 155 through 167 removed outlier: 3.755A pdb=" N GLY 3 160 " --> pdb=" O ASP 3 156 " (cutoff:3.500A) Processing helix chain '3' and resid 174 through 186 removed outlier: 4.205A pdb=" N GLN 3 179 " --> pdb=" O GLU 3 175 " (cutoff:3.500A) Processing helix chain '3' and resid 193 through 204 Processing helix chain '3' and resid 216 through 228 removed outlier: 4.009A pdb=" N THR 3 221 " --> pdb=" O ASP 3 217 " (cutoff:3.500A) Processing helix chain '3' and resid 234 through 243 removed outlier: 3.915A pdb=" N ARG 3 242 " --> pdb=" O ALA 3 238 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLY 3 243 " --> pdb=" O THR 3 239 " (cutoff:3.500A) Processing helix chain '3' and resid 246 through 250 Processing helix chain '3' and resid 254 through 271 removed outlier: 3.644A pdb=" N PHE 3 271 " --> pdb=" O ALA 3 267 " (cutoff:3.500A) Processing helix chain '3' and resid 276 through 286 removed outlier: 3.676A pdb=" N GLU 3 279 " --> pdb=" O GLU 3 276 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA 3 280 " --> pdb=" O SER 3 277 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE 3 282 " --> pdb=" O GLU 3 279 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA 3 284 " --> pdb=" O VAL 3 281 " (cutoff:3.500A) Processing helix chain '3' and resid 294 through 310 removed outlier: 3.677A pdb=" N VAL 3 303 " --> pdb=" O GLU 3 299 " (cutoff:3.500A) Processing helix chain '4' and resid 9 through 12 No H-bonds generated for 'chain '4' and resid 9 through 12' Processing helix chain '4' and resid 20 through 34 removed outlier: 3.531A pdb=" N ALA 4 25 " --> pdb=" O GLU 4 21 " (cutoff:3.500A) Processing helix chain '4' and resid 48 through 67 removed outlier: 4.187A pdb=" N GLN 4 61 " --> pdb=" O TYR 4 57 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL 4 62 " --> pdb=" O LEU 4 58 " (cutoff:3.500A) Proline residue: 4 65 - end of helix Processing helix chain '4' and resid 80 through 95 Processing helix chain '4' and resid 101 through 112 Processing helix chain '4' and resid 119 through 125 Processing helix chain '4' and resid 132 through 149 removed outlier: 3.988A pdb=" N ALA 4 137 " --> pdb=" O ASP 4 133 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL 4 141 " --> pdb=" O ALA 4 137 " (cutoff:3.500A) Processing helix chain '4' and resid 160 through 176 removed outlier: 3.981A pdb=" N PHE 4 165 " --> pdb=" O GLY 4 161 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS 4 168 " --> pdb=" O LYS 4 164 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA 4 171 " --> pdb=" O ALA 4 167 " (cutoff:3.500A) Processing helix chain '4' and resid 180 through 188 Processing helix chain '4' and resid 193 through 233 removed outlier: 3.759A pdb=" N LYS 4 198 " --> pdb=" O ASP 4 194 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N VAL 4 199 " --> pdb=" O ALA 4 195 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU 4 202 " --> pdb=" O LYS 4 198 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR 4 205 " --> pdb=" O LYS 4 201 " (cutoff:3.500A) Processing helix chain '4' and resid 238 through 257 removed outlier: 3.612A pdb=" N ALA 4 256 " --> pdb=" O LEU 4 252 " (cutoff:3.500A) Processing helix chain '4' and resid 263 through 284 Processing helix chain '5' and resid 8 through 58 removed outlier: 5.012A pdb=" N LEU 5 31 " --> pdb=" O ASP 5 27 " (cutoff:3.500A) Proline residue: 5 32 - end of helix removed outlier: 3.640A pdb=" N GLU 5 37 " --> pdb=" O THR 5 33 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N HIS 5 41 " --> pdb=" O GLU 5 37 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N LYS 5 49 " --> pdb=" O ALA 5 45 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N ARG 5 50 " --> pdb=" O ALA 5 46 " (cutoff:3.500A) Processing helix chain '5' and resid 64 through 66 No H-bonds generated for 'chain '5' and resid 64 through 66' Processing helix chain '5' and resid 73 through 80 Processing helix chain '5' and resid 88 through 105 removed outlier: 4.040A pdb=" N LEU 5 92 " --> pdb=" O PRO 5 88 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LYS 5 101 " --> pdb=" O SER 5 97 " (cutoff:3.500A) Processing helix chain '5' and resid 115 through 118 No H-bonds generated for 'chain '5' and resid 115 through 118' Processing helix chain '6' and resid 31 through 40 Processing helix chain '6' and resid 51 through 57 Processing helix chain '6' and resid 73 through 93 Processing helix chain '6' and resid 99 through 116 removed outlier: 3.811A pdb=" N VAL 6 107 " --> pdb=" O LEU 6 103 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TRP 6 112 " --> pdb=" O LEU 6 108 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU 6 113 " --> pdb=" O GLN 6 109 " (cutoff:3.500A) Processing helix chain '6' and resid 122 through 129 Processing helix chain '6' and resid 134 through 137 No H-bonds generated for 'chain '6' and resid 134 through 137' Processing helix chain '7' and resid 84 through 104 removed outlier: 3.733A pdb=" N GLU 7 99 " --> pdb=" O SER 7 95 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU 7 103 " --> pdb=" O GLU 7 99 " (cutoff:3.500A) Processing helix chain '7' and resid 110 through 112 No H-bonds generated for 'chain '7' and resid 110 through 112' Processing helix chain '7' and resid 116 through 120 removed outlier: 3.623A pdb=" N TYR 7 120 " --> pdb=" O LYS 7 116 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 116 through 120' Processing helix chain '7' and resid 124 through 144 Processing helix chain '7' and resid 150 through 156 removed outlier: 4.201A pdb=" N SER 7 155 " --> pdb=" O SER 7 151 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLN 7 156 " --> pdb=" O ALA 7 152 " (cutoff:3.500A) Processing helix chain '7' and resid 158 through 165 Processing helix chain '7' and resid 175 through 187 Processing helix chain '8' and resid 27 through 30 No H-bonds generated for 'chain '8' and resid 27 through 30' Processing helix chain '8' and resid 32 through 38 Processing helix chain '8' and resid 40 through 77 removed outlier: 3.755A pdb=" N TRP 8 45 " --> pdb=" O ILE 8 41 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N TYR 8 46 " --> pdb=" O PRO 8 42 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N LEU 8 47 " --> pdb=" O ARG 8 43 " (cutoff:3.500A) Processing helix chain '9' and resid 5 through 16 Processing helix chain '9' and resid 33 through 56 removed outlier: 4.020A pdb=" N ALA 9 38 " --> pdb=" O GLY 9 34 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL 9 42 " --> pdb=" O ALA 9 38 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ASN 9 56 " --> pdb=" O LEU 9 52 " (cutoff:3.500A) Processing helix chain '9' and resid 83 through 96 removed outlier: 3.619A pdb=" N GLU 9 92 " --> pdb=" O GLU 9 88 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS 9 95 " --> pdb=" O LYS 9 91 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER 9 96 " --> pdb=" O GLU 9 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 91 removed outlier: 4.684A pdb=" N MET A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ALA A 70 " --> pdb=" O CYS A 66 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N LEU A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ALA A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLY A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL A 74 " --> pdb=" O ALA A 70 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLY A 79 " --> pdb=" O GLY A 75 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE A 86 " --> pdb=" O PHE A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 95 No H-bonds generated for 'chain 'A' and resid 93 through 95' Processing helix chain 'A' and resid 98 through 125 removed outlier: 3.570A pdb=" N LEU A 105 " --> pdb=" O GLY A 101 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ILE A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 91 removed outlier: 4.386A pdb=" N MET B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N CYS B 66 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ILE B 69 " --> pdb=" O GLY B 65 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N ALA B 70 " --> pdb=" O CYS B 66 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N LEU B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ALA B 72 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N GLY B 73 " --> pdb=" O ILE B 69 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL B 74 " --> pdb=" O ALA B 70 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE B 86 " --> pdb=" O PHE B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 123 removed outlier: 3.948A pdb=" N VAL B 100 " --> pdb=" O ALA B 96 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY B 101 " --> pdb=" O LYS B 97 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 89 removed outlier: 3.786A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ILE C 69 " --> pdb=" O GLY C 65 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ALA C 70 " --> pdb=" O CYS C 66 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N LEU C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ALA C 72 " --> pdb=" O THR C 68 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLY C 73 " --> pdb=" O ILE C 69 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY C 79 " --> pdb=" O GLY C 75 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE C 86 " --> pdb=" O PHE C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 126 removed outlier: 3.754A pdb=" N LEU C 105 " --> pdb=" O GLY C 101 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ILE C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 65 Processing helix chain 'D' and resid 67 through 91 removed outlier: 3.663A pdb=" N ALA D 70 " --> pdb=" O ALA D 67 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU D 78 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLY D 79 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU D 85 " --> pdb=" O PHE D 82 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG D 91 " --> pdb=" O GLY D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 126 removed outlier: 3.921A pdb=" N GLY D 101 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL D 120 " --> pdb=" O PHE D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 89 removed outlier: 4.751A pdb=" N LYS E 60 " --> pdb=" O LEU E 56 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ILE E 69 " --> pdb=" O GLY E 65 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ALA E 70 " --> pdb=" O CYS E 66 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LEU E 71 " --> pdb=" O ALA E 67 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ALA E 72 " --> pdb=" O THR E 68 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLY E 73 " --> pdb=" O ILE E 69 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL E 74 " --> pdb=" O ALA E 70 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE E 86 " --> pdb=" O PHE E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 125 removed outlier: 3.777A pdb=" N SER E 112 " --> pdb=" O ALA E 108 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ILE E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA E 114 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL E 121 " --> pdb=" O SER E 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 65 Processing helix chain 'F' and resid 68 through 91 removed outlier: 3.595A pdb=" N LEU F 71 " --> pdb=" O THR F 68 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL F 74 " --> pdb=" O LEU F 71 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY F 77 " --> pdb=" O VAL F 74 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU F 85 " --> pdb=" O PHE F 82 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY F 88 " --> pdb=" O LEU F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 123 removed outlier: 5.558A pdb=" N LYS F 97 " --> pdb=" O ASN F 94 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LEU F 104 " --> pdb=" O GLY F 101 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU F 105 " --> pdb=" O TYR F 102 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU F 111 " --> pdb=" O ALA F 108 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER F 112 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU F 118 " --> pdb=" O LEU F 115 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU F 119 " --> pdb=" O PHE F 116 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL F 121 " --> pdb=" O LEU F 118 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE F 122 " --> pdb=" O LEU F 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 91 removed outlier: 4.442A pdb=" N MET G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N CYS G 66 " --> pdb=" O VAL G 62 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE G 69 " --> pdb=" O GLY G 65 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ALA G 70 " --> pdb=" O CYS G 66 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LEU G 71 " --> pdb=" O ALA G 67 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N ALA G 72 " --> pdb=" O THR G 68 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N GLY G 73 " --> pdb=" O ILE G 69 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE G 86 " --> pdb=" O PHE G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 123 removed outlier: 4.311A pdb=" N ILE G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 91 removed outlier: 3.855A pdb=" N THR H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ILE H 69 " --> pdb=" O GLY H 65 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ALA H 70 " --> pdb=" O CYS H 66 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N LEU H 71 " --> pdb=" O ALA H 67 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ALA H 72 " --> pdb=" O THR H 68 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N GLY H 73 " --> pdb=" O ILE H 69 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL H 74 " --> pdb=" O ALA H 70 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE H 86 " --> pdb=" O PHE H 82 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN H 87 " --> pdb=" O GLY H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 110 removed outlier: 3.665A pdb=" N LEU H 109 " --> pdb=" O LEU H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 125 removed outlier: 4.221A pdb=" N VAL H 120 " --> pdb=" O PHE H 116 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL H 121 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 65 removed outlier: 3.829A pdb=" N MET I 61 " --> pdb=" O ALA I 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 68 through 91 removed outlier: 3.591A pdb=" N PHE I 82 " --> pdb=" O GLY I 79 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LEU I 85 " --> pdb=" O PHE I 82 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN I 87 " --> pdb=" O SER I 84 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA I 89 " --> pdb=" O ILE I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 95 No H-bonds generated for 'chain 'I' and resid 93 through 95' Processing helix chain 'I' and resid 98 through 126 removed outlier: 3.698A pdb=" N SER I 112 " --> pdb=" O ALA I 108 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ILE I 113 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA I 114 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL I 120 " --> pdb=" O PHE I 116 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 89 removed outlier: 4.209A pdb=" N LYS J 60 " --> pdb=" O LEU J 56 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N MET J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL J 62 " --> pdb=" O ALA J 58 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE J 69 " --> pdb=" O GLY J 65 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ALA J 70 " --> pdb=" O CYS J 66 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N LEU J 71 " --> pdb=" O ALA J 67 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ALA J 72 " --> pdb=" O THR J 68 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLY J 73 " --> pdb=" O ILE J 69 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N VAL J 74 " --> pdb=" O ALA J 70 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE J 86 " --> pdb=" O PHE J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 95 No H-bonds generated for 'chain 'J' and resid 93 through 95' Processing helix chain 'J' and resid 98 through 108 removed outlier: 3.646A pdb=" N LEU J 105 " --> pdb=" O GLY J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 125 Processing helix chain 'M' and resid 105 through 118 Processing helix chain 'M' and resid 135 through 142 Processing helix chain 'M' and resid 148 through 167 removed outlier: 3.962A pdb=" N GLY M 166 " --> pdb=" O CYS M 162 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU M 167 " --> pdb=" O ASN M 163 " (cutoff:3.500A) Processing helix chain 'M' and resid 174 through 176 No H-bonds generated for 'chain 'M' and resid 174 through 176' Processing helix chain 'M' and resid 178 through 200 removed outlier: 3.526A pdb=" N LYS M 199 " --> pdb=" O LEU M 195 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N THR M 200 " --> pdb=" O GLY M 196 " (cutoff:3.500A) Processing helix chain 'M' and resid 222 through 264 removed outlier: 4.512A pdb=" N ARG M 232 " --> pdb=" O SER M 228 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ALA M 233 " --> pdb=" O TYR M 229 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL M 234 " --> pdb=" O THR M 230 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLY M 237 " --> pdb=" O ALA M 233 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY M 247 " --> pdb=" O ASN M 243 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N HIS M 248 " --> pdb=" O MET M 244 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA M 260 " --> pdb=" O GLY M 256 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU M 261 " --> pdb=" O MET M 257 " (cutoff:3.500A) Proline residue: M 262 - end of helix Processing helix chain 'M' and resid 271 through 308 removed outlier: 3.959A pdb=" N VAL M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU M 280 " --> pdb=" O GLY M 276 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER M 296 " --> pdb=" O ALA M 292 " (cutoff:3.500A) Processing helix chain 'P' and resid 51 through 57 removed outlier: 3.511A pdb=" N LEU P 56 " --> pdb=" O GLN P 52 " (cutoff:3.500A) Processing helix chain 'P' and resid 69 through 83 removed outlier: 3.573A pdb=" N PHE P 77 " --> pdb=" O GLU P 73 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS P 82 " --> pdb=" O ILE P 78 " (cutoff:3.500A) Processing helix chain 'P' and resid 85 through 92 removed outlier: 3.922A pdb=" N LEU P 90 " --> pdb=" O GLU P 86 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA P 91 " --> pdb=" O LEU P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 98 through 104 Processing helix chain 'P' and resid 118 through 127 removed outlier: 3.748A pdb=" N GLU P 123 " --> pdb=" O LYS P 119 " (cutoff:3.500A) Processing helix chain 'P' and resid 130 through 146 removed outlier: 4.050A pdb=" N LEU P 135 " --> pdb=" O SER P 132 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL P 137 " --> pdb=" O LEU P 134 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL P 139 " --> pdb=" O GLU P 136 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN P 140 " --> pdb=" O VAL P 137 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU P 143 " --> pdb=" O ASN P 140 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU P 146 " --> pdb=" O GLU P 143 " (cutoff:3.500A) Processing helix chain 'P' and resid 164 through 176 removed outlier: 4.092A pdb=" N LYS P 176 " --> pdb=" O LYS P 172 " (cutoff:3.500A) Processing helix chain 'P' and resid 211 through 225 Processing helix chain 'Q' and resid 16 through 30 removed outlier: 4.167A pdb=" N VAL Q 30 " --> pdb=" O LEU Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 33 through 36 No H-bonds generated for 'chain 'Q' and resid 33 through 36' Processing helix chain 'Q' and resid 41 through 43 No H-bonds generated for 'chain 'Q' and resid 41 through 43' Processing helix chain 'R' and resid 30 through 40 removed outlier: 4.364A pdb=" N LYS R 39 " --> pdb=" O GLU R 35 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS R 40 " --> pdb=" O VAL R 36 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 54 removed outlier: 3.726A pdb=" N TYR R 54 " --> pdb=" O PRO R 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 51 through 54' Processing helix chain 'R' and resid 152 through 154 No H-bonds generated for 'chain 'R' and resid 152 through 154' Processing helix chain 'R' and resid 159 through 167 removed outlier: 4.125A pdb=" N ALA R 166 " --> pdb=" O SER R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 195 Processing helix chain 'S' and resid 40 through 72 removed outlier: 3.842A pdb=" N LYS S 44 " --> pdb=" O ASN S 40 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS S 58 " --> pdb=" O GLY S 54 " (cutoff:3.500A) Processing helix chain 'S' and resid 75 through 78 No H-bonds generated for 'chain 'S' and resid 75 through 78' Processing helix chain 'S' and resid 81 through 89 removed outlier: 4.342A pdb=" N PHE S 85 " --> pdb=" O LEU S 81 " (cutoff:3.500A) Processing helix chain 'S' and resid 115 through 127 removed outlier: 3.617A pdb=" N ARG S 124 " --> pdb=" O THR S 120 " (cutoff:3.500A) Processing helix chain 'S' and resid 144 through 147 No H-bonds generated for 'chain 'S' and resid 144 through 147' Processing helix chain 'S' and resid 172 through 184 Processing helix chain 'S' and resid 228 through 230 No H-bonds generated for 'chain 'S' and resid 228 through 230' Processing helix chain 'S' and resid 239 through 312 removed outlier: 3.650A pdb=" N ARG S 244 " --> pdb=" O SER S 240 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU S 248 " --> pdb=" O ARG S 244 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN S 263 " --> pdb=" O MET S 259 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN S 276 " --> pdb=" O SER S 272 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU S 285 " --> pdb=" O ALA S 281 " (cutoff:3.500A) Processing helix chain 'T' and resid 58 through 75 removed outlier: 3.665A pdb=" N ILE T 67 " --> pdb=" O SER T 63 " (cutoff:3.500A) Proline residue: T 68 - end of helix removed outlier: 3.522A pdb=" N GLU T 72 " --> pdb=" O PRO T 68 " (cutoff:3.500A) Processing helix chain 'T' and resid 135 through 137 No H-bonds generated for 'chain 'T' and resid 135 through 137' Processing helix chain 'T' and resid 157 through 159 No H-bonds generated for 'chain 'T' and resid 157 through 159' Processing helix chain 'T' and resid 207 through 212 removed outlier: 3.708A pdb=" N LEU T 212 " --> pdb=" O ALA T 208 " (cutoff:3.500A) Processing helix chain 'T' and resid 231 through 246 removed outlier: 3.536A pdb=" N GLN T 242 " --> pdb=" O ALA T 238 " (cutoff:3.500A) Processing helix chain 'T' and resid 266 through 279 Processing helix chain 'T' and resid 281 through 283 No H-bonds generated for 'chain 'T' and resid 281 through 283' Processing helix chain 'T' and resid 296 through 315 Proline residue: T 303 - end of helix removed outlier: 3.610A pdb=" N TYR T 312 " --> pdb=" O ALA T 308 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N PHE T 313 " --> pdb=" O MET T 309 " (cutoff:3.500A) Processing helix chain 'T' and resid 327 through 340 removed outlier: 3.817A pdb=" N VAL T 332 " --> pdb=" O SER T 328 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET T 337 " --> pdb=" O ALA T 333 " (cutoff:3.500A) Processing helix chain 'T' and resid 352 through 364 removed outlier: 4.207A pdb=" N PHE T 355 " --> pdb=" O GLY T 352 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU T 357 " --> pdb=" O VAL T 354 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER T 359 " --> pdb=" O TYR T 356 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ARG T 360 " --> pdb=" O LEU T 357 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU T 362 " --> pdb=" O SER T 359 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLU T 363 " --> pdb=" O ARG T 360 " (cutoff:3.500A) Processing helix chain 'T' and resid 393 through 401 Processing helix chain 'T' and resid 410 through 414 removed outlier: 3.525A pdb=" N TYR T 414 " --> pdb=" O THR T 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 410 through 414' Processing helix chain 'T' and resid 431 through 433 No H-bonds generated for 'chain 'T' and resid 431 through 433' Processing helix chain 'T' and resid 437 through 460 removed outlier: 3.774A pdb=" N GLN T 441 " --> pdb=" O PRO T 437 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VAL T 442 " --> pdb=" O GLY T 438 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY T 444 " --> pdb=" O LYS T 440 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N THR T 445 " --> pdb=" O GLN T 441 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN T 452 " --> pdb=" O LEU T 448 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG T 454 " --> pdb=" O LEU T 450 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLU T 455 " --> pdb=" O ALA T 451 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL T 456 " --> pdb=" O GLN T 452 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA T 458 " --> pdb=" O ARG T 454 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE T 459 " --> pdb=" O GLU T 455 " (cutoff:3.500A) Processing helix chain 'T' and resid 470 through 483 removed outlier: 3.950A pdb=" N ALA T 478 " --> pdb=" O LEU T 474 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG T 479 " --> pdb=" O GLU T 475 " (cutoff:3.500A) Processing helix chain 'T' and resid 495 through 505 removed outlier: 3.562A pdb=" N ALA T 500 " --> pdb=" O ARG T 496 " (cutoff:3.500A) Processing helix chain 'T' and resid 514 through 526 removed outlier: 3.647A pdb=" N ILE T 517 " --> pdb=" O VAL T 514 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N VAL T 518 " --> pdb=" O GLN T 515 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLU T 521 " --> pdb=" O VAL T 518 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU T 522 " --> pdb=" O ALA T 519 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL T 524 " --> pdb=" O GLU T 521 " (cutoff:3.500A) Processing helix chain 'T' and resid 532 through 538 removed outlier: 3.551A pdb=" N LEU T 536 " --> pdb=" O VAL T 532 " (cutoff:3.500A) Processing helix chain 'T' and resid 544 through 553 removed outlier: 3.921A pdb=" N ALA T 548 " --> pdb=" O PRO T 544 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N HIS T 549 " --> pdb=" O ALA T 545 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA T 552 " --> pdb=" O ALA T 548 " (cutoff:3.500A) Processing helix chain 'U' and resid 42 through 46 Processing helix chain 'U' and resid 59 through 63 Processing helix chain 'U' and resid 66 through 71 Processing helix chain 'U' and resid 135 through 137 No H-bonds generated for 'chain 'U' and resid 135 through 137' Processing helix chain 'U' and resid 207 through 212 Processing helix chain 'U' and resid 231 through 246 removed outlier: 3.749A pdb=" N ALA U 235 " --> pdb=" O LYS U 231 " (cutoff:3.500A) Processing helix chain 'U' and resid 266 through 278 Processing helix chain 'U' and resid 281 through 283 No H-bonds generated for 'chain 'U' and resid 281 through 283' Processing helix chain 'U' and resid 296 through 315 Proline residue: U 303 - end of helix removed outlier: 3.603A pdb=" N TYR U 312 " --> pdb=" O ALA U 308 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N PHE U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) Processing helix chain 'U' and resid 327 through 340 removed outlier: 3.734A pdb=" N VAL U 332 " --> pdb=" O SER U 328 " (cutoff:3.500A) Processing helix chain 'U' and resid 354 through 364 removed outlier: 3.797A pdb=" N HIS U 358 " --> pdb=" O VAL U 354 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU U 361 " --> pdb=" O LEU U 357 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ARG U 364 " --> pdb=" O ARG U 360 " (cutoff:3.500A) Processing helix chain 'U' and resid 370 through 372 No H-bonds generated for 'chain 'U' and resid 370 through 372' Processing helix chain 'U' and resid 393 through 399 Processing helix chain 'U' and resid 410 through 414 Processing helix chain 'U' and resid 437 through 459 removed outlier: 4.001A pdb=" N GLY U 444 " --> pdb=" O LYS U 440 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N THR U 445 " --> pdb=" O GLN U 441 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU U 446 " --> pdb=" O VAL U 442 " (cutoff:3.500A) Processing helix chain 'U' and resid 470 through 484 Processing helix chain 'U' and resid 494 through 505 removed outlier: 3.570A pdb=" N ALA U 500 " --> pdb=" O ARG U 496 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA U 504 " --> pdb=" O ALA U 500 " (cutoff:3.500A) Processing helix chain 'U' and resid 517 through 527 removed outlier: 3.664A pdb=" N GLU U 522 " --> pdb=" O VAL U 518 " (cutoff:3.500A) Processing helix chain 'U' and resid 531 through 539 Processing helix chain 'U' and resid 544 through 553 Processing helix chain 'V' and resid 46 through 48 No H-bonds generated for 'chain 'V' and resid 46 through 48' Processing helix chain 'V' and resid 59 through 69 removed outlier: 3.972A pdb=" N GLN V 64 " --> pdb=" O GLN V 60 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS V 65 " --> pdb=" O HIS V 61 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE V 67 " --> pdb=" O SER V 63 " (cutoff:3.500A) Proline residue: V 68 - end of helix Processing helix chain 'V' and resid 135 through 137 No H-bonds generated for 'chain 'V' and resid 135 through 137' Processing helix chain 'V' and resid 157 through 159 No H-bonds generated for 'chain 'V' and resid 157 through 159' Processing helix chain 'V' and resid 207 through 212 Processing helix chain 'V' and resid 231 through 247 removed outlier: 3.981A pdb=" N GLU V 247 " --> pdb=" O LYS V 243 " (cutoff:3.500A) Processing helix chain 'V' and resid 266 through 279 Processing helix chain 'V' and resid 281 through 283 No H-bonds generated for 'chain 'V' and resid 281 through 283' Processing helix chain 'V' and resid 296 through 315 Proline residue: V 303 - end of helix removed outlier: 3.733A pdb=" N TYR V 312 " --> pdb=" O ALA V 308 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N PHE V 313 " --> pdb=" O MET V 309 " (cutoff:3.500A) Processing helix chain 'V' and resid 327 through 340 Processing helix chain 'V' and resid 352 through 364 removed outlier: 4.118A pdb=" N PHE V 355 " --> pdb=" O GLY V 352 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU V 357 " --> pdb=" O VAL V 354 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER V 359 " --> pdb=" O TYR V 356 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG V 360 " --> pdb=" O LEU V 357 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLU V 363 " --> pdb=" O ARG V 360 " (cutoff:3.500A) Processing helix chain 'V' and resid 370 through 372 No H-bonds generated for 'chain 'V' and resid 370 through 372' Processing helix chain 'V' and resid 393 through 401 Processing helix chain 'V' and resid 410 through 414 removed outlier: 3.997A pdb=" N TYR V 414 " --> pdb=" O THR V 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 410 through 414' Processing helix chain 'V' and resid 431 through 434 Processing helix chain 'V' and resid 439 through 455 removed outlier: 3.706A pdb=" N GLY V 444 " --> pdb=" O LYS V 440 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N THR V 445 " --> pdb=" O GLN V 441 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU V 448 " --> pdb=" O GLY V 444 " (cutoff:3.500A) Processing helix chain 'V' and resid 470 through 483 removed outlier: 3.681A pdb=" N GLU V 482 " --> pdb=" O ALA V 478 " (cutoff:3.500A) Processing helix chain 'V' and resid 494 through 505 Processing helix chain 'V' and resid 514 through 525 removed outlier: 4.214A pdb=" N ILE V 517 " --> pdb=" O VAL V 514 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N VAL V 518 " --> pdb=" O GLN V 515 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA V 519 " --> pdb=" O ASP V 516 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU V 521 " --> pdb=" O VAL V 518 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU V 522 " --> pdb=" O ALA V 519 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA V 523 " --> pdb=" O ALA V 520 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE V 525 " --> pdb=" O GLU V 522 " (cutoff:3.500A) Processing helix chain 'V' and resid 531 through 539 Processing helix chain 'V' and resid 544 through 553 removed outlier: 4.169A pdb=" N HIS V 549 " --> pdb=" O ALA V 545 " (cutoff:3.500A) Processing helix chain 'X' and resid 115 through 117 No H-bonds generated for 'chain 'X' and resid 115 through 117' Processing helix chain 'X' and resid 165 through 170 Processing helix chain 'X' and resid 189 through 203 removed outlier: 4.679A pdb=" N LYS X 202 " --> pdb=" O ASN X 198 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ALA X 203 " --> pdb=" O ASN X 199 " (cutoff:3.500A) Processing helix chain 'X' and resid 217 through 229 Processing helix chain 'X' and resid 236 through 241 removed outlier: 4.675A pdb=" N GLY X 240 " --> pdb=" O ALA X 237 " (cutoff:3.500A) Processing helix chain 'X' and resid 255 through 274 removed outlier: 3.528A pdb=" N ARG X 260 " --> pdb=" O GLY X 256 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N ALA X 262 " --> pdb=" O ARG X 258 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N LEU X 263 " --> pdb=" O ALA X 259 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE X 272 " --> pdb=" O VAL X 268 " (cutoff:3.500A) Processing helix chain 'X' and resid 288 through 298 Processing helix chain 'X' and resid 314 through 324 removed outlier: 4.033A pdb=" N ARG X 324 " --> pdb=" O GLY X 320 " (cutoff:3.500A) Processing helix chain 'X' and resid 349 through 357 removed outlier: 4.569A pdb=" N ALA X 356 " --> pdb=" O ALA X 352 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N HIS X 357 " --> pdb=" O THR X 353 " (cutoff:3.500A) Processing helix chain 'X' and resid 366 through 370 Processing helix chain 'X' and resid 389 through 392 No H-bonds generated for 'chain 'X' and resid 389 through 392' Processing helix chain 'X' and resid 394 through 420 removed outlier: 4.548A pdb=" N ASP X 415 " --> pdb=" O LYS X 411 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ILE X 416 " --> pdb=" O ASN X 412 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE X 419 " --> pdb=" O ASP X 415 " (cutoff:3.500A) Processing helix chain 'X' and resid 427 through 443 Processing helix chain 'X' and resid 451 through 454 No H-bonds generated for 'chain 'X' and resid 451 through 454' Processing helix chain 'X' and resid 463 through 475 Processing helix chain 'X' and resid 492 through 506 Processing helix chain 'X' and resid 527 through 532 Processing helix chain 'Y' and resid 115 through 117 No H-bonds generated for 'chain 'Y' and resid 115 through 117' Processing helix chain 'Y' and resid 165 through 170 Processing helix chain 'Y' and resid 189 through 200 Processing helix chain 'Y' and resid 217 through 229 Processing helix chain 'Y' and resid 236 through 241 removed outlier: 4.794A pdb=" N GLY Y 240 " --> pdb=" O ALA Y 237 " (cutoff:3.500A) Processing helix chain 'Y' and resid 255 through 258 No H-bonds generated for 'chain 'Y' and resid 255 through 258' Processing helix chain 'Y' and resid 261 through 274 Processing helix chain 'Y' and resid 288 through 296 Processing helix chain 'Y' and resid 314 through 324 removed outlier: 4.256A pdb=" N ARG Y 324 " --> pdb=" O GLY Y 320 " (cutoff:3.500A) Processing helix chain 'Y' and resid 349 through 357 removed outlier: 3.707A pdb=" N THR Y 354 " --> pdb=" O ALA Y 350 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ALA Y 356 " --> pdb=" O ALA Y 352 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N HIS Y 357 " --> pdb=" O THR Y 353 " (cutoff:3.500A) Processing helix chain 'Y' and resid 366 through 370 Processing helix chain 'Y' and resid 389 through 392 No H-bonds generated for 'chain 'Y' and resid 389 through 392' Processing helix chain 'Y' and resid 394 through 417 removed outlier: 3.903A pdb=" N VAL Y 399 " --> pdb=" O GLU Y 395 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS Y 411 " --> pdb=" O LEU Y 407 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASP Y 415 " --> pdb=" O LYS Y 411 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N ILE Y 416 " --> pdb=" O ASN Y 412 " (cutoff:3.500A) Processing helix chain 'Y' and resid 429 through 443 Processing helix chain 'Y' and resid 463 through 474 Processing helix chain 'Y' and resid 483 through 486 Processing helix chain 'Y' and resid 492 through 508 removed outlier: 3.894A pdb=" N LYS Y 501 " --> pdb=" O GLU Y 497 " (cutoff:3.500A) Processing helix chain 'Y' and resid 527 through 532 Processing helix chain 'Y' and resid 545 through 554 Processing helix chain 'Z' and resid 115 through 117 No H-bonds generated for 'chain 'Z' and resid 115 through 117' Processing helix chain 'Z' and resid 165 through 169 Processing helix chain 'Z' and resid 189 through 203 Processing helix chain 'Z' and resid 217 through 230 Processing helix chain 'Z' and resid 236 through 241 removed outlier: 3.571A pdb=" N ARG Z 239 " --> pdb=" O GLY Z 236 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLY Z 240 " --> pdb=" O ALA Z 237 " (cutoff:3.500A) Processing helix chain 'Z' and resid 255 through 274 removed outlier: 3.510A pdb=" N ARG Z 260 " --> pdb=" O GLY Z 256 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ALA Z 262 " --> pdb=" O ARG Z 258 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N LEU Z 263 " --> pdb=" O ALA Z 259 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE Z 272 " --> pdb=" O VAL Z 268 " (cutoff:3.500A) Processing helix chain 'Z' and resid 287 through 300 Processing helix chain 'Z' and resid 314 through 322 removed outlier: 4.080A pdb=" N LEU Z 321 " --> pdb=" O ASP Z 317 " (cutoff:3.500A) Processing helix chain 'Z' and resid 349 through 354 Processing helix chain 'Z' and resid 366 through 371 removed outlier: 3.613A pdb=" N LEU Z 371 " --> pdb=" O SER Z 367 " (cutoff:3.500A) Processing helix chain 'Z' and resid 393 through 420 removed outlier: 3.962A pdb=" N LEU Z 413 " --> pdb=" O ASP Z 409 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN Z 414 " --> pdb=" O TYR Z 410 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ASP Z 415 " --> pdb=" O LYS Z 411 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N ILE Z 416 " --> pdb=" O ASN Z 412 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE Z 419 " --> pdb=" O ASP Z 415 " (cutoff:3.500A) Processing helix chain 'Z' and resid 427 through 442 Processing helix chain 'Z' and resid 451 through 454 No H-bonds generated for 'chain 'Z' and resid 451 through 454' Processing helix chain 'Z' and resid 463 through 475 removed outlier: 3.615A pdb=" N GLY Z 472 " --> pdb=" O SER Z 468 " (cutoff:3.500A) Processing helix chain 'Z' and resid 483 through 486 Processing helix chain 'Z' and resid 492 through 507 removed outlier: 3.986A pdb=" N LYS Z 496 " --> pdb=" O ILE Z 492 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLU Z 497 " --> pdb=" O LYS Z 493 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE Z 506 " --> pdb=" O MET Z 502 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ALA Z 507 " --> pdb=" O ALA Z 503 " (cutoff:3.500A) Processing helix chain 'Z' and resid 527 through 531 Processing sheet with id= A, first strand: chain '2' and resid 369 through 372 removed outlier: 3.696A pdb=" N ALA 2 375 " --> pdb=" O LYS 2 372 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '2' and resid 379 through 382 removed outlier: 6.142A pdb=" N ALA 2 414 " --> pdb=" O GLN 2 380 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N VAL 2 382 " --> pdb=" O ALA 2 414 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL 2 416 " --> pdb=" O VAL 2 382 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain '7' and resid 36 through 41 removed outlier: 3.605A pdb=" N ASN 7 38 " --> pdb=" O THR 7 49 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL 7 61 " --> pdb=" O ALA 7 46 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL 7 48 " --> pdb=" O THR 7 59 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA 7 52 " --> pdb=" O ALA 7 55 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA 7 55 " --> pdb=" O ALA 7 52 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'P' and resid 188 through 190 removed outlier: 6.624A pdb=" N VAL P 156 " --> pdb=" O LYS P 189 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'Q' and resid 45 through 50 Processing sheet with id= F, first strand: chain 'R' and resid 97 through 100 removed outlier: 3.959A pdb=" N THR R 88 " --> pdb=" O HIS R 119 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL R 115 " --> pdb=" O PRO R 92 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'R' and resid 107 through 109 Processing sheet with id= H, first strand: chain 'S' and resid 203 through 211 removed outlier: 3.713A pdb=" N LYS S 204 " --> pdb=" O LYS S 196 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ASN S 195 " --> pdb=" O VAL S 105 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ASP S 136 " --> pdb=" O SER S 100 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N VAL S 102 " --> pdb=" O ASP S 136 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL S 138 " --> pdb=" O VAL S 102 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ALA S 104 " --> pdb=" O VAL S 138 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL S 140 " --> pdb=" O ALA S 104 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N SER S 141 " --> pdb=" O GLN S 159 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ALA S 161 " --> pdb=" O SER S 141 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'T' and resid 84 through 86 removed outlier: 3.872A pdb=" N GLU T 107 " --> pdb=" O ALA T 119 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LYS T 116 " --> pdb=" O PHE T 132 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLY T 128 " --> pdb=" O LEU T 120 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N TYR T 98 " --> pdb=" O VAL T 87 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N VAL T 87 " --> pdb=" O TYR T 98 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'T' and resid 152 through 155 Processing sheet with id= K, first strand: chain 'T' and resid 404 through 408 removed outlier: 3.650A pdb=" N LEU T 222 " --> pdb=" O GLY T 404 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'T' and resid 285 through 290 removed outlier: 8.883A pdb=" N ILE T 286 " --> pdb=" O VAL T 255 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N CYS T 257 " --> pdb=" O ILE T 286 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N VAL T 288 " --> pdb=" O CYS T 257 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N TYR T 259 " --> pdb=" O VAL T 288 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N ALA T 290 " --> pdb=" O TYR T 259 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ALA T 261 " --> pdb=" O ALA T 290 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N HIS T 319 " --> pdb=" O TYR T 256 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N VAL T 258 " --> pdb=" O HIS T 319 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU T 321 " --> pdb=" O VAL T 258 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL T 260 " --> pdb=" O LEU T 321 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE T 323 " --> pdb=" O VAL T 260 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL T 262 " --> pdb=" O ILE T 323 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASP T 325 " --> pdb=" O VAL T 262 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N SER T 376 " --> pdb=" O GLY T 320 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ILE T 322 " --> pdb=" O SER T 376 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N THR T 378 " --> pdb=" O ILE T 322 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N TYR T 324 " --> pdb=" O THR T 378 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N PHE T 380 " --> pdb=" O TYR T 324 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'U' and resid 85 through 91 removed outlier: 6.587A pdb=" N ARG U 96 " --> pdb=" O LEU U 88 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N VAL U 90 " --> pdb=" O ILE U 94 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE U 94 " --> pdb=" O VAL U 90 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL U 130 " --> pdb=" O ALA U 119 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ALA U 119 " --> pdb=" O VAL U 130 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N PHE U 132 " --> pdb=" O GLY U 117 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N GLY U 117 " --> pdb=" O PHE U 132 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'U' and resid 152 through 155 Processing sheet with id= O, first strand: chain 'U' and resid 404 through 408 Processing sheet with id= P, first strand: chain 'U' and resid 285 through 290 removed outlier: 8.681A pdb=" N ILE U 286 " --> pdb=" O VAL U 255 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N CYS U 257 " --> pdb=" O ILE U 286 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N VAL U 288 " --> pdb=" O CYS U 257 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N TYR U 259 " --> pdb=" O VAL U 288 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N ALA U 290 " --> pdb=" O TYR U 259 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ALA U 261 " --> pdb=" O ALA U 290 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N HIS U 319 " --> pdb=" O TYR U 256 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N VAL U 258 " --> pdb=" O HIS U 319 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LEU U 321 " --> pdb=" O VAL U 258 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N VAL U 260 " --> pdb=" O LEU U 321 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ILE U 323 " --> pdb=" O VAL U 260 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL U 262 " --> pdb=" O ILE U 323 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASP U 325 " --> pdb=" O VAL U 262 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N SER U 376 " --> pdb=" O GLY U 320 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N ILE U 322 " --> pdb=" O SER U 376 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N THR U 378 " --> pdb=" O ILE U 322 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N TYR U 324 " --> pdb=" O THR U 378 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE U 380 " --> pdb=" O TYR U 324 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'V' and resid 84 through 86 removed outlier: 3.804A pdb=" N GLU V 107 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLY V 128 " --> pdb=" O LEU V 120 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N LEU V 122 " --> pdb=" O HIS V 126 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N HIS V 126 " --> pdb=" O LEU V 122 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N TYR V 98 " --> pdb=" O VAL V 87 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N VAL V 87 " --> pdb=" O TYR V 98 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'V' and resid 152 through 155 Processing sheet with id= S, first strand: chain 'V' and resid 404 through 408 removed outlier: 3.511A pdb=" N LEU V 222 " --> pdb=" O GLY V 404 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'V' and resid 285 through 290 removed outlier: 8.975A pdb=" N ILE V 286 " --> pdb=" O VAL V 255 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N CYS V 257 " --> pdb=" O ILE V 286 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N VAL V 288 " --> pdb=" O CYS V 257 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N TYR V 259 " --> pdb=" O VAL V 288 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ALA V 290 " --> pdb=" O TYR V 259 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ALA V 261 " --> pdb=" O ALA V 290 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N HIS V 319 " --> pdb=" O TYR V 256 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N VAL V 258 " --> pdb=" O HIS V 319 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N LEU V 321 " --> pdb=" O VAL V 258 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N VAL V 260 " --> pdb=" O LEU V 321 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE V 323 " --> pdb=" O VAL V 260 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL V 262 " --> pdb=" O ILE V 323 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ASP V 325 " --> pdb=" O VAL V 262 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N SER V 376 " --> pdb=" O GLY V 320 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ILE V 322 " --> pdb=" O SER V 376 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N THR V 378 " --> pdb=" O ILE V 322 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N TYR V 324 " --> pdb=" O THR V 378 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N PHE V 380 " --> pdb=" O TYR V 324 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'X' and resid 37 through 39 removed outlier: 6.550A pdb=" N ARG X 86 " --> pdb=" O ALA X 77 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N HIS X 79 " --> pdb=" O THR X 84 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N THR X 84 " --> pdb=" O HIS X 79 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ARG X 51 " --> pdb=" O VAL X 40 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N VAL X 40 " --> pdb=" O ARG X 51 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'X' and resid 110 through 113 Processing sheet with id= W, first strand: chain 'X' and resid 360 through 363 removed outlier: 7.481A pdb=" N ILE X 179 " --> pdb=" O ILE X 333 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N SER X 335 " --> pdb=" O ILE X 179 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N LEU X 181 " --> pdb=" O SER X 335 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLN X 337 " --> pdb=" O LEU X 181 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N GLY X 183 " --> pdb=" O GLN X 337 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL X 339 " --> pdb=" O GLY X 183 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N PHE X 207 " --> pdb=" O LEU X 281 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N PHE X 283 " --> pdb=" O PHE X 207 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL X 209 " --> pdb=" O PHE X 283 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ASP X 285 " --> pdb=" O VAL X 209 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ALA X 211 " --> pdb=" O ASP X 285 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'X' and resid 559 through 561 Processing sheet with id= Y, first strand: chain 'Y' and resid 38 through 44 removed outlier: 6.429A pdb=" N ASP Y 49 " --> pdb=" O SER Y 41 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N VAL Y 43 " --> pdb=" O VAL Y 47 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL Y 47 " --> pdb=" O VAL Y 43 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ILE Y 88 " --> pdb=" O VAL Y 76 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N VAL Y 76 " --> pdb=" O ILE Y 88 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N LEU Y 72 " --> pdb=" O VAL Y 65 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'Y' and resid 360 through 363 removed outlier: 7.478A pdb=" N ILE Y 179 " --> pdb=" O ILE Y 333 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N SER Y 335 " --> pdb=" O ILE Y 179 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N LEU Y 181 " --> pdb=" O SER Y 335 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLN Y 337 " --> pdb=" O LEU Y 181 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N GLY Y 183 " --> pdb=" O GLN Y 337 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N VAL Y 339 " --> pdb=" O GLY Y 183 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N PHE Y 207 " --> pdb=" O LEU Y 281 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N PHE Y 283 " --> pdb=" O PHE Y 207 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL Y 209 " --> pdb=" O PHE Y 283 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N ASP Y 285 " --> pdb=" O VAL Y 209 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ALA Y 211 " --> pdb=" O ASP Y 285 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'Z' and resid 38 through 44 removed outlier: 6.428A pdb=" N ASP Z 49 " --> pdb=" O SER Z 41 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL Z 43 " --> pdb=" O VAL Z 47 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL Z 47 " --> pdb=" O VAL Z 43 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE Z 88 " --> pdb=" O VAL Z 76 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N VAL Z 76 " --> pdb=" O ILE Z 88 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'Z' and resid 110 through 113 Processing sheet with id= AC, first strand: chain 'Z' and resid 360 through 362 removed outlier: 8.329A pdb=" N ILE Z 179 " --> pdb=" O ILE Z 333 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N SER Z 335 " --> pdb=" O ILE Z 179 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N LEU Z 181 " --> pdb=" O SER Z 335 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLN Z 337 " --> pdb=" O LEU Z 181 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL Z 213 " --> pdb=" O ASP Z 285 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'Z' and resid 559 through 561 2412 hydrogen bonds defined for protein. 6864 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 15.37 Time building geometry restraints manager: 18.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 12615 1.33 - 1.45: 11629 1.45 - 1.58: 30167 1.58 - 1.70: 21 1.70 - 1.82: 254 Bond restraints: 54686 Sorted by residual: bond pdb=" C4 ATP V1001 " pdb=" C5 ATP V1001 " ideal model delta sigma weight residual 1.388 1.458 -0.070 1.00e-02 1.00e+04 4.95e+01 bond pdb=" C4 ATP U1001 " pdb=" C5 ATP U1001 " ideal model delta sigma weight residual 1.388 1.457 -0.069 1.00e-02 1.00e+04 4.76e+01 bond pdb=" C4 ATP T1001 " pdb=" C5 ATP T1001 " ideal model delta sigma weight residual 1.388 1.452 -0.064 1.00e-02 1.00e+04 4.07e+01 bond pdb=" C5 ATP V1001 " pdb=" C6 ATP V1001 " ideal model delta sigma weight residual 1.409 1.468 -0.059 1.00e-02 1.00e+04 3.47e+01 bond pdb=" C5 ATP U1001 " pdb=" C6 ATP U1001 " ideal model delta sigma weight residual 1.409 1.468 -0.059 1.00e-02 1.00e+04 3.46e+01 ... (remaining 54681 not shown) Histogram of bond angle deviations from ideal: 95.68 - 103.75: 737 103.75 - 111.83: 25394 111.83 - 119.91: 24348 119.91 - 127.99: 23350 127.99 - 136.07: 332 Bond angle restraints: 74161 Sorted by residual: angle pdb=" PB ATP U1001 " pdb=" O3B ATP U1001 " pdb=" PG ATP U1001 " ideal model delta sigma weight residual 139.87 120.81 19.06 1.00e+00 1.00e+00 3.63e+02 angle pdb=" PB ATP V1001 " pdb=" O3B ATP V1001 " pdb=" PG ATP V1001 " ideal model delta sigma weight residual 139.87 120.86 19.01 1.00e+00 1.00e+00 3.61e+02 angle pdb=" PB ATP T1001 " pdb=" O3B ATP T1001 " pdb=" PG ATP T1001 " ideal model delta sigma weight residual 139.87 122.01 17.86 1.00e+00 1.00e+00 3.19e+02 angle pdb=" PA ATP T1001 " pdb=" O3A ATP T1001 " pdb=" PB ATP T1001 " ideal model delta sigma weight residual 136.83 121.70 15.13 1.00e+00 1.00e+00 2.29e+02 angle pdb=" PA ATP U1001 " pdb=" O3A ATP U1001 " pdb=" PB ATP U1001 " ideal model delta sigma weight residual 136.83 123.59 13.24 1.00e+00 1.00e+00 1.75e+02 ... (remaining 74156 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.29: 31010 23.29 - 46.57: 1698 46.57 - 69.86: 171 69.86 - 93.15: 51 93.15 - 116.44: 2 Dihedral angle restraints: 32932 sinusoidal: 12574 harmonic: 20358 Sorted by residual: dihedral pdb=" CA ALA X 307 " pdb=" C ALA X 307 " pdb=" N VAL X 308 " pdb=" CA VAL X 308 " ideal model delta harmonic sigma weight residual -180.00 -119.20 -60.80 0 5.00e+00 4.00e-02 1.48e+02 dihedral pdb=" CA ALA Z 307 " pdb=" C ALA Z 307 " pdb=" N VAL Z 308 " pdb=" CA VAL Z 308 " ideal model delta harmonic sigma weight residual -180.00 -120.33 -59.67 0 5.00e+00 4.00e-02 1.42e+02 dihedral pdb=" CA ALA Y 307 " pdb=" C ALA Y 307 " pdb=" N VAL Y 308 " pdb=" CA VAL Y 308 " ideal model delta harmonic sigma weight residual -180.00 -123.12 -56.88 0 5.00e+00 4.00e-02 1.29e+02 ... (remaining 32929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 7786 0.098 - 0.196: 850 0.196 - 0.294: 49 0.294 - 0.392: 2 0.392 - 0.490: 2 Chirality restraints: 8689 Sorted by residual: chirality pdb=" CB VAL U 81 " pdb=" CA VAL U 81 " pdb=" CG1 VAL U 81 " pdb=" CG2 VAL U 81 " both_signs ideal model delta sigma weight residual False -2.63 -2.14 -0.49 2.00e-01 2.50e+01 5.99e+00 chirality pdb=" CB ILE P 157 " pdb=" CA ILE P 157 " pdb=" CG1 ILE P 157 " pdb=" CG2 ILE P 157 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.42 2.00e-01 2.50e+01 4.34e+00 chirality pdb=" CB VAL U 180 " pdb=" CA VAL U 180 " pdb=" CG1 VAL U 180 " pdb=" CG2 VAL U 180 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.65e+00 ... (remaining 8686 not shown) Planarity restraints: 9510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA Z 503 " 0.030 2.00e-02 2.50e+03 5.88e-02 3.45e+01 pdb=" C ALA Z 503 " -0.102 2.00e-02 2.50e+03 pdb=" O ALA Z 503 " 0.038 2.00e-02 2.50e+03 pdb=" N LYS Z 504 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA U 296 " 0.058 5.00e-02 4.00e+02 8.67e-02 1.20e+01 pdb=" N PRO U 297 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO U 297 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO U 297 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP X 348 " 0.055 5.00e-02 4.00e+02 8.42e-02 1.13e+01 pdb=" N PRO X 349 " -0.146 5.00e-02 4.00e+02 pdb=" CA PRO X 349 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO X 349 " 0.046 5.00e-02 4.00e+02 ... (remaining 9507 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 541 2.60 - 3.17: 44508 3.17 - 3.75: 86740 3.75 - 4.32: 125824 4.32 - 4.90: 204136 Nonbonded interactions: 461749 Sorted by model distance: nonbonded pdb=" OG1 THR V 232 " pdb="MG MG V1002 " model vdw 2.023 2.170 nonbonded pdb=" O2B ATP U1001 " pdb="MG MG U1002 " model vdw 2.063 2.170 nonbonded pdb=" OG1 THR U 232 " pdb="MG MG U1002 " model vdw 2.105 2.170 nonbonded pdb=" OG1 THR T 232 " pdb="MG MG T1002 " model vdw 2.114 2.170 nonbonded pdb=" O3G ATP V1001 " pdb="MG MG V1002 " model vdw 2.120 2.170 ... (remaining 461744 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = (chain 'T' and (resid 43 through 562 or resid 1001 through 1002)) selection = (chain 'U' and (resid 43 through 561 or (resid 562 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1001 through 1002)) selection = (chain 'V' and (resid 43 through 561 or (resid 562 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1001 through 1002)) } ncs_group { reference = (chain 'X' and resid 37 through 556) selection = (chain 'Y' and resid 37 through 556) selection = (chain 'Z' and resid 37 through 556) } 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 1 6.06 5 P 13 5.49 5 Mg 5 5.21 5 S 149 5.16 5 C 34297 2.51 5 N 9112 2.21 5 O 10171 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: 4.550 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: 0.040 Extract box with map and model: 25.850 Check model and map are aligned: 0.670 Process input model: 110.260 Find NCS groups from input model: 2.700 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Set scattering table: 0.380 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:2.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 146.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 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 : 0.011 0.123 54686 Z= 0.685 Angle : 1.021 19.062 74161 Z= 0.577 Chirality : 0.062 0.490 8689 Planarity : 0.008 0.087 9510 Dihedral : 14.442 116.437 19846 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.19 % Favored : 94.61 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.34 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.89 (0.08), residues: 7038 helix: -2.91 (0.06), residues: 3828 sheet: -1.33 (0.20), residues: 647 loop : -2.04 (0.11), residues: 2563 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1135 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 1112 time to evaluate : 5.017 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: 23 outliers final: 11 residues processed: 1128 average time/residue: 0.5656 time to fit residues: 1038.7197 Evaluate side-chains 672 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 661 time to evaluate : 6.589 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.3774 time to fit residues: 14.8760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 589 optimal weight: 5.9990 chunk 529 optimal weight: 5.9990 chunk 293 optimal weight: 0.9990 chunk 180 optimal weight: 1.9990 chunk 356 optimal weight: 0.9990 chunk 282 optimal weight: 1.9990 chunk 547 optimal weight: 0.9980 chunk 211 optimal weight: 0.9990 chunk 332 optimal weight: 0.7980 chunk 407 optimal weight: 5.9990 chunk 633 optimal weight: 3.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 29 ASN 0 48 ASN 0 60 GLN 1 257 HIS ** 1 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 313 GLN 1 316 ASN 1 346 GLN ** 1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 423 ASN 1 482 ASN 1 562 ASN 1 587 ASN 1 590 HIS 2 40 GLN 2 68 ASN 2 243 GLN 2 289 HIS ** 2 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 97 ASN 3 179 GLN 3 206 ASN 4 38 GLN 4 124 ASN 4 135 ASN 4 240 GLN 5 29 GLN 5 107 ASN 6 40 ASN 6 74 GLN 7 86 HIS 7 98 ASN 7 123 HIS ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 190 GLN 8 26 HIS 9 35 GLN D 94 ASN D 98 GLN G 87 ASN H 98 GLN I 94 ASN M 108 ASN M 163 ASN P 220 ASN P 223 ASN Q 21 ASN ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 38 ASN R 85 GLN ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 174 GLN S 293 ASN S 297 GLN T 64 GLN T 104 GLN T 134 ASN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 497 GLN U 152 ASN U 241 HIS U 242 GLN U 244 ASN U 248 GLN U 253 GLN U 319 HIS ** U 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 461 GLN U 497 GLN U 529 ASN V 60 GLN ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 126 HIS V 139 HIS V 149 GLN ** V 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 488 GLN V 497 GLN X 199 ASN X 408 GLN Y 68 HIS Y 132 GLN Y 440 GLN Z 132 GLN Z 199 ASN Z 278 GLN Z 294 ASN Z 398 ASN Total number of N/Q/H flips: 78 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 54686 Z= 0.189 Angle : 0.566 9.089 74161 Z= 0.296 Chirality : 0.042 0.214 8689 Planarity : 0.005 0.062 9510 Dihedral : 5.980 91.570 7577 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.75 % Favored : 96.06 % Rotamer Outliers : 1.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.99 (0.09), residues: 7038 helix: -1.15 (0.08), residues: 3841 sheet: -0.73 (0.21), residues: 583 loop : -1.48 (0.11), residues: 2614 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 888 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 788 time to evaluate : 5.258 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 outliers start: 100 outliers final: 54 residues processed: 857 average time/residue: 0.5471 time to fit residues: 789.2367 Evaluate side-chains 691 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 637 time to evaluate : 4.906 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 0 residues processed: 54 average time/residue: 0.3895 time to fit residues: 46.8403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 352 optimal weight: 0.0170 chunk 196 optimal weight: 1.9990 chunk 527 optimal weight: 1.9990 chunk 431 optimal weight: 0.0370 chunk 174 optimal weight: 2.9990 chunk 635 optimal weight: 10.0000 chunk 685 optimal weight: 1.9990 chunk 565 optimal weight: 2.9990 chunk 629 optimal weight: 7.9990 chunk 216 optimal weight: 0.2980 chunk 509 optimal weight: 2.9990 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 124 ASN ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 GLN P 59 GLN Q 40 GLN ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 38 ASN R 73 ASN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 152 ASN U 386 GLN ** U 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 241 HIS V 271 GLN V 386 GLN ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 440 GLN Z 132 GLN Z 198 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 54686 Z= 0.170 Angle : 0.534 10.543 74161 Z= 0.275 Chirality : 0.041 0.201 8689 Planarity : 0.004 0.055 9510 Dihedral : 5.442 88.067 7577 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.09 % Favored : 95.75 % Rotamer Outliers : 1.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.10), residues: 7038 helix: -0.28 (0.08), residues: 3844 sheet: -0.65 (0.21), residues: 610 loop : -1.07 (0.12), residues: 2584 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 704 time to evaluate : 4.918 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 outliers start: 88 outliers final: 42 residues processed: 766 average time/residue: 0.5251 time to fit residues: 685.4590 Evaluate side-chains 642 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 600 time to evaluate : 4.931 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 0 residues processed: 42 average time/residue: 0.4009 time to fit residues: 38.3630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 627 optimal weight: 4.9990 chunk 477 optimal weight: 9.9990 chunk 329 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 303 optimal weight: 0.4980 chunk 426 optimal weight: 5.9990 chunk 637 optimal weight: 8.9990 chunk 674 optimal weight: 3.9990 chunk 332 optimal weight: 4.9990 chunk 603 optimal weight: 4.9990 chunk 181 optimal weight: 0.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 189 HIS 4 124 ASN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 98 GLN E 98 GLN I 94 ASN P 66 GLN Q 21 ASN ** Q 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 38 ASN R 104 HIS S 116 ASN S 262 ASN U 152 ASN U 228 GLN ** U 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 441 GLN Y 144 HIS Y 337 GLN Y 440 GLN Z 414 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.065 54686 Z= 0.311 Angle : 0.597 9.546 74161 Z= 0.306 Chirality : 0.044 0.232 8689 Planarity : 0.004 0.056 9510 Dihedral : 5.565 89.944 7577 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.69 % Favored : 95.14 % Rotamer Outliers : 1.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.10), residues: 7038 helix: -0.08 (0.09), residues: 3824 sheet: -0.65 (0.21), residues: 624 loop : -0.95 (0.12), residues: 2590 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 751 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 641 time to evaluate : 5.303 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 outliers start: 110 outliers final: 68 residues processed: 714 average time/residue: 0.5323 time to fit residues: 647.0600 Evaluate side-chains 649 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 581 time to evaluate : 4.938 Switching outliers to nearest non-outliers outliers start: 68 outliers final: 0 residues processed: 68 average time/residue: 0.4108 time to fit residues: 59.2591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 561 optimal weight: 0.8980 chunk 382 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 502 optimal weight: 5.9990 chunk 278 optimal weight: 0.8980 chunk 575 optimal weight: 6.9990 chunk 466 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 344 optimal weight: 0.6980 chunk 605 optimal weight: 9.9990 chunk 170 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 365 GLN 4 124 ASN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 46 HIS ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 121 ASN T 358 HIS T 441 GLN U 152 ASN X 322 GLN X 337 GLN X 448 GLN Y 440 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 54686 Z= 0.165 Angle : 0.523 9.355 74161 Z= 0.268 Chirality : 0.041 0.183 8689 Planarity : 0.004 0.054 9510 Dihedral : 5.145 85.554 7577 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.86 % Favored : 95.99 % Rotamer Outliers : 0.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.10), residues: 7038 helix: 0.33 (0.09), residues: 3814 sheet: -0.58 (0.21), residues: 621 loop : -0.79 (0.12), residues: 2603 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 713 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 663 time to evaluate : 5.188 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 outliers start: 50 outliers final: 16 residues processed: 703 average time/residue: 0.5344 time to fit residues: 640.5744 Evaluate side-chains 616 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 600 time to evaluate : 4.950 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.3976 time to fit residues: 18.6638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 226 optimal weight: 0.6980 chunk 607 optimal weight: 10.0000 chunk 133 optimal weight: 0.9990 chunk 396 optimal weight: 4.9990 chunk 166 optimal weight: 0.6980 chunk 675 optimal weight: 5.9990 chunk 560 optimal weight: 2.9990 chunk 312 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 223 optimal weight: 1.9990 chunk 354 optimal weight: 9.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 124 ASN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN H 92 ASN ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 52 GLN P 59 GLN ** Q 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 49 GLN U 152 ASN ** Y 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 440 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 54686 Z= 0.186 Angle : 0.531 9.943 74161 Z= 0.270 Chirality : 0.041 0.199 8689 Planarity : 0.004 0.054 9510 Dihedral : 5.007 83.749 7577 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.22 % Favored : 95.64 % Rotamer Outliers : 1.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.10), residues: 7038 helix: 0.46 (0.09), residues: 3844 sheet: -0.50 (0.21), residues: 633 loop : -0.67 (0.13), residues: 2561 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 622 time to evaluate : 5.088 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 outliers start: 64 outliers final: 33 residues processed: 665 average time/residue: 0.5331 time to fit residues: 606.9430 Evaluate side-chains 620 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 587 time to evaluate : 4.987 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.4105 time to fit residues: 32.6750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 651 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 384 optimal weight: 0.7980 chunk 493 optimal weight: 2.9990 chunk 382 optimal weight: 2.9990 chunk 568 optimal weight: 6.9990 chunk 377 optimal weight: 5.9990 chunk 672 optimal weight: 0.9980 chunk 421 optimal weight: 4.9990 chunk 410 optimal weight: 0.3980 chunk 310 optimal weight: 1.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 124 ASN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 ASN I 92 ASN P 52 GLN Q 21 ASN ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 74 ASN T 358 HIS U 152 ASN ** U 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 440 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 54686 Z= 0.220 Angle : 0.546 9.362 74161 Z= 0.278 Chirality : 0.042 0.220 8689 Planarity : 0.004 0.054 9510 Dihedral : 5.013 82.324 7577 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.33 % Favored : 95.51 % Rotamer Outliers : 0.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.10), residues: 7038 helix: 0.53 (0.09), residues: 3828 sheet: -0.44 (0.22), residues: 633 loop : -0.64 (0.13), residues: 2577 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 617 time to evaluate : 5.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 30 residues processed: 646 average time/residue: 0.5412 time to fit residues: 601.2701 Evaluate side-chains 615 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 585 time to evaluate : 4.992 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.4012 time to fit residues: 29.9123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 416 optimal weight: 8.9990 chunk 268 optimal weight: 2.9990 chunk 401 optimal weight: 2.9990 chunk 202 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 130 optimal weight: 0.3980 chunk 427 optimal weight: 0.9980 chunk 458 optimal weight: 1.9990 chunk 332 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 528 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 124 ASN 6 104 ASN ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 41 HIS H 92 ASN I 92 ASN P 66 GLN ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 358 HIS U 152 ASN ** U 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 440 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 54686 Z= 0.181 Angle : 0.536 10.090 74161 Z= 0.272 Chirality : 0.041 0.236 8689 Planarity : 0.004 0.054 9510 Dihedral : 4.895 74.644 7577 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.19 % Favored : 95.67 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.10), residues: 7038 helix: 0.64 (0.09), residues: 3834 sheet: -0.38 (0.22), residues: 634 loop : -0.60 (0.13), residues: 2570 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 631 time to evaluate : 5.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 17 residues processed: 649 average time/residue: 0.5507 time to fit residues: 614.7875 Evaluate side-chains 600 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 583 time to evaluate : 4.953 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.4058 time to fit residues: 19.7292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 611 optimal weight: 0.9990 chunk 644 optimal weight: 3.9990 chunk 588 optimal weight: 0.0970 chunk 626 optimal weight: 2.9990 chunk 377 optimal weight: 5.9990 chunk 273 optimal weight: 0.8980 chunk 492 optimal weight: 5.9990 chunk 192 optimal weight: 3.9990 chunk 566 optimal weight: 3.9990 chunk 592 optimal weight: 7.9990 chunk 624 optimal weight: 0.8980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 124 ASN ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 41 HIS G 94 ASN J 98 GLN Q 49 GLN U 152 ASN ** U 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 440 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 54686 Z= 0.197 Angle : 0.547 12.949 74161 Z= 0.277 Chirality : 0.042 0.193 8689 Planarity : 0.004 0.065 9510 Dihedral : 4.855 63.147 7577 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.23 % Favored : 95.62 % Rotamer Outliers : 0.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.10), residues: 7038 helix: 0.68 (0.09), residues: 3834 sheet: -0.35 (0.22), residues: 632 loop : -0.59 (0.13), residues: 2572 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 618 time to evaluate : 4.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 13 residues processed: 636 average time/residue: 0.5419 time to fit residues: 594.9415 Evaluate side-chains 604 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 591 time to evaluate : 4.977 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.3994 time to fit residues: 16.6074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 411 optimal weight: 0.7980 chunk 662 optimal weight: 6.9990 chunk 404 optimal weight: 0.9990 chunk 314 optimal weight: 4.9990 chunk 460 optimal weight: 6.9990 chunk 695 optimal weight: 4.9990 chunk 640 optimal weight: 20.0000 chunk 553 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 427 optimal weight: 4.9990 chunk 339 optimal weight: 10.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 285 GLN ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 GLN Q 49 GLN S 185 HIS T 358 HIS U 152 ASN ** U 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 440 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.067 54686 Z= 0.297 Angle : 0.600 12.456 74161 Z= 0.304 Chirality : 0.044 0.198 8689 Planarity : 0.004 0.071 9510 Dihedral : 5.078 66.680 7577 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.96 % Favored : 94.90 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.10), residues: 7038 helix: 0.52 (0.09), residues: 3825 sheet: -0.35 (0.22), residues: 604 loop : -0.60 (0.13), residues: 2609 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 583 time to evaluate : 5.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 11 residues processed: 591 average time/residue: 0.5450 time to fit residues: 548.8273 Evaluate side-chains 578 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 567 time to evaluate : 4.948 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.4196 time to fit residues: 15.1358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 439 optimal weight: 0.7980 chunk 589 optimal weight: 3.9990 chunk 169 optimal weight: 0.1980 chunk 510 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 chunk 153 optimal weight: 8.9990 chunk 554 optimal weight: 0.1980 chunk 232 optimal weight: 4.9990 chunk 569 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 591 HIS ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 41 HIS Q 49 GLN S 185 HIS T 358 HIS U 152 ASN U 264 GLN ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 144 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.146723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.120943 restraints weight = 83818.010| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.12 r_work: 0.3269 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.045 54686 Z= 0.150 Angle : 0.540 14.779 74161 Z= 0.272 Chirality : 0.041 0.195 8689 Planarity : 0.004 0.080 9510 Dihedral : 4.710 61.452 7577 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.95 % Favored : 95.92 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.10), residues: 7038 helix: 0.80 (0.09), residues: 3831 sheet: -0.22 (0.23), residues: 589 loop : -0.52 (0.13), residues: 2618 =============================================================================== Job complete usr+sys time: 12109.50 seconds wall clock time: 214 minutes 4.44 seconds (12844.44 seconds total)