Starting phenix.real_space_refine on Tue Feb 13 08:02:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6re6_4843/02_2024/6re6_4843_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6re6_4843/02_2024/6re6_4843.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6re6_4843/02_2024/6re6_4843.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6re6_4843/02_2024/6re6_4843.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6re6_4843/02_2024/6re6_4843_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6re6_4843/02_2024/6re6_4843_updated.pdb" } resolution = 3.4 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned 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 34282 2.51 5 N 9107 2.21 5 O 10163 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 GLU 33": "OE1" <-> "OE2" Residue "1 GLU 34": "OE1" <-> "OE2" Residue "1 ASP 69": "OD1" <-> "OD2" Residue "1 ASP 91": "OD1" <-> "OD2" Residue "1 ARG 150": "NH1" <-> "NH2" Residue "1 GLU 165": "OE1" <-> "OE2" Residue "1 ASP 172": "OD1" <-> "OD2" Residue "1 ARG 182": "NH1" <-> "NH2" Residue "1 GLU 198": "OE1" <-> "OE2" Residue "1 PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 235": "OE1" <-> "OE2" Residue "1 ARG 259": "NH1" <-> "NH2" Residue "1 GLU 273": "OE1" <-> "OE2" Residue "1 GLU 329": "OE1" <-> "OE2" Residue "1 GLU 339": "OE1" <-> "OE2" Residue "1 GLU 350": "OE1" <-> "OE2" Residue "1 ARG 359": "NH1" <-> "NH2" Residue "1 ASP 373": "OD1" <-> "OD2" Residue "1 ARG 387": "NH1" <-> "NH2" Residue "1 GLU 409": "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 452": "OE1" <-> "OE2" Residue "1 GLU 457": "OE1" <-> "OE2" Residue "1 ASP 486": "OD1" <-> "OD2" Residue "1 GLU 496": "OE1" <-> "OE2" Residue "1 ASP 504": "OD1" <-> "OD2" Residue "1 GLU 513": "OE1" <-> "OE2" Residue "1 GLU 517": "OE1" <-> "OE2" Residue "1 ASP 572": "OD1" <-> "OD2" Residue "1 ASP 573": "OD1" <-> "OD2" Residue "1 ASP 601": "OD1" <-> "OD2" Residue "1 ARG 609": "NH1" <-> "NH2" Residue "2 GLU 5": "OE1" <-> "OE2" Residue "2 ASP 7": "OD1" <-> "OD2" Residue "2 TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 45": "NH1" <-> "NH2" Residue "2 TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 79": "OE1" <-> "OE2" Residue "2 GLU 86": "OE1" <-> "OE2" Residue "2 TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 149": "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 ASP 230": "OD1" <-> "OD2" Residue "2 GLU 260": "OE1" <-> "OE2" Residue "2 PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 281": "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 PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 346": "NH1" <-> "NH2" 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 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 92": "OE1" <-> "OE2" Residue "3 ASP 102": "OD1" <-> "OD2" Residue "3 PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 149": "NH1" <-> "NH2" Residue "3 ASP 154": "OD1" <-> "OD2" Residue "3 PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 175": "OE1" <-> "OE2" Residue "3 PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 197": "OD1" <-> "OD2" Residue "3 ARG 213": "NH1" <-> "NH2" Residue "3 ASP 217": "OD1" <-> "OD2" 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 "3 GLU 301": "OE1" <-> "OE2" Residue "3 GLU 314": "OE1" <-> "OE2" Residue "3 PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 21": "OE1" <-> "OE2" Residue "4 TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 45": "OD1" <-> "OD2" Residue "4 GLU 64": "OE1" <-> "OE2" Residue "4 ARG 84": "NH1" <-> "NH2" Residue "4 TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 121": "OD1" <-> "OD2" Residue "4 ASP 133": "OD1" <-> "OD2" Residue "4 TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 146": "OE1" <-> "OE2" Residue "4 ASP 156": "OD1" <-> "OD2" Residue "4 ARG 176": "NH1" <-> "NH2" Residue "4 TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 193": "OE1" <-> "OE2" Residue "4 GLU 202": "OE1" <-> "OE2" Residue "4 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 GLU 266": "OE1" <-> "OE2" Residue "4 GLU 270": "OE1" <-> "OE2" Residue "4 ASP 271": "OD1" <-> "OD2" Residue "4 PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 284": "OE1" <-> "OE2" Residue "5 ARG 36": "NH1" <-> "NH2" Residue "5 ARG 50": "NH1" <-> "NH2" Residue "5 ARG 112": "NH1" <-> "NH2" Residue "5 PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 91": "OD1" <-> "OD2" Residue "7 PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 47": "OE1" <-> "OE2" Residue "7 ARG 81": "NH1" <-> "NH2" Residue "7 GLU 99": "OE1" <-> "OE2" Residue "7 TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 109": "OD1" <-> "OD2" Residue "7 PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 117": "OD1" <-> "OD2" 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 ASP 10": "OD1" <-> "OD2" Residue "8 ARG 13": "NH1" <-> "NH2" Residue "8 ASP 62": "OD1" <-> "OD2" Residue "8 ARG 65": "NH1" <-> "NH2" Residue "8 ASP 66": "OD1" <-> "OD2" 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 PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ARG 28": "NH1" <-> "NH2" Residue "9 PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ARG 40": "NH1" <-> "NH2" Residue "9 PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ASP 82": "OD1" <-> "OD2" Residue "9 GLU 92": "OE1" <-> "OE2" Residue "A PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 115": "NH1" <-> "NH2" Residue "M ASP 143": "OD1" <-> "OD2" Residue "M ARG 145": "NH1" <-> "NH2" Residue "M PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 225": "OE1" <-> "OE2" Residue "M ARG 232": "NH1" <-> "NH2" Residue "M ARG 239": "NH1" <-> "NH2" Residue "M PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 288": "OE1" <-> "OE2" Residue "M PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 72": "OD1" <-> "OD2" Residue "P PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 163": "OD1" <-> "OD2" Residue "P ASP 179": "OD1" <-> "OD2" Residue "P PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "Q GLU 64": "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 PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 117": "OE1" <-> "OE2" Residue "R GLU 123": "OE1" <-> "OE2" Residue "R GLU 148": "OE1" <-> "OE2" Residue "R ASP 153": "OD1" <-> "OD2" Residue "R ASP 174": "OD1" <-> "OD2" Residue "R PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 177": "OE1" <-> "OE2" Residue "R GLU 186": "OE1" <-> "OE2" Residue "S ARG 46": "NH1" <-> "NH2" Residue "S ASP 83": "OD1" <-> "OD2" Residue "S GLU 131": "OE1" <-> "OE2" Residue "S ARG 147": "NH1" <-> "NH2" Residue "S ARG 152": "NH1" <-> "NH2" Residue "S GLU 154": "OE1" <-> "OE2" Residue "S ARG 157": "NH1" <-> "NH2" Residue "S TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 221": "OE1" <-> "OE2" Residue "S ASP 222": "OD1" <-> "OD2" Residue "S ASP 229": "OD1" <-> "OD2" Residue "S GLU 234": "OE1" <-> "OE2" Residue "S ASP 241": "OD1" <-> "OD2" Residue "S ARG 244": "NH1" <-> "NH2" Residue "S GLU 283": "OE1" <-> "OE2" Residue "S TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 306": "OE1" <-> "OE2" Residue "T GLU 47": "OE1" <-> "OE2" Residue "T ARG 49": "NH1" <-> "NH2" Residue "T GLU 72": "OE1" <-> "OE2" Residue "T GLU 74": "OE1" <-> "OE2" Residue "T ARG 86": "NH1" <-> "NH2" Residue "T ASP 125": "OD1" <-> "OD2" Residue "T ASP 142": "OD1" <-> "OD2" Residue "T ARG 162": "NH1" <-> "NH2" Residue "T ASP 165": "OD1" <-> "OD2" Residue "T ASP 172": "OD1" <-> "OD2" Residue "T ARG 195": "NH1" <-> "NH2" Residue "T ARG 199": "NH1" <-> "NH2" Residue "T PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 237": "OD1" <-> "OD2" Residue "T TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 283": "NH1" <-> "NH2" Residue "T TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 325": "OD1" <-> "OD2" Residue "T ASP 353": "OD1" <-> "OD2" Residue "T ASP 403": "OD1" <-> "OD2" Residue "T GLU 409": "OE1" <-> "OE2" Residue "T 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 PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 465": "OD1" <-> "OD2" Residue "T PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 547": "OD1" <-> "OD2" Residue "T ARG 555": "NH1" <-> "NH2" Residue "U ASP 46": "OD1" <-> "OD2" Residue "U ARG 49": "NH1" <-> "NH2" Residue "U PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 92": "OD1" <-> "OD2" Residue "U ARG 96": "NH1" <-> "NH2" Residue "U TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 125": "OD1" <-> "OD2" 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 ARG 227": "NH1" <-> "NH2" Residue "U ARG 254": "NH1" <-> "NH2" Residue "U TYR 256": "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 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 GLU 371": "OE1" <-> "OE2" Residue "U PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 409": "OE1" <-> "OE2" Residue "U GLU 411": "OE1" <-> "OE2" Residue "U PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 449": "OE1" <-> "OE2" Residue "U ARG 454": "NH1" <-> "NH2" Residue "U GLU 455": "OE1" <-> "OE2" Residue "U PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 475": "OE1" <-> "OE2" Residue "U ARG 479": "NH1" <-> "NH2" Residue "U ARG 496": "NH1" <-> "NH2" Residue "U ARG 513": "NH1" <-> "NH2" Residue "U GLU 521": "OE1" <-> "OE2" Residue "U PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 47": "OE1" <-> "OE2" Residue "V ARG 49": "NH1" <-> "NH2" Residue "V PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 74": "OE1" <-> "OE2" Residue "V PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 125": "OD1" <-> "OD2" Residue "V PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 135": "OD1" <-> "OD2" Residue "V ASP 142": "OD1" <-> "OD2" Residue "V ASP 165": "OD1" <-> "OD2" Residue "V ARG 181": "NH1" <-> "NH2" Residue "V GLU 186": "OE1" <-> "OE2" Residue "V ASP 210": "OD1" <-> "OD2" Residue "V ARG 217": "NH1" <-> "NH2" Residue "V ARG 220": "NH1" <-> "NH2" Residue "V ASP 226": "OD1" <-> "OD2" 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 ASP 326": "OD1" <-> "OD2" 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 GLU 371": "OE1" <-> "OE2" Residue "V ASP 403": "OD1" <-> "OD2" Residue "V PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 429": "NH1" <-> "NH2" Residue "V ARG 454": "NH1" <-> "NH2" Residue "V ASP 465": "OD1" <-> "OD2" Residue "V ASP 467": "OD1" <-> "OD2" Residue "V ARG 476": "NH1" <-> "NH2" Residue "V PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 496": "NH1" <-> "NH2" Residue "V ARG 513": "NH1" <-> "NH2" Residue "V ASP 547": "OD1" <-> "OD2" Residue "V GLU 553": "OE1" <-> "OE2" Residue "V ARG 555": "NH1" <-> "NH2" Residue "X TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 51": "NH1" <-> "NH2" Residue "X ARG 71": "NH1" <-> "NH2" Residue "X ASP 82": "OD1" <-> "OD2" Residue "X ARG 86": "NH1" <-> "NH2" Residue "X ASP 91": "OD1" <-> "OD2" Residue "X ASP 94": "OD1" <-> "OD2" Residue "X ARG 98": "NH1" <-> "NH2" Residue "X ASP 104": "OD1" <-> "OD2" Residue "X ARG 120": "NH1" <-> "NH2" Residue "X GLU 131": "OE1" <-> "OE2" Residue "X GLU 149": "OE1" <-> "OE2" Residue "X GLU 152": "OE1" <-> "OE2" Residue "X GLU 195": "OE1" <-> "OE2" Residue "X PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 216": "NH1" <-> "NH2" Residue "X ASP 222": "OD1" <-> "OD2" Residue "X GLU 229": "OE1" <-> "OE2" Residue "X GLU 238": "OE1" <-> "OE2" Residue "X ARG 258": "NH1" <-> "NH2" Residue "X GLU 270": "OE1" <-> "OE2" Residue "X PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 285": "OD1" <-> "OD2" Residue "X ASP 317": "OD1" <-> "OD2" Residue "X PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 359": "OD1" <-> "OD2" Residue "X GLU 370": "OE1" <-> "OE2" Residue "X ASP 378": "OD1" <-> "OD2" Residue "X ARG 385": "NH1" <-> "NH2" Residue "X GLU 395": "OE1" <-> "OE2" Residue "X ARG 401": "NH1" <-> "NH2" Residue "X TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 435": "NH1" <-> "NH2" Residue "X ARG 437": "NH1" <-> "NH2" Residue "X PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 480": "OD1" <-> "OD2" Residue "X GLU 497": "OE1" <-> "OE2" Residue "X ASP 500": "OD1" <-> "OD2" Residue "X ARG 509": "NH1" <-> "NH2" Residue "X ASP 513": "OD1" <-> "OD2" Residue "X GLU 519": "OE1" <-> "OE2" Residue "X GLU 520": "OE1" <-> "OE2" Residue "X ASP 523": "OD1" <-> "OD2" Residue "X ASP 543": "OD1" <-> "OD2" Residue "X ASP 548": "OD1" <-> "OD2" Residue "X PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 552": "OE1" <-> "OE2" Residue "X GLU 557": "OE1" <-> "OE2" Residue "X GLU 564": "OE1" <-> "OE2" Residue "Y ASP 36": "OD1" <-> "OD2" Residue "Y TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 51": "NH1" <-> "NH2" Residue "Y ASP 53": "OD1" <-> "OD2" Residue "Y GLU 146": "OE1" <-> "OE2" Residue "Y PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 168": "OD1" <-> "OD2" Residue "Y PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 218": "NH1" <-> "NH2" Residue "Y ARG 225": "NH1" <-> "NH2" Residue "Y ARG 239": "NH1" <-> "NH2" Residue "Y GLU 296": "OE1" <-> "OE2" Residue "Y TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 385": "NH1" <-> "NH2" Residue "Y TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 401": "NH1" <-> "NH2" Residue "Y ASP 409": "OD1" <-> "OD2" Residue "Y GLU 428": "OE1" <-> "OE2" Residue "Y ASP 429": "OD1" <-> "OD2" Residue "Y PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 479": "OD1" <-> "OD2" Residue "Y ASP 491": "OD1" <-> "OD2" Residue "Y GLU 494": "OE1" <-> "OE2" Residue "Y ARG 509": "NH1" <-> "NH2" Residue "Y GLU 519": "OE1" <-> "OE2" Residue "Y ASP 528": "OD1" <-> "OD2" Residue "Y GLU 533": "OE1" <-> "OE2" Residue "Y GLU 541": "OE1" <-> "OE2" Residue "Y ASP 548": "OD1" <-> "OD2" Residue "Y PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 36": "OD1" <-> "OD2" Residue "Z TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 71": "NH1" <-> "NH2" Residue "Z ASP 82": "OD1" <-> "OD2" Residue "Z ARG 86": "NH1" <-> "NH2" Residue "Z ARG 115": "NH1" <-> "NH2" Residue "Z ARG 120": "NH1" <-> "NH2" Residue "Z ARG 145": "NH1" <-> "NH2" Residue "Z PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 195": "OE1" <-> "OE2" Residue "Z GLU 229": "OE1" <-> "OE2" Residue "Z GLU 238": "OE1" <-> "OE2" Residue "Z ARG 258": "NH1" <-> "NH2" Residue "Z GLU 270": "OE1" <-> "OE2" Residue "Z TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 366": "NH1" <-> "NH2" Residue "Z GLU 370": "OE1" <-> "OE2" Residue "Z TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 385": "NH1" <-> "NH2" Residue "Z GLU 424": "OE1" <-> "OE2" Residue "Z GLU 427": "OE1" <-> "OE2" Residue "Z GLU 428": "OE1" <-> "OE2" Residue "Z GLU 451": "OE1" <-> "OE2" Residue "Z PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 462": "OD1" <-> "OD2" Residue "Z PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 479": "OD1" <-> "OD2" Residue "Z ASP 480": "OD1" <-> "OD2" Residue "Z TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 513": "OD1" <-> "OD2" Residue "Z GLU 536": "OE1" <-> "OE2" Residue "Z GLU 540": "OE1" <-> "OE2" Residue "Z GLU 547": "OE1" <-> "OE2" Residue "Z GLU 563": "OE1" <-> "OE2" Residue "Z GLU 564": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 53720 Number of models: 1 Model: "" Number of chains: 37 Chain: "0" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 607 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 8, 'TRANS': 72} Chain: "1" Number of atoms: 4661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4661 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 31, 'TRANS': 563} Chain: "2" Number of atoms: 3163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3163 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 17, 'TRANS': 423} Chain: "3" Number of atoms: 1874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1874 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 239} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 7 Chain: "4" Number of atoms: 2177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2177 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 9, 'TRANS': 280} Chain: "5" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 986 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "6" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 926 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "7" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1347 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 5, 'TRANS': 170} Chain: "8" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 692 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 7, 'TRANS': 80} Chain: "9" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 776 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 5, 'TRANS': 91} Chain: "A" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "B" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "C" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain breaks: 1 Chain: "D" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "E" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "F" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "G" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "H" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "I" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "J" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "M" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1640 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "P" Number of atoms: 1532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1532 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 5, 'TRANS': 187} Chain: "Q" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 561 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 5, 'TRANS': 66} Chain: "R" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1303 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 13, 'TRANS': 163} Chain: "S" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2130 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 271} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 3979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3979 Classifications: {'peptide': 523} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Chain: "U" Number of atoms: 3978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3978 Classifications: {'peptide': 523} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "V" Number of atoms: 3961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3961 Classifications: {'peptide': 520} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 494} Chain: "X" 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: "Y" Number of atoms: 3952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3952 Classifications: {'peptide': 520} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 497} Chain: "Z" Number of atoms: 4095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4095 Classifications: {'peptide': 539} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 514} 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: "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: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 20.50, per 1000 atoms: 0.38 Number of scatterers: 53720 At special positions: 0 Unit cell: (212.706, 130.572, 259.038, 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 10163 8.00 N 9107 7.00 C 34282 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: 15.56 Conformation dependent library (CDL) restraints added in 7.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN M 600 " pdb="ZN ZN M 600 " - pdb=" NE2 HIS M 248 " 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13076 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 284 helices and 32 sheets defined 52.1% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.38 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 49 Processing helix chain '0' and resid 52 through 55 No H-bonds generated for 'chain '0' and resid 52 through 55' Processing helix chain '1' and resid 46 through 72 Processing helix chain '1' and resid 106 through 138 Processing helix chain '1' and resid 164 through 175 removed outlier: 4.243A pdb=" N THR 1 169 " --> pdb=" O GLU 1 165 " (cutoff:3.500A) Processing helix chain '1' and resid 191 through 203 Processing helix chain '1' and resid 210 through 223 removed outlier: 3.718A pdb=" N SER 1 214 " --> pdb=" O ALA 1 210 " (cutoff:3.500A) Processing helix chain '1' and resid 242 through 270 Processing helix chain '1' and resid 272 through 276 removed outlier: 3.630A pdb=" N ALA 1 275 " --> pdb=" O PRO 1 272 " (cutoff:3.500A) Processing helix chain '1' and resid 283 through 285 No H-bonds generated for 'chain '1' and resid 283 through 285' Processing helix chain '1' and resid 298 through 304 Processing helix chain '1' and resid 311 through 316 Processing helix chain '1' and resid 324 through 326 No H-bonds generated for 'chain '1' and resid 324 through 326' Processing helix chain '1' and resid 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: 3.616A pdb=" N VAL 1 382 " --> pdb=" O GLU 1 378 " (cutoff:3.500A) Processing helix chain '1' and resid 393 through 420 removed outlier: 3.574A pdb=" N GLU 1 415 " --> pdb=" O ALA 1 411 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VAL 1 418 " --> pdb=" O GLU 1 414 " (cutoff:3.500A) removed outlier: 5.354A 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 removed outlier: 3.586A pdb=" N ARG 1 453 " --> pdb=" O ALA 1 449 " (cutoff:3.500A) Processing helix chain '1' and resid 464 through 477 Processing helix chain '1' and resid 480 through 482 No H-bonds generated for 'chain '1' and resid 480 through 482' Processing helix chain '1' and resid 486 through 489 No H-bonds generated for 'chain '1' and resid 486 through 489' Processing helix chain '1' and resid 491 through 516 removed outlier: 3.917A pdb=" N GLU 1 501 " --> pdb=" O LEU 1 497 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU 1 516 " --> pdb=" O LEU 1 512 " (cutoff:3.500A) Processing helix chain '1' and resid 519 through 535 Processing helix chain '1' and resid 542 through 548 Processing helix chain '1' and resid 550 through 561 Processing helix chain '1' and resid 567 through 573 Processing helix chain '1' and resid 578 through 587 Processing helix chain '1' and resid 593 through 605 Processing helix chain '2' and resid 8 through 18 Processing helix chain '2' and resid 26 through 37 Processing helix chain '2' and resid 45 through 57 Processing helix chain '2' and resid 63 through 75 Processing helix chain '2' and resid 81 through 93 removed outlier: 3.931A pdb=" N ALA 2 88 " --> pdb=" O VAL 2 84 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N GLY 2 89 " --> pdb=" O ALA 2 85 " (cutoff:3.500A) Proline residue: 2 90 - end of helix Processing helix chain '2' and resid 100 through 112 Processing helix chain '2' and resid 118 through 130 removed outlier: 3.596A pdb=" N VAL 2 127 " --> pdb=" O LYS 2 123 " (cutoff:3.500A) Processing helix chain '2' and resid 137 through 149 Processing helix chain '2' and resid 155 through 167 removed outlier: 3.651A pdb=" N VAL 2 164 " --> pdb=" O ALA 2 160 " (cutoff:3.500A) Processing helix chain '2' and resid 172 through 185 Processing helix chain '2' and resid 190 through 199 removed outlier: 4.196A pdb=" N ALA 2 195 " --> pdb=" O ALA 2 191 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N SER 2 199 " --> pdb=" O ALA 2 195 " (cutoff:3.500A) Processing helix chain '2' and resid 207 through 220 Processing helix chain '2' and resid 229 through 234 Processing helix chain '2' and resid 241 through 254 removed outlier: 3.667A pdb=" N GLU 2 246 " --> pdb=" O ALA 2 242 " (cutoff:3.500A) Processing helix chain '2' and resid 259 through 275 removed outlier: 3.570A pdb=" N VAL 2 268 " --> pdb=" O ALA 2 264 " (cutoff:3.500A) Proline residue: 2 271 - end of helix Processing helix chain '2' and resid 282 through 295 Processing helix chain '2' and resid 301 through 320 removed outlier: 4.344A pdb=" N SER 2 305 " --> pdb=" O ALA 2 301 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE 2 306 " --> pdb=" O ALA 2 302 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY 2 312 " --> pdb=" O ALA 2 308 " (cutoff:3.500A) Processing helix chain '2' and resid 326 through 340 Processing helix chain '2' and resid 346 through 355 removed outlier: 3.544A pdb=" N SER 2 355 " --> pdb=" O SER 2 351 " (cutoff:3.500A) Processing helix chain '2' and resid 397 through 409 removed outlier: 3.986A pdb=" N ALA 2 408 " --> pdb=" O LYS 2 404 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLN 2 409 " --> pdb=" O VAL 2 405 " (cutoff:3.500A) Processing helix chain '2' and resid 418 through 421 No H-bonds generated for 'chain '2' and resid 418 through 421' Processing helix chain '2' and resid 427 through 441 removed outlier: 3.779A pdb=" N VAL 2 441 " --> pdb=" O ALA 2 437 " (cutoff:3.500A) Processing helix chain '3' and resid 78 through 88 removed outlier: 3.744A pdb=" N LYS 3 88 " --> pdb=" O THR 3 84 " (cutoff:3.500A) 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 removed outlier: 3.750A pdb=" N TYR 3 108 " --> pdb=" O PRO 3 104 " (cutoff:3.500A) Processing helix chain '3' and resid 118 through 128 removed outlier: 4.290A pdb=" N LYS 3 123 " --> pdb=" O ASP 3 119 " (cutoff:3.500A) Processing helix chain '3' and resid 137 through 149 Processing helix chain '3' and resid 155 through 167 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: 3.822A pdb=" N GLN 3 179 " --> pdb=" O GLU 3 175 " (cutoff:3.500A) Processing helix chain '3' and resid 193 through 204 Processing helix chain '3' and resid 216 through 228 removed outlier: 3.857A pdb=" N THR 3 221 " --> pdb=" O ASP 3 217 " (cutoff:3.500A) Processing helix chain '3' and resid 234 through 243 removed outlier: 3.672A pdb=" N ARG 3 242 " --> pdb=" O ALA 3 238 " (cutoff:3.500A) removed outlier: 4.073A 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: 3.823A pdb=" N PHE 3 271 " --> pdb=" O ALA 3 267 " (cutoff:3.500A) Processing helix chain '3' and resid 276 through 286 removed outlier: 3.668A pdb=" N GLU 3 279 " --> pdb=" O GLU 3 276 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA 3 280 " --> pdb=" O SER 3 277 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE 3 282 " --> pdb=" O GLU 3 279 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY 3 283 " --> pdb=" O ALA 3 280 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA 3 284 " --> pdb=" O VAL 3 281 " (cutoff:3.500A) Processing helix chain '3' and resid 294 through 311 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 removed outlier: 3.753A pdb=" N ALA 4 25 " --> pdb=" O GLU 4 21 " (cutoff:3.500A) Processing helix chain '4' and resid 48 through 67 removed outlier: 3.609A pdb=" N ALA 4 60 " --> pdb=" O LYS 4 56 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLN 4 61 " --> pdb=" O TYR 4 57 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL 4 62 " --> pdb=" O LEU 4 58 " (cutoff:3.500A) Proline residue: 4 65 - end of helix Processing helix chain '4' and resid 80 through 95 Processing helix chain '4' and resid 101 through 112 Processing helix chain '4' and resid 119 through 125 Processing helix chain '4' and resid 132 through 149 removed outlier: 3.867A pdb=" N ALA 4 137 " --> pdb=" O ASP 4 133 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL 4 141 " --> pdb=" O ALA 4 137 " (cutoff:3.500A) Processing helix chain '4' and resid 160 through 176 removed outlier: 3.527A pdb=" N LYS 4 168 " --> pdb=" O LYS 4 164 " (cutoff:3.500A) removed outlier: 4.143A 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 193 through 233 removed outlier: 3.798A pdb=" N LYS 4 198 " --> pdb=" O ASP 4 194 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL 4 199 " --> pdb=" O ALA 4 195 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLU 4 202 " --> pdb=" O LYS 4 198 " (cutoff:3.500A) Processing helix chain '4' and resid 238 through 258 removed outlier: 3.811A pdb=" N ALA 4 256 " --> pdb=" O LEU 4 252 " (cutoff:3.500A) Processing helix chain '4' and resid 263 through 284 Processing helix chain '5' and resid 8 through 58 removed outlier: 4.817A pdb=" N LEU 5 31 " --> pdb=" O ASP 5 27 " (cutoff:3.500A) Proline residue: 5 32 - end of helix removed outlier: 3.602A pdb=" N GLU 5 37 " --> pdb=" O THR 5 33 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N HIS 5 41 " --> pdb=" O GLU 5 37 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N LYS 5 49 " --> pdb=" O ALA 5 45 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ARG 5 50 " --> pdb=" O ALA 5 46 " (cutoff:3.500A) Processing helix chain '5' and resid 64 through 66 No H-bonds generated for 'chain '5' and resid 64 through 66' Processing helix chain '5' and resid 73 through 80 Processing helix chain '5' and resid 88 through 105 removed outlier: 3.790A pdb=" N LEU 5 92 " --> pdb=" O PRO 5 88 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LYS 5 101 " --> pdb=" O SER 5 97 " (cutoff:3.500A) Processing helix chain '5' and resid 115 through 118 No H-bonds generated for 'chain '5' and resid 115 through 118' Processing helix chain '6' and resid 31 through 40 Processing helix chain '6' and resid 49 through 57 removed outlier: 4.232A pdb=" N LYS 6 52 " --> pdb=" O SER 6 49 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N THR 6 53 " --> pdb=" O SER 6 50 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA 6 56 " --> pdb=" O THR 6 53 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN 6 57 " --> pdb=" O ILE 6 54 " (cutoff:3.500A) Processing helix chain '6' and resid 73 through 95 removed outlier: 4.067A pdb=" N LYS 6 95 " --> pdb=" O ASP 6 91 " (cutoff:3.500A) Processing helix chain '6' and resid 99 through 119 removed outlier: 4.083A pdb=" N VAL 6 107 " --> pdb=" O LEU 6 103 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TRP 6 112 " --> pdb=" O LEU 6 108 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER 6 118 " --> pdb=" O ILE 6 114 " (cutoff:3.500A) Processing helix chain '6' and resid 122 through 130 Processing helix chain '7' and resid 69 through 71 No H-bonds generated for 'chain '7' and resid 69 through 71' Processing helix chain '7' and resid 84 through 104 removed outlier: 3.740A pdb=" N GLU 7 99 " --> pdb=" O SER 7 95 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU 7 103 " --> pdb=" O GLU 7 99 " (cutoff:3.500A) Processing helix chain '7' and resid 111 through 113 No H-bonds generated for 'chain '7' and resid 111 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 Processing helix chain '7' and resid 147 through 156 removed outlier: 3.673A pdb=" N LEU 7 150 " --> pdb=" O PHE 7 147 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER 7 151 " --> pdb=" O ASP 7 148 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ALA 7 154 " --> pdb=" O SER 7 151 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER 7 155 " --> pdb=" O ALA 7 152 " (cutoff:3.500A) Processing helix chain '7' and resid 158 through 164 Processing helix chain '7' and resid 175 through 186 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 79 removed outlier: 3.628A pdb=" N TRP 8 45 " --> pdb=" O ILE 8 41 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N TYR 8 46 " --> pdb=" O PRO 8 42 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N LEU 8 47 " --> pdb=" O ARG 8 43 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA 8 79 " --> pdb=" O GLU 8 75 " (cutoff:3.500A) Processing helix chain '9' and resid 6 through 16 Processing helix chain '9' and resid 33 through 56 removed outlier: 3.619A pdb=" N VAL 9 37 " --> pdb=" O LYS 9 33 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA 9 38 " --> pdb=" O GLY 9 34 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL 9 42 " --> pdb=" O ALA 9 38 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ASN 9 56 " --> pdb=" O LEU 9 52 " (cutoff:3.500A) Processing helix chain '9' and resid 83 through 96 removed outlier: 3.577A pdb=" N LYS 9 95 " --> pdb=" O LYS 9 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 91 removed outlier: 3.521A pdb=" N ALA A 64 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR A 68 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ILE A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ALA A 70 " --> pdb=" O CYS A 66 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N LEU A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ALA A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLY A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 125 removed outlier: 3.772A pdb=" N ALA A 96 " --> pdb=" O PRO A 93 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N LYS A 97 " --> pdb=" O ASN A 94 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N VAL A 100 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU A 104 " --> pdb=" O GLY A 101 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU A 105 " --> pdb=" O TYR A 102 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE A 107 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA A 108 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU A 111 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER A 112 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE A 113 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU A 119 " --> pdb=" O PHE A 116 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU A 125 " --> pdb=" O PHE A 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 91 removed outlier: 3.640A pdb=" N LYS B 60 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ILE B 69 " --> pdb=" O GLY B 65 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ALA B 70 " --> pdb=" O CYS B 66 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LEU B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA B 72 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY B 73 " --> pdb=" O ILE B 69 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE B 86 " --> pdb=" O PHE B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 125 removed outlier: 5.172A pdb=" N LYS B 97 " --> pdb=" O ASN B 94 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY B 106 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLU B 111 " --> pdb=" O ALA B 108 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N SER B 112 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE B 113 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU B 115 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE B 116 " --> pdb=" O ILE B 113 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU B 118 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU B 119 " --> pdb=" O PHE B 116 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU B 125 " --> pdb=" O PHE B 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 91 removed outlier: 3.871A pdb=" N LYS C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ILE C 69 " --> pdb=" O GLY C 65 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ALA C 70 " --> pdb=" O CYS C 66 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N LEU C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ALA C 72 " --> pdb=" O THR C 68 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLY C 73 " --> pdb=" O ILE C 69 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 125 removed outlier: 5.249A pdb=" N LYS C 97 " --> pdb=" O ASN C 94 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL C 100 " --> pdb=" O LYS C 97 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR C 110 " --> pdb=" O PHE C 107 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER C 112 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE C 113 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU C 119 " --> pdb=" O PHE C 116 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE C 122 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE C 124 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU C 125 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 91 removed outlier: 4.044A pdb=" N MET D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA D 64 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLY D 65 " --> pdb=" O MET D 61 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ILE D 69 " --> pdb=" O GLY D 65 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ALA D 70 " --> pdb=" O CYS D 66 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N LEU D 71 " --> pdb=" O ALA D 67 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ALA D 72 " --> pdb=" O THR D 68 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY D 73 " --> pdb=" O ILE D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 125 removed outlier: 5.049A pdb=" N LYS D 97 " --> pdb=" O ASN D 94 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL D 100 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLY D 101 " --> pdb=" O GLN D 98 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU D 104 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU D 111 " --> pdb=" O ALA D 108 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER D 112 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU D 119 " --> pdb=" O PHE D 116 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU D 125 " --> pdb=" O PHE D 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 91 removed outlier: 4.148A pdb=" N MET E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA E 64 " --> pdb=" O LYS E 60 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE E 69 " --> pdb=" O GLY E 65 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ALA E 70 " --> pdb=" O CYS E 66 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N LEU E 71 " --> pdb=" O ALA E 67 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ALA E 72 " --> pdb=" O THR E 68 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY E 73 " --> pdb=" O ILE E 69 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL E 74 " --> pdb=" O ALA E 70 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL E 80 " --> pdb=" O ALA E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 123 removed outlier: 4.959A pdb=" N LYS E 97 " --> pdb=" O ASN E 94 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL E 100 " --> pdb=" O LYS E 97 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER E 112 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU E 119 " --> pdb=" O PHE E 116 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL E 121 " --> pdb=" O LEU E 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 69 removed outlier: 3.782A pdb=" N MET F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL F 62 " --> pdb=" O ALA F 58 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE F 69 " --> pdb=" O GLY F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 91 removed outlier: 3.689A pdb=" N ILE F 86 " --> pdb=" O PHE F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 126 removed outlier: 5.117A pdb=" N LYS F 97 " --> pdb=" O ASN F 94 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL F 100 " --> pdb=" O LYS F 97 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU F 111 " --> pdb=" O ALA F 108 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N SER F 112 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU F 115 " --> pdb=" O SER F 112 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU F 119 " --> pdb=" O PHE F 116 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU F 125 " --> pdb=" O PHE F 122 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N PHE F 126 " --> pdb=" O LEU F 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 67 removed outlier: 4.019A pdb=" N MET G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL G 62 " --> pdb=" O ALA G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 91 removed outlier: 3.676A pdb=" N VAL G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE G 86 " --> pdb=" O PHE G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 126 removed outlier: 3.575A pdb=" N ALA G 96 " --> pdb=" O PRO G 93 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N LYS G 97 " --> pdb=" O ASN G 94 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N VAL G 100 " --> pdb=" O LYS G 97 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU G 104 " --> pdb=" O GLY G 101 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR G 110 " --> pdb=" O PHE G 107 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU G 111 " --> pdb=" O ALA G 108 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N SER G 112 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU G 125 " --> pdb=" O PHE G 122 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N PHE G 126 " --> pdb=" O LEU G 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 89 removed outlier: 3.799A pdb=" N MET H 61 " --> pdb=" O ALA H 57 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA H 64 " --> pdb=" O LYS H 60 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY H 65 " --> pdb=" O MET H 61 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ILE H 69 " --> pdb=" O GLY H 65 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ALA H 70 " --> pdb=" O CYS H 66 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N LEU H 71 " --> pdb=" O ALA H 67 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ALA H 72 " --> pdb=" O THR H 68 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLY H 73 " --> pdb=" O ILE H 69 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE H 86 " --> pdb=" O PHE H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 125 removed outlier: 5.192A pdb=" N LYS H 97 " --> pdb=" O ASN H 94 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE H 107 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU H 109 " --> pdb=" O GLY H 106 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU H 111 " --> pdb=" O ALA H 108 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER H 112 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEU H 125 " --> pdb=" O PHE H 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 91 removed outlier: 3.801A pdb=" N MET I 61 " --> pdb=" O ALA I 57 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL I 62 " --> pdb=" O ALA I 58 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE I 69 " --> pdb=" O GLY I 65 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ALA I 70 " --> pdb=" O CYS I 66 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N LEU I 71 " --> pdb=" O ALA I 67 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ALA I 72 " --> pdb=" O THR I 68 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY I 73 " --> pdb=" O ILE I 69 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE I 86 " --> pdb=" O PHE I 82 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG I 91 " --> pdb=" O ASN I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 125 removed outlier: 3.660A pdb=" N ALA I 96 " --> pdb=" O PRO I 93 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N LYS I 97 " --> pdb=" O ASN I 94 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL I 100 " --> pdb=" O LYS I 97 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N SER I 112 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU I 125 " --> pdb=" O PHE I 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 91 removed outlier: 4.409A pdb=" N MET J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL J 62 " --> pdb=" O ALA J 58 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE J 69 " --> pdb=" O GLY J 65 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ALA J 70 " --> pdb=" O CYS J 66 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N LEU J 71 " --> pdb=" O ALA J 67 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ALA J 72 " --> pdb=" O THR J 68 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLY J 73 " --> pdb=" O ILE J 69 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL J 74 " --> pdb=" O ALA J 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 125 removed outlier: 3.608A pdb=" N ALA J 96 " --> pdb=" O PRO J 93 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N LYS J 97 " --> pdb=" O ASN J 94 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU J 99 " --> pdb=" O ALA J 96 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL J 100 " --> pdb=" O LYS J 97 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU J 104 " --> pdb=" O GLY J 101 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU J 111 " --> pdb=" O ALA J 108 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER J 112 " --> pdb=" O LEU J 109 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU J 125 " --> pdb=" O PHE J 122 " (cutoff:3.500A) Processing helix chain 'M' and resid 105 through 118 Processing helix chain 'M' and resid 135 through 143 Processing helix chain 'M' and resid 148 through 164 Processing helix chain 'M' and resid 174 through 176 No H-bonds generated for 'chain 'M' and resid 174 through 176' Processing helix chain 'M' and resid 178 through 200 removed outlier: 3.593A pdb=" N THR M 200 " --> pdb=" O GLY M 196 " (cutoff:3.500A) Processing helix chain 'M' and resid 222 through 264 removed outlier: 4.313A pdb=" N ARG M 232 " --> pdb=" O SER M 228 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALA M 233 " --> pdb=" O TYR M 229 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N VAL M 234 " --> pdb=" O THR M 230 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLY M 237 " --> pdb=" O ALA M 233 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLY M 247 " --> pdb=" O ASN M 243 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N HIS M 248 " --> pdb=" O MET M 244 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA M 260 " --> pdb=" O GLY M 256 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU M 261 " --> pdb=" O MET M 257 " (cutoff:3.500A) Proline residue: M 262 - end of helix Processing helix chain 'M' and resid 271 through 308 removed outlier: 3.531A pdb=" N VAL M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU M 280 " --> pdb=" O GLY M 276 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER M 296 " --> pdb=" O ALA M 292 " (cutoff:3.500A) Processing helix chain 'P' and resid 51 through 63 Processing helix chain 'P' and resid 67 through 83 removed outlier: 3.531A pdb=" N GLN P 71 " --> pdb=" O LEU P 67 " (cutoff:3.500A) Processing helix chain 'P' and resid 85 through 92 removed outlier: 3.830A pdb=" N LEU P 90 " --> pdb=" O GLU P 86 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA P 91 " --> pdb=" O LEU P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 98 through 108 Processing helix chain 'P' and resid 116 through 127 Processing helix chain 'P' and resid 131 through 148 removed outlier: 3.906A pdb=" N LEU P 135 " --> pdb=" O SER P 132 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU P 136 " --> pdb=" O ALA P 133 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N THR P 138 " --> pdb=" O LEU P 135 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N VAL P 139 " --> pdb=" O GLU P 136 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN P 140 " --> pdb=" O VAL P 137 " (cutoff:3.500A) Processing helix chain 'P' and resid 168 through 177 removed outlier: 3.888A pdb=" N LYS P 172 " --> pdb=" O VAL P 168 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS P 173 " --> pdb=" O GLU P 169 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LYS P 176 " --> pdb=" O LYS P 172 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N PHE P 177 " --> pdb=" O LYS P 173 " (cutoff:3.500A) Processing helix chain 'P' and resid 214 through 226 removed outlier: 3.693A pdb=" N ASN P 219 " --> pdb=" O VAL P 215 " (cutoff:3.500A) Processing helix chain 'Q' and resid 16 through 30 removed outlier: 4.062A pdb=" N VAL Q 30 " --> pdb=" O LEU Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 33 through 39 removed outlier: 3.700A pdb=" N ALA Q 37 " --> pdb=" O GLU Q 33 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LYS Q 38 " --> pdb=" O PRO Q 34 " (cutoff:3.500A) Processing helix chain 'Q' and resid 41 through 43 No H-bonds generated for 'chain 'Q' and resid 41 through 43' Processing helix chain 'R' and resid 30 through 38 removed outlier: 3.533A pdb=" N THR R 34 " --> pdb=" O PRO R 30 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU R 35 " --> pdb=" O LYS R 31 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL R 36 " --> pdb=" O GLU R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 54 removed outlier: 3.611A pdb=" N TYR R 54 " --> pdb=" O PRO R 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 51 through 54' Processing helix chain 'R' and resid 152 through 154 No H-bonds generated for 'chain 'R' and resid 152 through 154' Processing helix chain 'R' and resid 159 through 168 removed outlier: 3.884A pdb=" N ALA R 166 " --> pdb=" O SER R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 195 removed outlier: 3.942A pdb=" N ALA R 190 " --> pdb=" O GLU R 186 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL R 195 " --> pdb=" O LEU R 191 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 78 removed outlier: 3.746A pdb=" N ARG S 48 " --> pdb=" O LYS S 44 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS S 55 " --> pdb=" O LYS S 51 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS S 58 " --> pdb=" O GLY S 54 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ILE S 73 " --> pdb=" O LYS S 69 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ALA S 74 " --> pdb=" O ASN S 70 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 88 Processing helix chain 'S' and resid 118 through 130 removed outlier: 3.503A pdb=" N ALA S 128 " --> pdb=" O ARG S 124 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR S 129 " --> pdb=" O ALA S 125 " (cutoff:3.500A) Processing helix chain 'S' and resid 144 through 147 No H-bonds generated for 'chain 'S' and resid 144 through 147' Processing helix chain 'S' and resid 150 through 153 No H-bonds generated for 'chain 'S' and resid 150 through 153' Processing helix chain 'S' and resid 172 through 184 Processing helix chain 'S' and resid 213 through 221 removed outlier: 5.375A pdb=" N LYS S 218 " --> pdb=" O ASP S 214 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N GLN S 219 " --> pdb=" O LEU S 215 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU S 221 " --> pdb=" O GLU S 217 " (cutoff:3.500A) Processing helix chain 'S' and resid 239 through 273 removed outlier: 3.650A pdb=" N ASN S 263 " --> pdb=" O MET S 259 " (cutoff:3.500A) Processing helix chain 'S' and resid 276 through 312 Processing helix chain 'T' and resid 58 through 63 Processing helix chain 'T' and resid 67 through 75 removed outlier: 4.028A pdb=" N GLU T 72 " --> pdb=" O PRO T 68 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TRP T 73 " --> pdb=" O ALA T 69 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS T 75 " --> pdb=" O LYS T 71 " (cutoff:3.500A) Processing helix chain 'T' and resid 135 through 137 No H-bonds generated for 'chain 'T' and resid 135 through 137' Processing helix chain 'T' and resid 157 through 159 No H-bonds generated for 'chain 'T' and resid 157 through 159' Processing helix chain 'T' and resid 207 through 212 Processing helix chain 'T' and resid 231 through 247 removed outlier: 3.900A pdb=" N GLU T 247 " --> pdb=" O LYS T 243 " (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: 4.265A pdb=" N PHE T 313 " --> pdb=" O MET T 309 " (cutoff:3.500A) Processing helix chain 'T' and resid 327 through 341 removed outlier: 3.715A 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 362 removed outlier: 4.311A pdb=" N PHE T 355 " --> pdb=" O GLY T 352 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR T 356 " --> pdb=" O ASP T 353 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU T 357 " --> pdb=" O VAL T 354 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ARG T 360 " --> pdb=" O LEU T 357 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU T 362 " --> pdb=" O SER T 359 " (cutoff:3.500A) Processing helix chain 'T' and resid 393 through 399 Processing helix chain 'T' and resid 410 through 414 Processing helix chain 'T' and resid 432 through 434 No H-bonds generated for 'chain 'T' and resid 432 through 434' Processing helix chain 'T' and resid 437 through 442 removed outlier: 3.530A pdb=" N GLN T 441 " --> pdb=" O PRO T 437 " (cutoff:3.500A) Processing helix chain 'T' and resid 444 through 457 Processing helix chain 'T' and resid 470 through 483 removed outlier: 3.652A pdb=" N ARG T 479 " --> pdb=" O GLU T 475 " (cutoff:3.500A) Processing helix chain 'T' and resid 494 through 505 removed outlier: 3.563A pdb=" N ALA T 500 " --> pdb=" O ARG T 496 " (cutoff:3.500A) Processing helix chain 'T' and resid 517 through 527 removed outlier: 4.362A pdb=" N GLU T 522 " --> pdb=" O VAL T 518 " (cutoff:3.500A) Processing helix chain 'T' and resid 530 through 539 Processing helix chain 'T' and resid 546 through 555 Processing helix chain 'U' and resid 46 through 48 No H-bonds generated for 'chain 'U' and resid 46 through 48' Processing helix chain 'U' and resid 59 through 73 removed outlier: 4.275A pdb=" N GLN U 64 " --> pdb=" O GLN U 60 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS U 65 " --> pdb=" O HIS U 61 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ILE U 67 " --> pdb=" O SER U 63 " (cutoff:3.500A) Proline residue: U 68 - end of helix removed outlier: 4.346A pdb=" N TRP U 73 " --> pdb=" O ALA U 69 " (cutoff:3.500A) 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 211 Processing helix chain 'U' and resid 231 through 246 Processing helix chain 'U' and resid 266 through 279 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: 3.880A pdb=" N TYR U 312 " --> pdb=" O ALA U 308 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N PHE U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) Processing helix chain 'U' and resid 327 through 340 removed outlier: 3.961A 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: 4.308A pdb=" N PHE U 355 " --> pdb=" O GLY U 352 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TYR U 356 " --> pdb=" O ASP U 353 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU U 357 " --> pdb=" O VAL U 354 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG U 360 " --> pdb=" O LEU U 357 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N GLU U 363 " --> pdb=" O ARG U 360 " (cutoff:3.500A) Processing helix chain 'U' and resid 393 through 401 Processing helix chain 'U' and resid 411 through 414 No H-bonds generated for 'chain 'U' and resid 411 through 414' Processing helix chain 'U' and resid 437 through 459 removed outlier: 4.017A pdb=" N VAL U 442 " --> pdb=" O GLY U 438 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLY U 444 " --> pdb=" O LYS U 440 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N THR U 445 " --> pdb=" O GLN U 441 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR U 453 " --> pdb=" O GLU U 449 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU U 455 " --> pdb=" O ALA U 451 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL U 456 " --> pdb=" O GLN U 452 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ALA U 458 " --> pdb=" O ARG U 454 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE U 459 " --> pdb=" O GLU U 455 " (cutoff:3.500A) Processing helix chain 'U' and resid 468 through 484 removed outlier: 3.646A pdb=" N TYR U 472 " --> pdb=" O ALA U 468 " (cutoff:3.500A) Processing helix chain 'U' and resid 494 through 505 removed outlier: 3.621A pdb=" N VAL U 499 " --> pdb=" O GLU U 495 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA U 500 " --> pdb=" O ARG U 496 " (cutoff:3.500A) Processing helix chain 'U' and resid 517 through 527 Processing helix chain 'U' and resid 531 through 539 removed outlier: 3.676A pdb=" N ILE U 535 " --> pdb=" O ALA U 531 " (cutoff:3.500A) Processing helix chain 'U' and resid 544 through 553 Processing helix chain 'V' and resid 44 through 48 removed outlier: 3.602A pdb=" N GLU V 47 " --> pdb=" O ALA V 44 " (cutoff:3.500A) Processing helix chain 'V' and resid 58 through 69 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 211 Processing helix chain 'V' and resid 231 through 246 removed outlier: 3.697A pdb=" N GLN V 242 " --> pdb=" O ALA V 238 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS V 243 " --> pdb=" O ILE V 239 " (cutoff:3.500A) Processing helix chain 'V' and resid 251 through 253 No H-bonds generated for 'chain 'V' and resid 251 through 253' Processing helix chain 'V' and resid 266 through 279 Processing helix chain 'V' and resid 281 through 284 Processing helix chain 'V' and resid 296 through 315 Proline residue: V 303 - end of helix removed outlier: 3.818A pdb=" N TYR V 312 " --> pdb=" O ALA V 308 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N PHE V 313 " --> pdb=" O MET V 309 " (cutoff:3.500A) Processing helix chain 'V' and resid 327 through 339 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: 4.230A pdb=" N PHE V 355 " --> pdb=" O GLY V 352 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU V 357 " --> pdb=" O VAL V 354 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG V 360 " --> pdb=" O LEU V 357 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLU V 363 " --> pdb=" O ARG V 360 " (cutoff:3.500A) Processing helix chain 'V' and resid 393 through 401 Processing helix chain 'V' and resid 410 through 415 removed outlier: 3.668A pdb=" N LYS V 415 " --> pdb=" O GLU V 411 " (cutoff:3.500A) Processing helix chain 'V' and resid 431 through 434 removed outlier: 3.699A 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 439 through 456 removed outlier: 3.808A pdb=" N GLY V 444 " --> pdb=" O LYS V 440 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N THR V 445 " --> pdb=" O GLN V 441 " (cutoff:3.500A) Processing helix chain 'V' and resid 470 through 483 Processing helix chain 'V' and resid 494 through 505 removed outlier: 3.644A pdb=" N ALA V 504 " --> pdb=" O ALA V 500 " (cutoff:3.500A) Processing helix chain 'V' and resid 514 through 527 removed outlier: 4.131A pdb=" N ILE V 517 " --> pdb=" O VAL V 514 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N VAL V 518 " --> pdb=" O GLN V 515 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA V 519 " --> pdb=" O ASP V 516 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLU V 521 " --> pdb=" O VAL V 518 " (cutoff:3.500A) Processing helix chain 'V' and resid 532 through 539 removed outlier: 3.871A pdb=" N ALA V 538 " --> pdb=" O LYS V 534 " (cutoff:3.500A) Processing helix chain 'V' and resid 549 through 553 Processing helix chain 'X' and resid 115 through 117 No H-bonds generated for 'chain 'X' and resid 115 through 117' Processing helix chain 'X' and resid 165 through 170 Processing helix chain 'X' and resid 189 through 203 Processing helix chain 'X' and resid 217 through 230 Processing helix chain 'X' and resid 236 through 241 removed outlier: 4.648A 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: 3.608A pdb=" N PHE X 272 " --> pdb=" O VAL X 268 " (cutoff:3.500A) Processing helix chain 'X' and resid 287 through 300 Processing helix chain 'X' and resid 314 through 322 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 356 removed outlier: 3.877A pdb=" N ALA X 356 " --> pdb=" O ALA X 352 " (cutoff:3.500A) Processing helix chain 'X' and resid 366 through 369 No H-bonds generated for 'chain 'X' and resid 366 through 369' 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 412 Processing helix chain 'X' and resid 415 through 419 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 443 removed outlier: 3.564A pdb=" N ARG X 441 " --> pdb=" O ARG X 437 " (cutoff:3.500A) Processing helix chain 'X' and resid 450 through 452 No H-bonds generated for 'chain 'X' and resid 450 through 452' Processing helix chain 'X' and resid 463 through 475 Processing helix chain 'X' and resid 483 through 486 No H-bonds generated for 'chain 'X' and resid 483 through 486' Processing helix chain 'X' and resid 492 through 506 removed outlier: 4.230A pdb=" N LYS X 496 " --> pdb=" O ILE X 492 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLU X 497 " --> pdb=" O LYS X 493 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ASP X 505 " --> pdb=" O LYS X 501 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ILE X 506 " --> pdb=" O MET X 502 " (cutoff:3.500A) Processing helix chain 'X' and resid 527 through 531 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 191 through 200 Processing helix chain 'Y' and resid 217 through 229 Processing helix chain 'Y' and resid 238 through 241 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 removed outlier: 3.600A pdb=" N PHE Y 272 " --> pdb=" O VAL Y 268 " (cutoff:3.500A) Processing helix chain 'Y' and resid 288 through 298 Processing helix chain 'Y' and resid 314 through 322 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: 4.451A pdb=" N ALA Y 356 " --> pdb=" O ALA Y 352 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N HIS Y 357 " --> pdb=" O THR Y 353 " (cutoff:3.500A) Processing helix chain 'Y' and resid 366 through 369 No H-bonds generated for 'chain 'Y' and resid 366 through 369' 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 419 removed outlier: 3.776A pdb=" N LEU Y 413 " --> pdb=" O ASP Y 409 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN Y 414 " --> pdb=" O TYR Y 410 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ASP Y 415 " --> pdb=" O LYS Y 411 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ILE Y 416 " --> pdb=" O ASN Y 412 " (cutoff:3.500A) Processing helix chain 'Y' and resid 422 through 424 No H-bonds generated for 'chain 'Y' and resid 422 through 424' Processing helix chain 'Y' and resid 427 through 443 removed outlier: 3.900A pdb=" N ALA Y 434 " --> pdb=" O LYS Y 430 " (cutoff:3.500A) Processing helix chain 'Y' and resid 463 through 475 removed outlier: 3.517A pdb=" N VAL Y 473 " --> pdb=" O GLY Y 469 " (cutoff:3.500A) Processing helix chain 'Y' and resid 483 through 485 No H-bonds generated for 'chain 'Y' and resid 483 through 485' Processing helix chain 'Y' and resid 492 through 507 removed outlier: 4.027A pdb=" N LYS Y 496 " --> pdb=" O ILE Y 492 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE Y 506 " --> pdb=" O MET Y 502 " (cutoff:3.500A) Processing helix chain 'Y' and resid 512 through 514 No H-bonds generated for 'chain 'Y' and resid 512 through 514' Processing helix chain 'Y' and resid 527 through 531 Processing helix chain 'Y' and resid 545 through 549 removed outlier: 3.618A pdb=" N PHE Y 549 " --> pdb=" O LEU Y 545 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 545 through 549' 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 170 Processing helix chain 'Z' and resid 189 through 200 Processing helix chain 'Z' and resid 217 through 229 Processing helix chain 'Z' and resid 236 through 241 removed outlier: 3.987A pdb=" N ARG Z 239 " --> pdb=" O GLY Z 236 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLY Z 240 " --> pdb=" O ALA Z 237 " (cutoff:3.500A) Processing helix chain 'Z' and resid 255 through 274 removed outlier: 4.874A pdb=" N ALA Z 262 " --> pdb=" O ARG Z 258 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU Z 263 " --> pdb=" O ALA Z 259 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE Z 272 " --> pdb=" O VAL Z 268 " (cutoff:3.500A) Processing helix chain 'Z' and resid 287 through 298 removed outlier: 3.579A pdb=" N GLN Z 292 " --> pdb=" O ARG Z 289 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER Z 298 " --> pdb=" O SER Z 295 " (cutoff:3.500A) Processing helix chain 'Z' and resid 314 through 324 removed outlier: 4.576A pdb=" N ARG Z 324 " --> pdb=" O GLY Z 320 " (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 353 Processing helix chain 'Z' and resid 366 through 370 Processing helix chain 'Z' and resid 389 through 417 removed outlier: 7.601A pdb=" N ALA Z 394 " --> pdb=" O ASN Z 390 " (cutoff:3.500A) removed outlier: 9.375A pdb=" N GLU Z 395 " --> pdb=" O VAL Z 391 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N HIS Z 396 " --> pdb=" O ILE Z 392 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR Z 397 " --> pdb=" O GLY Z 393 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ASP Z 415 " --> pdb=" O LYS Z 411 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ILE Z 416 " --> pdb=" O ASN Z 412 " (cutoff:3.500A) Processing helix chain 'Z' and resid 430 through 442 removed outlier: 3.601A pdb=" N ALA Z 434 " --> pdb=" O LYS Z 430 " (cutoff:3.500A) Processing helix chain 'Z' and resid 463 through 475 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 492 through 508 removed outlier: 4.011A pdb=" N LYS Z 496 " --> pdb=" O ILE Z 492 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS Z 501 " --> pdb=" O GLU Z 497 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALA Z 507 " --> pdb=" O ALA Z 503 " (cutoff:3.500A) Processing helix chain 'Z' and resid 527 through 533 removed outlier: 4.192A pdb=" N VAL Z 531 " --> pdb=" O LEU Z 527 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N SER Z 532 " --> pdb=" O ASP Z 528 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain '2' and resid 369 through 372 Processing sheet with id= B, first strand: chain '7' and resid 36 through 41 removed outlier: 3.892A pdb=" N GLU 7 47 " --> pdb=" O ALA 7 40 " (cutoff:3.500A) 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 151 through 153 removed outlier: 6.159A pdb=" N LYS P 183 " --> pdb=" O VAL P 152 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'P' and resid 188 through 190 removed outlier: 6.765A pdb=" N VAL P 156 " --> pdb=" O LYS P 189 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE P 198 " --> pdb=" O MET P 209 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'Q' and resid 45 through 50 Processing sheet with id= G, first strand: chain 'R' and resid 72 through 75 removed outlier: 6.745A pdb=" N THR R 142 " --> pdb=" O ASN R 73 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N TYR R 75 " --> pdb=" O THR R 142 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE R 144 " --> pdb=" O TYR R 75 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'R' and resid 96 through 100 removed outlier: 3.539A pdb=" N THR R 88 " --> pdb=" O HIS R 119 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL R 115 " --> pdb=" O PRO R 92 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'S' and resid 203 through 211 removed outlier: 5.111A pdb=" N ASN S 195 " --> pdb=" O VAL S 105 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ASP S 136 " --> pdb=" O SER S 100 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N VAL S 102 " --> pdb=" O ASP S 136 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL S 138 " --> pdb=" O VAL S 102 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ALA S 104 " --> pdb=" O VAL S 138 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL S 140 " --> pdb=" O ALA S 104 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N SER S 141 " --> pdb=" O GLN S 159 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ALA S 161 " --> pdb=" O SER S 141 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'T' and resid 94 through 98 removed outlier: 6.902A pdb=" N VAL T 130 " --> pdb=" O ALA T 119 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ALA T 119 " --> pdb=" O VAL T 130 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N PHE T 132 " --> pdb=" O GLY T 117 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N GLY T 117 " --> pdb=" O PHE T 132 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'T' and resid 152 through 155 Processing sheet with id= L, first strand: chain 'T' and resid 404 through 408 removed outlier: 3.825A pdb=" N LEU T 222 " --> pdb=" O GLY T 404 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'T' and resid 286 through 290 removed outlier: 6.863A pdb=" N HIS T 319 " --> pdb=" O TYR T 256 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N VAL T 258 " --> pdb=" O HIS T 319 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU T 321 " --> pdb=" O VAL T 258 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N VAL T 260 " --> pdb=" O LEU T 321 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE T 323 " --> pdb=" O VAL T 260 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL T 262 " --> pdb=" O ILE T 323 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ASP T 325 " --> pdb=" O VAL T 262 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N SER T 376 " --> pdb=" O GLY T 320 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ILE T 322 " --> pdb=" O SER T 376 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N THR T 378 " --> pdb=" O ILE T 322 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N TYR T 324 " --> pdb=" O THR T 378 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'U' and resid 85 through 91 removed outlier: 6.638A pdb=" N ARG U 96 " --> pdb=" O LEU U 88 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N VAL U 90 " --> pdb=" O ILE U 94 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE U 94 " --> pdb=" O VAL U 90 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN U 121 " --> pdb=" O GLY U 128 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL U 130 " --> pdb=" O ALA U 119 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ALA U 119 " --> pdb=" O VAL U 130 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'U' and resid 152 through 155 Processing sheet with id= P, first strand: chain 'U' and resid 405 through 408 removed outlier: 6.826A pdb=" N LEU U 222 " --> pdb=" O ILE U 406 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N LEU U 408 " --> pdb=" O LEU U 222 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ILE U 224 " --> pdb=" O LEU U 408 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'U' and resid 285 through 290 removed outlier: 8.723A pdb=" N ILE U 286 " --> pdb=" O VAL U 255 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N CYS U 257 " --> pdb=" O ILE U 286 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N VAL U 288 " --> pdb=" O CYS U 257 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N TYR U 259 " --> pdb=" O VAL U 288 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N ALA U 290 " --> pdb=" O TYR U 259 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ALA U 261 " --> pdb=" O ALA U 290 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N HIS U 319 " --> pdb=" O TYR U 256 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N VAL U 258 " --> pdb=" O HIS U 319 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU U 321 " --> pdb=" O VAL U 258 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N VAL U 260 " --> pdb=" O LEU U 321 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE U 323 " --> pdb=" O VAL U 260 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N VAL U 262 " --> pdb=" O ILE U 323 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ASP U 325 " --> pdb=" O VAL U 262 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N SER U 376 " --> pdb=" O GLY U 320 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ILE U 322 " --> pdb=" O SER U 376 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N THR U 378 " --> pdb=" O ILE U 322 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N TYR U 324 " --> pdb=" O THR U 378 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N PHE U 380 " --> pdb=" O TYR U 324 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'V' and resid 85 through 89 removed outlier: 6.526A pdb=" N ARG V 96 " --> pdb=" O LEU V 88 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL V 130 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ALA V 119 " --> pdb=" O VAL V 130 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU V 107 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLN V 149 " --> pdb=" O LEU V 108 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N CYS V 110 " --> pdb=" O THR V 147 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N THR V 147 " --> pdb=" O CYS V 110 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'V' and resid 152 through 155 Processing sheet with id= T, first strand: chain 'V' and resid 404 through 408 Processing sheet with id= U, first strand: chain 'V' and resid 285 through 290 removed outlier: 8.709A pdb=" N ILE V 286 " --> pdb=" O VAL V 255 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N CYS V 257 " --> pdb=" O ILE V 286 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N VAL V 288 " --> pdb=" O CYS V 257 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N TYR V 259 " --> pdb=" O VAL V 288 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ALA V 290 " --> pdb=" O TYR V 259 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ALA V 261 " --> pdb=" O ALA V 290 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N HIS V 319 " --> pdb=" O TYR V 256 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N VAL V 258 " --> pdb=" O HIS V 319 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LEU V 321 " --> pdb=" O VAL V 258 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N VAL V 260 " --> pdb=" O LEU V 321 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE V 323 " --> pdb=" O VAL V 260 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL V 262 " --> pdb=" O ILE V 323 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ASP V 325 " --> pdb=" O VAL V 262 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N SER V 376 " --> pdb=" O GLY V 320 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ILE V 322 " --> pdb=" O SER V 376 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N THR V 378 " --> pdb=" O ILE V 322 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N TYR V 324 " --> pdb=" O THR V 378 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'X' and resid 38 through 44 removed outlier: 6.386A pdb=" N ASP X 49 " --> pdb=" O SER X 41 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N VAL X 43 " --> pdb=" O VAL X 47 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL X 47 " --> pdb=" O VAL X 43 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ILE X 88 " --> pdb=" O VAL X 76 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL X 76 " --> pdb=" O ILE X 88 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'X' and resid 110 through 113 removed outlier: 3.620A pdb=" N ASP X 139 " --> pdb=" O VAL X 113 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'X' and resid 360 through 362 removed outlier: 8.497A pdb=" N ILE X 179 " --> pdb=" O ILE X 333 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N SER X 335 " --> pdb=" O ILE X 179 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LEU X 181 " --> pdb=" O SER X 335 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLN X 337 " --> pdb=" O LEU X 181 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL X 284 " --> pdb=" O VAL X 336 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'X' and resid 559 through 561 Processing sheet with id= Z, first strand: chain 'Y' and resid 37 through 39 removed outlier: 6.684A pdb=" N ARG Y 86 " --> pdb=" O ALA Y 77 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N HIS Y 79 " --> pdb=" O THR Y 84 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N THR Y 84 " --> pdb=" O HIS Y 79 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ARG Y 51 " --> pdb=" O VAL Y 40 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N VAL Y 40 " --> pdb=" O ARG Y 51 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'Y' and resid 110 through 113 Processing sheet with id= AB, first strand: chain 'Y' and resid 360 through 363 removed outlier: 7.442A pdb=" N ILE Y 179 " --> pdb=" O ILE Y 333 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N SER Y 335 " --> pdb=" O ILE Y 179 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N LEU Y 181 " --> pdb=" O SER Y 335 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLN Y 337 " --> pdb=" O LEU Y 181 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N GLY Y 183 " --> pdb=" O GLN Y 337 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N VAL Y 339 " --> pdb=" O GLY Y 183 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N PHE Y 207 " --> pdb=" O LEU Y 281 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N PHE Y 283 " --> pdb=" O PHE Y 207 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N VAL Y 209 " --> pdb=" O PHE Y 283 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ASP Y 285 " --> pdb=" O VAL Y 209 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ALA Y 211 " --> pdb=" O ASP Y 285 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'Z' and resid 38 through 44 removed outlier: 6.576A pdb=" N ASP Z 49 " --> pdb=" O SER Z 41 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N VAL Z 43 " --> pdb=" O VAL Z 47 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL Z 47 " --> pdb=" O VAL Z 43 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ILE Z 88 " --> pdb=" O VAL Z 76 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N VAL Z 76 " --> pdb=" O ILE Z 88 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N LEU Z 72 " --> pdb=" O VAL Z 65 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'Z' and resid 110 through 113 Processing sheet with id= AE, first strand: chain 'Z' and resid 360 through 363 removed outlier: 7.221A pdb=" N ILE Z 179 " --> pdb=" O ILE Z 333 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N SER Z 335 " --> pdb=" O ILE Z 179 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N LEU Z 181 " --> pdb=" O SER Z 335 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLN Z 337 " --> pdb=" O LEU Z 181 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N GLY Z 183 " --> pdb=" O GLN Z 337 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N VAL Z 339 " --> pdb=" O GLY Z 183 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'Z' and resid 559 through 561 2459 hydrogen bonds defined for protein. 6498 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 15.67 Time building geometry restraints manager: 17.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 13676 1.33 - 1.45: 9766 1.45 - 1.57: 30941 1.57 - 1.69: 21 1.69 - 1.81: 254 Bond restraints: 54658 Sorted by residual: bond pdb=" C4 ATP T1001 " pdb=" C5 ATP T1001 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.18e+01 bond pdb=" C4 ATP V1001 " pdb=" C5 ATP V1001 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.09e+01 bond pdb=" C4 ATP U1001 " pdb=" C5 ATP U1001 " ideal model delta sigma weight residual 1.388 1.458 -0.070 1.00e-02 1.00e+04 4.85e+01 bond pdb=" C5 ATP U1001 " pdb=" C6 ATP U1001 " ideal model delta sigma weight residual 1.409 1.470 -0.061 1.00e-02 1.00e+04 3.69e+01 bond pdb=" C5 ATP V1001 " pdb=" C6 ATP V1001 " ideal model delta sigma weight residual 1.409 1.468 -0.059 1.00e-02 1.00e+04 3.44e+01 ... (remaining 54653 not shown) Histogram of bond angle deviations from ideal: 95.74 - 103.79: 737 103.79 - 111.85: 25833 111.85 - 119.91: 23735 119.91 - 127.97: 23462 127.97 - 136.02: 354 Bond angle restraints: 74121 Sorted by residual: angle pdb=" PB ATP U1001 " pdb=" O3B ATP U1001 " pdb=" PG ATP U1001 " ideal model delta sigma weight residual 139.87 120.20 19.67 1.00e+00 1.00e+00 3.87e+02 angle pdb=" PB ATP T1001 " pdb=" O3B ATP T1001 " pdb=" PG ATP T1001 " ideal model delta sigma weight residual 139.87 120.51 19.36 1.00e+00 1.00e+00 3.75e+02 angle pdb=" PB ATP V1001 " pdb=" O3B ATP V1001 " pdb=" PG ATP V1001 " ideal model delta sigma weight residual 139.87 123.97 15.90 1.00e+00 1.00e+00 2.53e+02 angle pdb=" PA ATP T1001 " pdb=" O3A ATP T1001 " pdb=" PB ATP T1001 " ideal model delta sigma weight residual 136.83 121.22 15.61 1.00e+00 1.00e+00 2.44e+02 angle pdb=" PA ATP V1001 " pdb=" O3A ATP V1001 " pdb=" PB ATP V1001 " ideal model delta sigma weight residual 136.83 121.91 14.92 1.00e+00 1.00e+00 2.23e+02 ... (remaining 74116 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.83: 32349 35.83 - 71.66: 620 71.66 - 107.50: 35 107.50 - 143.33: 0 143.33 - 179.16: 1 Dihedral angle restraints: 33005 sinusoidal: 12661 harmonic: 20344 Sorted by residual: 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 -130.29 -49.71 0 5.00e+00 4.00e-02 9.88e+01 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 -135.45 -44.55 0 5.00e+00 4.00e-02 7.94e+01 dihedral pdb=" C5' ADP Z 601 " pdb=" O5' ADP Z 601 " pdb=" PA ADP Z 601 " pdb=" O2A ADP Z 601 " ideal model delta sinusoidal sigma weight residual -60.00 119.16 -179.16 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 33002 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 7547 0.086 - 0.172: 1077 0.172 - 0.258: 53 0.258 - 0.344: 3 0.344 - 0.430: 3 Chirality restraints: 8683 Sorted by residual: chirality pdb=" CB ILE 3 90 " pdb=" CA ILE 3 90 " pdb=" CG1 ILE 3 90 " pdb=" CG2 ILE 3 90 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.43 2.00e-01 2.50e+01 4.63e+00 chirality pdb=" CB ILE C 95 " pdb=" CA ILE C 95 " pdb=" CG1 ILE C 95 " pdb=" CG2 ILE C 95 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 3.03e+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 -2.28 -0.35 2.00e-01 2.50e+01 2.98e+00 ... (remaining 8680 not shown) Planarity restraints: 9504 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA Y 503 " 0.032 2.00e-02 2.50e+03 6.26e-02 3.92e+01 pdb=" C ALA Y 503 " -0.108 2.00e-02 2.50e+03 pdb=" O ALA Y 503 " 0.040 2.00e-02 2.50e+03 pdb=" N LYS Y 504 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA Z 503 " 0.030 2.00e-02 2.50e+03 5.82e-02 3.38e+01 pdb=" C ALA Z 503 " -0.101 2.00e-02 2.50e+03 pdb=" O ALA Z 503 " 0.037 2.00e-02 2.50e+03 pdb=" N LYS Z 504 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU T 509 " 0.015 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C LEU T 509 " -0.056 2.00e-02 2.50e+03 pdb=" O LEU T 509 " 0.022 2.00e-02 2.50e+03 pdb=" N ASP T 510 " 0.019 2.00e-02 2.50e+03 ... (remaining 9501 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 2544 2.71 - 3.26: 52605 3.26 - 3.81: 90733 3.81 - 4.35: 116031 4.35 - 4.90: 195594 Nonbonded interactions: 457507 Sorted by model distance: nonbonded pdb=" O3B ADP Z 601 " pdb="MG MG Z 602 " model vdw 2.163 2.170 nonbonded pdb=" OG1 THR Y 190 " pdb="MG MG Y 602 " model vdw 2.224 2.170 nonbonded pdb=" O3G ATP U1001 " pdb="MG MG U1002 " model vdw 2.225 2.170 nonbonded pdb=" OG1 THR T 232 " pdb="MG MG T1002 " model vdw 2.228 2.170 nonbonded pdb=" O LYS Z 515 " pdb=" N VAL Z 517 " model vdw 2.233 2.520 ... (remaining 457502 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 562 or resid 1001 through 1002)) selection = chain 'V' } ncs_group { reference = (chain 'X' and resid 37 through 552) selection = (chain 'Y' and resid 37 through 552) selection = (chain 'Z' and resid 37 through 552) } 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: 4.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 23.370 Check model and map are aligned: 0.590 Set scattering table: 0.390 Process input model: 110.600 Find NCS groups from input model: 2.470 Set up NCS constraints: 0.290 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:2.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 144.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 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 : 0.010 0.107 54658 Z= 0.655 Angle : 0.944 19.673 74121 Z= 0.541 Chirality : 0.059 0.430 8683 Planarity : 0.007 0.078 9504 Dihedral : 14.497 179.161 19929 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.85 % Favored : 94.97 % Rotamer: Outliers : 0.27 % Allowed : 9.95 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.94 (0.08), residues: 7034 helix: -2.75 (0.06), residues: 3825 sheet: -1.65 (0.20), residues: 606 loop : -2.32 (0.10), residues: 2603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP Y 141 HIS 0.012 0.002 HIS 7 123 PHE 0.034 0.003 PHE S 249 TYR 0.031 0.003 TYR 7 119 ARG 0.010 0.001 ARG U 454 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1190 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 1175 time to evaluate : 4.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 24 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.9108 (pp) REVERT: 1 313 GLN cc_start: 0.8620 (tt0) cc_final: 0.8335 (mt0) REVERT: 1 341 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7922 (mt-10) REVERT: 1 548 MET cc_start: 0.9078 (mtm) cc_final: 0.8740 (mtp) REVERT: 2 108 GLU cc_start: 0.7951 (tt0) cc_final: 0.7515 (tt0) REVERT: 4 124 ASN cc_start: 0.8558 (t0) cc_final: 0.8209 (t0) REVERT: 4 192 ASN cc_start: 0.7759 (p0) cc_final: 0.7408 (p0) REVERT: 6 91 ASP cc_start: 0.8394 (t70) cc_final: 0.8104 (t0) REVERT: 7 142 GLU cc_start: 0.7459 (mt-10) cc_final: 0.6927 (mt-10) REVERT: 8 60 ILE cc_start: 0.8991 (mm) cc_final: 0.8771 (mt) REVERT: 8 71 LYS cc_start: 0.8060 (tttp) cc_final: 0.7832 (ttmm) REVERT: 9 13 LYS cc_start: 0.7868 (mtmt) cc_final: 0.7465 (mmmt) REVERT: A 60 LYS cc_start: 0.7899 (mtmt) cc_final: 0.7677 (mtmt) REVERT: B 85 LEU cc_start: 0.8573 (tp) cc_final: 0.8306 (tt) REVERT: D 97 LYS cc_start: 0.7314 (mmtp) cc_final: 0.6989 (tptp) REVERT: E 78 LEU cc_start: 0.8464 (pp) cc_final: 0.8201 (pt) REVERT: F 66 CYS cc_start: 0.8196 (m) cc_final: 0.7815 (m) REVERT: F 97 LYS cc_start: 0.8841 (ttmt) cc_final: 0.8593 (mttt) REVERT: H 61 MET cc_start: 0.8316 (mtt) cc_final: 0.7522 (mtt) REVERT: H 81 MET cc_start: 0.8343 (ttp) cc_final: 0.8009 (ttp) REVERT: H 92 ASN cc_start: 0.8654 (p0) cc_final: 0.7969 (p0) REVERT: I 60 LYS cc_start: 0.7535 (mttt) cc_final: 0.7117 (mttt) REVERT: I 81 MET cc_start: 0.8839 (ttp) cc_final: 0.8390 (ttp) REVERT: S 60 MET cc_start: 0.6895 (ttm) cc_final: 0.6631 (ttm) REVERT: S 76 GLU cc_start: 0.6968 (mm-30) cc_final: 0.6675 (mm-30) REVERT: S 92 PHE cc_start: 0.7466 (m-80) cc_final: 0.7213 (m-80) REVERT: S 231 TYR cc_start: 0.8728 (m-80) cc_final: 0.8237 (m-80) REVERT: T 78 GLN cc_start: 0.8206 (mt0) cc_final: 0.7938 (mm110) REVERT: U 53 PHE cc_start: 0.6787 (p90) cc_final: 0.6312 (p90) REVERT: U 240 ILE cc_start: 0.7326 (mm) cc_final: 0.6912 (mt) REVERT: U 353 ASP cc_start: 0.8393 (p0) cc_final: 0.8029 (p0) REVERT: U 509 LEU cc_start: 0.5333 (mt) cc_final: 0.5034 (tp) REVERT: V 447 LYS cc_start: 0.6556 (tptt) cc_final: 0.6335 (ttmm) REVERT: V 530 PRO cc_start: 0.7098 (Cg_endo) cc_final: 0.6879 (Cg_exo) REVERT: X 452 VAL cc_start: 0.5936 (m) cc_final: 0.5699 (t) REVERT: Z 310 TYR cc_start: 0.8732 (m-80) cc_final: 0.8293 (m-80) REVERT: Z 500 ASP cc_start: 0.6956 (p0) cc_final: 0.6371 (m-30) REVERT: Z 501 LYS cc_start: 0.7786 (ttmt) cc_final: 0.6978 (tppt) outliers start: 15 outliers final: 6 residues processed: 1187 average time/residue: 0.5650 time to fit residues: 1089.1530 Evaluate side-chains 686 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 679 time to evaluate : 4.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 24 LEU Chi-restraints excluded: chain 2 residue 391 THR Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain T residue 430 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain Z residue 558 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 697 random chunks: chunk 588 optimal weight: 3.9990 chunk 528 optimal weight: 20.0000 chunk 293 optimal weight: 0.9980 chunk 180 optimal weight: 10.0000 chunk 356 optimal weight: 3.9990 chunk 282 optimal weight: 2.9990 chunk 546 optimal weight: 0.9980 chunk 211 optimal weight: 0.7980 chunk 332 optimal weight: 7.9990 chunk 406 optimal weight: 1.9990 chunk 632 optimal weight: 3.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 100 GLN 1 285 GLN 1 298 GLN 1 316 ASN ** 1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 394 GLN ** 1 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 482 ASN 1 590 HIS 1 606 ASN 2 68 ASN ** 2 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 243 GLN 2 289 HIS 2 380 GLN 2 432 GLN 3 94 ASN 3 179 GLN 3 206 ASN 3 229 ASN 5 107 ASN 6 40 ASN 6 57 GLN 6 74 GLN 7 38 ASN ** 7 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 86 HIS 7 106 GLN 7 123 HIS ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 184 ASN ** 8 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 78 HIS 9 60 ASN A 87 ASN A 98 GLN C 87 ASN E 98 GLN I 94 ASN M 108 ASN M 163 ASN P 52 GLN P 223 ASN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 73 ASN R 137 HIS ** R 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 40 ASN S 174 GLN S 262 ASN ** S 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 61 HIS T 64 GLN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 386 GLN T 405 GLN T 488 GLN U 83 HIS ** U 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 246 ASN U 248 GLN U 264 GLN ** U 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 278 GLN U 319 HIS ** U 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 386 GLN U 452 GLN V 121 ASN V 134 ASN V 139 HIS ** V 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 242 GLN V 244 ASN V 246 ASN V 264 GLN V 358 HIS V 486 GLN V 488 GLN V 497 GLN X 78 GLN X 132 GLN X 153 GLN X 252 ASN X 278 GLN X 286 ASN X 322 GLN X 337 GLN X 404 GLN ** X 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 157 GLN Y 174 GLN ** Y 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 408 GLN Z 174 GLN Z 278 GLN Z 390 ASN Z 408 GLN Total number of N/Q/H flips: 82 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 54658 Z= 0.214 Angle : 0.559 10.840 74121 Z= 0.294 Chirality : 0.041 0.160 8683 Planarity : 0.005 0.059 9504 Dihedral : 6.057 163.570 7672 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.30 % Favored : 96.56 % Rotamer: Outliers : 2.17 % Allowed : 14.18 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.09), residues: 7034 helix: -0.98 (0.08), residues: 3846 sheet: -1.28 (0.20), residues: 618 loop : -1.71 (0.11), residues: 2570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP Y 141 HIS 0.006 0.001 HIS 7 123 PHE 0.044 0.001 PHE 3 115 TYR 0.026 0.002 TYR 4 211 ARG 0.005 0.000 ARG S 124 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 919 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 797 time to evaluate : 4.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 24 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.9072 (pp) REVERT: 1 61 MET cc_start: 0.8208 (mtt) cc_final: 0.8004 (mtp) REVERT: 1 313 GLN cc_start: 0.8448 (tt0) cc_final: 0.8233 (mt0) REVERT: 1 341 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7942 (mt-10) REVERT: 1 548 MET cc_start: 0.8978 (mtm) cc_final: 0.8679 (mtp) REVERT: 2 108 GLU cc_start: 0.8016 (tt0) cc_final: 0.7563 (tt0) REVERT: 2 209 ASP cc_start: 0.7270 (OUTLIER) cc_final: 0.7025 (t0) REVERT: 3 106 TRP cc_start: 0.8547 (m100) cc_final: 0.8333 (m100) REVERT: 4 124 ASN cc_start: 0.8667 (t0) cc_final: 0.8241 (t0) REVERT: 7 142 GLU cc_start: 0.7345 (mt-10) cc_final: 0.6850 (mt-10) REVERT: 8 62 ASP cc_start: 0.7978 (OUTLIER) cc_final: 0.7577 (m-30) REVERT: 8 70 LYS cc_start: 0.7455 (tttm) cc_final: 0.6233 (mmtt) REVERT: 9 13 LYS cc_start: 0.7846 (mtmt) cc_final: 0.7447 (mmmt) REVERT: 9 66 ILE cc_start: 0.7889 (OUTLIER) cc_final: 0.7577 (mm) REVERT: A 60 LYS cc_start: 0.7726 (mtmt) cc_final: 0.7509 (mtmt) REVERT: D 97 LYS cc_start: 0.7320 (mmtp) cc_final: 0.7087 (tptp) REVERT: E 78 LEU cc_start: 0.8243 (pp) cc_final: 0.7802 (mt) REVERT: H 81 MET cc_start: 0.8236 (ttp) cc_final: 0.7954 (ttp) REVERT: H 92 ASN cc_start: 0.8474 (p0) cc_final: 0.7929 (p0) REVERT: I 60 LYS cc_start: 0.7516 (mttt) cc_final: 0.6988 (mttt) REVERT: I 81 MET cc_start: 0.8644 (ttp) cc_final: 0.8365 (ttp) REVERT: P 77 PHE cc_start: 0.6856 (m-80) cc_final: 0.6637 (m-10) REVERT: T 78 GLN cc_start: 0.8185 (mt0) cc_final: 0.7902 (mm110) REVERT: U 112 ASP cc_start: 0.8419 (p0) cc_final: 0.8187 (p0) REVERT: U 240 ILE cc_start: 0.7054 (mm) cc_final: 0.6740 (mt) REVERT: U 509 LEU cc_start: 0.5406 (mt) cc_final: 0.5058 (tp) REVERT: U 512 VAL cc_start: 0.5921 (m) cc_final: 0.5484 (m) REVERT: V 389 ASP cc_start: 0.8242 (t0) cc_final: 0.7413 (p0) REVERT: Y 90 MET cc_start: 0.8328 (mmt) cc_final: 0.8078 (mmt) REVERT: Y 195 GLU cc_start: 0.7532 (tp30) cc_final: 0.7145 (tp30) REVERT: Z 310 TYR cc_start: 0.8609 (m-80) cc_final: 0.8310 (m-80) REVERT: Z 478 TYR cc_start: 0.7535 (m-80) cc_final: 0.7217 (m-10) REVERT: Z 500 ASP cc_start: 0.6870 (p0) cc_final: 0.6456 (m-30) REVERT: Z 501 LYS cc_start: 0.7531 (ttmt) cc_final: 0.6763 (tppt) outliers start: 122 outliers final: 81 residues processed: 872 average time/residue: 0.5123 time to fit residues: 744.0649 Evaluate side-chains 732 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 647 time to evaluate : 4.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 1 residue 24 LEU Chi-restraints excluded: chain 1 residue 103 LYS Chi-restraints excluded: chain 1 residue 113 THR Chi-restraints excluded: chain 1 residue 216 LEU Chi-restraints excluded: chain 1 residue 578 ASP Chi-restraints excluded: chain 2 residue 24 VAL Chi-restraints excluded: chain 2 residue 209 ASP Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 377 VAL Chi-restraints excluded: chain 2 residue 391 THR Chi-restraints excluded: chain 3 residue 181 VAL Chi-restraints excluded: chain 4 residue 172 VAL Chi-restraints excluded: chain 4 residue 269 LEU Chi-restraints excluded: chain 6 residue 61 ILE Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 7 residue 15 LEU Chi-restraints excluded: chain 7 residue 60 GLN Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 62 ASP Chi-restraints excluded: chain 8 residue 82 THR Chi-restraints excluded: chain 9 residue 66 ILE Chi-restraints excluded: chain 9 residue 88 GLU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 314 LYS Chi-restraints excluded: chain P residue 123 GLU Chi-restraints excluded: chain P residue 163 ASP Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain S residue 126 THR Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 185 HIS Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 291 ASP Chi-restraints excluded: chain S residue 299 THR Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 120 LEU Chi-restraints excluded: chain T residue 272 LEU Chi-restraints excluded: chain T residue 484 LEU Chi-restraints excluded: chain U residue 66 LEU Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 163 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 260 VAL Chi-restraints excluded: chain U residue 273 VAL Chi-restraints excluded: chain U residue 278 GLN Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 177 LEU Chi-restraints excluded: chain V residue 257 CYS Chi-restraints excluded: chain V residue 279 THR Chi-restraints excluded: chain V residue 285 THR Chi-restraints excluded: chain X residue 195 GLU Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 286 ASN Chi-restraints excluded: chain X residue 295 SER Chi-restraints excluded: chain X residue 297 VAL Chi-restraints excluded: chain X residue 368 ILE Chi-restraints excluded: chain X residue 423 ASP Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 228 ILE Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 335 SER Chi-restraints excluded: chain Y residue 382 SER Chi-restraints excluded: chain Z residue 193 ILE Chi-restraints excluded: chain Z residue 251 MET Chi-restraints excluded: chain Z residue 367 SER Chi-restraints excluded: chain Z residue 558 THR Chi-restraints excluded: chain Z residue 567 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 697 random chunks: chunk 351 optimal weight: 4.9990 chunk 196 optimal weight: 0.7980 chunk 526 optimal weight: 3.9990 chunk 431 optimal weight: 8.9990 chunk 174 optimal weight: 1.9990 chunk 634 optimal weight: 0.0970 chunk 685 optimal weight: 5.9990 chunk 564 optimal weight: 0.9990 chunk 628 optimal weight: 10.0000 chunk 216 optimal weight: 0.0980 chunk 508 optimal weight: 8.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 450 ASN ** 2 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 38 ASN ** 7 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 78 HIS 9 41 HIS D 92 ASN D 98 GLN J 87 ASN Q 43 GLN R 83 GLN R 85 GLN ** R 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 40 ASN S 174 GLN ** S 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 64 GLN T 241 HIS T 435 GLN ** T 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 278 GLN U 358 HIS ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 529 ASN V 149 GLN ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 157 GLN ** Y 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 54658 Z= 0.152 Angle : 0.504 8.852 74121 Z= 0.262 Chirality : 0.040 0.159 8683 Planarity : 0.004 0.054 9504 Dihedral : 5.600 142.708 7671 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.54 % Favored : 96.36 % Rotamer: Outliers : 2.31 % Allowed : 16.17 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.10), residues: 7034 helix: -0.25 (0.08), residues: 3867 sheet: -1.10 (0.21), residues: 614 loop : -1.34 (0.12), residues: 2553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP 9 73 HIS 0.004 0.001 HIS Z 204 PHE 0.033 0.001 PHE 3 115 TYR 0.024 0.001 TYR 4 211 ARG 0.006 0.000 ARG Y 239 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 873 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 743 time to evaluate : 4.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 341 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7940 (mt-10) REVERT: 1 548 MET cc_start: 0.8930 (mtm) cc_final: 0.8672 (mtp) REVERT: 2 108 GLU cc_start: 0.8046 (tt0) cc_final: 0.7603 (tt0) REVERT: 3 106 TRP cc_start: 0.8488 (m100) cc_final: 0.8267 (m100) REVERT: 4 124 ASN cc_start: 0.8661 (t0) cc_final: 0.8247 (t0) REVERT: 4 269 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8236 (mm) REVERT: 7 142 GLU cc_start: 0.7346 (mt-10) cc_final: 0.6879 (mt-10) REVERT: 8 62 ASP cc_start: 0.7931 (OUTLIER) cc_final: 0.7619 (m-30) REVERT: 8 70 LYS cc_start: 0.7676 (tttm) cc_final: 0.6360 (mmtt) REVERT: 9 13 LYS cc_start: 0.7901 (mtmt) cc_final: 0.7397 (mmmt) REVERT: 9 17 ASP cc_start: 0.7634 (m-30) cc_final: 0.7424 (m-30) REVERT: 9 66 ILE cc_start: 0.7851 (OUTLIER) cc_final: 0.7427 (mm) REVERT: E 78 LEU cc_start: 0.8101 (pp) cc_final: 0.7823 (mt) REVERT: F 61 MET cc_start: 0.7925 (mmm) cc_final: 0.7589 (mmt) REVERT: H 81 MET cc_start: 0.8212 (ttp) cc_final: 0.7949 (ttp) REVERT: H 92 ASN cc_start: 0.8373 (p0) cc_final: 0.7905 (p0) REVERT: I 60 LYS cc_start: 0.7380 (mttt) cc_final: 0.7060 (mttt) REVERT: I 122 PHE cc_start: 0.7526 (m-10) cc_final: 0.7146 (t80) REVERT: Q 21 ASN cc_start: 0.8620 (m-40) cc_final: 0.8293 (m110) REVERT: S 159 GLN cc_start: 0.7651 (OUTLIER) cc_final: 0.7341 (mt0) REVERT: U 112 ASP cc_start: 0.8276 (p0) cc_final: 0.8013 (p0) REVERT: U 240 ILE cc_start: 0.6901 (mm) cc_final: 0.6516 (mt) REVERT: U 353 ASP cc_start: 0.8325 (p0) cc_final: 0.8011 (p0) REVERT: U 409 GLU cc_start: 0.6432 (mm-30) cc_final: 0.5789 (mm-30) REVERT: U 509 LEU cc_start: 0.5257 (mt) cc_final: 0.4942 (tp) REVERT: U 529 ASN cc_start: 0.5986 (OUTLIER) cc_final: 0.5583 (t0) REVERT: V 454 ARG cc_start: 0.6960 (mtm110) cc_final: 0.6758 (mtm110) REVERT: X 487 TYR cc_start: 0.5689 (t80) cc_final: 0.5390 (t80) REVERT: Y 90 MET cc_start: 0.8343 (mmt) cc_final: 0.8077 (mmt) REVERT: Z 219 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7627 (mt-10) REVERT: Z 310 TYR cc_start: 0.8395 (m-80) cc_final: 0.7787 (m-80) REVERT: Z 500 ASP cc_start: 0.6874 (p0) cc_final: 0.6569 (m-30) outliers start: 130 outliers final: 82 residues processed: 832 average time/residue: 0.5060 time to fit residues: 711.7824 Evaluate side-chains 720 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 632 time to evaluate : 4.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 1 residue 106 ASP Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 2 residue 24 VAL Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 377 VAL Chi-restraints excluded: chain 2 residue 391 THR Chi-restraints excluded: chain 3 residue 181 VAL Chi-restraints excluded: chain 3 residue 263 SER Chi-restraints excluded: chain 4 residue 269 LEU Chi-restraints excluded: chain 6 residue 108 LEU Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 15 LEU Chi-restraints excluded: chain 7 residue 49 THR Chi-restraints excluded: chain 7 residue 60 GLN Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 8 residue 62 ASP Chi-restraints excluded: chain 9 residue 66 ILE Chi-restraints excluded: chain 9 residue 88 GLU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain J residue 66 CYS Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 314 LYS Chi-restraints excluded: chain M residue 323 VAL Chi-restraints excluded: chain P residue 123 GLU Chi-restraints excluded: chain P residue 163 ASP Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain S residue 92 PHE Chi-restraints excluded: chain S residue 159 GLN Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 185 HIS Chi-restraints excluded: chain S residue 212 SER Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 291 ASP Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 272 LEU Chi-restraints excluded: chain T residue 315 ASP Chi-restraints excluded: chain T residue 427 VAL Chi-restraints excluded: chain T residue 529 ASN Chi-restraints excluded: chain U residue 66 LEU Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 163 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 187 VAL Chi-restraints excluded: chain U residue 273 VAL Chi-restraints excluded: chain U residue 278 GLN Chi-restraints excluded: chain U residue 300 PHE Chi-restraints excluded: chain U residue 331 SER Chi-restraints excluded: chain U residue 357 LEU Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 529 ASN Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 177 LEU Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 285 THR Chi-restraints excluded: chain X residue 62 SER Chi-restraints excluded: chain X residue 92 SER Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 295 SER Chi-restraints excluded: chain X residue 296 GLU Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 368 ILE Chi-restraints excluded: chain X residue 423 ASP Chi-restraints excluded: chain X residue 452 VAL Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 198 ASN Chi-restraints excluded: chain Y residue 335 SER Chi-restraints excluded: chain Y residue 528 ASP Chi-restraints excluded: chain Z residue 207 PHE Chi-restraints excluded: chain Z residue 219 GLU Chi-restraints excluded: chain Z residue 558 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 697 random chunks: chunk 626 optimal weight: 4.9990 chunk 476 optimal weight: 2.9990 chunk 329 optimal weight: 8.9990 chunk 70 optimal weight: 0.6980 chunk 302 optimal weight: 2.9990 chunk 425 optimal weight: 10.0000 chunk 636 optimal weight: 9.9990 chunk 673 optimal weight: 5.9990 chunk 332 optimal weight: 0.6980 chunk 603 optimal weight: 0.3980 chunk 181 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 527 GLN ** 2 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 38 ASN ** 7 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 78 HIS P 52 GLN P 66 GLN ** R 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 40 ASN S 174 GLN ** S 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 64 GLN ** T 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 278 GLN V 196 GLN ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 330 GLN ** V 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 539 ASN ** X 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 286 ASN Y 42 GLN Y 157 GLN ** Y 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 54658 Z= 0.189 Angle : 0.515 9.234 74121 Z= 0.265 Chirality : 0.041 0.175 8683 Planarity : 0.004 0.052 9504 Dihedral : 5.438 132.339 7669 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.65 % Favored : 96.23 % Rotamer: Outliers : 2.84 % Allowed : 17.04 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.10), residues: 7034 helix: 0.09 (0.09), residues: 3860 sheet: -0.94 (0.21), residues: 618 loop : -1.13 (0.12), residues: 2556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 9 73 HIS 0.005 0.001 HIS 7 123 PHE 0.032 0.001 PHE T 276 TYR 0.022 0.001 TYR 4 211 ARG 0.006 0.000 ARG 7 121 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 831 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 671 time to evaluate : 4.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 72 ASP cc_start: 0.7308 (OUTLIER) cc_final: 0.7062 (p0) REVERT: 1 341 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7933 (mt-10) REVERT: 1 548 MET cc_start: 0.8957 (mtm) cc_final: 0.8653 (mtp) REVERT: 2 108 GLU cc_start: 0.8038 (tt0) cc_final: 0.7566 (tt0) REVERT: 3 155 LYS cc_start: 0.8238 (ttpp) cc_final: 0.7788 (tptt) REVERT: 4 124 ASN cc_start: 0.8663 (t0) cc_final: 0.8287 (t0) REVERT: 4 269 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8313 (mm) REVERT: 7 142 GLU cc_start: 0.7380 (mt-10) cc_final: 0.6924 (mt-10) REVERT: 8 62 ASP cc_start: 0.7998 (OUTLIER) cc_final: 0.7547 (m-30) REVERT: 8 70 LYS cc_start: 0.7653 (tttm) cc_final: 0.6395 (mmtt) REVERT: 9 13 LYS cc_start: 0.7905 (mtmt) cc_final: 0.7390 (mmmt) REVERT: 9 17 ASP cc_start: 0.7622 (m-30) cc_final: 0.7399 (m-30) REVERT: 9 66 ILE cc_start: 0.7834 (OUTLIER) cc_final: 0.7542 (mm) REVERT: E 78 LEU cc_start: 0.8255 (pp) cc_final: 0.7912 (mt) REVERT: E 107 PHE cc_start: 0.6785 (t80) cc_final: 0.6575 (t80) REVERT: E 111 GLU cc_start: 0.7349 (mm-30) cc_final: 0.7007 (tp30) REVERT: F 61 MET cc_start: 0.7938 (mmm) cc_final: 0.7596 (mmt) REVERT: H 81 MET cc_start: 0.8247 (ttp) cc_final: 0.7960 (ttp) REVERT: H 92 ASN cc_start: 0.8412 (p0) cc_final: 0.7909 (p0) REVERT: H 97 LYS cc_start: 0.7887 (mmtt) cc_final: 0.7200 (tmtt) REVERT: I 60 LYS cc_start: 0.7383 (mttt) cc_final: 0.7022 (mttt) REVERT: S 203 PHE cc_start: 0.8734 (OUTLIER) cc_final: 0.7736 (m-10) REVERT: U 240 ILE cc_start: 0.7025 (mm) cc_final: 0.6587 (mt) REVERT: U 409 GLU cc_start: 0.6380 (mm-30) cc_final: 0.5794 (mm-30) REVERT: V 213 VAL cc_start: 0.8364 (m) cc_final: 0.8141 (p) REVERT: V 454 ARG cc_start: 0.6909 (mtm110) cc_final: 0.6699 (mtm110) REVERT: X 552 GLU cc_start: 0.5825 (OUTLIER) cc_final: 0.4878 (mm-30) REVERT: Y 195 GLU cc_start: 0.7415 (tp30) cc_final: 0.7050 (tp30) REVERT: Y 244 CYS cc_start: 0.7582 (OUTLIER) cc_final: 0.7348 (p) REVERT: Y 502 MET cc_start: 0.5736 (mtp) cc_final: 0.5196 (ttp) REVERT: Z 219 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7699 (mt-10) REVERT: Z 310 TYR cc_start: 0.8462 (m-80) cc_final: 0.7831 (m-80) outliers start: 160 outliers final: 107 residues processed: 779 average time/residue: 0.5101 time to fit residues: 670.9458 Evaluate side-chains 727 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 612 time to evaluate : 4.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 1 residue 72 ASP Chi-restraints excluded: chain 1 residue 103 LYS Chi-restraints excluded: chain 1 residue 216 LEU Chi-restraints excluded: chain 1 residue 271 SER Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 572 ASP Chi-restraints excluded: chain 2 residue 24 VAL Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 377 VAL Chi-restraints excluded: chain 2 residue 391 THR Chi-restraints excluded: chain 3 residue 181 VAL Chi-restraints excluded: chain 3 residue 263 SER Chi-restraints excluded: chain 3 residue 281 VAL Chi-restraints excluded: chain 4 residue 172 VAL Chi-restraints excluded: chain 4 residue 269 LEU Chi-restraints excluded: chain 6 residue 108 LEU Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 15 LEU Chi-restraints excluded: chain 7 residue 49 THR Chi-restraints excluded: chain 7 residue 61 VAL Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 8 residue 37 THR Chi-restraints excluded: chain 8 residue 62 ASP Chi-restraints excluded: chain 8 residue 82 THR Chi-restraints excluded: chain 9 residue 66 ILE Chi-restraints excluded: chain 9 residue 88 GLU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain J residue 66 CYS Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 314 LYS Chi-restraints excluded: chain M residue 323 VAL Chi-restraints excluded: chain P residue 163 ASP Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 130 SER Chi-restraints excluded: chain S residue 126 THR Chi-restraints excluded: chain S residue 185 HIS Chi-restraints excluded: chain S residue 203 PHE Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 259 MET Chi-restraints excluded: chain S residue 291 ASP Chi-restraints excluded: chain S residue 299 THR Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 372 LEU Chi-restraints excluded: chain T residue 425 LEU Chi-restraints excluded: chain T residue 427 VAL Chi-restraints excluded: chain T residue 484 LEU Chi-restraints excluded: chain T residue 529 ASN Chi-restraints excluded: chain U residue 66 LEU Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 163 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 187 VAL Chi-restraints excluded: chain U residue 209 VAL Chi-restraints excluded: chain U residue 260 VAL Chi-restraints excluded: chain U residue 273 VAL Chi-restraints excluded: chain U residue 278 GLN Chi-restraints excluded: chain U residue 300 PHE Chi-restraints excluded: chain U residue 331 SER Chi-restraints excluded: chain U residue 357 LEU Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain V residue 89 SER Chi-restraints excluded: chain V residue 155 ILE Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 177 LEU Chi-restraints excluded: chain V residue 279 THR Chi-restraints excluded: chain V residue 285 THR Chi-restraints excluded: chain X residue 62 SER Chi-restraints excluded: chain X residue 92 SER Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 222 ASP Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 286 ASN Chi-restraints excluded: chain X residue 291 THR Chi-restraints excluded: chain X residue 297 VAL Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 368 ILE Chi-restraints excluded: chain X residue 423 ASP Chi-restraints excluded: chain X residue 452 VAL Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain X residue 552 GLU Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 198 ASN Chi-restraints excluded: chain Y residue 244 CYS Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 335 SER Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Y residue 528 ASP Chi-restraints excluded: chain Z residue 87 CYS Chi-restraints excluded: chain Z residue 193 ILE Chi-restraints excluded: chain Z residue 219 GLU Chi-restraints excluded: chain Z residue 567 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 697 random chunks: chunk 561 optimal weight: 4.9990 chunk 382 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 501 optimal weight: 0.0470 chunk 277 optimal weight: 2.9990 chunk 574 optimal weight: 0.9990 chunk 465 optimal weight: 0.3980 chunk 0 optimal weight: 3.9990 chunk 344 optimal weight: 5.9990 chunk 604 optimal weight: 4.9990 chunk 170 optimal weight: 3.9990 overall best weight: 1.0682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 82 HIS ** 1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 38 ASN ** 7 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 78 HIS P 52 GLN ** R 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 40 ASN S 174 GLN ** S 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 271 GLN U 278 GLN V 149 GLN ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 488 GLN ** V 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 286 ASN ** Y 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 54658 Z= 0.165 Angle : 0.500 9.375 74121 Z= 0.256 Chirality : 0.040 0.236 8683 Planarity : 0.004 0.050 9504 Dihedral : 5.261 124.293 7668 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.51 % Favored : 96.39 % Rotamer: Outliers : 2.79 % Allowed : 17.75 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.10), residues: 7034 helix: 0.34 (0.09), residues: 3862 sheet: -0.78 (0.21), residues: 607 loop : -0.97 (0.12), residues: 2565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 9 73 HIS 0.004 0.001 HIS 7 123 PHE 0.028 0.001 PHE U 436 TYR 0.022 0.001 TYR 4 211 ARG 0.007 0.000 ARG 7 121 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 811 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 654 time to evaluate : 4.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 72 ASP cc_start: 0.7192 (OUTLIER) cc_final: 0.6957 (p0) REVERT: 1 341 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7933 (mt-10) REVERT: 1 490 TYR cc_start: 0.8712 (OUTLIER) cc_final: 0.8146 (m-80) REVERT: 1 548 MET cc_start: 0.8944 (mtm) cc_final: 0.8652 (mtp) REVERT: 2 108 GLU cc_start: 0.8024 (tt0) cc_final: 0.7571 (tt0) REVERT: 2 387 LEU cc_start: 0.8196 (mt) cc_final: 0.7995 (mt) REVERT: 3 155 LYS cc_start: 0.8153 (ttpp) cc_final: 0.7801 (tptt) REVERT: 4 124 ASN cc_start: 0.8662 (t0) cc_final: 0.8300 (t0) REVERT: 4 269 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8230 (mm) REVERT: 7 142 GLU cc_start: 0.7368 (mt-10) cc_final: 0.6907 (mt-10) REVERT: 8 62 ASP cc_start: 0.7941 (OUTLIER) cc_final: 0.7545 (m-30) REVERT: 8 70 LYS cc_start: 0.7655 (tttm) cc_final: 0.6438 (mmtt) REVERT: 9 13 LYS cc_start: 0.7983 (mtmt) cc_final: 0.7457 (mmmt) REVERT: 9 17 ASP cc_start: 0.7578 (m-30) cc_final: 0.7299 (m-30) REVERT: 9 66 ILE cc_start: 0.7843 (OUTLIER) cc_final: 0.7481 (mm) REVERT: E 78 LEU cc_start: 0.8212 (pp) cc_final: 0.7897 (mp) REVERT: E 107 PHE cc_start: 0.6937 (t80) cc_final: 0.6710 (t80) REVERT: E 111 GLU cc_start: 0.7461 (mm-30) cc_final: 0.6994 (tp30) REVERT: F 61 MET cc_start: 0.7960 (mmm) cc_final: 0.7634 (mmt) REVERT: H 81 MET cc_start: 0.8229 (ttp) cc_final: 0.7942 (ttp) REVERT: H 92 ASN cc_start: 0.8378 (p0) cc_final: 0.7915 (p0) REVERT: H 97 LYS cc_start: 0.7882 (mmtt) cc_final: 0.7192 (tmtt) REVERT: I 60 LYS cc_start: 0.7399 (mttt) cc_final: 0.7042 (mttt) REVERT: Q 21 ASN cc_start: 0.8493 (m-40) cc_final: 0.8186 (m110) REVERT: S 203 PHE cc_start: 0.8715 (OUTLIER) cc_final: 0.7695 (m-10) REVERT: S 231 TYR cc_start: 0.8732 (m-80) cc_final: 0.8193 (m-80) REVERT: T 217 ARG cc_start: 0.6114 (mtm-85) cc_final: 0.5772 (mtt180) REVERT: U 53 PHE cc_start: 0.6938 (OUTLIER) cc_final: 0.6665 (p90) REVERT: U 240 ILE cc_start: 0.6993 (mm) cc_final: 0.6547 (mt) REVERT: U 353 ASP cc_start: 0.8400 (p0) cc_final: 0.8114 (p0) REVERT: U 409 GLU cc_start: 0.6313 (mm-30) cc_final: 0.5765 (mm-30) REVERT: V 454 ARG cc_start: 0.6868 (mtm110) cc_final: 0.6661 (mtm110) REVERT: V 487 LYS cc_start: 0.8048 (mmtp) cc_final: 0.7501 (ttpp) REVERT: Y 141 TRP cc_start: 0.7960 (OUTLIER) cc_final: 0.7569 (m-10) REVERT: Y 244 CYS cc_start: 0.7496 (OUTLIER) cc_final: 0.7264 (p) REVERT: Y 435 ARG cc_start: 0.6590 (tpp80) cc_final: 0.6370 (tpp80) REVERT: Y 502 MET cc_start: 0.5579 (mtp) cc_final: 0.5129 (ttp) REVERT: Z 219 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7694 (mm-30) REVERT: Z 310 TYR cc_start: 0.8380 (m-80) cc_final: 0.7723 (m-80) outliers start: 157 outliers final: 104 residues processed: 768 average time/residue: 0.4937 time to fit residues: 648.2985 Evaluate side-chains 734 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 620 time to evaluate : 4.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 1 residue 72 ASP Chi-restraints excluded: chain 1 residue 103 LYS Chi-restraints excluded: chain 1 residue 271 SER Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 490 TYR Chi-restraints excluded: chain 2 residue 24 VAL Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 377 VAL Chi-restraints excluded: chain 2 residue 391 THR Chi-restraints excluded: chain 3 residue 181 VAL Chi-restraints excluded: chain 3 residue 263 SER Chi-restraints excluded: chain 3 residue 281 VAL Chi-restraints excluded: chain 4 residue 172 VAL Chi-restraints excluded: chain 4 residue 269 LEU Chi-restraints excluded: chain 5 residue 65 VAL Chi-restraints excluded: chain 5 residue 89 VAL Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 114 ILE Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 15 LEU Chi-restraints excluded: chain 7 residue 49 THR Chi-restraints excluded: chain 7 residue 61 VAL Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 8 residue 37 THR Chi-restraints excluded: chain 8 residue 62 ASP Chi-restraints excluded: chain 8 residue 82 THR Chi-restraints excluded: chain 9 residue 66 ILE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain J residue 66 CYS Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain M residue 202 PHE Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 314 LYS Chi-restraints excluded: chain M residue 323 VAL Chi-restraints excluded: chain P residue 123 GLU Chi-restraints excluded: chain P residue 163 ASP Chi-restraints excluded: chain P residue 179 ASP Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 130 SER Chi-restraints excluded: chain S residue 126 THR Chi-restraints excluded: chain S residue 159 GLN Chi-restraints excluded: chain S residue 185 HIS Chi-restraints excluded: chain S residue 203 PHE Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 291 ASP Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 315 ASP Chi-restraints excluded: chain T residue 427 VAL Chi-restraints excluded: chain T residue 529 ASN Chi-restraints excluded: chain U residue 53 PHE Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 163 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 187 VAL Chi-restraints excluded: chain U residue 209 VAL Chi-restraints excluded: chain U residue 273 VAL Chi-restraints excluded: chain U residue 278 GLN Chi-restraints excluded: chain U residue 300 PHE Chi-restraints excluded: chain U residue 325 ASP Chi-restraints excluded: chain U residue 331 SER Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 516 ASP Chi-restraints excluded: chain V residue 87 VAL Chi-restraints excluded: chain V residue 89 SER Chi-restraints excluded: chain V residue 149 GLN Chi-restraints excluded: chain V residue 155 ILE Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 177 LEU Chi-restraints excluded: chain V residue 206 VAL Chi-restraints excluded: chain X residue 62 SER Chi-restraints excluded: chain X residue 92 SER Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 295 SER Chi-restraints excluded: chain X residue 296 GLU Chi-restraints excluded: chain X residue 297 VAL Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 368 ILE Chi-restraints excluded: chain X residue 423 ASP Chi-restraints excluded: chain X residue 452 VAL Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain Y residue 122 MET Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 141 TRP Chi-restraints excluded: chain Y residue 196 LEU Chi-restraints excluded: chain Y residue 198 ASN Chi-restraints excluded: chain Y residue 244 CYS Chi-restraints excluded: chain Y residue 335 SER Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 528 ASP Chi-restraints excluded: chain Z residue 87 CYS Chi-restraints excluded: chain Z residue 193 ILE Chi-restraints excluded: chain Z residue 219 GLU Chi-restraints excluded: chain Z residue 558 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 697 random chunks: chunk 226 optimal weight: 0.5980 chunk 606 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 395 optimal weight: 0.3980 chunk 166 optimal weight: 1.9990 chunk 674 optimal weight: 1.9990 chunk 559 optimal weight: 10.0000 chunk 312 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 223 optimal weight: 8.9990 chunk 354 optimal weight: 10.0000 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 38 ASN ** 7 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 78 HIS C 87 ASN P 52 GLN Q 49 GLN ** R 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 174 GLN S 191 GLN ** S 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 179 ASN ** U 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 278 GLN ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 330 GLN ** V 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 286 ASN ** Y 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 144 HIS ** Z 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 54658 Z= 0.190 Angle : 0.515 14.057 74121 Z= 0.262 Chirality : 0.041 0.289 8683 Planarity : 0.004 0.050 9504 Dihedral : 5.174 117.988 7668 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.67 % Favored : 96.22 % Rotamer: Outliers : 2.88 % Allowed : 18.44 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.10), residues: 7034 helix: 0.45 (0.09), residues: 3868 sheet: -0.76 (0.21), residues: 609 loop : -0.88 (0.12), residues: 2557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 9 73 HIS 0.005 0.001 HIS 7 123 PHE 0.024 0.001 PHE T 489 TYR 0.021 0.001 TYR 4 211 ARG 0.007 0.000 ARG 7 121 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 828 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 666 time to evaluate : 4.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 72 ASP cc_start: 0.7203 (OUTLIER) cc_final: 0.6961 (p0) REVERT: 1 341 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7932 (mt-10) REVERT: 1 490 TYR cc_start: 0.8704 (OUTLIER) cc_final: 0.8076 (m-80) REVERT: 1 548 MET cc_start: 0.8968 (mtm) cc_final: 0.8659 (mtp) REVERT: 2 108 GLU cc_start: 0.7996 (tt0) cc_final: 0.7545 (tt0) REVERT: 2 387 LEU cc_start: 0.8214 (mt) cc_final: 0.7990 (mt) REVERT: 3 155 LYS cc_start: 0.8170 (ttpp) cc_final: 0.7803 (tptt) REVERT: 4 124 ASN cc_start: 0.8679 (t0) cc_final: 0.8310 (t0) REVERT: 4 269 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8237 (mm) REVERT: 7 142 GLU cc_start: 0.7374 (mt-10) cc_final: 0.6925 (mt-10) REVERT: 8 62 ASP cc_start: 0.7942 (OUTLIER) cc_final: 0.7528 (m-30) REVERT: 8 70 LYS cc_start: 0.7656 (tttm) cc_final: 0.6381 (mmtt) REVERT: 9 13 LYS cc_start: 0.7987 (mtmt) cc_final: 0.7459 (mmmt) REVERT: 9 17 ASP cc_start: 0.7588 (m-30) cc_final: 0.7300 (m-30) REVERT: 9 66 ILE cc_start: 0.7775 (OUTLIER) cc_final: 0.7466 (mm) REVERT: E 78 LEU cc_start: 0.8314 (pp) cc_final: 0.7944 (mp) REVERT: F 61 MET cc_start: 0.7945 (mmm) cc_final: 0.7624 (mmt) REVERT: H 81 MET cc_start: 0.8264 (ttp) cc_final: 0.7960 (ttp) REVERT: H 92 ASN cc_start: 0.8370 (p0) cc_final: 0.8033 (p0) REVERT: H 97 LYS cc_start: 0.7861 (mmtt) cc_final: 0.7245 (tmtt) REVERT: I 60 LYS cc_start: 0.7360 (mttt) cc_final: 0.7006 (mttt) REVERT: Q 21 ASN cc_start: 0.8462 (m-40) cc_final: 0.8168 (m110) REVERT: S 203 PHE cc_start: 0.8764 (OUTLIER) cc_final: 0.7681 (m-10) REVERT: S 231 TYR cc_start: 0.8757 (m-80) cc_final: 0.8236 (m-80) REVERT: U 53 PHE cc_start: 0.6981 (OUTLIER) cc_final: 0.6647 (p90) REVERT: U 240 ILE cc_start: 0.7121 (mm) cc_final: 0.6636 (mt) REVERT: U 409 GLU cc_start: 0.6289 (mm-30) cc_final: 0.5879 (mm-30) REVERT: X 370 GLU cc_start: 0.7094 (pp20) cc_final: 0.6669 (mm-30) REVERT: X 552 GLU cc_start: 0.5880 (OUTLIER) cc_final: 0.4979 (mm-30) REVERT: Y 141 TRP cc_start: 0.8018 (OUTLIER) cc_final: 0.7516 (m-10) REVERT: Y 244 CYS cc_start: 0.7519 (OUTLIER) cc_final: 0.7226 (p) REVERT: Y 502 MET cc_start: 0.5560 (mtp) cc_final: 0.4984 (ttp) REVERT: Z 219 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7735 (mm-30) REVERT: Z 310 TYR cc_start: 0.8418 (m-80) cc_final: 0.7691 (m-80) outliers start: 162 outliers final: 127 residues processed: 781 average time/residue: 0.4954 time to fit residues: 660.0399 Evaluate side-chains 758 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 620 time to evaluate : 4.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 1 residue 72 ASP Chi-restraints excluded: chain 1 residue 103 LYS Chi-restraints excluded: chain 1 residue 216 LEU Chi-restraints excluded: chain 1 residue 271 SER Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 490 TYR Chi-restraints excluded: chain 2 residue 24 VAL Chi-restraints excluded: chain 2 residue 144 LEU Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 377 VAL Chi-restraints excluded: chain 2 residue 391 THR Chi-restraints excluded: chain 3 residue 117 SER Chi-restraints excluded: chain 3 residue 181 VAL Chi-restraints excluded: chain 3 residue 263 SER Chi-restraints excluded: chain 3 residue 281 VAL Chi-restraints excluded: chain 4 residue 16 SER Chi-restraints excluded: chain 4 residue 172 VAL Chi-restraints excluded: chain 4 residue 269 LEU Chi-restraints excluded: chain 5 residue 65 VAL Chi-restraints excluded: chain 5 residue 89 VAL Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 114 ILE Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 15 LEU Chi-restraints excluded: chain 7 residue 49 THR Chi-restraints excluded: chain 7 residue 61 VAL Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 8 residue 37 THR Chi-restraints excluded: chain 8 residue 62 ASP Chi-restraints excluded: chain 8 residue 82 THR Chi-restraints excluded: chain 9 residue 66 ILE Chi-restraints excluded: chain 9 residue 88 GLU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain J residue 66 CYS Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain M residue 202 PHE Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 314 LYS Chi-restraints excluded: chain M residue 323 VAL Chi-restraints excluded: chain P residue 123 GLU Chi-restraints excluded: chain P residue 163 ASP Chi-restraints excluded: chain P residue 179 ASP Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 130 SER Chi-restraints excluded: chain S residue 126 THR Chi-restraints excluded: chain S residue 159 GLN Chi-restraints excluded: chain S residue 185 HIS Chi-restraints excluded: chain S residue 203 PHE Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 212 SER Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 266 GLU Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 427 VAL Chi-restraints excluded: chain T residue 529 ASN Chi-restraints excluded: chain U residue 53 PHE Chi-restraints excluded: chain U residue 66 LEU Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 163 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 187 VAL Chi-restraints excluded: chain U residue 209 VAL Chi-restraints excluded: chain U residue 273 VAL Chi-restraints excluded: chain U residue 278 GLN Chi-restraints excluded: chain U residue 300 PHE Chi-restraints excluded: chain U residue 331 SER Chi-restraints excluded: chain U residue 357 LEU Chi-restraints excluded: chain U residue 466 LEU 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 V residue 87 VAL Chi-restraints excluded: chain V residue 89 SER Chi-restraints excluded: chain V residue 155 ILE Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 177 LEU Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 206 VAL Chi-restraints excluded: chain V residue 210 ASP Chi-restraints excluded: chain V residue 257 CYS Chi-restraints excluded: chain V residue 279 THR Chi-restraints excluded: chain X residue 62 SER Chi-restraints excluded: chain X residue 92 SER Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 222 ASP Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 286 ASN Chi-restraints excluded: chain X residue 291 THR Chi-restraints excluded: chain X residue 295 SER Chi-restraints excluded: chain X residue 296 GLU Chi-restraints excluded: chain X residue 297 VAL Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 423 ASP Chi-restraints excluded: chain X residue 452 VAL Chi-restraints excluded: chain X residue 480 ASP Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain X residue 552 GLU Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain Y residue 103 VAL Chi-restraints excluded: chain Y residue 122 MET Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 141 TRP Chi-restraints excluded: chain Y residue 198 ASN Chi-restraints excluded: chain Y residue 244 CYS Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 335 SER Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Y residue 528 ASP Chi-restraints excluded: chain Z residue 87 CYS Chi-restraints excluded: chain Z residue 193 ILE Chi-restraints excluded: chain Z residue 219 GLU Chi-restraints excluded: chain Z residue 346 LEU Chi-restraints excluded: chain Z residue 558 THR Chi-restraints excluded: chain Z residue 567 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 697 random chunks: chunk 650 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 384 optimal weight: 0.7980 chunk 492 optimal weight: 2.9990 chunk 381 optimal weight: 0.9990 chunk 567 optimal weight: 4.9990 chunk 376 optimal weight: 0.8980 chunk 671 optimal weight: 0.0970 chunk 420 optimal weight: 8.9990 chunk 409 optimal weight: 2.9990 chunk 310 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 38 ASN ** 7 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 78 HIS ** J 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 52 GLN ** R 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 174 GLN ** S 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 405 GLN ** T 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 104 GLN U 179 ASN ** U 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 278 GLN ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 336 GLN ** V 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 337 GLN ** Y 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 54658 Z= 0.144 Angle : 0.501 12.512 74121 Z= 0.254 Chirality : 0.040 0.277 8683 Planarity : 0.004 0.050 9504 Dihedral : 5.030 112.426 7668 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.43 % Favored : 96.47 % Rotamer: Outliers : 2.45 % Allowed : 19.53 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.10), residues: 7034 helix: 0.62 (0.09), residues: 3869 sheet: -0.68 (0.21), residues: 600 loop : -0.76 (0.12), residues: 2565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 9 73 HIS 0.004 0.001 HIS T 241 PHE 0.027 0.001 PHE T 276 TYR 0.047 0.001 TYR Z 478 ARG 0.014 0.000 ARG X 289 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 833 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 695 time to evaluate : 4.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 72 ASP cc_start: 0.7301 (OUTLIER) cc_final: 0.7072 (p0) REVERT: 1 103 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7699 (tppt) REVERT: 1 341 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7934 (mt-10) REVERT: 1 490 TYR cc_start: 0.8718 (OUTLIER) cc_final: 0.8151 (m-80) REVERT: 1 548 MET cc_start: 0.8931 (mtm) cc_final: 0.8654 (mtp) REVERT: 2 108 GLU cc_start: 0.8005 (tt0) cc_final: 0.7555 (tt0) REVERT: 3 155 LYS cc_start: 0.8133 (ttpp) cc_final: 0.7786 (tptt) REVERT: 4 124 ASN cc_start: 0.8675 (t0) cc_final: 0.8296 (t0) REVERT: 4 269 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8200 (mm) REVERT: 6 80 PHE cc_start: 0.7686 (t80) cc_final: 0.7027 (m-10) REVERT: 7 142 GLU cc_start: 0.7348 (mt-10) cc_final: 0.6901 (mt-10) REVERT: 8 62 ASP cc_start: 0.7906 (OUTLIER) cc_final: 0.7581 (m-30) REVERT: 8 70 LYS cc_start: 0.7619 (tttm) cc_final: 0.6224 (mmtt) REVERT: 9 13 LYS cc_start: 0.7973 (mtmt) cc_final: 0.7450 (mmmt) REVERT: 9 17 ASP cc_start: 0.7534 (m-30) cc_final: 0.7231 (m-30) REVERT: 9 66 ILE cc_start: 0.7739 (OUTLIER) cc_final: 0.7440 (mm) REVERT: A 123 LEU cc_start: 0.8793 (mt) cc_final: 0.8504 (mp) REVERT: E 78 LEU cc_start: 0.8073 (pp) cc_final: 0.7815 (mt) REVERT: F 61 MET cc_start: 0.7962 (mmm) cc_final: 0.7680 (mmt) REVERT: H 81 MET cc_start: 0.8235 (ttp) cc_final: 0.7953 (ttp) REVERT: H 92 ASN cc_start: 0.8354 (p0) cc_final: 0.8063 (p0) REVERT: H 97 LYS cc_start: 0.7833 (mmtt) cc_final: 0.7210 (tmtt) REVERT: I 60 LYS cc_start: 0.7299 (mttt) cc_final: 0.6945 (mttt) REVERT: Q 21 ASN cc_start: 0.8444 (m-40) cc_final: 0.8145 (m110) REVERT: S 203 PHE cc_start: 0.8744 (OUTLIER) cc_final: 0.7719 (m-10) REVERT: S 231 TYR cc_start: 0.8749 (m-80) cc_final: 0.8163 (m-80) REVERT: U 240 ILE cc_start: 0.7099 (mm) cc_final: 0.6599 (mt) REVERT: U 409 GLU cc_start: 0.6253 (mm-30) cc_final: 0.5925 (mm-30) REVERT: V 213 VAL cc_start: 0.8396 (m) cc_final: 0.8156 (p) REVERT: V 471 GLN cc_start: 0.6815 (mp10) cc_final: 0.6484 (mp10) REVERT: X 370 GLU cc_start: 0.7040 (pp20) cc_final: 0.6620 (mm-30) REVERT: Y 141 TRP cc_start: 0.7988 (OUTLIER) cc_final: 0.7498 (m-10) REVERT: Y 244 CYS cc_start: 0.7538 (OUTLIER) cc_final: 0.7240 (p) REVERT: Y 310 TYR cc_start: 0.9053 (m-80) cc_final: 0.8053 (m-80) REVERT: Z 219 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7761 (mm-30) REVERT: Z 310 TYR cc_start: 0.8218 (m-80) cc_final: 0.7492 (m-80) outliers start: 138 outliers final: 101 residues processed: 793 average time/residue: 0.5087 time to fit residues: 690.8400 Evaluate side-chains 752 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 641 time to evaluate : 4.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 1 residue 72 ASP Chi-restraints excluded: chain 1 residue 103 LYS Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 490 TYR Chi-restraints excluded: chain 2 residue 24 VAL Chi-restraints excluded: chain 2 residue 144 LEU Chi-restraints excluded: chain 2 residue 290 VAL Chi-restraints excluded: chain 2 residue 377 VAL Chi-restraints excluded: chain 2 residue 391 THR Chi-restraints excluded: chain 3 residue 181 VAL Chi-restraints excluded: chain 3 residue 281 VAL Chi-restraints excluded: chain 4 residue 115 THR Chi-restraints excluded: chain 4 residue 172 VAL Chi-restraints excluded: chain 4 residue 269 LEU Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 15 LEU Chi-restraints excluded: chain 7 residue 49 THR Chi-restraints excluded: chain 7 residue 61 VAL Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 8 residue 37 THR Chi-restraints excluded: chain 8 residue 62 ASP Chi-restraints excluded: chain 8 residue 82 THR Chi-restraints excluded: chain 9 residue 66 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain J residue 66 CYS Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain M residue 202 PHE Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 314 LYS Chi-restraints excluded: chain M residue 323 VAL Chi-restraints excluded: chain P residue 123 GLU Chi-restraints excluded: chain P residue 179 ASP Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 130 SER Chi-restraints excluded: chain S residue 126 THR Chi-restraints excluded: chain S residue 159 GLN Chi-restraints excluded: chain S residue 203 PHE Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 266 GLU Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 115 VAL Chi-restraints excluded: chain T residue 427 VAL Chi-restraints excluded: chain T residue 529 ASN Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 163 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 187 VAL Chi-restraints excluded: chain U residue 273 VAL Chi-restraints excluded: chain U residue 278 GLN Chi-restraints excluded: chain U residue 331 SER Chi-restraints excluded: chain U residue 466 LEU Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain U residue 516 ASP Chi-restraints excluded: chain V residue 89 SER Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 177 LEU Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 206 VAL Chi-restraints excluded: chain V residue 257 CYS Chi-restraints excluded: chain X residue 62 SER Chi-restraints excluded: chain X residue 92 SER Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 222 ASP Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 291 THR Chi-restraints excluded: chain X residue 295 SER Chi-restraints excluded: chain X residue 296 GLU Chi-restraints excluded: chain X residue 297 VAL Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 423 ASP Chi-restraints excluded: chain X residue 452 VAL Chi-restraints excluded: chain X residue 480 ASP Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain Y residue 73 VAL Chi-restraints excluded: chain Y residue 103 VAL Chi-restraints excluded: chain Y residue 122 MET Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 141 TRP Chi-restraints excluded: chain Y residue 198 ASN Chi-restraints excluded: chain Y residue 244 CYS Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 335 SER Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Z residue 193 ILE Chi-restraints excluded: chain Z residue 219 GLU Chi-restraints excluded: chain Z residue 346 LEU Chi-restraints excluded: chain Z residue 558 THR Chi-restraints excluded: chain Z residue 567 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 697 random chunks: chunk 415 optimal weight: 8.9990 chunk 268 optimal weight: 3.9990 chunk 401 optimal weight: 10.0000 chunk 202 optimal weight: 0.9980 chunk 132 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 427 optimal weight: 9.9990 chunk 457 optimal weight: 10.0000 chunk 332 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 528 optimal weight: 0.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 189 HIS 5 10 GLN ** 5 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 38 ASN ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 78 HIS ** J 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 43 GLN ** R 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 64 GLN T 253 GLN U 179 ASN ** U 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 278 GLN X 199 ASN ** X 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 54658 Z= 0.198 Angle : 0.530 11.642 74121 Z= 0.268 Chirality : 0.041 0.225 8683 Planarity : 0.004 0.049 9504 Dihedral : 5.037 107.819 7667 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.80 % Favored : 96.09 % Rotamer: Outliers : 2.59 % Allowed : 19.79 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.10), residues: 7034 helix: 0.66 (0.09), residues: 3859 sheet: -0.62 (0.21), residues: 612 loop : -0.78 (0.12), residues: 2563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 9 73 HIS 0.005 0.001 HIS 7 123 PHE 0.024 0.001 PHE T 276 TYR 0.027 0.001 TYR Z 478 ARG 0.009 0.000 ARG Z 218 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 655 time to evaluate : 4.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 13 GLN cc_start: 0.7533 (tt0) cc_final: 0.7291 (mt0) REVERT: 1 72 ASP cc_start: 0.7317 (OUTLIER) cc_final: 0.7079 (p0) REVERT: 1 490 TYR cc_start: 0.8711 (OUTLIER) cc_final: 0.8079 (m-80) REVERT: 1 548 MET cc_start: 0.8970 (mtm) cc_final: 0.8642 (mtp) REVERT: 2 108 GLU cc_start: 0.8031 (tt0) cc_final: 0.7768 (tt0) REVERT: 3 155 LYS cc_start: 0.8161 (ttpp) cc_final: 0.7801 (tptt) REVERT: 4 124 ASN cc_start: 0.8685 (t0) cc_final: 0.8313 (t0) REVERT: 4 269 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8233 (mm) REVERT: 6 80 PHE cc_start: 0.7711 (t80) cc_final: 0.7034 (m-10) REVERT: 7 142 GLU cc_start: 0.7368 (mt-10) cc_final: 0.6924 (mt-10) REVERT: 8 62 ASP cc_start: 0.7969 (OUTLIER) cc_final: 0.7601 (m-30) REVERT: 8 70 LYS cc_start: 0.7540 (tttm) cc_final: 0.6254 (mmtt) REVERT: 9 13 LYS cc_start: 0.7959 (mtmt) cc_final: 0.7450 (mmmt) REVERT: 9 17 ASP cc_start: 0.7569 (m-30) cc_final: 0.7262 (m-30) REVERT: 9 66 ILE cc_start: 0.7825 (OUTLIER) cc_final: 0.7530 (mm) REVERT: E 78 LEU cc_start: 0.8314 (pp) cc_final: 0.7911 (mt) REVERT: F 61 MET cc_start: 0.7959 (mmm) cc_final: 0.7650 (mmt) REVERT: H 81 MET cc_start: 0.8290 (ttp) cc_final: 0.7975 (ttp) REVERT: H 92 ASN cc_start: 0.8393 (p0) cc_final: 0.8042 (p0) REVERT: H 97 LYS cc_start: 0.7871 (mmtt) cc_final: 0.7247 (tmtt) REVERT: I 60 LYS cc_start: 0.7347 (mttt) cc_final: 0.7010 (mttt) REVERT: Q 21 ASN cc_start: 0.8475 (m-40) cc_final: 0.8188 (m110) REVERT: S 203 PHE cc_start: 0.8764 (OUTLIER) cc_final: 0.7676 (m-10) REVERT: S 231 TYR cc_start: 0.8738 (m-80) cc_final: 0.8140 (m-80) REVERT: U 53 PHE cc_start: 0.7065 (OUTLIER) cc_final: 0.6743 (p90) REVERT: U 222 LEU cc_start: 0.7716 (tp) cc_final: 0.7483 (tp) REVERT: U 240 ILE cc_start: 0.7130 (mm) cc_final: 0.6659 (mt) REVERT: U 409 GLU cc_start: 0.6146 (mm-30) cc_final: 0.5770 (mm-30) REVERT: V 471 GLN cc_start: 0.6812 (mp10) cc_final: 0.6454 (mp10) REVERT: X 87 CYS cc_start: 0.7583 (m) cc_final: 0.7344 (m) REVERT: X 370 GLU cc_start: 0.7157 (pp20) cc_final: 0.6631 (mm-30) REVERT: Y 141 TRP cc_start: 0.8060 (OUTLIER) cc_final: 0.7577 (m-10) REVERT: Y 233 ILE cc_start: 0.5915 (mt) cc_final: 0.5695 (mt) REVERT: Y 244 CYS cc_start: 0.7560 (OUTLIER) cc_final: 0.7288 (p) REVERT: Y 310 TYR cc_start: 0.9026 (m-80) cc_final: 0.8087 (m-80) REVERT: Y 502 MET cc_start: 0.5662 (mtp) cc_final: 0.5119 (ttm) REVERT: Y 521 LEU cc_start: 0.4444 (OUTLIER) cc_final: 0.4200 (pt) REVERT: Z 219 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7565 (mm-30) REVERT: Z 310 TYR cc_start: 0.8395 (m-80) cc_final: 0.7658 (m-80) outliers start: 146 outliers final: 113 residues processed: 757 average time/residue: 0.5044 time to fit residues: 655.5871 Evaluate side-chains 746 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 622 time to evaluate : 4.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 1 residue 72 ASP Chi-restraints excluded: chain 1 residue 103 LYS Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 490 TYR Chi-restraints excluded: chain 2 residue 24 VAL Chi-restraints excluded: chain 2 residue 144 LEU Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 290 VAL Chi-restraints excluded: chain 2 residue 377 VAL Chi-restraints excluded: chain 2 residue 391 THR Chi-restraints excluded: chain 3 residue 117 SER Chi-restraints excluded: chain 3 residue 181 VAL Chi-restraints excluded: chain 3 residue 263 SER Chi-restraints excluded: chain 3 residue 281 VAL Chi-restraints excluded: chain 4 residue 16 SER Chi-restraints excluded: chain 4 residue 115 THR Chi-restraints excluded: chain 4 residue 172 VAL Chi-restraints excluded: chain 4 residue 269 LEU Chi-restraints excluded: chain 5 residue 65 VAL Chi-restraints excluded: chain 5 residue 89 VAL Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 15 LEU Chi-restraints excluded: chain 7 residue 49 THR Chi-restraints excluded: chain 7 residue 61 VAL Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 8 residue 37 THR Chi-restraints excluded: chain 8 residue 62 ASP Chi-restraints excluded: chain 8 residue 82 THR Chi-restraints excluded: chain 9 residue 66 ILE Chi-restraints excluded: chain 9 residue 88 GLU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain J residue 66 CYS Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain M residue 202 PHE Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 314 LYS Chi-restraints excluded: chain M residue 323 VAL Chi-restraints excluded: chain P residue 72 ASP Chi-restraints excluded: chain P residue 123 GLU Chi-restraints excluded: chain P residue 179 ASP Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 130 SER Chi-restraints excluded: chain S residue 126 THR Chi-restraints excluded: chain S residue 185 HIS Chi-restraints excluded: chain S residue 203 PHE Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 212 SER Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 266 GLU Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 115 VAL Chi-restraints excluded: chain T residue 425 LEU Chi-restraints excluded: chain T residue 427 VAL Chi-restraints excluded: chain T residue 529 ASN Chi-restraints excluded: chain U residue 53 PHE Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 163 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 187 VAL Chi-restraints excluded: chain U residue 209 VAL Chi-restraints excluded: chain U residue 273 VAL Chi-restraints excluded: chain U residue 278 GLN Chi-restraints excluded: chain U residue 331 SER Chi-restraints excluded: chain U residue 466 LEU Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain U residue 516 ASP Chi-restraints excluded: chain V residue 89 SER Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 177 LEU Chi-restraints excluded: chain V residue 206 VAL Chi-restraints excluded: chain V residue 337 MET Chi-restraints excluded: chain X residue 62 SER Chi-restraints excluded: chain X residue 92 SER Chi-restraints excluded: chain X residue 222 ASP Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 291 THR Chi-restraints excluded: chain X residue 295 SER Chi-restraints excluded: chain X residue 296 GLU Chi-restraints excluded: chain X residue 297 VAL Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 423 ASP Chi-restraints excluded: chain X residue 452 VAL Chi-restraints excluded: chain X residue 480 ASP Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain Y residue 73 VAL Chi-restraints excluded: chain Y residue 103 VAL Chi-restraints excluded: chain Y residue 122 MET Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 141 TRP Chi-restraints excluded: chain Y residue 198 ASN Chi-restraints excluded: chain Y residue 244 CYS Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 335 SER Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Z residue 193 ILE Chi-restraints excluded: chain Z residue 219 GLU Chi-restraints excluded: chain Z residue 346 LEU Chi-restraints excluded: chain Z residue 391 VAL Chi-restraints excluded: chain Z residue 558 THR Chi-restraints excluded: chain Z residue 567 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 697 random chunks: chunk 611 optimal weight: 0.4980 chunk 643 optimal weight: 0.6980 chunk 587 optimal weight: 10.0000 chunk 626 optimal weight: 2.9990 chunk 376 optimal weight: 0.8980 chunk 272 optimal weight: 3.9990 chunk 491 optimal weight: 2.9990 chunk 192 optimal weight: 20.0000 chunk 565 optimal weight: 3.9990 chunk 592 optimal weight: 8.9990 chunk 623 optimal weight: 0.5980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 38 ASN ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 78 HIS J 87 ASN ** R 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 278 GLN ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 252 ASN X 286 ASN ** Y 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 54658 Z= 0.172 Angle : 0.526 13.158 74121 Z= 0.265 Chirality : 0.040 0.227 8683 Planarity : 0.004 0.049 9504 Dihedral : 4.970 103.625 7667 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.55 % Favored : 96.35 % Rotamer: Outliers : 2.42 % Allowed : 19.94 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.10), residues: 7034 helix: 0.75 (0.09), residues: 3860 sheet: -0.56 (0.21), residues: 612 loop : -0.72 (0.13), residues: 2562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 9 73 HIS 0.004 0.001 HIS 7 123 PHE 0.026 0.001 PHE T 276 TYR 0.026 0.001 TYR Z 478 ARG 0.009 0.000 ARG Z 218 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 799 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 663 time to evaluate : 4.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 13 GLN cc_start: 0.7507 (tt0) cc_final: 0.7276 (mt0) REVERT: 1 72 ASP cc_start: 0.7270 (OUTLIER) cc_final: 0.7037 (p0) REVERT: 1 490 TYR cc_start: 0.8682 (OUTLIER) cc_final: 0.8115 (m-80) REVERT: 1 548 MET cc_start: 0.8941 (mtm) cc_final: 0.8650 (mtp) REVERT: 3 155 LYS cc_start: 0.8227 (ttpp) cc_final: 0.7878 (tptt) REVERT: 4 124 ASN cc_start: 0.8680 (t0) cc_final: 0.8319 (t0) REVERT: 4 269 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8214 (mm) REVERT: 6 80 PHE cc_start: 0.7685 (t80) cc_final: 0.6970 (m-10) REVERT: 7 142 GLU cc_start: 0.7356 (mt-10) cc_final: 0.6913 (mt-10) REVERT: 8 62 ASP cc_start: 0.7952 (OUTLIER) cc_final: 0.7593 (m-30) REVERT: 8 70 LYS cc_start: 0.7511 (tttm) cc_final: 0.6243 (mmtt) REVERT: 9 13 LYS cc_start: 0.7955 (mtmt) cc_final: 0.7449 (mmmt) REVERT: 9 17 ASP cc_start: 0.7561 (m-30) cc_final: 0.7248 (m-30) REVERT: 9 66 ILE cc_start: 0.7815 (OUTLIER) cc_final: 0.7532 (mm) REVERT: E 78 LEU cc_start: 0.8220 (pp) cc_final: 0.7867 (mt) REVERT: F 61 MET cc_start: 0.7977 (mmm) cc_final: 0.7707 (mmt) REVERT: H 81 MET cc_start: 0.8275 (ttp) cc_final: 0.7968 (ttp) REVERT: H 92 ASN cc_start: 0.8365 (p0) cc_final: 0.8037 (p0) REVERT: H 97 LYS cc_start: 0.7790 (mmtt) cc_final: 0.7262 (tmtt) REVERT: I 60 LYS cc_start: 0.7315 (mttt) cc_final: 0.6978 (mttt) REVERT: P 206 ARG cc_start: 0.7281 (ttp80) cc_final: 0.7009 (tpp80) REVERT: Q 21 ASN cc_start: 0.8469 (m-40) cc_final: 0.8170 (m110) REVERT: S 203 PHE cc_start: 0.8718 (OUTLIER) cc_final: 0.7652 (m-80) REVERT: S 231 TYR cc_start: 0.8738 (m-80) cc_final: 0.8155 (m-80) REVERT: U 53 PHE cc_start: 0.7058 (OUTLIER) cc_final: 0.6646 (p90) REVERT: U 222 LEU cc_start: 0.7743 (tp) cc_final: 0.7517 (tp) REVERT: U 240 ILE cc_start: 0.7130 (mm) cc_final: 0.6651 (mt) REVERT: V 213 VAL cc_start: 0.8376 (m) cc_final: 0.8102 (p) REVERT: V 471 GLN cc_start: 0.6750 (mp10) cc_final: 0.6426 (mp10) REVERT: Y 141 TRP cc_start: 0.8032 (OUTLIER) cc_final: 0.7508 (m-10) REVERT: Y 233 ILE cc_start: 0.6015 (mt) cc_final: 0.5788 (mt) REVERT: Y 244 CYS cc_start: 0.7557 (OUTLIER) cc_final: 0.7221 (p) REVERT: Y 310 TYR cc_start: 0.9039 (m-80) cc_final: 0.8193 (m-80) REVERT: Y 502 MET cc_start: 0.5670 (mtp) cc_final: 0.5142 (ttm) REVERT: Y 521 LEU cc_start: 0.4510 (OUTLIER) cc_final: 0.4231 (pt) REVERT: Z 55 GLU cc_start: 0.6595 (pt0) cc_final: 0.6383 (tt0) REVERT: Z 219 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7490 (mm-30) REVERT: Z 310 TYR cc_start: 0.8309 (m-80) cc_final: 0.7593 (m-80) outliers start: 136 outliers final: 115 residues processed: 761 average time/residue: 0.5019 time to fit residues: 651.5879 Evaluate side-chains 768 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 642 time to evaluate : 4.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 0 residue 43 SER Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 1 residue 72 ASP Chi-restraints excluded: chain 1 residue 103 LYS Chi-restraints excluded: chain 1 residue 271 SER Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 490 TYR Chi-restraints excluded: chain 2 residue 24 VAL Chi-restraints excluded: chain 2 residue 144 LEU Chi-restraints excluded: chain 2 residue 290 VAL Chi-restraints excluded: chain 2 residue 377 VAL Chi-restraints excluded: chain 2 residue 391 THR Chi-restraints excluded: chain 3 residue 117 SER Chi-restraints excluded: chain 3 residue 181 VAL Chi-restraints excluded: chain 3 residue 281 VAL Chi-restraints excluded: chain 4 residue 16 SER Chi-restraints excluded: chain 4 residue 42 THR Chi-restraints excluded: chain 4 residue 115 THR Chi-restraints excluded: chain 4 residue 172 VAL Chi-restraints excluded: chain 4 residue 269 LEU Chi-restraints excluded: chain 5 residue 65 VAL Chi-restraints excluded: chain 5 residue 89 VAL Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 49 THR Chi-restraints excluded: chain 7 residue 61 VAL Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 8 residue 37 THR Chi-restraints excluded: chain 8 residue 62 ASP Chi-restraints excluded: chain 8 residue 82 THR Chi-restraints excluded: chain 9 residue 66 ILE Chi-restraints excluded: chain 9 residue 88 GLU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain J residue 66 CYS Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain M residue 202 PHE Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 323 VAL Chi-restraints excluded: chain P residue 72 ASP Chi-restraints excluded: chain P residue 123 GLU Chi-restraints excluded: chain P residue 179 ASP Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 130 SER Chi-restraints excluded: chain R residue 185 ILE Chi-restraints excluded: chain S residue 126 THR Chi-restraints excluded: chain S residue 185 HIS Chi-restraints excluded: chain S residue 203 PHE Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 212 SER Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 266 GLU Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 115 VAL Chi-restraints excluded: chain T residue 315 ASP Chi-restraints excluded: chain T residue 425 LEU Chi-restraints excluded: chain T residue 427 VAL Chi-restraints excluded: chain T residue 529 ASN Chi-restraints excluded: chain U residue 53 PHE Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 163 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 187 VAL Chi-restraints excluded: chain U residue 209 VAL Chi-restraints excluded: chain U residue 273 VAL Chi-restraints excluded: chain U residue 278 GLN Chi-restraints excluded: chain U residue 331 SER Chi-restraints excluded: chain U residue 337 MET Chi-restraints excluded: chain U residue 466 LEU Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain U residue 516 ASP Chi-restraints excluded: chain V residue 89 SER Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 177 LEU Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain X residue 62 SER Chi-restraints excluded: chain X residue 92 SER Chi-restraints excluded: chain X residue 222 ASP Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 286 ASN Chi-restraints excluded: chain X residue 291 THR Chi-restraints excluded: chain X residue 295 SER Chi-restraints excluded: chain X residue 296 GLU Chi-restraints excluded: chain X residue 297 VAL Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 423 ASP Chi-restraints excluded: chain X residue 452 VAL Chi-restraints excluded: chain X residue 475 THR Chi-restraints excluded: chain X residue 480 ASP Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain Y residue 73 VAL Chi-restraints excluded: chain Y residue 103 VAL Chi-restraints excluded: chain Y residue 122 MET Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 141 TRP Chi-restraints excluded: chain Y residue 198 ASN Chi-restraints excluded: chain Y residue 244 CYS Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 335 SER Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Z residue 193 ILE Chi-restraints excluded: chain Z residue 219 GLU Chi-restraints excluded: chain Z residue 346 LEU Chi-restraints excluded: chain Z residue 391 VAL Chi-restraints excluded: chain Z residue 531 VAL Chi-restraints excluded: chain Z residue 558 THR Chi-restraints excluded: chain Z residue 567 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 697 random chunks: chunk 411 optimal weight: 2.9990 chunk 661 optimal weight: 2.9990 chunk 404 optimal weight: 1.9990 chunk 314 optimal weight: 7.9990 chunk 460 optimal weight: 9.9990 chunk 694 optimal weight: 0.0170 chunk 639 optimal weight: 5.9990 chunk 552 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 427 optimal weight: 9.9990 chunk 339 optimal weight: 9.9990 overall best weight: 2.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 38 ASN ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 78 HIS P 52 GLN R 181 ASN S 174 GLN ** S 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 64 GLN T 264 GLN ** U 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 278 GLN ** U 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 286 ASN X 337 GLN X 574 ASN ** Y 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 278 GLN ** Z 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 54658 Z= 0.279 Angle : 0.580 12.799 74121 Z= 0.294 Chirality : 0.043 0.260 8683 Planarity : 0.004 0.049 9504 Dihedral : 5.162 102.658 7667 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.22 % Favored : 95.64 % Rotamer: Outliers : 2.58 % Allowed : 20.11 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.10), residues: 7034 helix: 0.62 (0.09), residues: 3839 sheet: -0.61 (0.21), residues: 629 loop : -0.78 (0.12), residues: 2566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 3 109 HIS 0.007 0.001 HIS 7 123 PHE 0.023 0.002 PHE P 122 TYR 0.025 0.002 TYR U 356 ARG 0.011 0.000 ARG X 289 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 776 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 631 time to evaluate : 4.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 13 GLN cc_start: 0.7565 (tt0) cc_final: 0.7228 (mt0) REVERT: 1 72 ASP cc_start: 0.7381 (OUTLIER) cc_final: 0.7159 (p0) REVERT: 1 490 TYR cc_start: 0.8735 (OUTLIER) cc_final: 0.8119 (m-80) REVERT: 1 548 MET cc_start: 0.8981 (mtm) cc_final: 0.8663 (mtp) REVERT: 3 155 LYS cc_start: 0.8272 (ttpp) cc_final: 0.7846 (tptt) REVERT: 4 124 ASN cc_start: 0.8693 (t0) cc_final: 0.8309 (t0) REVERT: 6 80 PHE cc_start: 0.7729 (t80) cc_final: 0.7050 (m-10) REVERT: 7 142 GLU cc_start: 0.7355 (mt-10) cc_final: 0.6905 (mt-10) REVERT: 8 62 ASP cc_start: 0.8014 (OUTLIER) cc_final: 0.7680 (m-30) REVERT: 9 13 LYS cc_start: 0.7976 (mtmt) cc_final: 0.7459 (mmmt) REVERT: 9 17 ASP cc_start: 0.7596 (m-30) cc_final: 0.7289 (m-30) REVERT: 9 28 ARG cc_start: 0.6043 (ptt180) cc_final: 0.4317 (ptm160) REVERT: 9 66 ILE cc_start: 0.7844 (OUTLIER) cc_final: 0.7612 (mm) REVERT: C 97 LYS cc_start: 0.8242 (mptt) cc_final: 0.7717 (mmtt) REVERT: E 78 LEU cc_start: 0.8461 (pp) cc_final: 0.7856 (mt) REVERT: H 81 MET cc_start: 0.8375 (ttp) cc_final: 0.8062 (ttp) REVERT: H 97 LYS cc_start: 0.8014 (mmtt) cc_final: 0.7520 (tmtt) REVERT: I 60 LYS cc_start: 0.7376 (mttt) cc_final: 0.6899 (mttt) REVERT: Q 21 ASN cc_start: 0.8498 (m-40) cc_final: 0.8190 (m110) REVERT: S 98 ASN cc_start: 0.7199 (m110) cc_final: 0.6839 (t0) REVERT: S 203 PHE cc_start: 0.8814 (OUTLIER) cc_final: 0.7856 (m-10) REVERT: U 53 PHE cc_start: 0.7108 (OUTLIER) cc_final: 0.6638 (p90) REVERT: U 409 GLU cc_start: 0.6540 (mm-30) cc_final: 0.5971 (mm-30) REVERT: V 471 GLN cc_start: 0.6741 (mp10) cc_final: 0.6412 (mp10) REVERT: Y 141 TRP cc_start: 0.8076 (OUTLIER) cc_final: 0.7538 (m-10) REVERT: Y 195 GLU cc_start: 0.7428 (tp30) cc_final: 0.7106 (tp30) REVERT: Y 502 MET cc_start: 0.5775 (mtp) cc_final: 0.5111 (ttm) REVERT: Y 521 LEU cc_start: 0.4490 (OUTLIER) cc_final: 0.4152 (pt) REVERT: Z 55 GLU cc_start: 0.6801 (pt0) cc_final: 0.6418 (pt0) REVERT: Z 219 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7557 (mm-30) outliers start: 145 outliers final: 124 residues processed: 734 average time/residue: 0.5051 time to fit residues: 632.5380 Evaluate side-chains 746 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 613 time to evaluate : 4.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 0 residue 43 SER Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 1 residue 72 ASP Chi-restraints excluded: chain 1 residue 103 LYS Chi-restraints excluded: chain 1 residue 271 SER Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 490 TYR Chi-restraints excluded: chain 2 residue 75 THR Chi-restraints excluded: chain 2 residue 144 LEU Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 290 VAL Chi-restraints excluded: chain 2 residue 377 VAL Chi-restraints excluded: chain 2 residue 391 THR Chi-restraints excluded: chain 3 residue 117 SER Chi-restraints excluded: chain 3 residue 181 VAL Chi-restraints excluded: chain 3 residue 263 SER Chi-restraints excluded: chain 3 residue 281 VAL Chi-restraints excluded: chain 4 residue 16 SER Chi-restraints excluded: chain 4 residue 42 THR Chi-restraints excluded: chain 4 residue 111 GLN Chi-restraints excluded: chain 4 residue 115 THR Chi-restraints excluded: chain 4 residue 172 VAL Chi-restraints excluded: chain 4 residue 269 LEU Chi-restraints excluded: chain 5 residue 65 VAL Chi-restraints excluded: chain 5 residue 89 VAL Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 49 THR Chi-restraints excluded: chain 7 residue 61 VAL Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 8 residue 37 THR Chi-restraints excluded: chain 8 residue 62 ASP Chi-restraints excluded: chain 8 residue 82 THR Chi-restraints excluded: chain 9 residue 66 ILE Chi-restraints excluded: chain 9 residue 88 GLU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain J residue 66 CYS Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain M residue 202 PHE Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 323 VAL Chi-restraints excluded: chain P residue 72 ASP Chi-restraints excluded: chain P residue 123 GLU Chi-restraints excluded: chain P residue 179 ASP Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 130 SER Chi-restraints excluded: chain R residue 185 ILE Chi-restraints excluded: chain S residue 126 THR Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 185 HIS Chi-restraints excluded: chain S residue 203 PHE Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 212 SER Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 266 GLU Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 115 VAL Chi-restraints excluded: chain T residue 315 ASP Chi-restraints excluded: chain T residue 425 LEU Chi-restraints excluded: chain T residue 529 ASN Chi-restraints excluded: chain U residue 53 PHE Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 163 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 187 VAL Chi-restraints excluded: chain U residue 209 VAL Chi-restraints excluded: chain U residue 273 VAL Chi-restraints excluded: chain U residue 278 GLN Chi-restraints excluded: chain U residue 331 SER Chi-restraints excluded: chain U residue 337 MET Chi-restraints excluded: chain U residue 466 LEU Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain U residue 516 ASP Chi-restraints excluded: chain V residue 89 SER Chi-restraints excluded: chain V residue 155 ILE Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 177 LEU Chi-restraints excluded: chain V residue 257 CYS Chi-restraints excluded: chain V residue 337 MET Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain X residue 62 SER Chi-restraints excluded: chain X residue 92 SER Chi-restraints excluded: chain X residue 121 ILE Chi-restraints excluded: chain X residue 222 ASP Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 286 ASN Chi-restraints excluded: chain X residue 291 THR Chi-restraints excluded: chain X residue 295 SER Chi-restraints excluded: chain X residue 296 GLU Chi-restraints excluded: chain X residue 297 VAL Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 423 ASP Chi-restraints excluded: chain X residue 452 VAL Chi-restraints excluded: chain X residue 475 THR Chi-restraints excluded: chain X residue 480 ASP Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain Y residue 73 VAL Chi-restraints excluded: chain Y residue 103 VAL Chi-restraints excluded: chain Y residue 122 MET Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 141 TRP Chi-restraints excluded: chain Y residue 198 ASN Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 335 SER Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Z residue 193 ILE Chi-restraints excluded: chain Z residue 219 GLU Chi-restraints excluded: chain Z residue 332 SER Chi-restraints excluded: chain Z residue 391 VAL Chi-restraints excluded: chain Z residue 531 VAL Chi-restraints excluded: chain Z residue 558 THR Chi-restraints excluded: chain Z residue 567 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 697 random chunks: chunk 439 optimal weight: 2.9990 chunk 589 optimal weight: 6.9990 chunk 169 optimal weight: 0.6980 chunk 509 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 chunk 153 optimal weight: 9.9990 chunk 553 optimal weight: 10.0000 chunk 231 optimal weight: 0.9990 chunk 568 optimal weight: 5.9990 chunk 70 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 57 GLN 7 38 ASN ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 78 HIS P 52 GLN R 181 ASN ** S 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 278 GLN ** U 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 134 ASN X 286 ASN ** Y 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.133734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.108582 restraints weight = 90558.948| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.21 r_work: 0.3090 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 54658 Z= 0.253 Angle : 0.574 14.203 74121 Z= 0.290 Chirality : 0.042 0.248 8683 Planarity : 0.004 0.049 9504 Dihedral : 5.165 100.958 7667 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.99 % Favored : 95.88 % Rotamer: Outliers : 2.49 % Allowed : 20.49 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.10), residues: 7034 helix: 0.61 (0.09), residues: 3841 sheet: -0.64 (0.21), residues: 624 loop : -0.77 (0.13), residues: 2569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 3 109 HIS 0.007 0.001 HIS 7 123 PHE 0.039 0.002 PHE T 276 TYR 0.025 0.002 TYR Q 19 ARG 0.009 0.000 ARG Z 218 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12123.00 seconds wall clock time: 214 minutes 27.80 seconds (12867.80 seconds total)