Starting phenix.real_space_refine on Sun Mar 10 21:23:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rd9_4810/03_2024/6rd9_4810_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rd9_4810/03_2024/6rd9_4810.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rd9_4810/03_2024/6rd9_4810.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rd9_4810/03_2024/6rd9_4810.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rd9_4810/03_2024/6rd9_4810_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rd9_4810/03_2024/6rd9_4810_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.086 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 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 10199 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 ARG 150": "NH1" <-> "NH2" Residue "1 ASP 172": "OD1" <-> "OD2" Residue "1 ARG 182": "NH1" <-> "NH2" Residue "1 ASP 199": "OD1" <-> "OD2" Residue "1 GLU 215": "OE1" <-> "OE2" Residue "1 GLU 229": "OE1" <-> "OE2" Residue "1 ARG 259": "NH1" <-> "NH2" Residue "1 GLU 299": "OE1" <-> "OE2" Residue "1 PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 329": "OE1" <-> "OE2" Residue "1 GLU 341": "OE1" <-> "OE2" Residue "1 GLU 350": "OE1" <-> "OE2" Residue "1 GLU 352": "OE1" <-> "OE2" Residue "1 ASP 353": "OD1" <-> "OD2" Residue "1 ARG 359": "NH1" <-> "NH2" Residue "1 GLU 378": "OE1" <-> "OE2" Residue "1 GLU 385": "OE1" <-> "OE2" Residue "1 ARG 387": "NH1" <-> "NH2" Residue "1 TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 409": "OE1" <-> "OE2" Residue "1 GLU 414": "OE1" <-> "OE2" Residue "1 GLU 415": "OE1" <-> "OE2" Residue "1 TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 434": "NH1" <-> "NH2" Residue "1 PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 496": "OE1" <-> "OE2" Residue "1 ASP 504": "OD1" <-> "OD2" Residue "1 ASP 508": "OD1" <-> "OD2" Residue "1 GLU 513": "OE1" <-> "OE2" Residue "1 ASP 578": "OD1" <-> "OD2" Residue "1 ASP 601": "OD1" <-> "OD2" Residue "1 ARG 609": "NH1" <-> "NH2" Residue "2 ASP 7": "OD1" <-> "OD2" Residue "2 GLU 14": "OE1" <-> "OE2" Residue "2 ASP 16": "OD1" <-> "OD2" Residue "2 ASP 31": "OD1" <-> "OD2" Residue "2 TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 45": "NH1" <-> "NH2" Residue "2 GLU 86": "OE1" <-> "OE2" Residue "2 GLU 134": "OE1" <-> "OE2" Residue "2 TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 173": "NH1" <-> "NH2" Residue "2 ASP 194": "OD1" <-> "OD2" Residue "2 PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 225": "OE1" <-> "OE2" Residue "2 ASP 238": "OD1" <-> "OD2" Residue "2 PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 274": "OE1" <-> "OE2" Residue "2 PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 316": "OD1" <-> "OD2" Residue "2 GLU 326": "OE1" <-> "OE2" Residue "2 ASP 332": "OD1" <-> "OD2" Residue "2 PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 346": "NH1" <-> "NH2" Residue "2 ASP 367": "OD1" <-> "OD2" Residue "2 ASP 374": "OD1" <-> "OD2" Residue "2 TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 420": "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 ASP 139": "OD1" <-> "OD2" Residue "3 ARG 149": "NH1" <-> "NH2" 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 PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 19": "OD1" <-> "OD2" Residue "4 TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 64": "OE1" <-> "OE2" Residue "4 ARG 84": "NH1" <-> "NH2" Residue "4 TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 146": "OE1" <-> "OE2" Residue "4 GLU 160": "OE1" <-> "OE2" Residue "4 ARG 176": "NH1" <-> "NH2" Residue "4 ASP 181": "OD1" <-> "OD2" Residue "4 TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 193": "OE1" <-> "OE2" Residue "4 GLU 202": "OE1" <-> "OE2" Residue "4 PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 214": "OD1" <-> "OD2" 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 "5 GLU 6": "OE1" <-> "OE2" Residue "5 ARG 36": "NH1" <-> "NH2" Residue "5 ARG 50": "NH1" <-> "NH2" Residue "5 ARG 112": "NH1" <-> "NH2" Residue "6 PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 146": "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 GLU 75": "OE1" <-> "OE2" 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 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 74": "OE1" <-> "OE2" Residue "9 GLU 88": "OE1" <-> "OE2" Residue "C PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 111": "OE1" <-> "OE2" Residue "F GLU 111": "OE1" <-> "OE2" Residue "G GLU 111": "OE1" <-> "OE2" Residue "M ARG 115": "NH1" <-> "NH2" Residue "M ASP 132": "OD1" <-> "OD2" Residue "M ARG 145": "NH1" <-> "NH2" Residue "M PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 202": "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 ASP 72": "OD1" <-> "OD2" Residue "P PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 136": "OE1" <-> "OE2" Residue "P GLU 142": "OE1" <-> "OE2" Residue "P PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 191": "OD1" <-> "OD2" Residue "P PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 206": "NH1" <-> "NH2" 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 GLU 33": "OE1" <-> "OE2" Residue "Q ARG 42": "NH1" <-> "NH2" Residue "Q ARG 48": "NH1" <-> "NH2" Residue "Q TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 54": "OD1" <-> "OD2" Residue "R GLU 32": "OE1" <-> "OE2" Residue "R PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 35": "OE1" <-> "OE2" Residue "R PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 95": "OD1" <-> "OD2" Residue "R GLU 123": "OE1" <-> "OE2" 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 ASP 144": "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 ASP 164": "OD1" <-> "OD2" Residue "S PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 214": "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 306": "OE1" <-> "OE2" Residue "T ARG 49": "NH1" <-> "NH2" Residue "T GLU 74": "OE1" <-> "OE2" 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 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 403": "OD1" <-> "OD2" Residue "T PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 418": "NH1" <-> "NH2" Residue "T ARG 429": "NH1" <-> "NH2" Residue "T PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 454": "NH1" <-> "NH2" Residue "T GLU 455": "OE1" <-> "OE2" Residue "T PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 510": "OD1" <-> "OD2" Residue "T GLU 522": "OE1" <-> "OE2" Residue "T ASP 547": "OD1" <-> "OD2" Residue "T ARG 555": "NH1" <-> "NH2" Residue "U GLU 47": "OE1" <-> "OE2" Residue "U ARG 49": "NH1" <-> "NH2" Residue "U ASP 92": "OD1" <-> "OD2" Residue "U ARG 96": "NH1" <-> "NH2" Residue "U TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 146": "NH1" <-> "NH2" Residue "U ARG 162": "NH1" <-> "NH2" 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 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 PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 467": "OD1" <-> "OD2" Residue "U GLU 475": "OE1" <-> "OE2" 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 GLU 521": "OE1" <-> "OE2" Residue "U PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 547": "OD1" <-> "OD2" Residue "V GLU 47": "OE1" <-> "OE2" Residue "V ARG 49": "NH1" <-> "NH2" Residue "V PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 142": "OD1" <-> "OD2" Residue "V TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 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 GLU 409": "OE1" <-> "OE2" Residue "V PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 429": "NH1" <-> "NH2" Residue "V ARG 454": "NH1" <-> "NH2" Residue "V PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 465": "OD1" <-> "OD2" Residue "V GLU 475": "OE1" <-> "OE2" Residue "V ARG 476": "NH1" <-> "NH2" Residue "V GLU 482": "OE1" <-> "OE2" Residue "V PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 496": "NH1" <-> "NH2" Residue "V TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 513": "NH1" <-> "NH2" Residue "V GLU 521": "OE1" <-> "OE2" Residue "V GLU 522": "OE1" <-> "OE2" Residue "V GLU 553": "OE1" <-> "OE2" Residue "V ARG 555": "NH1" <-> "NH2" Residue "X ARG 51": "NH1" <-> "NH2" Residue "X ASP 82": "OD1" <-> "OD2" Residue "X ASP 91": "OD1" <-> "OD2" Residue "X ASP 94": "OD1" <-> "OD2" Residue "X ASP 136": "OD1" <-> "OD2" Residue "X GLU 149": "OE1" <-> "OE2" Residue "X PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 210": "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 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 ASP 279": "OD1" <-> "OD2" Residue "X ASP 285": "OD1" <-> "OD2" Residue "X GLU 296": "OE1" <-> "OE2" Residue "X ASP 317": "OD1" <-> "OD2" Residue "X PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 359": "OD1" <-> "OD2" 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 409": "OD1" <-> "OD2" Residue "X ASP 423": "OD1" <-> "OD2" Residue "X GLU 424": "OE1" <-> "OE2" Residue "X PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 494": "OE1" <-> "OE2" Residue "X GLU 497": "OE1" <-> "OE2" Residue "X ARG 509": "NH1" <-> "NH2" Residue "X GLU 541": "OE1" <-> "OE2" Residue "X ASP 542": "OD1" <-> "OD2" Residue "X GLU 547": "OE1" <-> "OE2" Residue "X GLU 552": "OE1" <-> "OE2" Residue "Y ASP 36": "OD1" <-> "OD2" Residue "Y TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 71": "NH1" <-> "NH2" Residue "Y ARG 86": "NH1" <-> "NH2" Residue "Y ARG 115": "NH1" <-> "NH2" Residue "Y ARG 120": "NH1" <-> "NH2" Residue "Y GLU 131": "OE1" <-> "OE2" Residue "Y ASP 139": "OD1" <-> "OD2" Residue "Y ARG 145": "NH1" <-> "NH2" Residue "Y PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 156": "OE1" <-> "OE2" Residue "Y TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 195": "OE1" <-> "OE2" Residue "Y GLU 215": "OE1" <-> "OE2" Residue "Y ARG 258": "NH1" <-> "NH2" Residue "Y GLU 270": "OE1" <-> "OE2" Residue "Y GLU 296": "OE1" <-> "OE2" Residue "Y TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 366": "NH1" <-> "NH2" Residue "Y TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 378": "OD1" <-> "OD2" Residue "Y ARG 385": "NH1" <-> "NH2" Residue "Y ASP 415": "OD1" <-> "OD2" Residue "Y ASP 423": "OD1" <-> "OD2" Residue "Y ASP 429": "OD1" <-> "OD2" Residue "Y PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 451": "OE1" <-> "OE2" Residue "Y PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 465": "OD1" <-> "OD2" Residue "Y PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 528": "OD1" <-> "OD2" Residue "Y ASP 543": "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 ARG 71": "NH1" <-> "NH2" Residue "Z ASP 82": "OD1" <-> "OD2" Residue "Z ARG 86": "NH1" <-> "NH2" Residue "Z ASP 94": "OD1" <-> "OD2" Residue "Z ARG 98": "NH1" <-> "NH2" Residue "Z ASP 104": "OD1" <-> "OD2" Residue "Z ARG 120": "NH1" <-> "NH2" Residue "Z ASP 130": "OD1" <-> "OD2" 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 PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 359": "OD1" <-> "OD2" Residue "Z ASP 378": "OD1" <-> "OD2" Residue "Z ARG 385": "NH1" <-> "NH2" Residue "Z ARG 401": "NH1" <-> "NH2" Residue "Z TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 423": "OD1" <-> "OD2" Residue "Z ARG 435": "NH1" <-> "NH2" Residue "Z ARG 437": "NH1" <-> "NH2" Residue "Z PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 480": "OD1" <-> "OD2" Residue "Z GLU 483": "OE1" <-> "OE2" Residue "Z ARG 509": "NH1" <-> "NH2" Residue "Z ASP 513": "OD1" <-> "OD2" Residue "Z GLU 546": "OE1" <-> "OE2" Residue "Z GLU 547": "OE1" <-> "OE2" Residue "Z PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 53776 Number of models: 1 Model: "" Number of chains: 41 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} Chain: "1" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "6" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "M" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Time building chain proxies: 20.80, per 1000 atoms: 0.39 Number of scatterers: 53776 At special positions: 0 Unit cell: (210.6, 132.678, 264.303, 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 10199 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: 16.45 Conformation dependent library (CDL) restraints added in 7.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN M 600 " pdb="ZN ZN M 600 " - pdb=" NE2 HIS M 248 " 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: 300 helices and 31 sheets defined 50.3% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.82 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 29 Processing helix chain '0' and resid 44 through 47 No H-bonds generated for 'chain '0' and resid 44 through 47' 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 47 through 72 removed outlier: 3.643A pdb=" N ASN 1 52 " --> pdb=" O ASN 1 48 " (cutoff:3.500A) 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 104 through 141 removed outlier: 4.202A pdb=" N VAL 1 107 " --> pdb=" O ALA 1 104 " (cutoff:3.500A) Proline residue: 1 108 - end of helix removed outlier: 3.690A pdb=" N ASP 1 112 " --> pdb=" O LYS 1 109 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL 1 114 " --> pdb=" O PHE 1 111 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N SER 1 116 " --> pdb=" O THR 1 113 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR 1 117 " --> pdb=" O VAL 1 114 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA 1 119 " --> pdb=" O SER 1 116 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA 1 121 " --> pdb=" O ARG 1 118 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ALA 1 124 " --> pdb=" O ALA 1 121 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASP 1 127 " --> pdb=" O ALA 1 124 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS 1 128 " --> pdb=" O SER 1 125 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA 1 131 " --> pdb=" O LYS 1 128 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS 1 134 " --> pdb=" O ALA 1 131 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR 1 135 " --> pdb=" O GLY 1 132 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU 1 138 " --> pdb=" O THR 1 135 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA 1 139 " --> pdb=" O GLU 1 136 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER 1 141 " --> pdb=" O GLU 1 138 " (cutoff:3.500A) Processing helix chain '1' and resid 164 through 175 removed outlier: 3.957A pdb=" N THR 1 169 " --> pdb=" O GLU 1 165 " (cutoff:3.500A) Processing helix chain '1' and resid 191 through 194 No H-bonds generated for 'chain '1' and resid 191 through 194' Processing helix chain '1' and resid 198 through 204 removed outlier: 3.740A pdb=" N VAL 1 204 " --> pdb=" O PHE 1 200 " (cutoff:3.500A) Processing helix chain '1' and resid 212 through 223 removed outlier: 4.161A pdb=" N LEU 1 217 " --> pdb=" O VAL 1 213 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU 1 221 " --> pdb=" O LEU 1 217 " (cutoff:3.500A) Processing helix chain '1' and resid 245 through 270 removed outlier: 4.032A pdb=" N ARG 1 259 " --> pdb=" O GLU 1 255 " (cutoff:3.500A) Processing helix chain '1' and resid 272 through 276 removed outlier: 3.537A pdb=" N ALA 1 275 " --> pdb=" O PRO 1 272 " (cutoff:3.500A) 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 removed outlier: 3.542A pdb=" N ALA 1 303 " --> pdb=" O GLU 1 299 " (cutoff:3.500A) 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 352 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: 3.568A pdb=" N ARG 1 381 " --> pdb=" O SER 1 377 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL 1 382 " --> pdb=" O GLU 1 378 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS 1 386 " --> pdb=" O VAL 1 382 " (cutoff:3.500A) Processing helix chain '1' and resid 393 through 420 removed outlier: 3.589A pdb=" N LEU 1 401 " --> pdb=" O GLU 1 397 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL 1 418 " --> pdb=" O GLU 1 414 " (cutoff:3.500A) removed outlier: 5.276A 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 459 Processing helix chain '1' and resid 464 through 477 removed outlier: 3.711A pdb=" N TYR 1 468 " --> pdb=" O PRO 1 464 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR 1 471 " --> pdb=" O ALA 1 467 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN 1 474 " --> pdb=" O VAL 1 470 " (cutoff:3.500A) 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 514 removed outlier: 4.213A pdb=" N GLU 1 501 " --> pdb=" O LEU 1 497 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER 1 503 " --> pdb=" O GLU 1 499 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP 1 508 " --> pdb=" O ASP 1 504 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU 1 512 " --> pdb=" O ASP 1 508 " (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 removed outlier: 3.591A pdb=" N GLU 1 559 " --> pdb=" O LYS 1 555 " (cutoff:3.500A) Processing helix chain '1' and resid 567 through 573 Processing helix chain '1' and resid 577 through 585 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 596 No H-bonds generated for 'chain '1' and resid 593 through 596' Processing helix chain '1' and resid 598 through 605 removed outlier: 3.646A pdb=" N LYS 1 605 " --> pdb=" O ASP 1 601 " (cutoff:3.500A) Processing helix chain '2' and resid 9 through 19 removed outlier: 3.519A pdb=" N LYS 2 13 " --> pdb=" O PRO 2 9 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU 2 14 " --> pdb=" O ALA 2 10 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU 2 18 " --> pdb=" O GLU 2 14 " (cutoff:3.500A) Processing helix chain '2' and resid 26 through 38 Processing helix chain '2' and resid 45 through 57 Processing helix chain '2' and resid 63 through 76 removed outlier: 3.514A pdb=" N THR 2 67 " --> pdb=" O ALA 2 63 " (cutoff:3.500A) Processing helix chain '2' and resid 81 through 86 Processing helix chain '2' and resid 88 through 93 removed outlier: 3.553A pdb=" N SER 2 93 " --> pdb=" O GLY 2 89 " (cutoff:3.500A) Processing helix chain '2' and resid 100 through 112 removed outlier: 3.714A pdb=" N SER 2 104 " --> pdb=" O PRO 2 100 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ILE 2 105 " --> pdb=" O VAL 2 101 " (cutoff:3.500A) Processing helix chain '2' and resid 118 through 130 removed outlier: 3.653A pdb=" N VAL 2 128 " --> pdb=" O ALA 2 124 " (cutoff:3.500A) Processing helix chain '2' and resid 137 through 149 Processing helix chain '2' and resid 155 through 167 removed outlier: 3.510A 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 200 removed outlier: 3.577A pdb=" N ASP 2 194 " --> pdb=" O LYS 2 190 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA 2 195 " --> pdb=" O ALA 2 191 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS 2 198 " --> pdb=" O ASP 2 194 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N SER 2 199 " --> pdb=" O ALA 2 195 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N PHE 2 200 " --> pdb=" O LEU 2 196 " (cutoff:3.500A) Processing helix chain '2' and resid 208 through 220 Processing helix chain '2' and resid 228 through 232 Processing helix chain '2' and resid 241 through 254 removed outlier: 3.540A pdb=" N VAL 2 245 " --> pdb=" O PRO 2 241 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU 2 246 " --> pdb=" O ALA 2 242 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY 2 250 " --> pdb=" O GLU 2 246 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER 2 254 " --> pdb=" O GLY 2 250 " (cutoff:3.500A) Processing helix chain '2' and resid 259 through 275 removed outlier: 3.703A 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 277 through 279 No H-bonds generated for 'chain '2' and resid 277 through 279' Processing helix chain '2' and resid 282 through 294 removed outlier: 3.548A pdb=" N THR 2 293 " --> pdb=" O HIS 2 289 " (cutoff:3.500A) Processing helix chain '2' and resid 306 through 320 removed outlier: 3.613A pdb=" N GLY 2 312 " --> pdb=" O ALA 2 308 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA 2 318 " --> pdb=" O ALA 2 314 " (cutoff:3.500A) Processing helix chain '2' and resid 327 through 340 removed outlier: 3.501A pdb=" N ALA 2 335 " --> pdb=" O ALA 2 331 " (cutoff:3.500A) Processing helix chain '2' and resid 346 through 352 removed outlier: 3.501A pdb=" N SER 2 351 " --> pdb=" O PRO 2 347 " (cutoff:3.500A) Processing helix chain '2' and resid 397 through 409 removed outlier: 3.599A pdb=" N GLN 2 409 " --> pdb=" O VAL 2 405 " (cutoff:3.500A) Processing helix chain '2' and resid 418 through 423 removed outlier: 4.270A pdb=" N ALA 2 423 " --> pdb=" O ASN 2 419 " (cutoff:3.500A) Processing helix chain '2' and resid 427 through 439 Processing helix chain '3' and resid 78 through 86 Processing helix chain '3' and resid 92 through 95 No H-bonds generated for 'chain '3' and resid 92 through 95' Processing helix chain '3' and resid 103 through 112 Processing helix chain '3' and resid 121 through 127 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 158 through 165 Processing helix chain '3' and resid 169 through 171 No H-bonds generated for 'chain '3' and resid 169 through 171' Processing helix chain '3' and resid 174 through 186 removed outlier: 4.003A pdb=" N GLN 3 179 " --> pdb=" O GLU 3 175 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA 3 182 " --> pdb=" O LEU 3 178 " (cutoff:3.500A) Processing helix chain '3' and resid 192 through 203 removed outlier: 3.566A pdb=" N SER 3 201 " --> pdb=" O ASP 3 197 " (cutoff:3.500A) Processing helix chain '3' and resid 216 through 228 removed outlier: 3.716A pdb=" N THR 3 221 " --> pdb=" O ASP 3 217 " (cutoff:3.500A) Processing helix chain '3' and resid 234 through 243 removed outlier: 3.533A pdb=" N ALA 3 238 " --> pdb=" O ALA 3 234 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG 3 242 " --> pdb=" O ALA 3 238 " (cutoff:3.500A) removed outlier: 4.102A 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: 3.733A pdb=" N SER 3 263 " --> pdb=" O ASP 3 259 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA 3 267 " --> pdb=" O SER 3 263 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR 3 270 " --> pdb=" O LYS 3 266 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE 3 271 " --> pdb=" O ALA 3 267 " (cutoff:3.500A) Processing helix chain '3' and resid 276 through 278 No H-bonds generated for 'chain '3' and resid 276 through 278' Processing helix chain '3' and resid 283 through 286 No H-bonds generated for 'chain '3' and resid 283 through 286' Processing helix chain '3' and resid 289 through 291 No H-bonds generated for 'chain '3' and resid 289 through 291' Processing helix chain '3' and resid 294 through 311 removed outlier: 3.728A pdb=" N ASN 3 309 " --> pdb=" O VAL 3 305 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA 3 310 " --> pdb=" O ALA 3 306 " (cutoff:3.500A) Processing helix chain '4' and resid 10 through 13 No H-bonds generated for 'chain '4' and resid 10 through 13' Processing helix chain '4' and resid 20 through 34 Processing helix chain '4' and resid 48 through 67 removed outlier: 4.153A pdb=" N GLN 4 61 " --> pdb=" O TYR 4 57 " (cutoff:3.500A) removed outlier: 3.634A 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 removed outlier: 3.536A pdb=" N LYS 4 107 " --> pdb=" O ILE 4 103 " (cutoff:3.500A) Processing helix chain '4' and resid 119 through 125 removed outlier: 3.653A pdb=" N ASN 4 124 " --> pdb=" O LYS 4 120 " (cutoff:3.500A) Processing helix chain '4' and resid 132 through 145 removed outlier: 3.641A pdb=" N ALA 4 137 " --> pdb=" O ASP 4 133 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N VAL 4 141 " --> pdb=" O ALA 4 137 " (cutoff:3.500A) Processing helix chain '4' and resid 160 through 176 removed outlier: 4.122A pdb=" N PHE 4 165 " --> pdb=" O GLY 4 161 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS 4 168 " --> pdb=" O LYS 4 164 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA 4 171 " --> pdb=" O ALA 4 167 " (cutoff:3.500A) Processing helix chain '4' and resid 180 through 187 Processing helix chain '4' and resid 197 through 233 removed outlier: 3.747A pdb=" N GLU 4 202 " --> pdb=" O LYS 4 198 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR 4 205 " --> pdb=" O LYS 4 201 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TRP 4 206 " --> pdb=" O GLU 4 202 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA 4 213 " --> pdb=" O SER 4 209 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA 4 224 " --> pdb=" O LYS 4 220 " (cutoff:3.500A) Processing helix chain '4' and resid 238 through 257 removed outlier: 3.603A pdb=" N LYS 4 243 " --> pdb=" O ALA 4 239 " (cutoff:3.500A) removed outlier: 3.608A 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 28 Processing helix chain '5' and resid 30 through 56 removed outlier: 3.542A pdb=" N GLU 5 37 " --> pdb=" O THR 5 33 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N HIS 5 41 " --> pdb=" O GLU 5 37 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LYS 5 49 " --> pdb=" O ALA 5 45 " (cutoff:3.500A) removed outlier: 5.121A 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 77 Processing helix chain '5' and resid 92 through 105 removed outlier: 4.067A pdb=" N SER 5 97 " --> pdb=" O GLU 5 93 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA 5 98 " --> pdb=" O LYS 5 94 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS 5 101 " --> pdb=" O SER 5 97 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL 5 102 " --> pdb=" O ALA 5 98 " (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 50 through 55 removed outlier: 3.999A pdb=" N ILE 6 54 " --> pdb=" O LEU 6 51 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS 6 55 " --> pdb=" O LYS 6 52 " (cutoff:3.500A) Processing helix chain '6' and resid 75 through 93 removed outlier: 3.542A pdb=" N TYR 6 88 " --> pdb=" O SER 6 84 " (cutoff:3.500A) Processing helix chain '6' and resid 99 through 117 removed outlier: 3.525A pdb=" N ASN 6 106 " --> pdb=" O ASP 6 102 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL 6 107 " --> pdb=" O LEU 6 103 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N TRP 6 112 " --> pdb=" O LEU 6 108 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU 6 113 " --> pdb=" O GLN 6 109 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER 6 117 " --> pdb=" O LEU 6 113 " (cutoff:3.500A) Processing helix chain '6' and resid 122 through 129 Processing helix chain '7' and resid 84 through 104 removed outlier: 3.711A pdb=" N GLU 7 99 " --> pdb=" O SER 7 95 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU 7 103 " --> pdb=" O GLU 7 99 " (cutoff:3.500A) Processing helix chain '7' and resid 110 through 113 Processing helix chain '7' and resid 116 through 119 No H-bonds generated for 'chain '7' and resid 116 through 119' Processing helix chain '7' and resid 124 through 144 removed outlier: 3.574A pdb=" N LYS 7 128 " --> pdb=" O PRO 7 124 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR 7 137 " --> pdb=" O ALA 7 133 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR 7 138 " --> pdb=" O ALA 7 134 " (cutoff:3.500A) Processing helix chain '7' and resid 147 through 156 removed outlier: 4.405A pdb=" N SER 7 151 " --> pdb=" O ASP 7 148 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA 7 152 " --> pdb=" O SER 7 149 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA 7 154 " --> pdb=" O SER 7 151 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER 7 155 " --> 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 186 removed outlier: 3.633A pdb=" N ASN 7 184 " --> pdb=" O GLY 7 180 " (cutoff:3.500A) 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: 3.727A pdb=" N TRP 8 45 " --> pdb=" O ILE 8 41 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TYR 8 46 " --> pdb=" O PRO 8 42 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N LEU 8 47 " --> pdb=" O ARG 8 43 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA 8 76 " --> pdb=" O ALA 8 72 " (cutoff:3.500A) Processing helix chain '9' and resid 6 through 15 Processing helix chain '9' and resid 37 through 56 removed outlier: 4.170A pdb=" N VAL 9 42 " --> pdb=" O ALA 9 38 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASN 9 56 " --> pdb=" O LEU 9 52 " (cutoff:3.500A) Processing helix chain '9' and resid 83 through 96 removed outlier: 3.637A pdb=" N GLU 9 88 " --> pdb=" O ALA 9 84 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS 9 95 " --> pdb=" O LYS 9 91 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER 9 96 " --> pdb=" O GLU 9 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 91 removed outlier: 3.907A pdb=" N MET A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY A 65 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ILE A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ALA A 70 " --> pdb=" O CYS A 66 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LEU A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N ALA A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLY A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL A 74 " --> pdb=" O ALA A 70 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY A 79 " --> pdb=" O GLY A 75 " (cutoff:3.500A) removed outlier: 3.713A 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: 3.582A pdb=" N LEU A 105 " --> pdb=" O GLY A 101 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 91 removed outlier: 3.921A pdb=" N MET B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE B 69 " --> pdb=" O GLY B 65 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ALA B 70 " --> pdb=" O CYS B 66 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N LEU B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ALA B 72 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N GLY B 73 " --> pdb=" O ILE B 69 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL B 74 " --> pdb=" O ALA B 70 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER B 84 " --> pdb=" O VAL B 80 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE B 86 " --> pdb=" O PHE B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 95 No H-bonds generated for 'chain 'B' and resid 93 through 95' Processing helix chain 'B' and resid 99 through 125 removed outlier: 4.173A pdb=" N ILE B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU B 118 " --> pdb=" O ALA B 114 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL B 120 " --> pdb=" O PHE B 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 89 removed outlier: 3.628A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ILE C 69 " --> pdb=" O GLY C 65 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ALA C 70 " --> pdb=" O CYS C 66 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N LEU C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ALA C 72 " --> pdb=" O THR C 68 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY C 73 " --> pdb=" O ILE C 69 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY C 79 " --> pdb=" O GLY C 75 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE C 86 " --> pdb=" O PHE C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 125 removed outlier: 3.751A pdb=" N LEU C 105 " --> pdb=" O GLY C 101 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER C 112 " --> pdb=" O ALA C 108 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ILE C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU C 119 " --> pdb=" O LEU C 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 65 removed outlier: 4.021A pdb=" N MET D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 89 removed outlier: 3.623A pdb=" N ALA D 70 " --> pdb=" O ALA D 67 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL D 74 " --> pdb=" O LEU D 71 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU D 78 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY D 79 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET D 81 " --> pdb=" O LEU D 78 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE D 82 " --> pdb=" O GLY D 79 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU D 85 " --> pdb=" O PHE D 82 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASN D 87 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA D 89 " --> pdb=" O ILE D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 124 removed outlier: 3.671A pdb=" N VAL D 100 " --> pdb=" O ALA D 96 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLY D 101 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL D 120 " --> pdb=" O PHE D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 89 removed outlier: 3.995A pdb=" N MET E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N CYS E 66 " --> pdb=" O VAL E 62 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ILE E 69 " --> pdb=" O GLY E 65 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ALA E 70 " --> pdb=" O CYS E 66 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N LEU E 71 " --> pdb=" O ALA E 67 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ALA E 72 " --> pdb=" O THR E 68 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLY E 73 " --> pdb=" O ILE E 69 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL E 74 " --> pdb=" O ALA E 70 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL E 80 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE E 86 " --> pdb=" O PHE E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 123 removed outlier: 4.208A pdb=" N LEU E 105 " --> pdb=" O GLY E 101 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER E 112 " --> pdb=" O ALA E 108 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA E 114 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE E 122 " --> pdb=" O LEU E 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 91 removed outlier: 3.986A pdb=" N MET F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE F 69 " --> pdb=" O GLY F 65 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N ALA F 70 " --> pdb=" O CYS F 66 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N LEU F 71 " --> pdb=" O ALA F 67 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ALA F 72 " --> pdb=" O THR F 68 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLY F 73 " --> pdb=" O ILE F 69 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY F 79 " --> pdb=" O GLY F 75 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE F 86 " --> pdb=" O PHE F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 95 No H-bonds generated for 'chain 'F' and resid 93 through 95' Processing helix chain 'F' and resid 99 through 123 removed outlier: 4.105A pdb=" N LEU F 105 " --> pdb=" O GLY F 101 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ILE F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE F 122 " --> pdb=" O LEU F 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 91 removed outlier: 3.958A pdb=" N MET G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE G 69 " --> pdb=" O GLY G 65 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ALA G 70 " --> pdb=" O CYS G 66 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N LEU G 71 " --> pdb=" O ALA G 67 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ALA G 72 " --> pdb=" O THR G 68 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLY G 73 " --> pdb=" O ILE G 69 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY G 79 " --> pdb=" O GLY G 75 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL G 80 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE G 86 " --> pdb=" O PHE G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 123 removed outlier: 3.640A pdb=" N LEU G 105 " --> pdb=" O GLY G 101 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA G 114 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE G 116 " --> pdb=" O SER G 112 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE G 122 " --> pdb=" O LEU G 118 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 91 removed outlier: 3.787A pdb=" N MET H 61 " --> pdb=" O ALA H 57 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE H 69 " --> pdb=" O GLY H 65 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ALA H 70 " --> pdb=" O CYS H 66 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N LEU H 71 " --> pdb=" O ALA H 67 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ALA H 72 " --> pdb=" O THR H 68 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N GLY H 73 " --> pdb=" O ILE H 69 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL H 74 " --> pdb=" O ALA H 70 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU H 85 " --> pdb=" O MET H 81 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE H 86 " --> pdb=" O PHE H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 95 No H-bonds generated for 'chain 'H' and resid 93 through 95' Processing helix chain 'H' and resid 99 through 125 removed outlier: 4.531A pdb=" N ILE H 113 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL H 120 " --> pdb=" O PHE H 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 65 removed outlier: 4.072A pdb=" N MET I 61 " --> pdb=" O ALA I 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 68 through 91 removed outlier: 3.752A pdb=" N GLY I 73 " --> pdb=" O ALA I 70 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL I 74 " --> pdb=" O LEU I 71 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA I 76 " --> pdb=" O GLY I 73 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU I 78 " --> pdb=" O GLY I 75 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N MET I 81 " --> pdb=" O LEU I 78 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE I 82 " --> pdb=" O GLY I 79 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY I 83 " --> pdb=" O VAL I 80 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU I 85 " --> pdb=" O PHE I 82 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASN I 87 " --> pdb=" O SER I 84 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA I 89 " --> pdb=" O ILE I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 118 removed outlier: 3.668A pdb=" N SER I 112 " --> pdb=" O ALA I 108 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ILE I 113 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA I 114 " --> pdb=" O THR I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 123 No H-bonds generated for 'chain 'I' and resid 120 through 123' Processing helix chain 'J' and resid 55 through 91 removed outlier: 3.818A pdb=" N MET J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL J 62 " --> pdb=" O ALA J 58 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR J 68 " --> pdb=" O ALA J 64 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ILE J 69 " --> pdb=" O GLY J 65 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ALA J 70 " --> pdb=" O CYS J 66 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N LEU J 71 " --> pdb=" O ALA J 67 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ALA J 72 " --> pdb=" O THR J 68 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLY J 73 " --> pdb=" O ILE J 69 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY J 79 " --> pdb=" O GLY J 75 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE J 86 " --> pdb=" O PHE J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 125 removed outlier: 5.172A pdb=" N LYS J 97 " --> pdb=" O ASN J 94 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU J 99 " --> pdb=" O ALA J 96 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL J 100 " --> pdb=" O LYS J 97 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU J 104 " --> pdb=" O GLY J 101 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU J 105 " --> pdb=" O TYR J 102 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE J 107 " --> pdb=" O LEU J 104 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU J 109 " --> pdb=" O GLY J 106 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLU J 111 " --> pdb=" O ALA J 108 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER J 112 " --> pdb=" O LEU J 109 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU J 115 " --> pdb=" O SER J 112 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE J 116 " --> pdb=" O ILE J 113 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU J 118 " --> pdb=" O LEU J 115 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL J 121 " --> pdb=" O LEU J 118 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LEU J 125 " --> pdb=" O PHE J 122 " (cutoff:3.500A) Processing helix chain 'M' and resid 105 through 120 removed outlier: 3.546A pdb=" N GLN M 120 " --> pdb=" O PHE M 116 " (cutoff:3.500A) Processing helix chain 'M' and resid 135 through 144 Processing helix chain 'M' and resid 148 through 167 removed outlier: 3.697A pdb=" N THR M 153 " --> pdb=" O GLY M 149 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER M 161 " --> pdb=" O CYS M 157 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N CYS M 162 " --> pdb=" O THR M 158 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY M 166 " --> pdb=" O CYS M 162 " (cutoff:3.500A) removed outlier: 4.161A 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 198 removed outlier: 3.579A pdb=" N SER M 187 " --> pdb=" O GLY M 183 " (cutoff:3.500A) Processing helix chain 'M' and resid 222 through 264 removed outlier: 3.591A pdb=" N SER M 228 " --> pdb=" O LEU M 224 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ARG M 232 " --> pdb=" O SER M 228 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA M 233 " --> pdb=" O TYR M 229 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL M 234 " --> pdb=" O THR M 230 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY M 237 " --> pdb=" O ALA M 233 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N HIS M 248 " --> pdb=" O MET M 244 " (cutoff:3.500A) removed outlier: 3.914A 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 310 removed outlier: 3.917A pdb=" N GLY M 276 " --> pdb=" O PRO M 272 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU M 280 " --> pdb=" O GLY M 276 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU M 290 " --> pdb=" O GLY M 286 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL M 293 " --> pdb=" O TYR M 289 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER M 296 " --> pdb=" O ALA M 292 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER M 300 " --> pdb=" O SER M 296 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE M 310 " --> pdb=" O TYR M 306 " (cutoff:3.500A) Processing helix chain 'P' and resid 51 through 63 removed outlier: 3.510A pdb=" N THR P 55 " --> pdb=" O ALA P 51 " (cutoff:3.500A) Processing helix chain 'P' and resid 69 through 83 removed outlier: 3.563A pdb=" N LYS P 82 " --> pdb=" O ILE P 78 " (cutoff:3.500A) Processing helix chain 'P' and resid 85 through 92 removed outlier: 3.810A pdb=" N LEU P 90 " --> pdb=" O GLU P 86 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA P 91 " --> pdb=" O LEU P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 98 through 108 removed outlier: 3.701A pdb=" N ILE P 105 " --> pdb=" O ARG P 101 " (cutoff:3.500A) Processing helix chain 'P' and resid 116 through 127 removed outlier: 3.617A pdb=" N GLU P 123 " --> pdb=" O LYS P 119 " (cutoff:3.500A) Processing helix chain 'P' and resid 131 through 148 removed outlier: 3.539A pdb=" N LEU P 134 " --> pdb=" O LEU P 131 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU P 135 " --> pdb=" O SER P 132 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL P 137 " --> pdb=" O LEU P 134 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR P 138 " --> pdb=" O LEU P 135 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL P 139 " --> pdb=" O GLU P 136 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU P 143 " --> pdb=" O ASN P 140 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU P 144 " --> pdb=" O TYR P 141 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU P 146 " --> pdb=" O GLU P 143 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA P 147 " --> pdb=" O LEU P 144 " (cutoff:3.500A) Processing helix chain 'P' and resid 164 through 176 removed outlier: 3.595A pdb=" N VAL P 168 " --> pdb=" O LYS P 164 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU P 170 " --> pdb=" O GLU P 166 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS P 172 " --> pdb=" O VAL P 168 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LYS P 176 " --> pdb=" O LYS P 172 " (cutoff:3.500A) Processing helix chain 'P' and resid 211 through 225 removed outlier: 3.767A pdb=" N GLU P 216 " --> pdb=" O ALA P 212 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE P 221 " --> pdb=" O GLU P 217 " (cutoff:3.500A) Processing helix chain 'Q' and resid 16 through 30 removed outlier: 3.503A pdb=" N LEU Q 27 " --> pdb=" O CYS Q 23 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL Q 30 " --> pdb=" O LEU Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 33 through 39 removed outlier: 3.872A pdb=" N ALA Q 37 " --> pdb=" O GLU Q 33 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N LYS Q 38 " --> pdb=" O PRO Q 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 30 through 40 removed outlier: 3.915A pdb=" N GLU R 35 " --> pdb=" O LYS R 31 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LYS R 39 " --> pdb=" O GLU R 35 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS R 40 " --> pdb=" O VAL R 36 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 53 No H-bonds generated for 'chain 'R' and resid 51 through 53' 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: 3.877A pdb=" N ALA R 166 " --> pdb=" O SER R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 193 removed outlier: 3.790A pdb=" N ALA R 179 " --> pdb=" O GLU R 175 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 69 removed outlier: 3.538A pdb=" N ILE S 47 " --> pdb=" O VAL S 43 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS S 58 " --> pdb=" O GLY S 54 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET S 62 " --> pdb=" O LYS S 58 " (cutoff:3.500A) Processing helix chain 'S' and resid 72 through 75 No H-bonds generated for 'chain 'S' and resid 72 through 75' Processing helix chain 'S' and resid 81 through 88 removed outlier: 4.437A pdb=" N PHE S 85 " --> pdb=" O LEU S 81 " (cutoff:3.500A) Processing helix chain 'S' and resid 115 through 127 removed outlier: 3.519A pdb=" N ILE S 119 " --> pdb=" O LEU S 115 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR S 120 " --> pdb=" O ASN S 116 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG S 124 " --> pdb=" O THR S 120 " (cutoff:3.500A) Processing helix chain 'S' and resid 147 through 150 No H-bonds generated for 'chain 'S' and resid 147 through 150' Processing helix chain 'S' and resid 172 through 184 Processing helix chain 'S' and resid 217 through 221 removed outlier: 3.725A pdb=" N GLU S 221 " --> pdb=" O GLU S 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 217 through 221' Processing helix chain 'S' and resid 239 through 312 removed outlier: 3.700A pdb=" N ARG S 244 " --> pdb=" O SER S 240 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU S 248 " --> pdb=" O ARG S 244 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN S 263 " --> pdb=" O MET S 259 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA S 268 " --> pdb=" O CYS S 264 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER S 272 " --> pdb=" O ALA S 268 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR S 278 " --> pdb=" O MET S 274 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU S 285 " --> pdb=" O ALA S 281 " (cutoff:3.500A) Processing helix chain 'T' and resid 61 through 64 No H-bonds generated for 'chain 'T' and resid 61 through 64' Processing helix chain 'T' and resid 67 through 75 removed outlier: 4.094A 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 192 through 194 No H-bonds generated for 'chain 'T' and resid 192 through 194' Processing helix chain 'T' and resid 207 through 212 removed outlier: 3.580A pdb=" N LEU T 212 " --> pdb=" O ALA T 208 " (cutoff:3.500A) Processing helix chain 'T' and resid 231 through 246 removed outlier: 3.575A pdb=" N LYS T 243 " --> pdb=" O ILE T 239 " (cutoff:3.500A) Processing helix chain 'T' and resid 266 through 278 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: 3.600A pdb=" N TYR T 312 " --> pdb=" O ALA T 308 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N PHE T 313 " --> pdb=" O MET T 309 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG T 314 " --> pdb=" O ALA T 310 " (cutoff:3.500A) Processing helix chain 'T' and resid 327 through 340 removed outlier: 3.542A pdb=" N VAL T 332 " --> pdb=" O SER T 328 " (cutoff:3.500A) Processing helix chain 'T' and resid 347 through 349 No H-bonds generated for 'chain 'T' and resid 347 through 349' Processing helix chain 'T' and resid 352 through 364 removed outlier: 4.227A pdb=" N PHE T 355 " --> pdb=" O GLY T 352 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER T 359 " --> pdb=" O TYR T 356 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ARG T 360 " --> pdb=" O LEU T 357 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU T 362 " --> pdb=" O SER T 359 " (cutoff:3.500A) removed outlier: 4.117A 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 Processing helix chain 'T' and resid 431 through 434 removed outlier: 3.749A pdb=" N ALA T 434 " --> pdb=" O GLY T 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 431 through 434' Processing helix chain 'T' and resid 437 through 440 No H-bonds generated for 'chain 'T' and resid 437 through 440' Processing helix chain 'T' and resid 443 through 459 removed outlier: 4.438A pdb=" N GLU T 455 " --> pdb=" O ALA T 451 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL T 456 " --> pdb=" O GLN T 452 " (cutoff:3.500A) Processing helix chain 'T' and resid 470 through 483 removed outlier: 3.701A pdb=" N ALA T 478 " --> pdb=" O LEU T 474 " (cutoff:3.500A) Processing helix chain 'T' and resid 494 through 505 Processing helix chain 'T' and resid 514 through 527 removed outlier: 3.891A pdb=" N ILE T 517 " --> pdb=" O VAL T 514 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL T 518 " --> pdb=" O GLN T 515 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU T 521 " --> pdb=" O VAL T 518 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU T 522 " --> pdb=" O ALA T 519 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ILE T 525 " --> pdb=" O GLU T 522 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLN T 527 " --> pdb=" O VAL T 524 " (cutoff:3.500A) Processing helix chain 'T' and resid 532 through 539 Processing helix chain 'T' and resid 544 through 551 removed outlier: 4.217A pdb=" N ALA T 548 " --> pdb=" O PRO T 544 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N HIS T 549 " --> pdb=" O ALA T 545 " (cutoff:3.500A) Processing helix chain 'U' and resid 42 through 48 removed outlier: 3.784A pdb=" N GLU U 47 " --> pdb=" O LYS U 43 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU U 48 " --> pdb=" O ALA U 44 " (cutoff:3.500A) Processing helix chain 'U' and resid 59 through 62 No H-bonds generated for 'chain 'U' and resid 59 through 62' 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: 3.584A pdb=" N ALA U 235 " --> pdb=" O LYS U 231 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS U 243 " --> pdb=" O ILE U 239 " (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: 3.599A pdb=" N TYR U 312 " --> pdb=" O ALA U 308 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N PHE U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) Processing helix chain 'U' and resid 328 through 340 removed outlier: 3.630A pdb=" N VAL U 332 " --> pdb=" O SER U 328 " (cutoff:3.500A) Processing helix chain 'U' and resid 347 through 349 No H-bonds generated for 'chain 'U' and resid 347 through 349' Processing helix chain 'U' and resid 352 through 364 removed outlier: 4.330A pdb=" N PHE U 355 " --> pdb=" O GLY U 352 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU U 357 " --> pdb=" O VAL U 354 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER U 359 " --> pdb=" O TYR U 356 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ARG U 360 " --> pdb=" O LEU U 357 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU U 362 " --> pdb=" O SER U 359 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLU U 363 " --> 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 457 removed outlier: 3.565A pdb=" N VAL U 442 " --> pdb=" O GLY U 438 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY U 444 " --> pdb=" O LYS U 440 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N THR U 445 " --> pdb=" O GLN U 441 " (cutoff:3.500A) Processing helix chain 'U' and resid 470 through 484 Processing helix chain 'U' and resid 494 through 505 removed outlier: 3.520A pdb=" N ALA U 500 " --> pdb=" O ARG U 496 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA U 504 " --> pdb=" O ALA U 500 " (cutoff:3.500A) Processing helix chain 'U' and resid 517 through 527 removed outlier: 3.939A pdb=" N GLU U 522 " --> pdb=" O VAL U 518 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN U 527 " --> pdb=" O ALA U 523 " (cutoff:3.500A) Processing helix chain 'U' and resid 532 through 539 Processing helix chain 'U' and resid 544 through 553 removed outlier: 3.727A pdb=" N ALA U 548 " --> pdb=" O PRO U 544 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N HIS U 549 " --> pdb=" O ALA U 545 " (cutoff:3.500A) 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 58 through 69 removed outlier: 3.951A pdb=" N GLN V 64 " --> pdb=" O GLN V 60 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS V 65 " --> pdb=" O HIS V 61 " (cutoff:3.500A) removed outlier: 3.602A 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: 3.888A pdb=" N GLU V 247 " --> pdb=" O LYS V 243 " (cutoff:3.500A) Processing helix chain 'V' and resid 266 through 278 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 300 Processing helix chain 'V' and resid 302 through 315 removed outlier: 3.523A pdb=" N TYR V 312 " --> pdb=" O ALA V 308 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N PHE V 313 " --> pdb=" O MET V 309 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG V 314 " --> pdb=" O ALA V 310 " (cutoff:3.500A) Processing helix chain 'V' and resid 327 through 340 removed outlier: 3.544A pdb=" N VAL V 332 " --> pdb=" O SER V 328 " (cutoff:3.500A) Processing helix chain 'V' and resid 347 through 349 No H-bonds generated for 'chain 'V' and resid 347 through 349' Processing helix chain 'V' and resid 352 through 364 removed outlier: 4.159A pdb=" N PHE V 355 " --> pdb=" O GLY V 352 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR V 356 " --> pdb=" O ASP V 353 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU V 357 " --> pdb=" O VAL V 354 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER V 359 " --> pdb=" O TYR V 356 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG V 360 " --> pdb=" O LEU V 357 " (cutoff:3.500A) removed outlier: 4.277A 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: 3.566A 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 removed outlier: 3.599A pdb=" N ALA V 434 " --> pdb=" O GLY V 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 431 through 434' Processing helix chain 'V' and resid 440 through 456 removed outlier: 3.699A pdb=" N GLY V 444 " --> pdb=" O LYS V 440 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N THR V 445 " --> pdb=" O GLN V 441 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU V 448 " --> pdb=" O GLY V 444 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU V 455 " --> pdb=" O ALA V 451 " (cutoff:3.500A) Processing helix chain 'V' and resid 470 through 481 Processing helix chain 'V' and resid 494 through 505 removed outlier: 3.736A pdb=" N ALA V 500 " --> pdb=" O ARG V 496 " (cutoff:3.500A) Processing helix chain 'V' and resid 514 through 516 No H-bonds generated for 'chain 'V' and resid 514 through 516' Processing helix chain 'V' and resid 520 through 523 No H-bonds generated for 'chain 'V' and resid 520 through 523' Processing helix chain 'V' and resid 530 through 539 removed outlier: 3.530A pdb=" N LYS V 534 " --> pdb=" O ALA V 531 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU V 536 " --> pdb=" O PHE V 533 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS V 537 " --> pdb=" O LYS V 534 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASN V 539 " --> pdb=" O LEU V 536 " (cutoff:3.500A) Processing helix chain 'V' and resid 544 through 553 removed outlier: 3.794A 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 150 through 152 No H-bonds generated for 'chain 'X' and resid 150 through 152' Processing helix chain 'X' and resid 165 through 170 Processing helix chain 'X' and resid 189 through 199 removed outlier: 3.528A pdb=" N ILE X 193 " --> pdb=" O LYS X 189 " (cutoff:3.500A) Processing helix chain 'X' and resid 217 through 228 Processing helix chain 'X' and resid 236 through 241 removed outlier: 4.880A pdb=" N GLY X 240 " --> pdb=" O ALA X 237 " (cutoff:3.500A) Processing helix chain 'X' and resid 255 through 258 No H-bonds generated for 'chain 'X' and resid 255 through 258' Processing helix chain 'X' and resid 261 through 274 removed outlier: 3.672A pdb=" N VAL X 268 " --> pdb=" O THR X 264 " (cutoff:3.500A) removed outlier: 3.595A 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: 3.549A pdb=" N LEU X 321 " --> pdb=" O ASP X 317 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ARG X 324 " --> pdb=" O GLY X 320 " (cutoff:3.500A) Processing helix chain 'X' and resid 342 through 344 No H-bonds generated for 'chain 'X' and resid 342 through 344' Processing helix chain 'X' and resid 349 through 357 removed outlier: 3.654A pdb=" N THR X 354 " --> pdb=" O ALA X 350 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE X 355 " --> pdb=" O PRO X 351 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ALA X 356 " --> pdb=" O ALA X 352 " (cutoff:3.500A) removed outlier: 4.457A 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 419 removed outlier: 4.711A pdb=" N ASP X 415 " --> pdb=" O LYS X 411 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ILE X 416 " --> pdb=" O ASN X 412 " (cutoff:3.500A) Processing helix chain 'X' and resid 422 through 424 No H-bonds generated for 'chain 'X' and resid 422 through 424' Processing helix chain 'X' and resid 427 through 442 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 505 removed outlier: 3.803A pdb=" N LYS X 496 " --> pdb=" O ILE X 492 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS X 501 " --> pdb=" O GLU X 497 " (cutoff:3.500A) Processing helix chain 'X' and resid 527 through 532 removed outlier: 3.647A pdb=" N VAL X 531 " --> pdb=" O LEU X 527 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER X 532 " --> pdb=" O ASP X 528 " (cutoff:3.500A) No H-bonds generated for '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: 4.765A 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 322 removed outlier: 3.560A pdb=" N LEU Y 321 " --> pdb=" O ASP Y 317 " (cutoff:3.500A) Processing helix chain 'Y' and resid 342 through 344 No H-bonds generated for 'chain 'Y' and resid 342 through 344' Processing helix chain 'Y' and resid 349 through 357 removed outlier: 3.672A pdb=" N THR Y 354 " --> pdb=" O ALA Y 350 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ALA Y 356 " --> pdb=" O ALA Y 352 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N HIS Y 357 " --> pdb=" O THR Y 353 " (cutoff:3.500A) Processing helix chain 'Y' and resid 366 through 371 removed outlier: 3.694A pdb=" N LEU Y 371 " --> pdb=" O SER Y 367 " (cutoff:3.500A) 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: 4.226A pdb=" N VAL Y 399 " --> pdb=" O GLU Y 395 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP Y 415 " --> pdb=" O LYS Y 411 " (cutoff:3.500A) removed outlier: 4.751A 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 492 through 506 removed outlier: 3.775A pdb=" N LYS Y 501 " --> pdb=" O GLU Y 497 " (cutoff:3.500A) Processing helix chain 'Y' and resid 527 through 531 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 202 Processing helix chain 'Z' and resid 217 through 230 Processing helix chain 'Z' and resid 236 through 241 removed outlier: 4.635A pdb=" N GLY Z 240 " --> pdb=" O ALA Z 237 " (cutoff:3.500A) Processing helix chain 'Z' and resid 255 through 274 removed outlier: 4.477A pdb=" N ALA Z 262 " --> pdb=" O ARG Z 258 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N LEU Z 263 " --> pdb=" O ALA Z 259 " (cutoff:3.500A) removed outlier: 3.553A 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: 3.859A pdb=" N LEU Z 321 " --> pdb=" O ASP Z 317 " (cutoff:3.500A) Processing helix chain 'Z' and resid 342 through 344 No H-bonds generated for 'chain 'Z' and resid 342 through 344' Processing helix chain 'Z' and resid 349 through 354 Processing helix chain 'Z' and resid 366 through 369 No H-bonds generated for 'chain 'Z' and resid 366 through 369' Processing helix chain 'Z' and resid 394 through 411 removed outlier: 3.816A pdb=" N VAL Z 399 " --> pdb=" O GLU Z 395 " (cutoff:3.500A) Processing helix chain 'Z' and resid 414 through 417 No H-bonds generated for 'chain 'Z' and resid 414 through 417' Processing helix chain 'Z' and resid 427 through 440 removed outlier: 3.501A pdb=" N LYS Z 438 " --> pdb=" O ALA Z 434 " (cutoff:3.500A) Processing helix chain 'Z' and resid 448 through 454 removed outlier: 3.762A pdb=" N GLU Z 451 " --> pdb=" O GLN Z 448 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N VAL Z 452 " --> pdb=" O VAL Z 449 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N THR Z 454 " --> pdb=" O GLU Z 451 " (cutoff:3.500A) Processing helix chain 'Z' and resid 463 through 475 removed outlier: 3.686A pdb=" N GLY Z 472 " --> pdb=" O SER Z 468 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL Z 473 " --> pdb=" O GLY Z 469 " (cutoff:3.500A) Processing helix chain 'Z' and resid 483 through 485 No H-bonds generated for 'chain 'Z' and resid 483 through 485' Processing helix chain 'Z' and resid 496 through 508 removed outlier: 4.177A pdb=" N LYS Z 501 " --> pdb=" O GLU Z 497 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ILE Z 506 " --> pdb=" O MET Z 502 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ALA Z 507 " --> pdb=" O ALA Z 503 " (cutoff:3.500A) Processing helix chain 'Z' and resid 527 through 533 removed outlier: 3.888A pdb=" N SER Z 532 " --> pdb=" O ASP Z 528 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU Z 533 " --> pdb=" O LYS Z 529 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain '2' and resid 368 through 372 removed outlier: 4.457A pdb=" N ILE 2 368 " --> pdb=" O VAL 2 379 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '7' and resid 35 through 41 Processing sheet with id= C, first strand: chain '7' and resid 50 through 52 Processing sheet with id= D, first strand: chain 'P' and resid 188 through 190 removed outlier: 6.235A 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 removed outlier: 3.520A pdb=" N PHE Q 47 " --> pdb=" O TYR Q 63 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'R' and resid 72 through 75 removed outlier: 6.648A pdb=" N THR R 142 " --> pdb=" O ASN R 73 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N TYR R 75 " --> pdb=" O THR R 142 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE R 144 " --> pdb=" O TYR R 75 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'R' and resid 97 through 100 removed outlier: 3.793A pdb=" N THR R 88 " --> pdb=" O HIS R 119 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL R 115 " --> pdb=" O PRO R 92 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'S' and resid 203 through 211 removed outlier: 3.516A pdb=" N LYS S 204 " --> pdb=" O LYS S 196 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ASN S 195 " --> pdb=" O VAL S 105 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ASP S 136 " --> pdb=" O SER S 100 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N VAL S 102 " --> pdb=" O ASP S 136 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N VAL S 138 " --> pdb=" O VAL S 102 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ALA S 104 " --> pdb=" O VAL S 138 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL S 140 " --> pdb=" O ALA S 104 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N SER S 141 " --> pdb=" O GLN S 159 " (cutoff:3.500A) removed outlier: 4.487A 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: 3.772A pdb=" N GLU T 107 " --> pdb=" O ALA T 119 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LYS T 116 " --> pdb=" O PHE T 132 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N GLY T 128 " --> pdb=" O LEU T 120 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N TYR T 98 " --> pdb=" O VAL T 87 " (cutoff:3.500A) removed outlier: 5.458A 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: 3.580A 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: 8.805A pdb=" N ILE T 286 " --> pdb=" O VAL T 255 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N CYS T 257 " --> pdb=" O ILE T 286 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N VAL T 288 " --> pdb=" O CYS T 257 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N TYR T 259 " --> pdb=" O VAL T 288 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N ALA T 290 " --> pdb=" O TYR T 259 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ALA T 261 " --> pdb=" O ALA T 290 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N HIS T 319 " --> pdb=" O TYR T 256 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N VAL T 258 " --> pdb=" O HIS T 319 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N LEU T 321 " --> pdb=" O VAL T 258 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL T 260 " --> pdb=" O LEU T 321 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE T 323 " --> pdb=" O VAL T 260 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL T 262 " --> pdb=" O ILE T 323 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ASP T 325 " --> pdb=" O VAL T 262 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N SER T 376 " --> pdb=" O GLY T 320 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ILE T 322 " --> pdb=" O SER T 376 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N THR T 378 " --> pdb=" O ILE T 322 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N TYR T 324 " --> pdb=" O THR T 378 " (cutoff:3.500A) removed outlier: 6.802A 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: 6.475A pdb=" N ARG U 96 " --> pdb=" O LEU U 88 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N VAL U 90 " --> pdb=" O ILE U 94 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE U 94 " --> pdb=" O VAL U 90 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN U 121 " --> pdb=" O GLY U 128 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL U 130 " --> pdb=" O ALA U 119 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ALA U 119 " --> pdb=" O VAL U 130 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N PHE U 132 " --> pdb=" O GLY U 117 " (cutoff:3.500A) removed outlier: 5.969A 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 removed outlier: 3.992A pdb=" N ASP U 226 " --> pdb=" O LEU U 408 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'U' and resid 285 through 290 removed outlier: 8.848A pdb=" N ILE U 286 " --> pdb=" O VAL U 255 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N CYS U 257 " --> pdb=" O ILE U 286 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N VAL U 288 " --> pdb=" O CYS U 257 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N TYR U 259 " --> pdb=" O VAL U 288 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ALA U 290 " --> pdb=" O TYR U 259 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ALA U 261 " --> pdb=" O ALA U 290 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N HIS U 319 " --> pdb=" O TYR U 256 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N VAL U 258 " --> pdb=" O HIS U 319 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU U 321 " --> pdb=" O VAL U 258 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N VAL U 260 " --> pdb=" O LEU U 321 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ILE U 323 " --> pdb=" O VAL U 260 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL U 262 " --> pdb=" O ILE U 323 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ASP U 325 " --> pdb=" O VAL U 262 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N SER U 376 " --> pdb=" O GLY U 320 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ILE U 322 " --> pdb=" O SER U 376 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N THR U 378 " --> pdb=" O ILE U 322 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N TYR U 324 " --> pdb=" O THR U 378 " (cutoff:3.500A) removed outlier: 6.789A 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 143 through 145 removed outlier: 6.481A pdb=" N ARG V 96 " --> pdb=" O LEU V 88 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N VAL V 90 " --> pdb=" O ILE V 94 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE V 94 " --> pdb=" O VAL V 90 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL V 130 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ALA V 119 " --> pdb=" O VAL V 130 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU V 107 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLN V 149 " --> pdb=" O LEU V 108 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N CYS V 110 " --> pdb=" O THR V 147 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N THR V 147 " --> pdb=" O CYS V 110 " (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: 3.530A 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: 9.005A pdb=" N ILE V 286 " --> pdb=" O VAL V 255 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N CYS V 257 " --> pdb=" O ILE V 286 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N VAL V 288 " --> pdb=" O CYS V 257 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N TYR V 259 " --> pdb=" O VAL V 288 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ALA V 290 " --> pdb=" O TYR V 259 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ALA V 261 " --> pdb=" O ALA V 290 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N HIS V 319 " --> pdb=" O TYR V 256 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N VAL V 258 " --> pdb=" O HIS V 319 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU V 321 " --> pdb=" O VAL V 258 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N VAL V 260 " --> pdb=" O LEU V 321 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE V 323 " --> pdb=" O VAL V 260 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N VAL V 262 " --> pdb=" O ILE V 323 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ASP V 325 " --> pdb=" O VAL V 262 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N SER V 376 " --> pdb=" O GLY V 320 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ILE V 322 " --> pdb=" O SER V 376 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N THR V 378 " --> pdb=" O ILE V 322 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N TYR V 324 " --> pdb=" O THR V 378 " (cutoff:3.500A) removed outlier: 6.868A 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: 6.577A pdb=" N ARG X 86 " --> pdb=" O ALA X 77 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N HIS X 79 " --> pdb=" O THR X 84 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N THR X 84 " --> pdb=" O HIS X 79 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ARG X 51 " --> pdb=" O VAL X 40 " (cutoff:3.500A) removed outlier: 5.665A 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: 7.448A pdb=" N ILE X 179 " --> pdb=" O ILE X 333 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N SER X 335 " --> pdb=" O ILE X 179 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LEU X 181 " --> pdb=" O SER X 335 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLN X 337 " --> pdb=" O LEU X 181 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N GLY X 183 " --> pdb=" O GLN X 337 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N VAL X 339 " --> pdb=" O GLY X 183 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N PHE X 207 " --> pdb=" O LEU X 281 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N PHE X 283 " --> pdb=" O PHE X 207 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL X 209 " --> pdb=" O PHE X 283 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ASP X 285 " --> pdb=" O VAL X 209 " (cutoff:3.500A) removed outlier: 7.230A 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: 6.390A pdb=" N ASP Y 49 " --> pdb=" O SER Y 41 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL Y 43 " --> pdb=" O VAL Y 47 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL Y 47 " --> pdb=" O VAL Y 43 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILE Y 88 " --> pdb=" O VAL Y 76 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N VAL Y 76 " --> pdb=" O ILE Y 88 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LEU Y 72 " --> pdb=" O VAL Y 65 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'Y' and resid 110 through 113 Processing sheet with id= AA, first strand: chain 'Y' and resid 360 through 363 removed outlier: 7.394A pdb=" N ILE Y 179 " --> pdb=" O ILE Y 333 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N SER Y 335 " --> pdb=" O ILE Y 179 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N LEU Y 181 " --> pdb=" O SER Y 335 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N GLN Y 337 " --> pdb=" O LEU Y 181 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N GLY Y 183 " --> pdb=" O GLN Y 337 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N VAL Y 339 " --> pdb=" O GLY Y 183 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N PHE Y 207 " --> pdb=" O LEU Y 281 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N PHE Y 283 " --> pdb=" O PHE Y 207 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL Y 209 " --> pdb=" O PHE Y 283 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ASP Y 285 " --> pdb=" O VAL Y 209 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ALA Y 211 " --> pdb=" O ASP Y 285 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'Z' and resid 38 through 44 removed outlier: 6.374A pdb=" N ASP Z 49 " --> pdb=" O SER Z 41 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N VAL Z 43 " --> pdb=" O VAL Z 47 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL Z 47 " --> pdb=" O VAL Z 43 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ILE Z 88 " --> pdb=" O VAL Z 76 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N VAL Z 76 " --> pdb=" O ILE Z 88 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'Z' and resid 110 through 113 Processing sheet with id= AD, first strand: chain 'Z' and resid 360 through 362 removed outlier: 8.569A pdb=" N ILE Z 179 " --> pdb=" O ILE Z 333 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N SER Z 335 " --> pdb=" O ILE Z 179 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N LEU Z 181 " --> pdb=" O SER Z 335 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLN Z 337 " --> pdb=" O LEU Z 181 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL Z 284 " --> pdb=" O VAL Z 336 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'Z' and resid 559 through 561 2208 hydrogen bonds defined for protein. 6273 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: 16.97 Time building geometry restraints manager: 17.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 11679 1.32 - 1.45: 11563 1.45 - 1.57: 31169 1.57 - 1.69: 21 1.69 - 1.81: 254 Bond restraints: 54686 Sorted by residual: bond pdb=" C4 ATP U1001 " pdb=" C5 ATP U1001 " ideal model delta sigma weight residual 1.388 1.455 -0.067 1.00e-02 1.00e+04 4.56e+01 bond pdb=" C4 ATP V1000 " pdb=" C5 ATP V1000 " ideal model delta sigma weight residual 1.388 1.455 -0.067 1.00e-02 1.00e+04 4.53e+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 4.06e+01 bond pdb=" C5 ATP U1001 " pdb=" N7 ATP U1001 " ideal model delta sigma weight residual 1.387 1.327 0.060 1.00e-02 1.00e+04 3.64e+01 bond pdb=" C4 ATP V1000 " pdb=" N9 ATP V1000 " ideal model delta sigma weight residual 1.374 1.314 0.060 1.00e-02 1.00e+04 3.57e+01 ... (remaining 54681 not shown) Histogram of bond angle deviations from ideal: 95.70 - 103.75: 752 103.75 - 111.81: 25262 111.81 - 119.86: 24264 119.86 - 127.92: 23499 127.92 - 135.98: 384 Bond angle restraints: 74161 Sorted by residual: angle pdb=" PB ATP V1000 " pdb=" O3B ATP V1000 " pdb=" PG ATP V1000 " ideal model delta sigma weight residual 139.87 123.34 16.53 1.00e+00 1.00e+00 2.73e+02 angle pdb=" PB ATP U1001 " pdb=" O3B ATP U1001 " pdb=" PG ATP U1001 " ideal model delta sigma weight residual 139.87 126.36 13.51 1.00e+00 1.00e+00 1.83e+02 angle pdb=" PA ATP T1001 " pdb=" O3A ATP T1001 " pdb=" PB ATP T1001 " ideal model delta sigma weight residual 136.83 123.71 13.12 1.00e+00 1.00e+00 1.72e+02 angle pdb=" PA ATP U1001 " pdb=" O3A ATP U1001 " pdb=" PB ATP U1001 " ideal model delta sigma weight residual 136.83 124.75 12.08 1.00e+00 1.00e+00 1.46e+02 angle pdb=" PA ATP V1000 " pdb=" O3A ATP V1000 " pdb=" PB ATP V1000 " ideal model delta sigma weight residual 136.83 126.28 10.55 1.00e+00 1.00e+00 1.11e+02 ... (remaining 74156 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.43: 32195 32.43 - 64.86: 767 64.86 - 97.29: 60 97.29 - 129.72: 1 129.72 - 162.15: 2 Dihedral angle restraints: 33025 sinusoidal: 12667 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 -122.78 -57.22 0 5.00e+00 4.00e-02 1.31e+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 -123.40 -56.60 0 5.00e+00 4.00e-02 1.28e+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 -124.58 -55.42 0 5.00e+00 4.00e-02 1.23e+02 ... (remaining 33022 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 7203 0.088 - 0.177: 1356 0.177 - 0.265: 115 0.265 - 0.354: 11 0.354 - 0.442: 4 Chirality restraints: 8689 Sorted by residual: 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 -2.19 -0.44 2.00e-01 2.50e+01 4.88e+00 chirality pdb=" CB VAL T 180 " pdb=" CA VAL T 180 " pdb=" CG1 VAL T 180 " pdb=" CG2 VAL T 180 " both_signs ideal model delta sigma weight residual False -2.63 -2.21 -0.42 2.00e-01 2.50e+01 4.40e+00 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 -2.23 -0.40 2.00e-01 2.50e+01 4.00e+00 ... (remaining 8686 not shown) Planarity restraints: 9510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA Y 503 " 0.031 2.00e-02 2.50e+03 5.94e-02 3.52e+01 pdb=" C ALA Y 503 " -0.103 2.00e-02 2.50e+03 pdb=" O ALA Y 503 " 0.038 2.00e-02 2.50e+03 pdb=" N LYS Y 504 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU 5 31 " -0.058 5.00e-02 4.00e+02 8.57e-02 1.17e+01 pdb=" N PRO 5 32 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO 5 32 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO 5 32 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA Z 307 " -0.017 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C ALA Z 307 " 0.058 2.00e-02 2.50e+03 pdb=" O ALA Z 307 " -0.021 2.00e-02 2.50e+03 pdb=" N VAL Z 308 " -0.020 2.00e-02 2.50e+03 ... (remaining 9507 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 281 2.48 - 3.09: 34604 3.09 - 3.69: 85248 3.69 - 4.30: 132294 4.30 - 4.90: 213156 Nonbonded interactions: 465583 Sorted by model distance: nonbonded pdb=" O LYS P 149 " pdb=" N GLU P 151 " model vdw 1.876 2.520 nonbonded pdb=" O LYS Q 56 " pdb=" O ALA Q 57 " model vdw 1.904 3.040 nonbonded pdb=" OG1 THR U 232 " pdb="MG MG U1002 " model vdw 1.990 2.170 nonbonded pdb=" OG1 THR V 232 " pdb="MG MG V1001 " model vdw 1.992 2.170 nonbonded pdb=" OG1 THR T 232 " pdb="MG MG T1002 " model vdw 2.016 2.170 ... (remaining 465578 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 1000 through 1001)) } 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 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: 4.350 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: 0.050 Extract box with map and model: 23.610 Check model and map are aligned: 0.660 Set scattering table: 0.400 Process input model: 114.270 Find NCS groups from input model: 2.790 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 156.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 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 : 0.014 0.143 54686 Z= 0.938 Angle : 1.114 16.530 74161 Z= 0.619 Chirality : 0.069 0.442 8689 Planarity : 0.008 0.086 9510 Dihedral : 14.327 162.148 19939 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.75 % Favored : 95.01 % Rotamer: Outliers : 0.69 % Allowed : 6.70 % Favored : 92.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -5.13 (0.07), residues: 7038 helix: -4.32 (0.04), residues: 3851 sheet: -1.38 (0.19), residues: 657 loop : -1.98 (0.11), residues: 2530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP R 37 HIS 0.017 0.003 HIS Y 79 PHE 0.042 0.003 PHE R 74 TYR 0.027 0.003 TYR 4 211 ARG 0.019 0.001 ARG 3 242 *********************** 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 865 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 826 time to evaluate : 4.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 41 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7017 (pm20) REVERT: 0 46 GLU cc_start: 0.8527 (tt0) cc_final: 0.8297 (tt0) REVERT: 1 143 LYS cc_start: 0.8248 (mtmm) cc_final: 0.7969 (mttm) REVERT: 1 181 LYS cc_start: 0.8058 (mmtp) cc_final: 0.7735 (tppt) REVERT: 1 572 ASP cc_start: 0.8219 (m-30) cc_final: 0.7848 (m-30) REVERT: 4 13 TYR cc_start: 0.9062 (OUTLIER) cc_final: 0.8738 (m-80) REVERT: 4 194 ASP cc_start: 0.8059 (m-30) cc_final: 0.7858 (m-30) REVERT: 4 198 LYS cc_start: 0.8773 (mptt) cc_final: 0.8434 (mmmt) REVERT: 4 214 ASP cc_start: 0.8032 (m-30) cc_final: 0.7800 (m-30) REVERT: 5 11 GLU cc_start: 0.8335 (mt-10) cc_final: 0.8068 (mt-10) REVERT: 7 135 ASP cc_start: 0.8300 (m-30) cc_final: 0.8063 (m-30) REVERT: 9 9 LYS cc_start: 0.8244 (mtmm) cc_final: 0.7556 (tttm) REVERT: 9 80 GLN cc_start: 0.8733 (tp40) cc_final: 0.8487 (tp40) REVERT: A 81 MET cc_start: 0.8611 (ttp) cc_final: 0.8364 (ttm) REVERT: A 119 LEU cc_start: 0.7606 (mp) cc_final: 0.7396 (tt) REVERT: B 84 SER cc_start: 0.8238 (m) cc_final: 0.7975 (p) REVERT: F 81 MET cc_start: 0.8337 (ttp) cc_final: 0.8118 (ttp) REVERT: G 81 MET cc_start: 0.7898 (ttp) cc_final: 0.7630 (ttp) REVERT: G 115 LEU cc_start: 0.6953 (pp) cc_final: 0.6630 (mt) REVERT: J 81 MET cc_start: 0.8576 (ttp) cc_final: 0.7962 (ttp) REVERT: J 84 SER cc_start: 0.8359 (m) cc_final: 0.7774 (p) REVERT: P 145 MET cc_start: 0.8649 (mmm) cc_final: 0.8299 (mmm) REVERT: Q 18 ARG cc_start: 0.8442 (ttm-80) cc_final: 0.8179 (tpp80) REVERT: Q 40 GLN cc_start: 0.7945 (tp-100) cc_final: 0.7660 (tp-100) REVERT: Q 48 ARG cc_start: 0.7845 (ptt180) cc_final: 0.7611 (ptt-90) REVERT: Q 49 GLN cc_start: 0.8339 (pt0) cc_final: 0.8092 (pt0) REVERT: Q 52 TYR cc_start: 0.6425 (m-80) cc_final: 0.6103 (m-10) REVERT: R 126 LYS cc_start: 0.7905 (mttm) cc_final: 0.7683 (mttp) REVERT: R 127 PHE cc_start: 0.8067 (m-80) cc_final: 0.7673 (m-80) REVERT: S 62 MET cc_start: 0.7379 (ptp) cc_final: 0.7006 (ptt) REVERT: S 186 ASN cc_start: 0.8074 (p0) cc_final: 0.7739 (p0) REVERT: S 206 THR cc_start: 0.8207 (m) cc_final: 0.7945 (p) REVERT: S 218 LYS cc_start: 0.7469 (tmtt) cc_final: 0.7245 (tptp) REVERT: S 229 ASP cc_start: 0.7304 (m-30) cc_final: 0.6927 (m-30) REVERT: S 234 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7959 (tm-30) REVERT: S 244 ARG cc_start: 0.8097 (tpp-160) cc_final: 0.7742 (ttp-110) REVERT: T 101 LYS cc_start: 0.8208 (tptt) cc_final: 0.7969 (mmmt) REVERT: T 199 ARG cc_start: 0.7616 (mmm160) cc_final: 0.7220 (ptp90) REVERT: T 487 LYS cc_start: 0.8290 (mtpp) cc_final: 0.7668 (ttmt) REVERT: T 496 ARG cc_start: 0.8088 (mtt-85) cc_final: 0.7678 (mtt90) REVERT: T 556 LYS cc_start: 0.7622 (mtmt) cc_final: 0.7339 (mtmm) REVERT: U 71 LYS cc_start: 0.8492 (tppt) cc_final: 0.8145 (tppp) REVERT: U 75 LYS cc_start: 0.8298 (mtmt) cc_final: 0.8017 (mmpt) REVERT: U 96 ARG cc_start: 0.8102 (mtp-110) cc_final: 0.7902 (mtm-85) REVERT: U 149 GLN cc_start: 0.7857 (mt0) cc_final: 0.7345 (mm110) REVERT: U 200 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7610 (mt-10) REVERT: U 326 ASP cc_start: 0.7990 (m-30) cc_final: 0.7600 (m-30) REVERT: U 474 LEU cc_start: 0.8207 (mp) cc_final: 0.7961 (mm) REVERT: U 511 LYS cc_start: 0.8152 (mmmm) cc_final: 0.7905 (mmpt) REVERT: U 550 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8277 (tm) REVERT: V 50 LYS cc_start: 0.8477 (ttmt) cc_final: 0.7971 (tmmt) REVERT: V 61 HIS cc_start: 0.8042 (t70) cc_final: 0.7497 (m170) REVERT: V 283 ARG cc_start: 0.8009 (ptm-80) cc_final: 0.7582 (ttt90) REVERT: V 515 GLN cc_start: 0.7190 (pp30) cc_final: 0.6882 (tm130) REVERT: V 534 LYS cc_start: 0.8500 (mtpt) cc_final: 0.8282 (mtpm) REVERT: X 131 GLU cc_start: 0.8277 (mt-10) cc_final: 0.8061 (mt-10) REVERT: X 215 GLU cc_start: 0.7444 (mm-30) cc_final: 0.6930 (mm-30) REVERT: X 227 MET cc_start: 0.8172 (mtt) cc_final: 0.7970 (mtt) REVERT: X 415 ASP cc_start: 0.8151 (t70) cc_final: 0.7888 (t0) REVERT: X 448 GLN cc_start: 0.7837 (mt0) cc_final: 0.7533 (mp10) REVERT: X 550 LYS cc_start: 0.8046 (ptpp) cc_final: 0.7450 (pptt) REVERT: X 573 LYS cc_start: 0.7732 (mtmt) cc_final: 0.7414 (mmmt) REVERT: Y 251 MET cc_start: 0.8762 (mtm) cc_final: 0.8513 (mtt) REVERT: Y 359 ASP cc_start: 0.8069 (m-30) cc_final: 0.7790 (m-30) REVERT: Y 427 GLU cc_start: 0.6094 (mt-10) cc_final: 0.5857 (mp0) REVERT: Y 437 ARG cc_start: 0.7458 (mtt-85) cc_final: 0.7024 (mtp85) REVERT: Y 441 ARG cc_start: 0.7847 (mmt-90) cc_final: 0.7516 (mmt90) REVERT: Y 497 GLU cc_start: 0.6766 (mt-10) cc_final: 0.6484 (mt-10) REVERT: Y 539 ILE cc_start: 0.7089 (pt) cc_final: 0.6759 (mt) REVERT: Y 547 GLU cc_start: 0.7191 (mp0) cc_final: 0.6967 (mp0) REVERT: Z 88 ILE cc_start: 0.9060 (tp) cc_final: 0.8774 (tp) REVERT: Z 292 GLN cc_start: 0.7917 (tt0) cc_final: 0.7582 (tt0) REVERT: Z 411 LYS cc_start: 0.8741 (mttp) cc_final: 0.8187 (tmmt) REVERT: Z 427 GLU cc_start: 0.7395 (tp30) cc_final: 0.7115 (pp20) REVERT: Z 441 ARG cc_start: 0.7557 (mmt-90) cc_final: 0.7167 (mmt-90) REVERT: Z 484 MET cc_start: 0.6921 (mmm) cc_final: 0.6370 (tmt) REVERT: Z 566 LYS cc_start: 0.8257 (tttm) cc_final: 0.7908 (tptp) outliers start: 39 outliers final: 21 residues processed: 855 average time/residue: 1.4550 time to fit residues: 1545.6825 Evaluate side-chains 611 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 588 time to evaluate : 4.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 3 residue 259 ASP Chi-restraints excluded: chain 3 residue 316 VAL Chi-restraints excluded: chain 4 residue 13 TYR Chi-restraints excluded: chain 5 residue 32 PRO Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain T residue 144 VAL Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 427 VAL Chi-restraints excluded: chain U residue 550 LEU Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 406 VAL Chi-restraints excluded: chain Y residue 452 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 589 optimal weight: 6.9990 chunk 529 optimal weight: 7.9990 chunk 293 optimal weight: 0.8980 chunk 180 optimal weight: 0.9990 chunk 356 optimal weight: 0.9990 chunk 282 optimal weight: 0.0030 chunk 547 optimal weight: 0.9990 chunk 211 optimal weight: 0.9990 chunk 332 optimal weight: 0.9990 chunk 407 optimal weight: 0.9990 chunk 633 optimal weight: 0.8980 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 44 ASN 1 100 GLN 1 257 HIS 1 285 GLN 1 298 GLN 1 316 ASN 1 346 GLN ** 1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 527 GLN 1 562 ASN 1 587 ASN 1 590 HIS 2 74 ASN 2 122 ASN 2 243 GLN 2 289 HIS ** 2 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 179 GLN 3 206 ASN 3 229 ASN 3 269 GLN 4 240 GLN 5 29 GLN 5 107 ASN 6 40 ASN 6 74 GLN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 86 HIS 7 98 ASN 7 123 HIS 7 170 HIS 7 184 ASN 8 26 HIS 8 78 HIS 9 35 GLN A 94 ASN B 98 GLN C 98 GLN D 98 GLN G 87 ASN G 94 ASN H 94 ASN M 108 ASN M 131 ASN M 163 ASN P 223 ASN Q 46 HIS R 38 ASN R 73 ASN R 104 HIS R 137 HIS ** R 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 181 ASN S 96 ASN ** S 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 188 GLN T 64 GLN T 104 GLN T 241 HIS T 264 GLN T 386 GLN T 405 GLN T 435 GLN ** T 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 539 ASN U 61 HIS U 121 ASN U 196 GLN U 246 ASN U 248 GLN U 319 HIS U 386 GLN ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 539 ASN U 549 HIS ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 139 HIS V 152 ASN V 244 ASN V 264 GLN V 278 GLN V 441 GLN ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 488 GLN V 497 GLN V 529 ASN X 199 ASN X 278 GLN X 311 GLN X 337 GLN X 398 ASN X 408 GLN ** X 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 574 ASN Y 174 GLN Y 241 ASN Y 398 ASN Y 448 GLN Z 144 HIS Z 199 ASN Z 241 ASN Z 278 GLN ** Z 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 294 ASN Z 337 GLN Z 574 ASN Total number of N/Q/H flips: 95 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 54686 Z= 0.195 Angle : 0.588 10.176 74161 Z= 0.306 Chirality : 0.042 0.160 8689 Planarity : 0.005 0.062 9510 Dihedral : 7.353 152.443 7700 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.05 % Favored : 96.76 % Rotamer: Outliers : 2.42 % Allowed : 12.06 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.09), residues: 7038 helix: -2.24 (0.07), residues: 3815 sheet: -1.12 (0.20), residues: 639 loop : -1.36 (0.11), residues: 2584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP 4 206 HIS 0.017 0.001 HIS 8 78 PHE 0.023 0.001 PHE H 107 TYR 0.024 0.001 TYR 4 211 ARG 0.011 0.000 ARG P 167 *********************** 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 851 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 715 time to evaluate : 4.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 41 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7025 (pm20) REVERT: 0 46 GLU cc_start: 0.8444 (tt0) cc_final: 0.8193 (tt0) REVERT: 1 143 LYS cc_start: 0.8078 (mtmm) cc_final: 0.7820 (mttm) REVERT: 1 181 LYS cc_start: 0.8026 (mmtp) cc_final: 0.7632 (tppt) REVERT: 1 352 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7294 (mm-30) REVERT: 1 496 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7750 (mt-10) REVERT: 1 572 ASP cc_start: 0.8139 (m-30) cc_final: 0.7800 (m-30) REVERT: 2 13 LYS cc_start: 0.7717 (mtpm) cc_final: 0.7336 (ptmm) REVERT: 2 31 ASP cc_start: 0.7531 (m-30) cc_final: 0.7290 (m-30) REVERT: 3 274 TYR cc_start: 0.8480 (m-80) cc_final: 0.8259 (m-80) REVERT: 4 13 TYR cc_start: 0.9070 (OUTLIER) cc_final: 0.8591 (m-80) REVERT: 4 156 ASP cc_start: 0.7029 (t70) cc_final: 0.6798 (t0) REVERT: 4 198 LYS cc_start: 0.8739 (mptt) cc_final: 0.8458 (mmmt) REVERT: 4 255 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.7799 (ttp80) REVERT: 5 11 GLU cc_start: 0.8277 (mt-10) cc_final: 0.8038 (mt-10) REVERT: 9 9 LYS cc_start: 0.8040 (mtmm) cc_final: 0.7401 (tttm) REVERT: 9 80 GLN cc_start: 0.8681 (tp40) cc_final: 0.8427 (tp40) REVERT: E 60 LYS cc_start: 0.7942 (mtmt) cc_final: 0.7719 (mttm) REVERT: E 115 LEU cc_start: 0.7136 (pp) cc_final: 0.6778 (mm) REVERT: G 95 ILE cc_start: 0.7993 (mm) cc_final: 0.7763 (mm) REVERT: H 61 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.8005 (mpp) REVERT: H 109 LEU cc_start: 0.7852 (mm) cc_final: 0.7620 (mt) REVERT: J 81 MET cc_start: 0.8131 (ttp) cc_final: 0.7660 (ttm) REVERT: M 232 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.7111 (mtp180) REVERT: P 99 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7835 (tp) REVERT: P 143 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7595 (mm-30) REVERT: P 145 MET cc_start: 0.8547 (mmm) cc_final: 0.8300 (mmm) REVERT: P 151 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7135 (tm-30) REVERT: P 175 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7202 (tm-30) REVERT: Q 18 ARG cc_start: 0.8391 (ttm-80) cc_final: 0.8179 (tpp80) REVERT: Q 40 GLN cc_start: 0.7819 (tp-100) cc_final: 0.7438 (tp-100) REVERT: Q 49 GLN cc_start: 0.8111 (pt0) cc_final: 0.7816 (pt0) REVERT: Q 52 TYR cc_start: 0.6443 (m-80) cc_final: 0.5769 (m-10) REVERT: R 86 LYS cc_start: 0.7566 (mptp) cc_final: 0.7361 (mmtm) REVERT: R 127 PHE cc_start: 0.7984 (m-80) cc_final: 0.7627 (m-80) REVERT: S 48 ARG cc_start: 0.6948 (tpp-160) cc_final: 0.6272 (ttm110) REVERT: S 62 MET cc_start: 0.7363 (ptp) cc_final: 0.7096 (mtp) REVERT: S 96 ASN cc_start: 0.6863 (OUTLIER) cc_final: 0.6332 (p0) REVERT: S 169 ARG cc_start: 0.7865 (ptm160) cc_final: 0.7441 (ptm160) REVERT: S 206 THR cc_start: 0.7919 (m) cc_final: 0.7576 (p) REVERT: S 229 ASP cc_start: 0.7429 (m-30) cc_final: 0.7016 (m-30) REVERT: S 234 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7735 (tm-30) REVERT: S 244 ARG cc_start: 0.8023 (tpp-160) cc_final: 0.7548 (ttp-110) REVERT: T 72 GLU cc_start: 0.6992 (tp30) cc_final: 0.6775 (tp30) REVERT: T 199 ARG cc_start: 0.7596 (mmm160) cc_final: 0.7258 (ptp90) REVERT: T 237 ASP cc_start: 0.7595 (m-30) cc_final: 0.7287 (m-30) REVERT: T 479 ARG cc_start: 0.7191 (mmt180) cc_final: 0.6988 (mmt180) REVERT: T 487 LYS cc_start: 0.8210 (mtpp) cc_final: 0.7640 (ttmt) REVERT: T 496 ARG cc_start: 0.7589 (mtt-85) cc_final: 0.7282 (mtt90) REVERT: T 509 LEU cc_start: 0.8150 (mp) cc_final: 0.7947 (mm) REVERT: T 551 LYS cc_start: 0.7816 (ptpp) cc_final: 0.7246 (pttp) REVERT: T 553 GLU cc_start: 0.7595 (tp30) cc_final: 0.7359 (tp30) REVERT: T 556 LYS cc_start: 0.7420 (mtmt) cc_final: 0.7175 (mtmm) REVERT: U 71 LYS cc_start: 0.8482 (tppt) cc_final: 0.8128 (tppp) REVERT: U 75 LYS cc_start: 0.8140 (mtmt) cc_final: 0.7919 (mmpt) REVERT: U 96 ARG cc_start: 0.8096 (mtp-110) cc_final: 0.7770 (mtp-110) REVERT: U 149 GLN cc_start: 0.7719 (mt0) cc_final: 0.7255 (mm110) REVERT: U 371 GLU cc_start: 0.7765 (pm20) cc_final: 0.7495 (pm20) REVERT: U 427 VAL cc_start: 0.8247 (OUTLIER) cc_final: 0.8025 (m) REVERT: U 502 TYR cc_start: 0.8151 (t80) cc_final: 0.7904 (t80) REVERT: U 511 LYS cc_start: 0.7943 (mmmm) cc_final: 0.7708 (mmpt) REVERT: V 50 LYS cc_start: 0.8344 (ttmt) cc_final: 0.7868 (tmmt) REVERT: V 61 HIS cc_start: 0.8019 (t70) cc_final: 0.7677 (m-70) REVERT: V 278 GLN cc_start: 0.7895 (mt0) cc_final: 0.7530 (mm-40) REVERT: V 283 ARG cc_start: 0.7859 (ptm-80) cc_final: 0.7472 (ttt90) REVERT: V 475 GLU cc_start: 0.6442 (OUTLIER) cc_final: 0.6236 (pp20) REVERT: V 539 ASN cc_start: 0.8727 (m-40) cc_final: 0.8477 (m-40) REVERT: X 131 GLU cc_start: 0.8224 (mt-10) cc_final: 0.8002 (mt-10) REVERT: X 359 ASP cc_start: 0.7849 (m-30) cc_final: 0.7551 (m-30) REVERT: X 385 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.7138 (tpt90) REVERT: X 493 LYS cc_start: 0.8093 (ttpt) cc_final: 0.7721 (ttmm) REVERT: X 550 LYS cc_start: 0.8105 (ptpp) cc_final: 0.7565 (pptt) REVERT: Y 359 ASP cc_start: 0.7746 (m-30) cc_final: 0.7494 (m-30) REVERT: Y 411 LYS cc_start: 0.8170 (mtpp) cc_final: 0.7963 (ttpt) REVERT: Y 437 ARG cc_start: 0.6863 (mtt-85) cc_final: 0.6357 (mmm-85) REVERT: Y 441 ARG cc_start: 0.7397 (mmt-90) cc_final: 0.7111 (mmt90) REVERT: Y 484 MET cc_start: 0.7489 (mmt) cc_final: 0.7273 (tpt) REVERT: Y 497 GLU cc_start: 0.6642 (mt-10) cc_final: 0.6254 (tt0) REVERT: Y 539 ILE cc_start: 0.7210 (pt) cc_final: 0.6955 (mt) REVERT: Z 88 ILE cc_start: 0.8991 (tp) cc_final: 0.8744 (pt) REVERT: Z 292 GLN cc_start: 0.7699 (tt0) cc_final: 0.7289 (tt0) REVERT: Z 359 ASP cc_start: 0.7500 (m-30) cc_final: 0.7075 (m-30) REVERT: Z 404 GLN cc_start: 0.8775 (mt0) cc_final: 0.8567 (mt0) REVERT: Z 411 LYS cc_start: 0.8373 (mttp) cc_final: 0.8116 (tmmt) REVERT: Z 427 GLU cc_start: 0.7522 (tp30) cc_final: 0.7160 (pp20) REVERT: Z 435 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7533 (mtt90) REVERT: Z 437 ARG cc_start: 0.7843 (mtp85) cc_final: 0.7608 (mmm160) REVERT: Z 484 MET cc_start: 0.6706 (mmm) cc_final: 0.6490 (tmt) REVERT: Z 566 LYS cc_start: 0.8253 (tttm) cc_final: 0.7992 (mppt) outliers start: 136 outliers final: 44 residues processed: 807 average time/residue: 1.3565 time to fit residues: 1379.1915 Evaluate side-chains 668 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 613 time to evaluate : 4.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 499 GLU Chi-restraints excluded: chain 2 residue 128 VAL Chi-restraints excluded: chain 2 residue 168 THR Chi-restraints excluded: chain 3 residue 156 ASP Chi-restraints excluded: chain 3 residue 316 VAL Chi-restraints excluded: chain 4 residue 13 TYR Chi-restraints excluded: chain 4 residue 19 ASP Chi-restraints excluded: chain 4 residue 247 SER Chi-restraints excluded: chain 4 residue 255 ARG Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 7 residue 39 VAL Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 9 residue 32 SER Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain H residue 61 MET Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 232 ARG Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 149 LYS Chi-restraints excluded: chain P residue 175 GLU Chi-restraints excluded: chain P residue 205 ARG Chi-restraints excluded: chain S residue 96 ASN Chi-restraints excluded: chain T residue 144 VAL Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 339 LEU Chi-restraints excluded: chain T residue 517 ILE Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 427 VAL Chi-restraints excluded: chain U residue 550 LEU Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 287 MET Chi-restraints excluded: chain V residue 475 GLU Chi-restraints excluded: chain V residue 517 ILE Chi-restraints excluded: chain V residue 529 ASN Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 385 ARG Chi-restraints excluded: chain X residue 480 ASP Chi-restraints excluded: chain X residue 491 ASP Chi-restraints excluded: chain Y residue 414 GLN Chi-restraints excluded: chain Z residue 435 ARG Chi-restraints excluded: chain Z residue 532 SER Chi-restraints excluded: chain Z residue 557 GLU Chi-restraints excluded: chain Z residue 568 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 352 optimal weight: 10.0000 chunk 196 optimal weight: 0.9990 chunk 527 optimal weight: 0.9990 chunk 431 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 635 optimal weight: 10.0000 chunk 685 optimal weight: 4.9990 chunk 565 optimal weight: 0.8980 chunk 629 optimal weight: 0.9990 chunk 216 optimal weight: 6.9990 chunk 509 optimal weight: 2.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 346 GLN ** 1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 482 ASN 2 74 ASN 2 427 GLN 5 59 ASN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 78 HIS 9 27 ASN C 98 GLN D 94 ASN D 98 GLN F 98 GLN ** H 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 185 HIS T 405 GLN ** T 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 539 ASN ** U 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 435 GLN V 471 GLN ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 448 GLN Z 198 ASN Z 398 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 54686 Z= 0.268 Angle : 0.582 13.498 74161 Z= 0.298 Chirality : 0.043 0.173 8689 Planarity : 0.004 0.056 9510 Dihedral : 7.020 143.584 7689 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.71 % Favored : 96.12 % Rotamer: Outliers : 2.52 % Allowed : 14.26 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.75 (0.09), residues: 7038 helix: -1.06 (0.08), residues: 3826 sheet: -1.06 (0.20), residues: 646 loop : -1.04 (0.12), residues: 2566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 9 73 HIS 0.007 0.001 HIS 4 233 PHE 0.025 0.001 PHE H 107 TYR 0.023 0.001 TYR 4 211 ARG 0.011 0.000 ARG P 167 *********************** 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 770 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 628 time to evaluate : 4.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 41 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7048 (pm20) REVERT: 1 39 LYS cc_start: 0.7956 (mmtm) cc_final: 0.7698 (mptp) REVERT: 1 143 LYS cc_start: 0.8051 (mtmm) cc_final: 0.7821 (mttm) REVERT: 1 181 LYS cc_start: 0.8066 (mmtp) cc_final: 0.7688 (tppt) REVERT: 1 352 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7260 (mm-30) REVERT: 1 452 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7772 (tm-30) REVERT: 1 496 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7759 (mt-10) REVERT: 1 572 ASP cc_start: 0.8094 (m-30) cc_final: 0.7778 (m-30) REVERT: 2 226 LYS cc_start: 0.8293 (tptt) cc_final: 0.7945 (tptp) REVERT: 4 13 TYR cc_start: 0.9078 (OUTLIER) cc_final: 0.8651 (m-80) REVERT: 4 198 LYS cc_start: 0.8754 (mptt) cc_final: 0.8470 (mmmt) REVERT: 5 11 GLU cc_start: 0.8279 (mt-10) cc_final: 0.8040 (mt-10) REVERT: 9 13 LYS cc_start: 0.7324 (pttt) cc_final: 0.7108 (pttt) REVERT: E 115 LEU cc_start: 0.7223 (pp) cc_final: 0.6845 (mm) REVERT: J 81 MET cc_start: 0.8254 (ttp) cc_final: 0.7666 (ttp) REVERT: M 232 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.7124 (mtp180) REVERT: M 284 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8677 (mm) REVERT: P 99 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7930 (tp) REVERT: P 143 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7611 (mm-30) REVERT: P 145 MET cc_start: 0.8466 (mmm) cc_final: 0.8215 (mmm) REVERT: P 151 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7357 (tm-30) REVERT: P 169 GLU cc_start: 0.7688 (tp30) cc_final: 0.7397 (tp30) REVERT: P 175 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7204 (tm-30) REVERT: Q 40 GLN cc_start: 0.7831 (tp-100) cc_final: 0.7572 (tp40) REVERT: Q 49 GLN cc_start: 0.8202 (pt0) cc_final: 0.7879 (pt0) REVERT: Q 52 TYR cc_start: 0.6369 (m-80) cc_final: 0.6064 (m-10) REVERT: R 127 PHE cc_start: 0.7877 (m-80) cc_final: 0.7584 (m-80) REVERT: S 48 ARG cc_start: 0.6935 (tpp-160) cc_final: 0.6461 (ttm110) REVERT: S 62 MET cc_start: 0.7300 (ptp) cc_final: 0.7063 (mtp) REVERT: S 217 GLU cc_start: 0.6391 (tp30) cc_final: 0.6094 (tp30) REVERT: S 229 ASP cc_start: 0.7177 (m-30) cc_final: 0.6702 (m-30) REVERT: S 234 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7627 (tm-30) REVERT: S 244 ARG cc_start: 0.7984 (tpp-160) cc_final: 0.7488 (ttp-110) REVERT: T 72 GLU cc_start: 0.7016 (tp30) cc_final: 0.6670 (tp30) REVERT: T 199 ARG cc_start: 0.7624 (mmm160) cc_final: 0.7207 (ptp90) REVERT: T 237 ASP cc_start: 0.7651 (m-30) cc_final: 0.7329 (m-30) REVERT: T 487 LYS cc_start: 0.8217 (mtpp) cc_final: 0.7596 (ttmt) REVERT: T 496 ARG cc_start: 0.7622 (mtt-85) cc_final: 0.7315 (mtt90) REVERT: T 509 LEU cc_start: 0.8177 (mp) cc_final: 0.7973 (mm) REVERT: T 551 LYS cc_start: 0.7790 (ptpp) cc_final: 0.7342 (pttp) REVERT: T 553 GLU cc_start: 0.7550 (tp30) cc_final: 0.7289 (tp30) REVERT: U 45 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7831 (mp) REVERT: U 75 LYS cc_start: 0.8260 (mtmt) cc_final: 0.7967 (mmpt) REVERT: U 96 ARG cc_start: 0.8067 (mtp-110) cc_final: 0.7695 (mtp-110) REVERT: U 149 GLN cc_start: 0.7740 (mt0) cc_final: 0.7267 (mm110) REVERT: U 371 GLU cc_start: 0.7759 (pm20) cc_final: 0.7442 (pm20) REVERT: U 502 TYR cc_start: 0.8073 (t80) cc_final: 0.7850 (t80) REVERT: V 50 LYS cc_start: 0.8336 (ttmt) cc_final: 0.7838 (tmmt) REVERT: V 283 ARG cc_start: 0.7846 (ptm-80) cc_final: 0.7483 (ttt90) REVERT: V 449 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7110 (mt-10) REVERT: V 539 ASN cc_start: 0.8733 (m-40) cc_final: 0.8482 (m-40) REVERT: X 131 GLU cc_start: 0.8295 (mt-10) cc_final: 0.8004 (mt-10) REVERT: X 359 ASP cc_start: 0.7886 (m-30) cc_final: 0.7568 (m-30) REVERT: X 385 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.7211 (tpt90) REVERT: X 493 LYS cc_start: 0.8116 (ttpt) cc_final: 0.7757 (ttmm) REVERT: X 550 LYS cc_start: 0.8099 (ptpp) cc_final: 0.7555 (pptt) REVERT: Y 140 ILE cc_start: 0.8769 (pt) cc_final: 0.8371 (pp) REVERT: Y 359 ASP cc_start: 0.7793 (m-30) cc_final: 0.7548 (m-30) REVERT: Y 414 GLN cc_start: 0.7725 (OUTLIER) cc_final: 0.7464 (mt0) REVERT: Y 437 ARG cc_start: 0.6889 (mtt-85) cc_final: 0.6381 (mmm-85) REVERT: Y 441 ARG cc_start: 0.7573 (mmt-90) cc_final: 0.7346 (mmt90) REVERT: Y 497 GLU cc_start: 0.6636 (mt-10) cc_final: 0.6332 (mt-10) REVERT: Y 539 ILE cc_start: 0.7274 (pt) cc_final: 0.6936 (mm) REVERT: Z 88 ILE cc_start: 0.8993 (tp) cc_final: 0.8781 (pt) REVERT: Z 292 GLN cc_start: 0.7624 (tt0) cc_final: 0.7220 (tt0) REVERT: Z 359 ASP cc_start: 0.7537 (m-30) cc_final: 0.7133 (m-30) REVERT: Z 411 LYS cc_start: 0.8274 (mttp) cc_final: 0.8069 (tmmt) REVERT: Z 427 GLU cc_start: 0.7538 (tp30) cc_final: 0.7183 (pp20) REVERT: Z 566 LYS cc_start: 0.8265 (tttm) cc_final: 0.7971 (mppt) outliers start: 142 outliers final: 64 residues processed: 722 average time/residue: 1.3589 time to fit residues: 1236.3160 Evaluate side-chains 654 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 581 time to evaluate : 4.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 1 residue 193 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 499 GLU Chi-restraints excluded: chain 2 residue 128 VAL Chi-restraints excluded: chain 2 residue 168 THR Chi-restraints excluded: chain 2 residue 440 LYS Chi-restraints excluded: chain 3 residue 156 ASP Chi-restraints excluded: chain 3 residue 316 VAL Chi-restraints excluded: chain 4 residue 13 TYR Chi-restraints excluded: chain 4 residue 19 ASP Chi-restraints excluded: chain 4 residue 247 SER Chi-restraints excluded: chain 5 residue 59 ASN Chi-restraints excluded: chain 5 residue 61 SER Chi-restraints excluded: chain 5 residue 112 ARG Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 7 residue 23 LEU Chi-restraints excluded: chain 7 residue 34 SER Chi-restraints excluded: chain 7 residue 61 VAL Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 92 ASN Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 232 ARG Chi-restraints excluded: chain M residue 284 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 175 GLU Chi-restraints excluded: chain P residue 205 ARG Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain S residue 86 VAL Chi-restraints excluded: chain T residue 144 VAL Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 185 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 339 LEU Chi-restraints excluded: chain U residue 45 LEU Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 152 ASN Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 510 ASP Chi-restraints excluded: chain U residue 516 ASP Chi-restraints excluded: chain U residue 550 LEU Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 287 MET Chi-restraints excluded: chain V residue 449 GLU Chi-restraints excluded: chain V residue 499 VAL Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 385 ARG Chi-restraints excluded: chain X residue 452 VAL Chi-restraints excluded: chain X residue 480 ASP Chi-restraints excluded: chain X residue 491 ASP Chi-restraints excluded: chain X residue 505 ASP Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 325 ILE Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 414 GLN Chi-restraints excluded: chain Z residue 50 VAL Chi-restraints excluded: chain Z residue 337 GLN Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 528 ASP Chi-restraints excluded: chain Z residue 568 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 627 optimal weight: 3.9990 chunk 477 optimal weight: 9.9990 chunk 329 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 303 optimal weight: 0.9980 chunk 426 optimal weight: 0.7980 chunk 637 optimal weight: 5.9990 chunk 674 optimal weight: 0.8980 chunk 332 optimal weight: 0.8980 chunk 603 optimal weight: 3.9990 chunk 181 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 346 GLN ** 1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 74 ASN 5 59 ASN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 78 HIS 9 27 ASN B 98 GLN C 98 GLN D 98 GLN J 92 ASN J 98 GLN ** R 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 435 GLN ** T 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 539 ASN U 152 ASN ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 529 ASN X 574 ASN Y 144 HIS Y 448 GLN Z 286 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2120 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= 0.203 Angle : 0.543 13.432 74161 Z= 0.276 Chirality : 0.041 0.157 8689 Planarity : 0.004 0.058 9510 Dihedral : 6.644 125.332 7688 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.44 % Favored : 96.42 % Rotamer: Outliers : 2.70 % Allowed : 15.13 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.07 (0.10), residues: 7038 helix: -0.42 (0.08), residues: 3835 sheet: -0.90 (0.21), residues: 613 loop : -0.86 (0.12), residues: 2590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 9 73 HIS 0.009 0.001 HIS 8 78 PHE 0.034 0.001 PHE H 107 TYR 0.021 0.001 TYR 4 211 ARG 0.006 0.000 ARG S 124 *********************** 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 769 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 617 time to evaluate : 4.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 41 GLU cc_start: 0.8324 (mt-10) cc_final: 0.7064 (pm20) REVERT: 1 143 LYS cc_start: 0.7914 (mtmm) cc_final: 0.7708 (mttm) REVERT: 1 181 LYS cc_start: 0.8015 (mmtp) cc_final: 0.7614 (tppt) REVERT: 1 216 LEU cc_start: 0.8699 (mm) cc_final: 0.8477 (tt) REVERT: 1 452 GLU cc_start: 0.7946 (tm-30) cc_final: 0.7685 (tm-30) REVERT: 1 572 ASP cc_start: 0.8062 (m-30) cc_final: 0.7759 (m-30) REVERT: 2 226 LYS cc_start: 0.8139 (tptt) cc_final: 0.7772 (tptp) REVERT: 4 13 TYR cc_start: 0.9102 (OUTLIER) cc_final: 0.8587 (m-80) REVERT: 4 198 LYS cc_start: 0.8781 (mptt) cc_final: 0.8472 (mmmt) REVERT: 5 11 GLU cc_start: 0.8279 (mt-10) cc_final: 0.8038 (mt-10) REVERT: 9 13 LYS cc_start: 0.7412 (pttt) cc_final: 0.7104 (pttt) REVERT: E 62 VAL cc_start: 0.8195 (p) cc_final: 0.7964 (p) REVERT: E 115 LEU cc_start: 0.7296 (pp) cc_final: 0.6947 (mm) REVERT: F 95 ILE cc_start: 0.7608 (OUTLIER) cc_final: 0.7222 (mm) REVERT: G 95 ILE cc_start: 0.8100 (mm) cc_final: 0.7782 (mm) REVERT: J 81 MET cc_start: 0.8229 (ttp) cc_final: 0.7615 (ttp) REVERT: M 232 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.7052 (mtp180) REVERT: M 284 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8674 (mm) REVERT: P 99 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7852 (tp) REVERT: P 145 MET cc_start: 0.8464 (mmm) cc_final: 0.8202 (mmm) REVERT: P 151 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7528 (pp20) REVERT: P 169 GLU cc_start: 0.7646 (tp30) cc_final: 0.7349 (tp30) REVERT: P 175 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7258 (tm-30) REVERT: P 186 MET cc_start: 0.5277 (OUTLIER) cc_final: 0.5054 (mmm) REVERT: Q 40 GLN cc_start: 0.7866 (tp-100) cc_final: 0.7581 (tp40) REVERT: Q 49 GLN cc_start: 0.8173 (pt0) cc_final: 0.7882 (pt0) REVERT: Q 52 TYR cc_start: 0.6378 (m-80) cc_final: 0.6037 (m-10) REVERT: R 127 PHE cc_start: 0.7717 (m-80) cc_final: 0.7474 (m-80) REVERT: S 48 ARG cc_start: 0.6767 (tpp-160) cc_final: 0.6389 (ttm110) REVERT: S 62 MET cc_start: 0.7311 (ptp) cc_final: 0.7068 (mtm) REVERT: S 217 GLU cc_start: 0.6228 (tp30) cc_final: 0.5805 (tp30) REVERT: S 229 ASP cc_start: 0.7201 (m-30) cc_final: 0.6756 (m-30) REVERT: S 234 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7666 (tm-30) REVERT: S 244 ARG cc_start: 0.7991 (tpp-160) cc_final: 0.7505 (ttp-110) REVERT: S 283 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.7071 (mm-30) REVERT: T 72 GLU cc_start: 0.7120 (tp30) cc_final: 0.6790 (tp30) REVERT: T 199 ARG cc_start: 0.7615 (mmm160) cc_final: 0.7188 (ptp90) REVERT: T 237 ASP cc_start: 0.7630 (m-30) cc_final: 0.7316 (m-30) REVERT: T 487 LYS cc_start: 0.8226 (mtpp) cc_final: 0.7636 (ttmt) REVERT: T 496 ARG cc_start: 0.7645 (mtt-85) cc_final: 0.7350 (mtt90) REVERT: T 542 ILE cc_start: 0.7722 (OUTLIER) cc_final: 0.7502 (pt) REVERT: T 551 LYS cc_start: 0.7773 (ptpp) cc_final: 0.7141 (pttp) REVERT: T 553 GLU cc_start: 0.7425 (tp30) cc_final: 0.7219 (tp30) REVERT: U 96 ARG cc_start: 0.8036 (mtp-110) cc_final: 0.7697 (mtp-110) REVERT: U 149 GLN cc_start: 0.7665 (mt0) cc_final: 0.7118 (mm110) REVERT: U 371 GLU cc_start: 0.7765 (pm20) cc_final: 0.7449 (pm20) REVERT: U 467 ASP cc_start: 0.7026 (t0) cc_final: 0.6801 (t0) REVERT: U 511 LYS cc_start: 0.7581 (mmpt) cc_final: 0.6963 (mttt) REVERT: V 50 LYS cc_start: 0.8336 (ttmt) cc_final: 0.7831 (tmmt) REVERT: V 283 ARG cc_start: 0.7877 (ptm-80) cc_final: 0.7561 (ttt90) REVERT: V 449 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.7105 (mt-10) REVERT: V 539 ASN cc_start: 0.8722 (m-40) cc_final: 0.8458 (m-40) REVERT: X 131 GLU cc_start: 0.8282 (mt-10) cc_final: 0.8041 (mt-10) REVERT: X 359 ASP cc_start: 0.7876 (m-30) cc_final: 0.7551 (m-30) REVERT: X 493 LYS cc_start: 0.8046 (ttpt) cc_final: 0.7686 (ttmm) REVERT: X 550 LYS cc_start: 0.8082 (ptpp) cc_final: 0.7572 (pptt) REVERT: Y 140 ILE cc_start: 0.8683 (pt) cc_final: 0.8309 (pp) REVERT: Y 359 ASP cc_start: 0.7784 (m-30) cc_final: 0.7515 (m-30) REVERT: Y 385 ARG cc_start: 0.7872 (mmt90) cc_final: 0.7494 (mmm-85) REVERT: Y 414 GLN cc_start: 0.7752 (tt0) cc_final: 0.7472 (mt0) REVERT: Y 437 ARG cc_start: 0.6871 (mtt-85) cc_final: 0.6366 (mmm-85) REVERT: Y 441 ARG cc_start: 0.7394 (mmt-90) cc_final: 0.7125 (mmt90) REVERT: Y 497 GLU cc_start: 0.6609 (mt-10) cc_final: 0.6304 (mt-10) REVERT: Y 501 LYS cc_start: 0.6452 (OUTLIER) cc_final: 0.6247 (tmmm) REVERT: Y 533 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7290 (pm20) REVERT: Y 539 ILE cc_start: 0.7256 (pt) cc_final: 0.6974 (mm) REVERT: Z 88 ILE cc_start: 0.8962 (tp) cc_final: 0.8753 (pt) REVERT: Z 292 GLN cc_start: 0.7588 (tt0) cc_final: 0.7174 (tt0) REVERT: Z 359 ASP cc_start: 0.7553 (m-30) cc_final: 0.7114 (m-30) REVERT: Z 411 LYS cc_start: 0.8300 (mttp) cc_final: 0.8066 (tmmt) REVERT: Z 427 GLU cc_start: 0.7476 (tp30) cc_final: 0.7181 (pp20) REVERT: Z 566 LYS cc_start: 0.8238 (tttm) cc_final: 0.7986 (mppt) outliers start: 152 outliers final: 72 residues processed: 715 average time/residue: 1.3547 time to fit residues: 1224.9386 Evaluate side-chains 658 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 574 time to evaluate : 4.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 1 residue 193 VAL Chi-restraints excluded: chain 1 residue 226 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 499 GLU Chi-restraints excluded: chain 2 residue 128 VAL Chi-restraints excluded: chain 2 residue 168 THR Chi-restraints excluded: chain 2 residue 440 LYS Chi-restraints excluded: chain 3 residue 156 ASP Chi-restraints excluded: chain 3 residue 297 LEU Chi-restraints excluded: chain 3 residue 316 VAL Chi-restraints excluded: chain 4 residue 13 TYR Chi-restraints excluded: chain 4 residue 19 ASP Chi-restraints excluded: chain 5 residue 59 ASN Chi-restraints excluded: chain 5 residue 61 SER Chi-restraints excluded: chain 5 residue 83 THR Chi-restraints excluded: chain 5 residue 112 ARG Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 7 residue 23 LEU Chi-restraints excluded: chain 7 residue 34 SER Chi-restraints excluded: chain 7 residue 61 VAL Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 6 VAL Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 232 ARG Chi-restraints excluded: chain M residue 284 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 157 ILE Chi-restraints excluded: chain P residue 175 GLU Chi-restraints excluded: chain P residue 186 MET Chi-restraints excluded: chain P residue 205 ARG Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain S residue 185 HIS Chi-restraints excluded: chain S residue 283 GLU Chi-restraints excluded: chain T residue 144 VAL Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 185 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 339 LEU Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 152 ASN Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain U residue 510 ASP Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 516 ASP Chi-restraints excluded: chain U residue 550 LEU Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 287 MET Chi-restraints excluded: chain V residue 449 GLU Chi-restraints excluded: chain V residue 529 ASN Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 74 LEU Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 297 VAL Chi-restraints excluded: chain X residue 354 THR Chi-restraints excluded: chain X residue 452 VAL Chi-restraints excluded: chain X residue 480 ASP Chi-restraints excluded: chain X residue 505 ASP Chi-restraints excluded: chain Y residue 193 ILE Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 325 ILE Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 501 LYS Chi-restraints excluded: chain Y residue 533 GLU Chi-restraints excluded: chain Z residue 50 VAL Chi-restraints excluded: chain Z residue 337 GLN Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 431 LEU Chi-restraints excluded: chain Z residue 528 ASP Chi-restraints excluded: chain Z residue 568 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 561 optimal weight: 0.6980 chunk 382 optimal weight: 0.8980 chunk 9 optimal weight: 6.9990 chunk 502 optimal weight: 0.4980 chunk 278 optimal weight: 9.9990 chunk 575 optimal weight: 4.9990 chunk 466 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 344 optimal weight: 0.9990 chunk 605 optimal weight: 5.9990 chunk 170 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 346 GLN ** 1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 74 ASN 4 135 ASN 5 59 ASN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 78 HIS 9 27 ASN D 98 GLN F 98 GLN ** H 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 92 ASN ** Q 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 174 GLN ** T 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 539 ASN U 152 ASN ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 61 HIS ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 448 GLN Z 132 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 54686 Z= 0.181 Angle : 0.528 15.601 74161 Z= 0.268 Chirality : 0.041 0.172 8689 Planarity : 0.004 0.076 9510 Dihedral : 6.341 105.086 7688 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.55 % Favored : 96.31 % Rotamer: Outliers : 2.84 % Allowed : 15.98 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.58 (0.10), residues: 7038 helix: 0.03 (0.09), residues: 3835 sheet: -0.81 (0.21), residues: 610 loop : -0.70 (0.12), residues: 2593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 9 73 HIS 0.006 0.001 HIS 8 78 PHE 0.024 0.001 PHE H 107 TYR 0.021 0.001 TYR 9 14 ARG 0.009 0.000 ARG X 441 *********************** 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 773 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 613 time to evaluate : 4.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 41 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7066 (pm20) REVERT: 1 118 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7996 (ttp-170) REVERT: 1 181 LYS cc_start: 0.7992 (mmtp) cc_final: 0.7590 (tppt) REVERT: 1 216 LEU cc_start: 0.8760 (mm) cc_final: 0.8548 (tt) REVERT: 1 452 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7698 (tm-30) REVERT: 1 572 ASP cc_start: 0.8089 (m-30) cc_final: 0.7794 (m-30) REVERT: 2 197 LEU cc_start: 0.8503 (tp) cc_final: 0.8267 (mt) REVERT: 2 226 LYS cc_start: 0.8038 (tptt) cc_final: 0.7637 (tptp) REVERT: 2 394 LYS cc_start: 0.8362 (ttpt) cc_final: 0.7777 (ttpt) REVERT: 4 13 TYR cc_start: 0.9089 (OUTLIER) cc_final: 0.8498 (m-80) REVERT: 4 198 LYS cc_start: 0.8782 (mptt) cc_final: 0.8476 (mmmt) REVERT: 5 11 GLU cc_start: 0.8271 (mt-10) cc_final: 0.8048 (mt-10) REVERT: 6 79 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8612 (mt) REVERT: 8 9 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8334 (ttpt) REVERT: B 92 ASN cc_start: 0.7582 (p0) cc_final: 0.7137 (p0) REVERT: C 97 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.8090 (mmpt) REVERT: E 60 LYS cc_start: 0.7656 (OUTLIER) cc_final: 0.7354 (tptm) REVERT: E 115 LEU cc_start: 0.7214 (pp) cc_final: 0.6947 (mm) REVERT: F 95 ILE cc_start: 0.7767 (OUTLIER) cc_final: 0.7563 (mm) REVERT: G 95 ILE cc_start: 0.8105 (mm) cc_final: 0.7821 (mm) REVERT: I 61 MET cc_start: 0.7360 (OUTLIER) cc_final: 0.6092 (mpt) REVERT: J 81 MET cc_start: 0.8222 (ttp) cc_final: 0.7604 (ttp) REVERT: M 284 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8655 (mm) REVERT: P 99 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7836 (tp) REVERT: P 145 MET cc_start: 0.8412 (mmm) cc_final: 0.8141 (mmm) REVERT: P 151 GLU cc_start: 0.7814 (tm-30) cc_final: 0.7541 (pp20) REVERT: P 169 GLU cc_start: 0.7664 (tp30) cc_final: 0.7386 (tp30) REVERT: P 175 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7205 (tm-30) REVERT: Q 40 GLN cc_start: 0.7850 (tp-100) cc_final: 0.7592 (tp40) REVERT: Q 49 GLN cc_start: 0.8157 (pt0) cc_final: 0.7875 (pt0) REVERT: Q 52 TYR cc_start: 0.6404 (m-80) cc_final: 0.6068 (m-10) REVERT: R 127 PHE cc_start: 0.7617 (m-80) cc_final: 0.7404 (m-80) REVERT: S 62 MET cc_start: 0.7268 (ptp) cc_final: 0.7010 (mtp) REVERT: S 217 GLU cc_start: 0.6447 (tp30) cc_final: 0.6033 (tp30) REVERT: S 229 ASP cc_start: 0.7258 (m-30) cc_final: 0.6820 (m-30) REVERT: S 244 ARG cc_start: 0.7979 (tpp-160) cc_final: 0.7598 (ttp-110) REVERT: S 283 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.7049 (mm-30) REVERT: T 72 GLU cc_start: 0.7158 (tp30) cc_final: 0.6809 (tp30) REVERT: T 199 ARG cc_start: 0.7603 (mmm160) cc_final: 0.7173 (ptp90) REVERT: T 237 ASP cc_start: 0.7632 (m-30) cc_final: 0.7318 (m-30) REVERT: T 487 LYS cc_start: 0.8212 (mtpp) cc_final: 0.7635 (ttmt) REVERT: T 542 ILE cc_start: 0.7731 (OUTLIER) cc_final: 0.7508 (pt) REVERT: T 551 LYS cc_start: 0.7774 (ptpp) cc_final: 0.7151 (pttp) REVERT: T 553 GLU cc_start: 0.7394 (tp30) cc_final: 0.7161 (tp30) REVERT: U 96 ARG cc_start: 0.8015 (mtp-110) cc_final: 0.7764 (mtm-85) REVERT: U 149 GLN cc_start: 0.7742 (mt0) cc_final: 0.7136 (mm110) REVERT: U 371 GLU cc_start: 0.7763 (pm20) cc_final: 0.7542 (pm20) REVERT: U 553 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7692 (mm-30) REVERT: V 50 LYS cc_start: 0.8337 (ttmt) cc_final: 0.7812 (tmmt) REVERT: V 283 ARG cc_start: 0.7882 (ptm-80) cc_final: 0.7568 (ttt90) REVERT: V 515 GLN cc_start: 0.7334 (tm130) cc_final: 0.7108 (pt0) REVERT: V 534 LYS cc_start: 0.8484 (mtpm) cc_final: 0.8254 (mtpp) REVERT: X 131 GLU cc_start: 0.8285 (mt-10) cc_final: 0.8045 (mt-10) REVERT: X 359 ASP cc_start: 0.7856 (m-30) cc_final: 0.7538 (m-30) REVERT: X 493 LYS cc_start: 0.8019 (ttpt) cc_final: 0.7657 (ttmm) REVERT: X 550 LYS cc_start: 0.8089 (ptpp) cc_final: 0.7566 (pptt) REVERT: Y 140 ILE cc_start: 0.8621 (pt) cc_final: 0.8246 (pp) REVERT: Y 359 ASP cc_start: 0.7780 (m-30) cc_final: 0.7495 (m-30) REVERT: Y 385 ARG cc_start: 0.7892 (mmt90) cc_final: 0.7499 (mmm-85) REVERT: Y 414 GLN cc_start: 0.7739 (OUTLIER) cc_final: 0.7463 (mt0) REVERT: Y 437 ARG cc_start: 0.6868 (mtt-85) cc_final: 0.6313 (mmm-85) REVERT: Y 441 ARG cc_start: 0.7354 (mmt-90) cc_final: 0.7090 (mmt90) REVERT: Y 497 GLU cc_start: 0.6619 (mt-10) cc_final: 0.6293 (mt-10) REVERT: Y 501 LYS cc_start: 0.6474 (OUTLIER) cc_final: 0.6256 (tmmm) REVERT: Y 533 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7272 (pm20) REVERT: Y 539 ILE cc_start: 0.7223 (pt) cc_final: 0.6992 (mm) REVERT: Z 292 GLN cc_start: 0.7543 (tt0) cc_final: 0.7167 (tt0) REVERT: Z 359 ASP cc_start: 0.7499 (m-30) cc_final: 0.7160 (m-30) REVERT: Z 411 LYS cc_start: 0.8313 (mttp) cc_final: 0.8040 (tmmt) REVERT: Z 427 GLU cc_start: 0.7515 (tp30) cc_final: 0.7129 (pp20) REVERT: Z 566 LYS cc_start: 0.8178 (tttm) cc_final: 0.7972 (tttt) outliers start: 160 outliers final: 78 residues processed: 723 average time/residue: 1.3511 time to fit residues: 1233.2474 Evaluate side-chains 665 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 571 time to evaluate : 4.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 1 residue 118 ARG Chi-restraints excluded: chain 1 residue 193 VAL Chi-restraints excluded: chain 1 residue 226 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 393 LEU Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 499 GLU Chi-restraints excluded: chain 2 residue 128 VAL Chi-restraints excluded: chain 2 residue 168 THR Chi-restraints excluded: chain 3 residue 156 ASP Chi-restraints excluded: chain 3 residue 297 LEU Chi-restraints excluded: chain 3 residue 316 VAL Chi-restraints excluded: chain 4 residue 13 TYR Chi-restraints excluded: chain 4 residue 33 LEU Chi-restraints excluded: chain 4 residue 44 THR Chi-restraints excluded: chain 4 residue 118 THR Chi-restraints excluded: chain 5 residue 59 ASN Chi-restraints excluded: chain 5 residue 61 SER Chi-restraints excluded: chain 5 residue 83 THR Chi-restraints excluded: chain 5 residue 112 ARG Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 79 LEU Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 7 residue 23 LEU Chi-restraints excluded: chain 7 residue 34 SER Chi-restraints excluded: chain 7 residue 61 VAL Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 9 LYS Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain G residue 92 ASN Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain I residue 61 MET Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 284 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 175 GLU Chi-restraints excluded: chain P residue 205 ARG Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain S residue 185 HIS Chi-restraints excluded: chain S residue 283 GLU Chi-restraints excluded: chain T residue 41 ASP Chi-restraints excluded: chain T residue 144 VAL Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 182 SER Chi-restraints excluded: chain T residue 185 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 339 LEU Chi-restraints excluded: chain T residue 509 LEU Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain U residue 510 ASP Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 516 ASP Chi-restraints excluded: chain U residue 550 LEU Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 287 MET Chi-restraints excluded: chain V residue 409 GLU Chi-restraints excluded: chain V residue 481 THR Chi-restraints excluded: chain V residue 510 ASP Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 74 LEU Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 297 VAL Chi-restraints excluded: chain X residue 354 THR Chi-restraints excluded: chain X residue 431 LEU Chi-restraints excluded: chain X residue 452 VAL Chi-restraints excluded: chain X residue 480 ASP Chi-restraints excluded: chain X residue 505 ASP Chi-restraints excluded: chain Y residue 193 ILE Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 414 GLN Chi-restraints excluded: chain Y residue 501 LYS Chi-restraints excluded: chain Y residue 533 GLU Chi-restraints excluded: chain Z residue 50 VAL Chi-restraints excluded: chain Z residue 337 GLN Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 559 VAL Chi-restraints excluded: chain Z residue 568 VAL 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: 6.9990 chunk 133 optimal weight: 3.9990 chunk 396 optimal weight: 0.8980 chunk 166 optimal weight: 1.9990 chunk 675 optimal weight: 4.9990 chunk 560 optimal weight: 2.9990 chunk 312 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 223 optimal weight: 1.9990 chunk 354 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 346 GLN 1 365 GLN 2 74 ASN 5 59 ASN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 78 HIS 9 27 ASN D 98 GLN F 98 GLN ** H 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 92 ASN ** Q 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 96 ASN ** S 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 539 ASN U 152 ASN U 471 GLN ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 121 ASN ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 529 ASN V 539 ASN Y 448 GLN Z 322 GLN Z 337 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 54686 Z= 0.310 Angle : 0.589 16.324 74161 Z= 0.297 Chirality : 0.044 0.194 8689 Planarity : 0.004 0.080 9510 Dihedral : 6.553 97.221 7688 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.86 % Favored : 95.99 % Rotamer: Outliers : 3.16 % Allowed : 16.28 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.50 (0.10), residues: 7038 helix: 0.10 (0.09), residues: 3850 sheet: -0.82 (0.20), residues: 637 loop : -0.66 (0.12), residues: 2551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 37 HIS 0.007 0.001 HIS 4 233 PHE 0.029 0.002 PHE H 107 TYR 0.025 0.002 TYR T 453 ARG 0.012 0.000 ARG S 124 *********************** 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 752 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 574 time to evaluate : 4.612 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 41 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7058 (pm20) REVERT: 1 109 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.8114 (tppp) REVERT: 1 118 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7997 (ttp-170) REVERT: 1 181 LYS cc_start: 0.8067 (mmtp) cc_final: 0.7701 (tppt) REVERT: 1 216 LEU cc_start: 0.8794 (mm) cc_final: 0.8564 (tt) REVERT: 1 283 ASP cc_start: 0.8208 (OUTLIER) cc_final: 0.7883 (p0) REVERT: 1 452 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7676 (tm-30) REVERT: 1 572 ASP cc_start: 0.8052 (m-30) cc_final: 0.7758 (m-30) REVERT: 2 226 LYS cc_start: 0.8171 (tptt) cc_final: 0.7728 (tptp) REVERT: 4 13 TYR cc_start: 0.9103 (OUTLIER) cc_final: 0.8609 (m-80) REVERT: 4 198 LYS cc_start: 0.8748 (mptt) cc_final: 0.8470 (mmmt) REVERT: 5 11 GLU cc_start: 0.8272 (mt-10) cc_final: 0.8043 (mt-10) REVERT: 6 79 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8567 (mt) REVERT: B 92 ASN cc_start: 0.7744 (p0) cc_final: 0.7237 (p0) REVERT: C 95 ILE cc_start: 0.6972 (OUTLIER) cc_final: 0.6762 (OUTLIER) REVERT: E 60 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.7504 (tptm) REVERT: E 81 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.7546 (tpp) REVERT: E 115 LEU cc_start: 0.7272 (pp) cc_final: 0.6917 (mm) REVERT: F 95 ILE cc_start: 0.7882 (OUTLIER) cc_final: 0.7671 (mm) REVERT: G 95 ILE cc_start: 0.8037 (mm) cc_final: 0.7807 (mm) REVERT: J 81 MET cc_start: 0.8240 (ttp) cc_final: 0.7648 (ttp) REVERT: M 284 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8742 (mm) REVERT: P 68 ASP cc_start: 0.7919 (OUTLIER) cc_final: 0.7584 (m-30) REVERT: P 99 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7890 (tp) REVERT: P 143 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7791 (mp0) REVERT: P 145 MET cc_start: 0.8480 (mmm) cc_final: 0.8215 (mmm) REVERT: P 151 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7576 (pp20) REVERT: P 169 GLU cc_start: 0.7732 (tp30) cc_final: 0.7448 (tp30) REVERT: P 175 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7208 (tm-30) REVERT: Q 40 GLN cc_start: 0.7794 (tp-100) cc_final: 0.7505 (tp-100) REVERT: Q 49 GLN cc_start: 0.8159 (pt0) cc_final: 0.7880 (pt0) REVERT: Q 52 TYR cc_start: 0.6573 (m-80) cc_final: 0.6343 (m-10) REVERT: R 127 PHE cc_start: 0.7713 (m-80) cc_final: 0.7460 (m-80) REVERT: S 62 MET cc_start: 0.7307 (ptp) cc_final: 0.7077 (mtp) REVERT: S 96 ASN cc_start: 0.6883 (OUTLIER) cc_final: 0.6423 (p0) REVERT: S 217 GLU cc_start: 0.6520 (tp30) cc_final: 0.6066 (tp30) REVERT: S 229 ASP cc_start: 0.7301 (m-30) cc_final: 0.6714 (m-30) REVERT: S 244 ARG cc_start: 0.8063 (tpp-160) cc_final: 0.7701 (ttp-110) REVERT: S 283 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.7076 (mm-30) REVERT: T 72 GLU cc_start: 0.7170 (tp30) cc_final: 0.6922 (tp30) REVERT: T 199 ARG cc_start: 0.7621 (mmm160) cc_final: 0.7183 (ptp90) REVERT: T 237 ASP cc_start: 0.7661 (m-30) cc_final: 0.7357 (m-30) REVERT: T 487 LYS cc_start: 0.8193 (mtpp) cc_final: 0.7588 (ttmt) REVERT: T 542 ILE cc_start: 0.7713 (OUTLIER) cc_final: 0.7469 (pt) REVERT: T 551 LYS cc_start: 0.7751 (ptpp) cc_final: 0.7132 (pttp) REVERT: T 553 GLU cc_start: 0.7510 (tp30) cc_final: 0.7267 (tp30) REVERT: U 45 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7767 (mp) REVERT: U 149 GLN cc_start: 0.7722 (mt0) cc_final: 0.7142 (mm110) REVERT: U 371 GLU cc_start: 0.7756 (pm20) cc_final: 0.7549 (pm20) REVERT: U 511 LYS cc_start: 0.7595 (mmpt) cc_final: 0.7000 (mttt) REVERT: V 50 LYS cc_start: 0.8317 (ttmt) cc_final: 0.7794 (tmmt) REVERT: V 278 GLN cc_start: 0.7925 (mt0) cc_final: 0.7543 (mm-40) REVERT: V 283 ARG cc_start: 0.7921 (ptm-80) cc_final: 0.7595 (ttt90) REVERT: V 482 GLU cc_start: 0.8160 (tp30) cc_final: 0.7906 (tp30) REVERT: V 515 GLN cc_start: 0.7329 (tm130) cc_final: 0.7098 (pt0) REVERT: V 534 LYS cc_start: 0.8496 (mtpm) cc_final: 0.8258 (mtpp) REVERT: X 131 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8023 (mt-10) REVERT: X 359 ASP cc_start: 0.7876 (m-30) cc_final: 0.7584 (m-30) REVERT: X 385 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.7254 (tpt90) REVERT: X 493 LYS cc_start: 0.8024 (ttpt) cc_final: 0.7683 (ttmm) REVERT: X 550 LYS cc_start: 0.8145 (ptpp) cc_final: 0.7558 (pptt) REVERT: Y 140 ILE cc_start: 0.8615 (pt) cc_final: 0.8235 (pp) REVERT: Y 149 GLU cc_start: 0.6162 (OUTLIER) cc_final: 0.5889 (mp0) REVERT: Y 359 ASP cc_start: 0.7800 (m-30) cc_final: 0.7546 (m-30) REVERT: Y 385 ARG cc_start: 0.7882 (mmt90) cc_final: 0.7486 (mmm-85) REVERT: Y 414 GLN cc_start: 0.7767 (OUTLIER) cc_final: 0.7493 (mt0) REVERT: Y 437 ARG cc_start: 0.6932 (mtt-85) cc_final: 0.6360 (mmm-85) REVERT: Y 441 ARG cc_start: 0.7479 (mmt-90) cc_final: 0.7224 (mmt90) REVERT: Y 497 GLU cc_start: 0.6628 (mt-10) cc_final: 0.6295 (mt-10) REVERT: Y 501 LYS cc_start: 0.6428 (OUTLIER) cc_final: 0.6213 (tmmm) REVERT: Y 533 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7195 (pm20) REVERT: Y 539 ILE cc_start: 0.7310 (pt) cc_final: 0.7093 (mm) REVERT: Z 292 GLN cc_start: 0.7601 (tt0) cc_final: 0.7173 (tt0) REVERT: Z 359 ASP cc_start: 0.7511 (m-30) cc_final: 0.7096 (m-30) REVERT: Z 411 LYS cc_start: 0.8278 (mttp) cc_final: 0.8034 (tmmt) REVERT: Z 427 GLU cc_start: 0.7526 (tp30) cc_final: 0.7218 (pp20) REVERT: Z 433 VAL cc_start: 0.6974 (t) cc_final: 0.6738 (t) outliers start: 178 outliers final: 101 residues processed: 700 average time/residue: 1.3661 time to fit residues: 1214.7607 Evaluate side-chains 674 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 552 time to evaluate : 4.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 1 residue 109 LYS Chi-restraints excluded: chain 1 residue 118 ARG Chi-restraints excluded: chain 1 residue 193 VAL Chi-restraints excluded: chain 1 residue 226 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 283 ASP Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 499 GLU Chi-restraints excluded: chain 2 residue 128 VAL Chi-restraints excluded: chain 2 residue 168 THR Chi-restraints excluded: chain 2 residue 440 LYS Chi-restraints excluded: chain 3 residue 156 ASP Chi-restraints excluded: chain 3 residue 316 VAL Chi-restraints excluded: chain 4 residue 13 TYR Chi-restraints excluded: chain 4 residue 19 ASP Chi-restraints excluded: chain 4 residue 33 LEU Chi-restraints excluded: chain 4 residue 44 THR Chi-restraints excluded: chain 4 residue 118 THR Chi-restraints excluded: chain 4 residue 247 SER Chi-restraints excluded: chain 5 residue 59 ASN Chi-restraints excluded: chain 5 residue 61 SER Chi-restraints excluded: chain 5 residue 83 THR Chi-restraints excluded: chain 5 residue 112 ARG Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain 6 residue 69 THR Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 79 LEU Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 7 residue 23 LEU Chi-restraints excluded: chain 7 residue 61 VAL Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 6 VAL Chi-restraints excluded: chain 9 residue 17 ASP Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain G residue 92 ASN Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain H residue 95 ILE Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 284 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 157 ILE Chi-restraints excluded: chain P residue 175 GLU Chi-restraints excluded: chain P residue 205 ARG Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 96 ASN Chi-restraints excluded: chain S residue 176 SER Chi-restraints excluded: chain S residue 185 HIS Chi-restraints excluded: chain S residue 227 SER Chi-restraints excluded: chain S residue 243 LEU Chi-restraints excluded: chain S residue 283 GLU Chi-restraints excluded: chain T residue 144 VAL Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 185 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 300 PHE Chi-restraints excluded: chain T residue 339 LEU Chi-restraints excluded: chain T residue 473 VAL Chi-restraints excluded: chain T residue 509 LEU Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain U residue 45 LEU Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 115 VAL Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain U residue 510 ASP Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 516 ASP Chi-restraints excluded: chain U residue 550 LEU Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 287 MET Chi-restraints excluded: chain V residue 409 GLU Chi-restraints excluded: chain V residue 465 ASP Chi-restraints excluded: chain V residue 481 THR Chi-restraints excluded: chain V residue 510 ASP Chi-restraints excluded: chain V residue 529 ASN Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 74 LEU Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 297 VAL Chi-restraints excluded: chain X residue 341 VAL Chi-restraints excluded: chain X residue 354 THR Chi-restraints excluded: chain X residue 385 ARG Chi-restraints excluded: chain X residue 406 VAL Chi-restraints excluded: chain X residue 431 LEU Chi-restraints excluded: chain X residue 452 VAL Chi-restraints excluded: chain X residue 480 ASP Chi-restraints excluded: chain X residue 491 ASP Chi-restraints excluded: chain X residue 505 ASP Chi-restraints excluded: chain Y residue 149 GLU Chi-restraints excluded: chain Y residue 193 ILE Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 414 GLN Chi-restraints excluded: chain Y residue 501 LYS Chi-restraints excluded: chain Y residue 533 GLU Chi-restraints excluded: chain Z residue 50 VAL Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 492 ILE Chi-restraints excluded: chain Z residue 528 ASP Chi-restraints excluded: chain Z residue 532 SER Chi-restraints excluded: chain Z residue 557 GLU Chi-restraints excluded: chain Z residue 559 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 651 optimal weight: 0.7980 chunk 76 optimal weight: 0.2980 chunk 384 optimal weight: 1.9990 chunk 493 optimal weight: 0.5980 chunk 382 optimal weight: 2.9990 chunk 568 optimal weight: 0.8980 chunk 377 optimal weight: 0.9980 chunk 672 optimal weight: 0.0970 chunk 421 optimal weight: 0.0570 chunk 410 optimal weight: 0.9990 chunk 310 optimal weight: 0.6980 overall best weight: 0.3496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 313 GLN 1 346 GLN 2 74 ASN 5 59 ASN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 184 ASN 8 78 HIS 9 27 ASN D 98 GLN J 92 ASN ** R 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 96 ASN ** S 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 539 ASN ** U 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 497 GLN ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 529 ASN X 398 ASN Z 286 ASN Z 322 GLN Z 337 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 54686 Z= 0.138 Angle : 0.519 17.722 74161 Z= 0.261 Chirality : 0.040 0.173 8689 Planarity : 0.004 0.075 9510 Dihedral : 6.055 91.603 7688 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.18 % Favored : 96.70 % Rotamer: Outliers : 2.52 % Allowed : 17.44 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.10), residues: 7038 helix: 0.52 (0.09), residues: 3858 sheet: -0.67 (0.21), residues: 621 loop : -0.47 (0.13), residues: 2559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP 9 73 HIS 0.006 0.001 HIS 8 78 PHE 0.036 0.001 PHE H 107 TYR 0.022 0.001 TYR 4 211 ARG 0.009 0.000 ARG S 124 *********************** 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 768 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 626 time to evaluate : 4.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 41 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7073 (pm20) REVERT: 1 118 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7929 (ttp-170) REVERT: 1 181 LYS cc_start: 0.7975 (mmtp) cc_final: 0.7764 (tppt) REVERT: 1 216 LEU cc_start: 0.8836 (mm) cc_final: 0.8623 (tt) REVERT: 1 283 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7638 (p0) REVERT: 1 452 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7661 (tm-30) REVERT: 1 572 ASP cc_start: 0.8080 (m-30) cc_final: 0.7791 (m-30) REVERT: 2 31 ASP cc_start: 0.7601 (OUTLIER) cc_final: 0.7368 (m-30) REVERT: 2 41 VAL cc_start: 0.7746 (OUTLIER) cc_final: 0.7484 (t) REVERT: 4 13 TYR cc_start: 0.9088 (OUTLIER) cc_final: 0.8398 (m-80) REVERT: 4 198 LYS cc_start: 0.8760 (mptt) cc_final: 0.8512 (mmmt) REVERT: 5 1 MET cc_start: 0.7416 (pmm) cc_final: 0.6996 (pmm) REVERT: 5 11 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7993 (mt-10) REVERT: 6 79 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8515 (mt) REVERT: 8 9 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8325 (ttpt) REVERT: B 92 ASN cc_start: 0.7563 (p0) cc_final: 0.7128 (p0) REVERT: E 60 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.7460 (tptm) REVERT: E 115 LEU cc_start: 0.7263 (pp) cc_final: 0.7012 (mm) REVERT: G 95 ILE cc_start: 0.7936 (mm) cc_final: 0.7735 (mm) REVERT: I 61 MET cc_start: 0.7429 (OUTLIER) cc_final: 0.6176 (mpt) REVERT: I 115 LEU cc_start: 0.7007 (mm) cc_final: 0.6775 (pp) REVERT: J 81 MET cc_start: 0.8229 (ttp) cc_final: 0.7607 (ttp) REVERT: M 284 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8645 (mm) REVERT: M 314 LYS cc_start: 0.8600 (ttpp) cc_final: 0.8199 (tttp) REVERT: P 68 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.7604 (m-30) REVERT: P 99 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7803 (tp) REVERT: P 143 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7772 (mp0) REVERT: P 145 MET cc_start: 0.8465 (mmm) cc_final: 0.8162 (mmm) REVERT: P 169 GLU cc_start: 0.7702 (tp30) cc_final: 0.7427 (tp30) REVERT: P 175 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7242 (tm-30) REVERT: Q 40 GLN cc_start: 0.7832 (tp-100) cc_final: 0.7542 (tp40) REVERT: Q 49 GLN cc_start: 0.8108 (pt0) cc_final: 0.7836 (pt0) REVERT: Q 52 TYR cc_start: 0.6249 (m-80) cc_final: 0.5932 (m-10) REVERT: Q 63 TYR cc_start: 0.7956 (m-80) cc_final: 0.7732 (m-80) REVERT: S 48 ARG cc_start: 0.6739 (tpp-160) cc_final: 0.6471 (ttm110) REVERT: S 203 PHE cc_start: 0.7982 (m-80) cc_final: 0.7483 (m-80) REVERT: S 217 GLU cc_start: 0.6379 (tp30) cc_final: 0.5933 (tp30) REVERT: S 229 ASP cc_start: 0.7288 (m-30) cc_final: 0.6835 (m-30) REVERT: S 244 ARG cc_start: 0.8006 (tpp-160) cc_final: 0.7601 (ttp-110) REVERT: S 283 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.7041 (mm-30) REVERT: S 303 GLU cc_start: 0.7504 (mm-30) cc_final: 0.7271 (mm-30) REVERT: T 72 GLU cc_start: 0.7154 (tp30) cc_final: 0.6876 (tp30) REVERT: T 199 ARG cc_start: 0.7588 (mmm160) cc_final: 0.7187 (ptp90) REVERT: T 237 ASP cc_start: 0.7572 (m-30) cc_final: 0.7256 (m-30) REVERT: T 487 LYS cc_start: 0.8207 (mtpp) cc_final: 0.7630 (ttmt) REVERT: T 551 LYS cc_start: 0.7759 (ptpp) cc_final: 0.7025 (pttp) REVERT: T 553 GLU cc_start: 0.7389 (tp30) cc_final: 0.7154 (tp30) REVERT: U 96 ARG cc_start: 0.8159 (mtm-85) cc_final: 0.7879 (mtm-85) REVERT: U 112 ASP cc_start: 0.8308 (p0) cc_final: 0.8083 (p0) REVERT: U 149 GLN cc_start: 0.7661 (mt0) cc_final: 0.7102 (mm110) REVERT: U 371 GLU cc_start: 0.7758 (pm20) cc_final: 0.7428 (pm20) REVERT: U 511 LYS cc_start: 0.7620 (mmpt) cc_final: 0.6972 (mttt) REVERT: U 553 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7729 (mm-30) REVERT: V 43 LYS cc_start: 0.6196 (OUTLIER) cc_final: 0.4958 (mmtp) REVERT: V 50 LYS cc_start: 0.8331 (ttmt) cc_final: 0.7817 (tmmt) REVERT: V 278 GLN cc_start: 0.7885 (mt0) cc_final: 0.7516 (mm-40) REVERT: V 283 ARG cc_start: 0.7896 (ptm-80) cc_final: 0.7570 (ttt90) REVERT: V 515 GLN cc_start: 0.7242 (tm130) cc_final: 0.6882 (pt0) REVERT: V 534 LYS cc_start: 0.8459 (mtpm) cc_final: 0.8240 (mtpp) REVERT: X 131 GLU cc_start: 0.8281 (mt-10) cc_final: 0.8020 (mt-10) REVERT: X 359 ASP cc_start: 0.7827 (m-30) cc_final: 0.7505 (m-30) REVERT: X 493 LYS cc_start: 0.8025 (ttpt) cc_final: 0.7633 (ttmm) REVERT: X 550 LYS cc_start: 0.8103 (ptpp) cc_final: 0.7544 (pptt) REVERT: Y 149 GLU cc_start: 0.5981 (OUTLIER) cc_final: 0.5761 (mp0) REVERT: Y 359 ASP cc_start: 0.7780 (m-30) cc_final: 0.7238 (m-30) REVERT: Y 385 ARG cc_start: 0.7916 (mmt90) cc_final: 0.7508 (mmm-85) REVERT: Y 414 GLN cc_start: 0.7746 (tt0) cc_final: 0.7456 (mt0) REVERT: Y 437 ARG cc_start: 0.7031 (mtt-85) cc_final: 0.6447 (mmm-85) REVERT: Y 441 ARG cc_start: 0.7211 (mmt-90) cc_final: 0.6927 (mmt90) REVERT: Y 533 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7269 (pm20) REVERT: Z 82 ASP cc_start: 0.7360 (t0) cc_final: 0.6796 (t0) REVERT: Z 292 GLN cc_start: 0.7536 (tt0) cc_final: 0.7159 (tt0) REVERT: Z 359 ASP cc_start: 0.7405 (m-30) cc_final: 0.7064 (m-30) REVERT: Z 411 LYS cc_start: 0.8245 (mttp) cc_final: 0.7994 (tmmt) REVERT: Z 427 GLU cc_start: 0.7454 (tp30) cc_final: 0.7208 (pp20) REVERT: Z 429 ASP cc_start: 0.6267 (m-30) cc_final: 0.6017 (m-30) REVERT: Z 433 VAL cc_start: 0.6943 (t) cc_final: 0.6726 (t) outliers start: 142 outliers final: 63 residues processed: 713 average time/residue: 1.3669 time to fit residues: 1241.7498 Evaluate side-chains 649 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 569 time to evaluate : 4.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 1 residue 92 TYR Chi-restraints excluded: chain 1 residue 118 ARG Chi-restraints excluded: chain 1 residue 226 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 283 ASP Chi-restraints excluded: chain 1 residue 393 LEU Chi-restraints excluded: chain 1 residue 499 GLU Chi-restraints excluded: chain 2 residue 31 ASP Chi-restraints excluded: chain 2 residue 41 VAL Chi-restraints excluded: chain 2 residue 168 THR Chi-restraints excluded: chain 3 residue 316 VAL Chi-restraints excluded: chain 4 residue 13 TYR Chi-restraints excluded: chain 4 residue 33 LEU Chi-restraints excluded: chain 4 residue 44 THR Chi-restraints excluded: chain 4 residue 118 THR Chi-restraints excluded: chain 4 residue 247 SER Chi-restraints excluded: chain 5 residue 59 ASN Chi-restraints excluded: chain 5 residue 61 SER Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 79 LEU Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 7 residue 61 VAL Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 6 VAL Chi-restraints excluded: chain 8 residue 9 LYS Chi-restraints excluded: chain 9 residue 17 ASP Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain G residue 92 ASN Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain H residue 95 ILE Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 61 MET Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 284 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 175 GLU Chi-restraints excluded: chain P residue 205 ARG Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain S residue 185 HIS Chi-restraints excluded: chain S residue 283 GLU Chi-restraints excluded: chain T residue 144 VAL Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 473 VAL Chi-restraints excluded: chain U residue 152 ASN Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 516 ASP Chi-restraints excluded: chain U residue 550 LEU Chi-restraints excluded: chain V residue 43 LYS Chi-restraints excluded: chain V residue 115 VAL Chi-restraints excluded: chain V residue 134 ASN Chi-restraints excluded: chain V residue 287 MET Chi-restraints excluded: chain V residue 409 GLU Chi-restraints excluded: chain V residue 465 ASP Chi-restraints excluded: chain V residue 529 ASN Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 297 VAL Chi-restraints excluded: chain X residue 354 THR Chi-restraints excluded: chain X residue 431 LEU Chi-restraints excluded: chain X residue 452 VAL Chi-restraints excluded: chain X residue 505 ASP Chi-restraints excluded: chain Y residue 149 GLU Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 325 ILE Chi-restraints excluded: chain Y residue 533 GLU Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 532 SER Chi-restraints excluded: chain Z residue 559 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 416 optimal weight: 0.9990 chunk 268 optimal weight: 0.0030 chunk 401 optimal weight: 0.9990 chunk 202 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 427 optimal weight: 1.9990 chunk 458 optimal weight: 0.7980 chunk 332 optimal weight: 0.0980 chunk 62 optimal weight: 0.6980 chunk 528 optimal weight: 0.3980 overall best weight: 0.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 346 GLN 2 74 ASN 5 59 ASN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 102 GLN 8 78 HIS 9 27 ASN B 98 GLN C 98 GLN F 98 GLN ** H 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 154 GLN ** R 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 441 GLN ** T 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 539 ASN ** U 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 539 ASN ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 529 ASN Z 337 GLN ** Z 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 448 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 54686 Z= 0.143 Angle : 0.519 17.456 74161 Z= 0.260 Chirality : 0.040 0.216 8689 Planarity : 0.004 0.066 9510 Dihedral : 5.847 91.172 7687 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.38 % Favored : 96.50 % Rotamer: Outliers : 2.10 % Allowed : 18.61 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.10), residues: 7038 helix: 0.74 (0.09), residues: 3859 sheet: -0.60 (0.21), residues: 623 loop : -0.41 (0.13), residues: 2556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 9 73 HIS 0.007 0.001 HIS 8 78 PHE 0.037 0.001 PHE H 107 TYR 0.023 0.001 TYR 9 14 ARG 0.009 0.000 ARG 1 359 *********************** 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 706 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 588 time to evaluate : 4.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 41 GLU cc_start: 0.8315 (mt-10) cc_final: 0.7081 (pm20) REVERT: 1 118 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7899 (ttp-170) REVERT: 1 181 LYS cc_start: 0.7941 (mmtp) cc_final: 0.7684 (tppt) REVERT: 1 216 LEU cc_start: 0.8835 (mm) cc_final: 0.8623 (tt) REVERT: 1 283 ASP cc_start: 0.7838 (OUTLIER) cc_final: 0.7577 (p0) REVERT: 1 452 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7647 (tm-30) REVERT: 1 572 ASP cc_start: 0.8079 (m-30) cc_final: 0.7783 (m-30) REVERT: 2 41 VAL cc_start: 0.7683 (OUTLIER) cc_final: 0.7418 (t) REVERT: 4 13 TYR cc_start: 0.9080 (OUTLIER) cc_final: 0.8367 (m-80) REVERT: 4 198 LYS cc_start: 0.8749 (mptt) cc_final: 0.8506 (mmmt) REVERT: 5 1 MET cc_start: 0.7366 (pmm) cc_final: 0.6878 (pmm) REVERT: 5 11 GLU cc_start: 0.8257 (mt-10) cc_final: 0.8029 (mt-10) REVERT: 9 13 LYS cc_start: 0.7251 (pttt) cc_final: 0.6725 (tttm) REVERT: B 92 ASN cc_start: 0.7480 (p0) cc_final: 0.7127 (p0) REVERT: E 60 LYS cc_start: 0.7694 (OUTLIER) cc_final: 0.7416 (tptm) REVERT: E 115 LEU cc_start: 0.7314 (pp) cc_final: 0.6968 (mm) REVERT: G 95 ILE cc_start: 0.7914 (mm) cc_final: 0.7703 (mm) REVERT: G 115 LEU cc_start: 0.7206 (pp) cc_final: 0.6737 (mt) REVERT: G 118 LEU cc_start: 0.7944 (mt) cc_final: 0.7665 (mt) REVERT: I 61 MET cc_start: 0.7440 (OUTLIER) cc_final: 0.6193 (mpt) REVERT: I 115 LEU cc_start: 0.7008 (mm) cc_final: 0.6778 (pp) REVERT: J 81 MET cc_start: 0.8232 (ttp) cc_final: 0.7595 (ttp) REVERT: P 68 ASP cc_start: 0.7857 (OUTLIER) cc_final: 0.7489 (m-30) REVERT: P 72 ASP cc_start: 0.7540 (t0) cc_final: 0.7080 (t70) REVERT: P 99 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7789 (tp) REVERT: P 143 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7708 (mp0) REVERT: P 145 MET cc_start: 0.8433 (mmm) cc_final: 0.8128 (mmm) REVERT: P 169 GLU cc_start: 0.7674 (tp30) cc_final: 0.7451 (tp30) REVERT: Q 40 GLN cc_start: 0.7808 (tp-100) cc_final: 0.7513 (tp40) REVERT: Q 49 GLN cc_start: 0.8103 (pt0) cc_final: 0.7797 (pt0) REVERT: Q 52 TYR cc_start: 0.6300 (m-80) cc_final: 0.5884 (m-10) REVERT: Q 63 TYR cc_start: 0.7937 (m-80) cc_final: 0.7683 (m-80) REVERT: R 120 SER cc_start: 0.6671 (p) cc_final: 0.6360 (t) REVERT: S 203 PHE cc_start: 0.7886 (m-80) cc_final: 0.7559 (m-80) REVERT: S 217 GLU cc_start: 0.6313 (tp30) cc_final: 0.5755 (tp30) REVERT: S 229 ASP cc_start: 0.7209 (m-30) cc_final: 0.6778 (m-30) REVERT: S 244 ARG cc_start: 0.8028 (tpp-160) cc_final: 0.7626 (ttp-110) REVERT: S 283 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.7033 (mm-30) REVERT: S 303 GLU cc_start: 0.7481 (mm-30) cc_final: 0.7264 (mm-30) REVERT: T 72 GLU cc_start: 0.7184 (tp30) cc_final: 0.6881 (tp30) REVERT: T 199 ARG cc_start: 0.7600 (mmm160) cc_final: 0.7186 (ptp90) REVERT: T 237 ASP cc_start: 0.7570 (m-30) cc_final: 0.7256 (m-30) REVERT: T 487 LYS cc_start: 0.8199 (mtpp) cc_final: 0.7633 (ttmt) REVERT: T 551 LYS cc_start: 0.7816 (ptpp) cc_final: 0.7405 (ptmm) REVERT: T 553 GLU cc_start: 0.7351 (tp30) cc_final: 0.7108 (tp30) REVERT: U 96 ARG cc_start: 0.8190 (mtm-85) cc_final: 0.7938 (mtp-110) REVERT: U 112 ASP cc_start: 0.8249 (p0) cc_final: 0.8037 (p0) REVERT: U 149 GLN cc_start: 0.7672 (mt0) cc_final: 0.7177 (mm110) REVERT: U 371 GLU cc_start: 0.7751 (pm20) cc_final: 0.7425 (pm20) REVERT: U 511 LYS cc_start: 0.7588 (mmpt) cc_final: 0.6942 (mttt) REVERT: U 541 LYS cc_start: 0.8545 (ptmt) cc_final: 0.7805 (pmtt) REVERT: U 553 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7687 (mm-30) REVERT: V 50 LYS cc_start: 0.8325 (ttmt) cc_final: 0.7822 (tmmt) REVERT: V 278 GLN cc_start: 0.7887 (mt0) cc_final: 0.7504 (mm-40) REVERT: V 283 ARG cc_start: 0.7888 (ptm-80) cc_final: 0.7564 (ttt90) REVERT: V 508 PHE cc_start: 0.7576 (m-80) cc_final: 0.7367 (m-80) REVERT: V 515 GLN cc_start: 0.7249 (tm130) cc_final: 0.6845 (pt0) REVERT: V 534 LYS cc_start: 0.8452 (mtpm) cc_final: 0.8240 (mttm) REVERT: X 131 GLU cc_start: 0.8299 (mt-10) cc_final: 0.8020 (mt-10) REVERT: X 359 ASP cc_start: 0.7798 (m-30) cc_final: 0.7485 (m-30) REVERT: X 493 LYS cc_start: 0.8038 (ttpt) cc_final: 0.7622 (ttmm) REVERT: X 550 LYS cc_start: 0.8080 (ptpp) cc_final: 0.7535 (pptt) REVERT: Y 149 GLU cc_start: 0.5951 (OUTLIER) cc_final: 0.5722 (mp0) REVERT: Y 359 ASP cc_start: 0.7795 (m-30) cc_final: 0.7265 (m-30) REVERT: Y 385 ARG cc_start: 0.7875 (mmt90) cc_final: 0.7515 (mmm-85) REVERT: Y 414 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.7528 (mt0) REVERT: Y 437 ARG cc_start: 0.6906 (mtt-85) cc_final: 0.6313 (mmm-85) REVERT: Y 441 ARG cc_start: 0.7275 (mmt-90) cc_final: 0.6972 (mmt90) REVERT: Y 533 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7266 (pm20) REVERT: Z 82 ASP cc_start: 0.7388 (t0) cc_final: 0.6815 (t0) REVERT: Z 226 GLU cc_start: 0.7425 (mt-10) cc_final: 0.6973 (mt-10) REVERT: Z 292 GLN cc_start: 0.7500 (tt0) cc_final: 0.7094 (tt0) REVERT: Z 359 ASP cc_start: 0.7460 (m-30) cc_final: 0.7130 (m-30) REVERT: Z 411 LYS cc_start: 0.8209 (mttp) cc_final: 0.7983 (tmmt) REVERT: Z 427 GLU cc_start: 0.7437 (tp30) cc_final: 0.7194 (pp20) REVERT: Z 429 ASP cc_start: 0.6249 (m-30) cc_final: 0.6015 (m-30) REVERT: Z 433 VAL cc_start: 0.6806 (t) cc_final: 0.6598 (t) outliers start: 118 outliers final: 72 residues processed: 670 average time/residue: 1.4046 time to fit residues: 1197.8682 Evaluate side-chains 656 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 572 time to evaluate : 4.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 1 residue 24 LEU Chi-restraints excluded: chain 1 residue 92 TYR Chi-restraints excluded: chain 1 residue 118 ARG Chi-restraints excluded: chain 1 residue 193 VAL Chi-restraints excluded: chain 1 residue 226 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 283 ASP Chi-restraints excluded: chain 1 residue 393 LEU Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 499 GLU Chi-restraints excluded: chain 2 residue 41 VAL Chi-restraints excluded: chain 2 residue 168 THR Chi-restraints excluded: chain 2 residue 359 THR Chi-restraints excluded: chain 2 residue 440 LYS Chi-restraints excluded: chain 3 residue 297 LEU Chi-restraints excluded: chain 3 residue 316 VAL Chi-restraints excluded: chain 4 residue 13 TYR Chi-restraints excluded: chain 4 residue 33 LEU Chi-restraints excluded: chain 4 residue 44 THR Chi-restraints excluded: chain 4 residue 118 THR Chi-restraints excluded: chain 5 residue 61 SER Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 69 THR Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 7 residue 23 LEU Chi-restraints excluded: chain 7 residue 61 VAL Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 6 VAL Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 61 MET Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 157 ILE Chi-restraints excluded: chain P residue 205 ARG Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain S residue 96 ASN Chi-restraints excluded: chain S residue 185 HIS Chi-restraints excluded: chain S residue 283 GLU Chi-restraints excluded: chain T residue 144 VAL Chi-restraints excluded: chain T residue 339 LEU Chi-restraints excluded: chain T residue 473 VAL Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 516 ASP Chi-restraints excluded: chain U residue 550 LEU Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 115 VAL Chi-restraints excluded: chain V residue 134 ASN Chi-restraints excluded: chain V residue 287 MET Chi-restraints excluded: chain V residue 409 GLU Chi-restraints excluded: chain V residue 465 ASP Chi-restraints excluded: chain V residue 529 ASN Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 74 LEU Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 297 VAL Chi-restraints excluded: chain X residue 354 THR Chi-restraints excluded: chain X residue 452 VAL Chi-restraints excluded: chain X residue 491 ASP Chi-restraints excluded: chain X residue 505 ASP Chi-restraints excluded: chain Y residue 149 GLU Chi-restraints excluded: chain Y residue 193 ILE Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 325 ILE Chi-restraints excluded: chain Y residue 414 GLN Chi-restraints excluded: chain Y residue 533 GLU Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 492 ILE Chi-restraints excluded: chain Z residue 532 SER Chi-restraints excluded: chain Z residue 559 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 611 optimal weight: 0.8980 chunk 644 optimal weight: 1.9990 chunk 588 optimal weight: 0.5980 chunk 626 optimal weight: 2.9990 chunk 377 optimal weight: 4.9990 chunk 273 optimal weight: 9.9990 chunk 492 optimal weight: 1.9990 chunk 192 optimal weight: 0.7980 chunk 566 optimal weight: 5.9990 chunk 592 optimal weight: 3.9990 chunk 624 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 346 GLN 2 74 ASN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 78 HIS D 98 GLN F 98 GLN ** Q 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 85 GLN R 154 GLN ** R 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 539 ASN U 152 ASN ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 529 ASN Z 448 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 54686 Z= 0.246 Angle : 0.566 17.529 74161 Z= 0.283 Chirality : 0.042 0.209 8689 Planarity : 0.004 0.078 9510 Dihedral : 6.046 89.407 7685 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.68 % Favored : 96.19 % Rotamer: Outliers : 2.13 % Allowed : 18.88 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.18 (0.10), residues: 7038 helix: 0.70 (0.09), residues: 3869 sheet: -0.66 (0.20), residues: 653 loop : -0.41 (0.13), residues: 2516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 37 HIS 0.006 0.001 HIS 4 233 PHE 0.038 0.001 PHE H 107 TYR 0.022 0.001 TYR 4 211 ARG 0.010 0.000 ARG T 496 *********************** 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 686 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 566 time to evaluate : 4.671 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 41 GLU cc_start: 0.8322 (mt-10) cc_final: 0.7075 (pm20) REVERT: 1 118 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7913 (ttp-170) REVERT: 1 181 LYS cc_start: 0.8044 (mmtp) cc_final: 0.7701 (tppt) REVERT: 1 216 LEU cc_start: 0.8791 (mm) cc_final: 0.8561 (tt) REVERT: 1 283 ASP cc_start: 0.8025 (OUTLIER) cc_final: 0.7731 (p0) REVERT: 1 452 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7591 (tm-30) REVERT: 1 572 ASP cc_start: 0.8049 (m-30) cc_final: 0.7764 (m-30) REVERT: 4 13 TYR cc_start: 0.9121 (OUTLIER) cc_final: 0.8509 (m-80) REVERT: 4 198 LYS cc_start: 0.8756 (mptt) cc_final: 0.8497 (mmmt) REVERT: 5 1 MET cc_start: 0.7365 (pmm) cc_final: 0.7051 (pmm) REVERT: 5 11 GLU cc_start: 0.8257 (mt-10) cc_final: 0.8036 (mt-10) REVERT: 9 13 LYS cc_start: 0.7294 (pttt) cc_final: 0.6764 (tttm) REVERT: A 123 LEU cc_start: 0.7968 (tp) cc_final: 0.7477 (mp) REVERT: B 92 ASN cc_start: 0.7499 (p0) cc_final: 0.7085 (p0) REVERT: E 60 LYS cc_start: 0.7723 (OUTLIER) cc_final: 0.7424 (tptm) REVERT: E 115 LEU cc_start: 0.7362 (pp) cc_final: 0.6983 (mm) REVERT: I 61 MET cc_start: 0.7455 (OUTLIER) cc_final: 0.6186 (mpt) REVERT: J 81 MET cc_start: 0.8260 (ttp) cc_final: 0.7630 (ttp) REVERT: M 314 LYS cc_start: 0.8547 (ttpp) cc_final: 0.8229 (tttp) REVERT: P 72 ASP cc_start: 0.7575 (t0) cc_final: 0.7125 (t70) REVERT: P 99 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7873 (tp) REVERT: P 143 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7756 (mp0) REVERT: P 145 MET cc_start: 0.8474 (mmm) cc_final: 0.8178 (mmm) REVERT: Q 40 GLN cc_start: 0.7892 (tp-100) cc_final: 0.7525 (mm-40) REVERT: Q 49 GLN cc_start: 0.8111 (pt0) cc_final: 0.7790 (pt0) REVERT: Q 52 TYR cc_start: 0.6538 (m-80) cc_final: 0.6223 (m-10) REVERT: R 120 SER cc_start: 0.6695 (p) cc_final: 0.6363 (t) REVERT: S 169 ARG cc_start: 0.7921 (ptm160) cc_final: 0.7550 (ptm160) REVERT: S 203 PHE cc_start: 0.8025 (m-80) cc_final: 0.7729 (m-80) REVERT: S 217 GLU cc_start: 0.6299 (tp30) cc_final: 0.5757 (tp30) REVERT: S 229 ASP cc_start: 0.7227 (m-30) cc_final: 0.6776 (m-30) REVERT: S 244 ARG cc_start: 0.8024 (tpp-160) cc_final: 0.7639 (ttp-110) REVERT: S 283 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.7028 (mm-30) REVERT: S 303 GLU cc_start: 0.7521 (mm-30) cc_final: 0.7284 (mm-30) REVERT: T 72 GLU cc_start: 0.7195 (tp30) cc_final: 0.6904 (tp30) REVERT: T 199 ARG cc_start: 0.7559 (mmm160) cc_final: 0.7134 (ptp90) REVERT: T 237 ASP cc_start: 0.7599 (m-30) cc_final: 0.7281 (m-30) REVERT: T 487 LYS cc_start: 0.8162 (mtpp) cc_final: 0.7606 (ttmt) REVERT: T 551 LYS cc_start: 0.7835 (ptpp) cc_final: 0.7079 (pttp) REVERT: T 553 GLU cc_start: 0.7350 (tp30) cc_final: 0.7077 (tp30) REVERT: U 112 ASP cc_start: 0.8277 (p0) cc_final: 0.8075 (p0) REVERT: U 149 GLN cc_start: 0.7770 (mt0) cc_final: 0.7212 (mm110) REVERT: U 371 GLU cc_start: 0.7763 (pm20) cc_final: 0.7544 (pm20) REVERT: U 511 LYS cc_start: 0.7601 (mmpt) cc_final: 0.6950 (mttt) REVERT: U 553 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7694 (mm-30) REVERT: V 50 LYS cc_start: 0.8327 (ttmt) cc_final: 0.7790 (tmmt) REVERT: V 278 GLN cc_start: 0.7909 (mt0) cc_final: 0.7521 (mm-40) REVERT: V 283 ARG cc_start: 0.7903 (ptm-80) cc_final: 0.7573 (ttt90) REVERT: V 414 TYR cc_start: 0.7767 (m-80) cc_final: 0.7540 (m-80) REVERT: V 515 GLN cc_start: 0.7246 (tm130) cc_final: 0.6837 (pt0) REVERT: V 534 LYS cc_start: 0.8473 (mtpm) cc_final: 0.8240 (mttm) REVERT: X 131 GLU cc_start: 0.8319 (mt-10) cc_final: 0.8048 (mt-10) REVERT: X 264 THR cc_start: 0.9143 (OUTLIER) cc_final: 0.8897 (p) REVERT: X 359 ASP cc_start: 0.7822 (m-30) cc_final: 0.7519 (m-30) REVERT: X 395 GLU cc_start: 0.8108 (tp30) cc_final: 0.7875 (tm-30) REVERT: X 493 LYS cc_start: 0.7996 (ttpt) cc_final: 0.7592 (ttmm) REVERT: X 550 LYS cc_start: 0.8099 (ptpp) cc_final: 0.7545 (pptt) REVERT: Y 149 GLU cc_start: 0.6121 (OUTLIER) cc_final: 0.5884 (mp0) REVERT: Y 359 ASP cc_start: 0.7821 (m-30) cc_final: 0.7556 (m-30) REVERT: Y 385 ARG cc_start: 0.7893 (mmt90) cc_final: 0.7530 (mmm-85) REVERT: Y 414 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.7504 (mt0) REVERT: Y 437 ARG cc_start: 0.6950 (mtt-85) cc_final: 0.6365 (mmm-85) REVERT: Y 441 ARG cc_start: 0.7377 (mmt-90) cc_final: 0.7065 (mmt90) REVERT: Y 533 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7278 (pm20) REVERT: Z 82 ASP cc_start: 0.7563 (t0) cc_final: 0.6994 (t0) REVERT: Z 226 GLU cc_start: 0.7421 (mt-10) cc_final: 0.7048 (mt-10) REVERT: Z 292 GLN cc_start: 0.7540 (tt0) cc_final: 0.7149 (tt0) REVERT: Z 359 ASP cc_start: 0.7497 (m-30) cc_final: 0.7064 (m-30) REVERT: Z 411 LYS cc_start: 0.8233 (mttp) cc_final: 0.7990 (tmmt) REVERT: Z 429 ASP cc_start: 0.6320 (m-30) cc_final: 0.6055 (m-30) REVERT: Z 430 LYS cc_start: 0.5836 (mtmp) cc_final: 0.5374 (ptpt) outliers start: 120 outliers final: 78 residues processed: 644 average time/residue: 1.3499 time to fit residues: 1097.9848 Evaluate side-chains 645 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 556 time to evaluate : 4.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 1 residue 92 TYR Chi-restraints excluded: chain 1 residue 118 ARG Chi-restraints excluded: chain 1 residue 193 VAL Chi-restraints excluded: chain 1 residue 226 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 283 ASP Chi-restraints excluded: chain 1 residue 393 LEU Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 499 GLU Chi-restraints excluded: chain 2 residue 168 THR Chi-restraints excluded: chain 2 residue 359 THR Chi-restraints excluded: chain 2 residue 440 LYS Chi-restraints excluded: chain 3 residue 156 ASP Chi-restraints excluded: chain 3 residue 173 GLU Chi-restraints excluded: chain 3 residue 316 VAL Chi-restraints excluded: chain 4 residue 13 TYR Chi-restraints excluded: chain 4 residue 19 ASP Chi-restraints excluded: chain 4 residue 33 LEU Chi-restraints excluded: chain 4 residue 44 THR Chi-restraints excluded: chain 4 residue 118 THR Chi-restraints excluded: chain 5 residue 61 SER Chi-restraints excluded: chain 5 residue 83 THR Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 69 THR Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 7 residue 23 LEU Chi-restraints excluded: chain 7 residue 61 VAL Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 6 VAL Chi-restraints excluded: chain 9 residue 17 ASP Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 61 MET Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 172 GLU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 157 ILE Chi-restraints excluded: chain P residue 205 ARG Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain S residue 185 HIS Chi-restraints excluded: chain S residue 283 GLU Chi-restraints excluded: chain T residue 144 VAL Chi-restraints excluded: chain T residue 179 ASN Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 339 LEU Chi-restraints excluded: chain T residue 473 VAL Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 516 ASP Chi-restraints excluded: chain U residue 550 LEU Chi-restraints excluded: chain V residue 115 VAL Chi-restraints excluded: chain V residue 287 MET Chi-restraints excluded: chain V residue 409 GLU Chi-restraints excluded: chain V residue 465 ASP Chi-restraints excluded: chain V residue 529 ASN Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 74 LEU Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 264 THR Chi-restraints excluded: chain X residue 297 VAL Chi-restraints excluded: chain X residue 354 THR Chi-restraints excluded: chain X residue 452 VAL Chi-restraints excluded: chain X residue 505 ASP Chi-restraints excluded: chain Y residue 149 GLU Chi-restraints excluded: chain Y residue 193 ILE Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 325 ILE Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 414 GLN Chi-restraints excluded: chain Y residue 533 GLU Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 492 ILE Chi-restraints excluded: chain Z residue 523 ASP Chi-restraints excluded: chain Z residue 532 SER Chi-restraints excluded: chain Z residue 559 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 411 optimal weight: 0.0970 chunk 662 optimal weight: 4.9990 chunk 404 optimal weight: 0.9980 chunk 314 optimal weight: 5.9990 chunk 460 optimal weight: 4.9990 chunk 695 optimal weight: 0.9980 chunk 640 optimal weight: 4.9990 chunk 553 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 427 optimal weight: 0.6980 chunk 339 optimal weight: 20.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 346 GLN 2 74 ASN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 78 HIS 9 27 ASN D 98 GLN F 98 GLN I 92 ASN P 71 GLN ** Q 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 154 GLN ** R 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 174 GLN ** T 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 539 ASN U 152 ASN ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 529 ASN ** Z 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 448 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 54686 Z= 0.181 Angle : 0.547 19.681 74161 Z= 0.272 Chirality : 0.041 0.197 8689 Planarity : 0.004 0.071 9510 Dihedral : 5.899 90.512 7685 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.37 % Favored : 96.52 % Rotamer: Outliers : 1.78 % Allowed : 19.37 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.82 (0.09), residues: 3866 sheet: -0.51 (0.21), residues: 632 loop : -0.36 (0.13), residues: 2540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 9 73 HIS 0.005 0.001 HIS 4 233 PHE 0.040 0.001 PHE H 107 TYR 0.024 0.001 TYR 9 14 ARG 0.009 0.000 ARG T 496 ********************** 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 683 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 583 time to evaluate : 4.647 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 41 GLU cc_start: 0.8311 (mt-10) cc_final: 0.7069 (pm20) REVERT: 1 181 LYS cc_start: 0.7959 (mmtp) cc_final: 0.7520 (tppt) REVERT: 1 216 LEU cc_start: 0.8809 (mm) cc_final: 0.8577 (tt) REVERT: 1 283 ASP cc_start: 0.7917 (OUTLIER) cc_final: 0.7622 (p0) REVERT: 1 452 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7609 (tm-30) REVERT: 1 572 ASP cc_start: 0.8053 (m-30) cc_final: 0.7763 (m-30) REVERT: 2 226 LYS cc_start: 0.8045 (tptt) cc_final: 0.7622 (tptp) REVERT: 4 13 TYR cc_start: 0.9095 (OUTLIER) cc_final: 0.8422 (m-80) REVERT: 4 198 LYS cc_start: 0.8737 (mptt) cc_final: 0.8491 (mmmt) REVERT: 5 1 MET cc_start: 0.7292 (pmm) cc_final: 0.7076 (pmm) REVERT: 5 11 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7995 (mt-10) REVERT: 9 13 LYS cc_start: 0.7270 (pttt) cc_final: 0.6768 (tttm) REVERT: A 123 LEU cc_start: 0.7960 (tp) cc_final: 0.7483 (mp) REVERT: B 92 ASN cc_start: 0.7366 (p0) cc_final: 0.7047 (p0) REVERT: E 60 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7417 (tptm) REVERT: E 115 LEU cc_start: 0.7353 (pp) cc_final: 0.7014 (mm) REVERT: I 61 MET cc_start: 0.7373 (OUTLIER) cc_final: 0.6143 (mpt) REVERT: J 81 MET cc_start: 0.8249 (ttp) cc_final: 0.7625 (ttp) REVERT: M 314 LYS cc_start: 0.8506 (ttpp) cc_final: 0.8202 (tttp) REVERT: P 72 ASP cc_start: 0.7524 (t0) cc_final: 0.7073 (t70) REVERT: P 99 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7834 (tp) REVERT: P 143 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7604 (mp0) REVERT: Q 40 GLN cc_start: 0.7888 (tp-100) cc_final: 0.7524 (mm-40) REVERT: Q 49 GLN cc_start: 0.8087 (pt0) cc_final: 0.7811 (pt0) REVERT: Q 52 TYR cc_start: 0.6542 (m-80) cc_final: 0.6209 (m-10) REVERT: R 120 SER cc_start: 0.6626 (p) cc_final: 0.6303 (t) REVERT: S 169 ARG cc_start: 0.7871 (ptm160) cc_final: 0.7581 (ptm160) REVERT: S 203 PHE cc_start: 0.7941 (m-80) cc_final: 0.7720 (m-80) REVERT: S 217 GLU cc_start: 0.6292 (tp30) cc_final: 0.6005 (tp30) REVERT: S 229 ASP cc_start: 0.7251 (m-30) cc_final: 0.6791 (m-30) REVERT: S 244 ARG cc_start: 0.8001 (tpp-160) cc_final: 0.7646 (ttp-110) REVERT: S 283 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6922 (mm-30) REVERT: S 303 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7288 (mm-30) REVERT: T 72 GLU cc_start: 0.7212 (tp30) cc_final: 0.6921 (tp30) REVERT: T 199 ARG cc_start: 0.7586 (mmm160) cc_final: 0.7135 (ptp90) REVERT: T 237 ASP cc_start: 0.7596 (m-30) cc_final: 0.7286 (m-30) REVERT: T 487 LYS cc_start: 0.8186 (mtpp) cc_final: 0.7626 (ttmt) REVERT: T 551 LYS cc_start: 0.7845 (ptpp) cc_final: 0.7472 (ptmm) REVERT: T 553 GLU cc_start: 0.7300 (tp30) cc_final: 0.7037 (tp30) REVERT: U 112 ASP cc_start: 0.8273 (p0) cc_final: 0.8069 (p0) REVERT: U 149 GLN cc_start: 0.7779 (mt0) cc_final: 0.7223 (mm110) REVERT: U 371 GLU cc_start: 0.7755 (pm20) cc_final: 0.7431 (pm20) REVERT: U 511 LYS cc_start: 0.7588 (mmpt) cc_final: 0.6947 (mttt) REVERT: U 553 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7707 (mm-30) REVERT: V 50 LYS cc_start: 0.8321 (ttmt) cc_final: 0.7791 (tmmt) REVERT: V 278 GLN cc_start: 0.7900 (mt0) cc_final: 0.7512 (mm-40) REVERT: V 283 ARG cc_start: 0.7905 (ptm-80) cc_final: 0.7552 (ttt90) REVERT: V 414 TYR cc_start: 0.7821 (m-80) cc_final: 0.7569 (m-80) REVERT: V 515 GLN cc_start: 0.7226 (tm130) cc_final: 0.6787 (pt0) REVERT: V 534 LYS cc_start: 0.8457 (mtpm) cc_final: 0.8234 (mttm) REVERT: X 131 GLU cc_start: 0.8281 (mt-10) cc_final: 0.8002 (mt-10) REVERT: X 359 ASP cc_start: 0.7788 (m-30) cc_final: 0.7473 (m-30) REVERT: X 493 LYS cc_start: 0.8001 (ttpt) cc_final: 0.7594 (ttmm) REVERT: X 550 LYS cc_start: 0.8060 (ptpp) cc_final: 0.7541 (pptt) REVERT: X 572 LYS cc_start: 0.7938 (tmmt) cc_final: 0.7618 (tmtt) REVERT: Y 149 GLU cc_start: 0.6045 (OUTLIER) cc_final: 0.5826 (mp0) REVERT: Y 359 ASP cc_start: 0.7818 (m-30) cc_final: 0.7531 (m-30) REVERT: Y 385 ARG cc_start: 0.7885 (mmt90) cc_final: 0.7570 (mmm-85) REVERT: Y 414 GLN cc_start: 0.7756 (OUTLIER) cc_final: 0.7480 (mt0) REVERT: Y 431 LEU cc_start: 0.7786 (tp) cc_final: 0.7568 (tm) REVERT: Y 437 ARG cc_start: 0.6930 (mtt-85) cc_final: 0.6322 (mmm-85) REVERT: Y 441 ARG cc_start: 0.7305 (mmt-90) cc_final: 0.6985 (mmt90) REVERT: Y 533 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7258 (pm20) REVERT: Z 82 ASP cc_start: 0.7455 (t0) cc_final: 0.6866 (t0) REVERT: Z 226 GLU cc_start: 0.7415 (mt-10) cc_final: 0.7044 (mt-10) REVERT: Z 292 GLN cc_start: 0.7545 (tt0) cc_final: 0.7145 (tt0) REVERT: Z 359 ASP cc_start: 0.7430 (m-30) cc_final: 0.6980 (m-30) REVERT: Z 411 LYS cc_start: 0.8215 (mttp) cc_final: 0.7984 (tmmt) REVERT: Z 430 LYS cc_start: 0.5703 (mtmp) cc_final: 0.5201 (ptpt) outliers start: 100 outliers final: 75 residues processed: 649 average time/residue: 1.3479 time to fit residues: 1105.1738 Evaluate side-chains 653 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 569 time to evaluate : 4.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 1 residue 92 TYR Chi-restraints excluded: chain 1 residue 193 VAL Chi-restraints excluded: chain 1 residue 226 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 283 ASP Chi-restraints excluded: chain 1 residue 393 LEU Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 499 GLU Chi-restraints excluded: chain 2 residue 128 VAL Chi-restraints excluded: chain 2 residue 168 THR Chi-restraints excluded: chain 2 residue 359 THR Chi-restraints excluded: chain 2 residue 440 LYS Chi-restraints excluded: chain 3 residue 156 ASP Chi-restraints excluded: chain 3 residue 316 VAL Chi-restraints excluded: chain 4 residue 13 TYR Chi-restraints excluded: chain 4 residue 33 LEU Chi-restraints excluded: chain 4 residue 44 THR Chi-restraints excluded: chain 4 residue 118 THR Chi-restraints excluded: chain 5 residue 61 SER Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 69 THR Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 7 residue 23 LEU Chi-restraints excluded: chain 7 residue 61 VAL Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 6 VAL Chi-restraints excluded: chain 8 residue 66 ASP Chi-restraints excluded: chain 9 residue 17 ASP Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 61 MET Chi-restraints excluded: chain I residue 92 ASN Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 157 ILE Chi-restraints excluded: chain P residue 205 ARG Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain S residue 185 HIS Chi-restraints excluded: chain S residue 243 LEU Chi-restraints excluded: chain S residue 283 GLU Chi-restraints excluded: chain T residue 144 VAL Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 339 LEU Chi-restraints excluded: chain T residue 473 VAL Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 516 ASP Chi-restraints excluded: chain U residue 550 LEU Chi-restraints excluded: chain V residue 115 VAL Chi-restraints excluded: chain V residue 134 ASN Chi-restraints excluded: chain V residue 287 MET Chi-restraints excluded: chain V residue 409 GLU Chi-restraints excluded: chain V residue 465 ASP Chi-restraints excluded: chain V residue 529 ASN Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 74 LEU Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 297 VAL Chi-restraints excluded: chain X residue 354 THR Chi-restraints excluded: chain X residue 452 VAL Chi-restraints excluded: chain X residue 505 ASP Chi-restraints excluded: chain Y residue 149 GLU Chi-restraints excluded: chain Y residue 193 ILE Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 325 ILE Chi-restraints excluded: chain Y residue 414 GLN Chi-restraints excluded: chain Y residue 533 GLU Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 492 ILE Chi-restraints excluded: chain Z residue 523 ASP Chi-restraints excluded: chain Z residue 532 SER Chi-restraints excluded: chain Z residue 559 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 439 optimal weight: 0.1980 chunk 589 optimal weight: 10.0000 chunk 169 optimal weight: 0.5980 chunk 510 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 153 optimal weight: 9.9990 chunk 554 optimal weight: 4.9990 chunk 232 optimal weight: 6.9990 chunk 569 optimal weight: 0.8980 chunk 70 optimal weight: 0.4980 chunk 102 optimal weight: 7.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 48 ASN 1 346 GLN 2 74 ASN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 78 HIS C 98 GLN F 98 GLN ** H 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 71 GLN ** Q 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 154 GLN ** R 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 539 ASN ** U 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 152 ASN U 471 GLN ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 529 ASN Z 448 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.136380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.102744 restraints weight = 71661.619| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.69 r_work: 0.2927 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 54686 Z= 0.217 Angle : 0.559 19.130 74161 Z= 0.279 Chirality : 0.042 0.213 8689 Planarity : 0.004 0.085 9510 Dihedral : 5.928 91.908 7685 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.55 % Favored : 96.33 % Rotamer: Outliers : 1.69 % Allowed : 19.62 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.34 (0.10), residues: 7038 helix: 0.83 (0.09), residues: 3857 sheet: -0.51 (0.21), residues: 624 loop : -0.37 (0.13), residues: 2557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 9 73 HIS 0.010 0.001 HIS T 549 PHE 0.038 0.001 PHE H 107 TYR 0.021 0.001 TYR 4 211 ARG 0.019 0.000 ARG P 167 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18474.86 seconds wall clock time: 321 minutes 46.87 seconds (19306.87 seconds total)