Starting phenix.real_space_refine on Sun Mar 10 17:41:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdc_4813/03_2024/6rdc_4813_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdc_4813/03_2024/6rdc_4813.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdc_4813/03_2024/6rdc_4813.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdc_4813/03_2024/6rdc_4813.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdc_4813/03_2024/6rdc_4813_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdc_4813/03_2024/6rdc_4813_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.070 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 13 5.49 5 Mg 5 5.21 5 S 149 5.16 5 C 34297 2.51 5 N 9112 2.21 5 O 10199 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 28": "NH1" <-> "NH2" Residue "1 PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 69": "OD1" <-> "OD2" Residue "1 ASP 106": "OD1" <-> "OD2" Residue "1 GLU 136": "OE1" <-> "OE2" 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 215": "OE1" <-> "OE2" Residue "1 GLU 229": "OE1" <-> "OE2" Residue "1 ARG 259": "NH1" <-> "NH2" Residue "1 GLU 281": "OE1" <-> "OE2" Residue "1 GLU 299": "OE1" <-> "OE2" Residue "1 GLU 329": "OE1" <-> "OE2" Residue "1 GLU 343": "OE1" <-> "OE2" Residue "1 GLU 350": "OE1" <-> "OE2" Residue "1 ASP 353": "OD1" <-> "OD2" Residue "1 ARG 359": "NH1" <-> "NH2" Residue "1 ARG 387": "NH1" <-> "NH2" Residue "1 GLU 409": "OE1" <-> "OE2" Residue "1 TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 422": "OD1" <-> "OD2" Residue "1 ASP 425": "OD1" <-> "OD2" Residue "1 ARG 434": "NH1" <-> "NH2" Residue "1 PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 479": "OD1" <-> "OD2" Residue "1 GLU 496": "OE1" <-> "OE2" Residue "1 ASP 508": "OD1" <-> "OD2" Residue "1 GLU 513": "OE1" <-> "OE2" Residue "1 GLU 516": "OE1" <-> "OE2" Residue "1 GLU 577": "OE1" <-> "OE2" Residue "1 ARG 609": "NH1" <-> "NH2" Residue "2 GLU 14": "OE1" <-> "OE2" Residue "2 GLU 22": "OE1" <-> "OE2" Residue "2 TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 45": "NH1" <-> "NH2" Residue "2 GLU 86": "OE1" <-> "OE2" Residue "2 TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 154": "OD1" <-> "OD2" Residue "2 ARG 173": "NH1" <-> "NH2" Residue "2 ASP 194": "OD1" <-> "OD2" Residue "2 PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 225": "OE1" <-> "OE2" Residue "2 TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 274": "OE1" <-> "OE2" Residue "2 PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 316": "OD1" <-> "OD2" Residue "2 GLU 326": "OE1" <-> "OE2" Residue "2 PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 346": "NH1" <-> "NH2" Residue "2 ASP 374": "OD1" <-> "OD2" Residue "2 TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 426": "OD1" <-> "OD2" Residue "2 TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 102": "OD1" <-> "OD2" Residue "3 ASP 119": "OD1" <-> "OD2" Residue "3 PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 126": "OE1" <-> "OE2" Residue "3 ARG 149": "NH1" <-> "NH2" Residue "3 ASP 156": "OD1" <-> "OD2" Residue "3 PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 213": "NH1" <-> "NH2" Residue "3 TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 233": "NH1" <-> "NH2" Residue "3 ARG 242": "NH1" <-> "NH2" Residue "3 ARG 257": "NH1" <-> "NH2" Residue "3 PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 276": "OE1" <-> "OE2" Residue "3 GLU 295": "OE1" <-> "OE2" Residue "3 PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 10": "OE1" <-> "OE2" Residue "4 GLU 21": "OE1" <-> "OE2" Residue "4 TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 40": "OE1" <-> "OE2" Residue "4 TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 64": "OE1" <-> "OE2" Residue "4 ARG 84": "NH1" <-> "NH2" Residue "4 TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 133": "OD1" <-> "OD2" Residue "4 TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 176": "NH1" <-> "NH2" Residue "4 TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 197": "OD1" <-> "OD2" Residue "4 PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 218": "OE1" <-> "OE2" 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 "5 GLU 6": "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 PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 81": "NH1" <-> "NH2" Residue "7 TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ARG 13": "NH1" <-> "NH2" Residue "8 TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 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 "B GLU 111": "OE1" <-> "OE2" Residue "D GLU 111": "OE1" <-> "OE2" Residue "E GLU 111": "OE1" <-> "OE2" Residue "F GLU 111": "OE1" <-> "OE2" Residue "J GLU 111": "OE1" <-> "OE2" Residue "M ARG 115": "NH1" <-> "NH2" Residue "M ARG 145": "NH1" <-> "NH2" Residue "M PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 232": "NH1" <-> "NH2" Residue "M ARG 239": "NH1" <-> "NH2" Residue "M 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 GLU 143": "OE1" <-> "OE2" Residue "P TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 179": "OD1" <-> "OD2" Residue "P PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 201": "OE1" <-> "OE2" 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 ASP 25": "OD1" <-> "OD2" Residue "Q ARG 42": "NH1" <-> "NH2" Residue "Q ARG 48": "NH1" <-> "NH2" Residue "Q TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 66": "OE1" <-> "OE2" Residue "R PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "S ARG 46": "NH1" <-> "NH2" Residue "S TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 147": "NH1" <-> "NH2" Residue "S ARG 152": "NH1" <-> "NH2" Residue "S ARG 157": "NH1" <-> "NH2" Residue "S TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 164": "OD1" <-> "OD2" Residue "S PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 222": "OD1" <-> "OD2" Residue "S ARG 244": "NH1" <-> "NH2" Residue "S ASP 291": "OD1" <-> "OD2" 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 ARG 86": "NH1" <-> "NH2" Residue "T ASP 112": "OD1" <-> "OD2" Residue "T ASP 142": "OD1" <-> "OD2" Residue "T ARG 162": "NH1" <-> "NH2" Residue "T ASP 172": "OD1" <-> "OD2" Residue "T ARG 195": "NH1" <-> "NH2" Residue "T ARG 199": "NH1" <-> "NH2" Residue "T PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T 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 PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 418": "NH1" <-> "NH2" Residue "T PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 454": "NH1" <-> "NH2" Residue "T ASP 467": "OD1" <-> "OD2" Residue "T PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 555": "NH1" <-> "NH2" Residue "U ARG 49": "NH1" <-> "NH2" Residue "U TYR 57": "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 112": "OD1" <-> "OD2" Residue "U TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 146": "NH1" <-> "NH2" Residue "U ARG 162": "NH1" <-> "NH2" Residue "U ASP 165": "OD1" <-> "OD2" Residue "U ARG 181": "NH1" <-> "NH2" Residue "U ARG 199": "NH1" <-> "NH2" Residue "U PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 227": "NH1" <-> "NH2" Residue "U ARG 254": "NH1" <-> "NH2" Residue "U TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 283": "NH1" <-> "NH2" Residue "U TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 311": "OE1" <-> "OE2" Residue "U PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 314": "NH1" <-> "NH2" Residue "U ARG 342": "NH1" <-> "NH2" Residue "U ARG 343": "NH1" <-> "NH2" Residue "U ARG 364": "NH1" <-> "NH2" Residue "U GLU 371": "OE1" <-> "OE2" Residue "U PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 389": "OD1" <-> "OD2" Residue "U PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 465": "OD1" <-> "OD2" Residue "U ASP 467": "OD1" <-> "OD2" Residue "U ARG 479": "NH1" <-> "NH2" Residue "U GLU 482": "OE1" <-> "OE2" Residue "U ARG 496": "NH1" <-> "NH2" Residue "U TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 513": "NH1" <-> "NH2" Residue "U GLU 522": "OE1" <-> "OE2" Residue "U PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 49": "NH1" <-> "NH2" Residue "V PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 74": "OE1" <-> "OE2" Residue "V TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 142": "OD1" <-> "OD2" Residue "V ARG 181": "NH1" <-> "NH2" Residue "V ASP 210": "OD1" <-> "OD2" Residue "V ARG 217": "NH1" <-> "NH2" Residue "V ARG 220": "NH1" <-> "NH2" Residue "V ASP 237": "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 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 409": "OE1" <-> "OE2" Residue "V PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 429": "NH1" <-> "NH2" Residue "V ARG 454": "NH1" <-> "NH2" Residue "V PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 476": "NH1" <-> "NH2" Residue "V PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 496": "NH1" <-> "NH2" Residue "V TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 513": "NH1" <-> "NH2" Residue "V GLU 522": "OE1" <-> "OE2" 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 ASP 53": "OD1" <-> "OD2" Residue "X ARG 71": "NH1" <-> "NH2" Residue "X ARG 86": "NH1" <-> "NH2" Residue "X ARG 98": "NH1" <-> "NH2" Residue "X ASP 104": "OD1" <-> "OD2" Residue "X ARG 120": "NH1" <-> "NH2" Residue "X ASP 130": "OD1" <-> "OD2" Residue "X GLU 131": "OE1" <-> "OE2" Residue "X GLU 146": "OE1" <-> "OE2" Residue "X GLU 152": "OE1" <-> "OE2" Residue "X PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 215": "OE1" <-> "OE2" Residue "X ARG 216": "NH1" <-> "NH2" Residue "X GLU 229": "OE1" <-> "OE2" Residue "X ARG 258": "NH1" <-> "NH2" Residue "X GLU 270": "OE1" <-> "OE2" Residue "X ASP 285": "OD1" <-> "OD2" Residue "X PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 359": "OD1" <-> "OD2" Residue "X GLU 370": "OE1" <-> "OE2" Residue "X TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 378": "OD1" <-> "OD2" Residue "X ASP 381": "OD1" <-> "OD2" Residue "X ARG 385": "NH1" <-> "NH2" Residue "X ARG 401": "NH1" <-> "NH2" Residue "X ASP 409": "OD1" <-> "OD2" 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 462": "OD1" <-> "OD2" Residue "X PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 480": "OD1" <-> "OD2" Residue "X ASP 500": "OD1" <-> "OD2" Residue "X ARG 509": "NH1" <-> "NH2" Residue "X ASP 528": "OD1" <-> "OD2" Residue "X GLU 547": "OE1" <-> "OE2" Residue "X ASP 548": "OD1" <-> "OD2" Residue "X PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 564": "OE1" <-> "OE2" Residue "Y ARG 51": "NH1" <-> "NH2" Residue "Y ASP 104": "OD1" <-> "OD2" Residue "Y GLU 146": "OE1" <-> "OE2" Residue "Y PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 156": "OE1" <-> "OE2" Residue "Y PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 218": "NH1" <-> "NH2" Residue "Y GLU 219": "OE1" <-> "OE2" Residue "Y ARG 225": "NH1" <-> "NH2" Residue "Y ARG 239": "NH1" <-> "NH2" Residue "Y TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 296": "OE1" <-> "OE2" Residue "Y ASP 317": "OD1" <-> "OD2" 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 415": "OD1" <-> "OD2" Residue "Y ASP 429": "OD1" <-> "OD2" Residue "Y PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 494": "OE1" <-> "OE2" Residue "Y ASP 505": "OD1" <-> "OD2" Residue "Y ARG 509": "NH1" <-> "NH2" Residue "Y GLU 511": "OE1" <-> "OE2" Residue "Y GLU 533": "OE1" <-> "OE2" Residue "Y ASP 543": "OD1" <-> "OD2" Residue "Y PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 71": "NH1" <-> "NH2" 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 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 ASP 359": "OD1" <-> "OD2" Residue "Z ARG 366": "NH1" <-> "NH2" Residue "Z TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 378": "OD1" <-> "OD2" Residue "Z ASP 381": "OD1" <-> "OD2" Residue "Z ARG 385": "NH1" <-> "NH2" Residue "Z GLU 451": "OE1" <-> "OE2" Residue "Z PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 462": "OD1" <-> "OD2" Residue "Z ASP 465": "OD1" <-> "OD2" Residue "Z PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 505": "OD1" <-> "OD2" Residue "Z ASP 523": "OD1" <-> "OD2" Residue "Z ASP 528": "OD1" <-> "OD2" Residue "Z GLU 536": "OE1" <-> "OE2" Residue "Z GLU 540": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 53776 Number of models: 1 Model: "" Number of chains: 44 Chain: "0" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 607 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 8, 'TRANS': 72} Chain: "1" Number of atoms: 4661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4661 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 31, 'TRANS': 563} Chain: "2" Number of atoms: 3163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3163 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 17, 'TRANS': 423} Chain: "3" Number of atoms: 1874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1874 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 239} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 7 Chain: "4" Number of atoms: 2177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2177 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 9, 'TRANS': 280} Chain: "5" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 986 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "6" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 926 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "7" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1347 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 5, 'TRANS': 170} Chain: "8" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 692 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 7, 'TRANS': 80} Chain: "9" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 776 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 5, 'TRANS': 91} Chain: "A" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "B" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "C" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain breaks: 1 Chain: "D" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "E" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "F" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "G" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "H" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "I" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "J" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "M" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1640 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "P" Number of atoms: 1532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1532 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 5, 'TRANS': 187} Chain: "Q" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 561 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 5, 'TRANS': 66} Chain: "R" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1303 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 13, 'TRANS': 163} Chain: "S" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2130 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 271} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 3979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3979 Classifications: {'peptide': 523} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Chain: "U" Number of atoms: 3980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3980 Classifications: {'peptide': 523} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Chain: "V" Number of atoms: 3962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3962 Classifications: {'peptide': 520} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 494} Chain: "X" Number of atoms: 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: 3977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3977 Classifications: {'peptide': 524} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 501} 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 breaks: 2 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} Chain: "1" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "5" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "6" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "8" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "M" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Time building chain proxies: 20.78, per 1000 atoms: 0.39 Number of scatterers: 53776 At special positions: 0 Unit cell: (214.812, 129.519, 262.197, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 149 16.00 P 13 15.00 Mg 5 11.99 O 10199 8.00 N 9112 7.00 C 34297 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.88 Conformation dependent library (CDL) restraints added in 7.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN M 600 " pdb="ZN ZN M 600 " - pdb=" NE2 HIS M 248 " pdb="ZN ZN M 600 " - pdb=" NE2 HIS M 252 " 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: 13086 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 298 helices and 31 sheets defined 51.0% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.88 Creating SS restraints... Processing helix chain '0' and resid 18 through 29 Processing helix chain '0' and resid 44 through 48 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 97 through 99 No H-bonds generated for 'chain '1' and resid 97 through 99' Processing helix chain '1' and resid 106 through 123 removed outlier: 3.503A pdb=" N ALA 1 122 " --> pdb=" O ARG 1 118 " (cutoff:3.500A) Processing helix chain '1' and resid 127 through 138 removed outlier: 4.009A pdb=" N THR 1 135 " --> pdb=" O ALA 1 131 " (cutoff:3.500A) Processing helix chain '1' and resid 164 through 175 removed outlier: 3.671A pdb=" N THR 1 169 " --> pdb=" O GLU 1 165 " (cutoff:3.500A) Processing helix chain '1' and resid 191 through 203 removed outlier: 4.588A pdb=" N ALA 1 196 " --> pdb=" O GLY 1 192 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASP 1 199 " --> pdb=" O LYS 1 195 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE 1 200 " --> pdb=" O ALA 1 196 " (cutoff:3.500A) Processing helix chain '1' and resid 210 through 223 removed outlier: 3.785A pdb=" N LEU 1 221 " --> pdb=" O LEU 1 217 " (cutoff:3.500A) Processing helix chain '1' and resid 242 through 270 removed outlier: 3.599A pdb=" N ALA 1 250 " --> pdb=" O ALA 1 246 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG 1 259 " --> pdb=" O GLU 1 255 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL 1 270 " --> pdb=" O LYS 1 266 " (cutoff:3.500A) Processing helix chain '1' and resid 272 through 276 removed outlier: 3.613A 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 290 through 292 No H-bonds generated for 'chain '1' and resid 290 through 292' Processing helix chain '1' and resid 298 through 304 Processing helix chain '1' and resid 311 through 315 Processing helix chain '1' and resid 324 through 326 No H-bonds generated for 'chain '1' and resid 324 through 326' Processing helix chain '1' and resid 331 through 333 No H-bonds generated for 'chain '1' and resid 331 through 333' Processing helix chain '1' and resid 339 through 350 removed outlier: 3.520A pdb=" N GLU 1 350 " --> pdb=" O GLN 1 346 " (cutoff:3.500A) Processing helix chain '1' and resid 354 through 361 removed outlier: 3.622A pdb=" N LEU 1 358 " --> pdb=" O PRO 1 354 " (cutoff:3.500A) Processing helix chain '1' and resid 363 through 366 Processing helix chain '1' and resid 376 through 387 removed outlier: 3.564A pdb=" N ARG 1 381 " --> pdb=" O SER 1 377 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL 1 382 " --> pdb=" O GLU 1 378 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS 1 386 " --> pdb=" O VAL 1 382 " (cutoff:3.500A) Processing helix chain '1' and resid 393 through 420 removed outlier: 3.563A pdb=" N LEU 1 401 " --> pdb=" O GLU 1 397 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N VAL 1 418 " --> pdb=" O GLU 1 414 " (cutoff:3.500A) removed outlier: 5.167A 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: 3.643A pdb=" N ARG 1 453 " --> pdb=" O ALA 1 449 " (cutoff:3.500A) Processing helix chain '1' and resid 466 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 514 removed outlier: 3.777A pdb=" N LEU 1 498 " --> pdb=" O SER 1 494 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU 1 501 " --> pdb=" O LEU 1 497 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP 1 504 " --> pdb=" O LEU 1 500 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE 1 505 " --> pdb=" O GLU 1 501 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA 1 511 " --> pdb=" O GLU 1 507 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU 1 512 " --> pdb=" O ASP 1 508 " (cutoff:3.500A) Processing helix chain '1' and resid 519 through 535 removed outlier: 3.681A pdb=" N THR 1 526 " --> pdb=" O LEU 1 522 " (cutoff:3.500A) Processing helix chain '1' and resid 542 through 548 Processing helix chain '1' and resid 550 through 561 removed outlier: 3.549A pdb=" N GLU 1 559 " --> pdb=" O LYS 1 555 " (cutoff:3.500A) Processing helix chain '1' and resid 567 through 573 Processing helix chain '1' and resid 578 through 587 Processing helix chain '1' and resid 589 through 591 No H-bonds generated for 'chain '1' and resid 589 through 591' Processing helix chain '1' and resid 593 through 605 removed outlier: 3.716A pdb=" N LYS 1 605 " --> pdb=" O ASP 1 601 " (cutoff:3.500A) Processing helix chain '1' and resid 611 through 613 No H-bonds generated for 'chain '1' and resid 611 through 613' 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 removed outlier: 3.701A pdb=" N GLY 2 56 " --> pdb=" O LEU 2 52 " (cutoff:3.500A) Processing helix chain '2' and resid 63 through 75 Processing helix chain '2' and resid 81 through 93 removed outlier: 3.861A pdb=" N ALA 2 88 " --> pdb=" O VAL 2 84 " (cutoff:3.500A) removed outlier: 4.928A 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: 3.625A pdb=" N VAL 2 127 " --> pdb=" O LYS 2 123 " (cutoff:3.500A) Processing helix chain '2' and resid 137 through 149 removed outlier: 3.773A pdb=" N ALA 2 141 " --> pdb=" O PRO 2 137 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL 2 143 " --> pdb=" O GLU 2 139 " (cutoff:3.500A) Processing helix chain '2' and resid 155 through 160 Processing helix chain '2' and resid 162 through 167 removed outlier: 3.786A pdb=" N ALA 2 166 " --> pdb=" O GLY 2 162 " (cutoff:3.500A) Processing helix chain '2' and resid 173 through 185 removed outlier: 3.675A pdb=" N ALA 2 178 " --> pdb=" O THR 2 174 " (cutoff:3.500A) Processing helix chain '2' and resid 190 through 196 removed outlier: 3.802A pdb=" N ALA 2 195 " --> pdb=" O ALA 2 191 " (cutoff:3.500A) Processing helix chain '2' and resid 210 through 219 Processing helix chain '2' and resid 228 through 234 removed outlier: 3.535A pdb=" N LYS 2 233 " --> pdb=" O VAL 2 229 " (cutoff:3.500A) Processing helix chain '2' and resid 241 through 254 removed outlier: 3.601A pdb=" N GLU 2 246 " --> pdb=" O ALA 2 242 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY 2 250 " --> pdb=" O GLU 2 246 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER 2 254 " --> pdb=" O GLY 2 250 " (cutoff:3.500A) Processing helix chain '2' and resid 261 through 275 removed outlier: 3.531A pdb=" N VAL 2 268 " --> pdb=" O ALA 2 264 " (cutoff:3.500A) Proline residue: 2 271 - end of helix removed outlier: 3.514A pdb=" N LYS 2 275 " --> pdb=" O PRO 2 271 " (cutoff:3.500A) Processing helix chain '2' and resid 282 through 294 Processing helix chain '2' and resid 301 through 304 No H-bonds generated for 'chain '2' and resid 301 through 304' Processing helix chain '2' and resid 306 through 320 removed outlier: 3.833A pdb=" N GLY 2 312 " --> pdb=" O ALA 2 308 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA 2 314 " --> pdb=" O ALA 2 310 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA 2 318 " --> pdb=" O ALA 2 314 " (cutoff:3.500A) Processing helix chain '2' and resid 326 through 336 Processing helix chain '2' and resid 346 through 355 removed outlier: 3.509A pdb=" N ALA 2 350 " --> pdb=" O ARG 2 346 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER 2 351 " --> pdb=" O PRO 2 347 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA 2 354 " --> pdb=" O ALA 2 350 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER 2 355 " --> pdb=" O SER 2 351 " (cutoff:3.500A) Processing helix chain '2' and resid 397 through 409 removed outlier: 3.809A pdb=" N ALA 2 408 " --> pdb=" O LYS 2 404 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN 2 409 " --> pdb=" O VAL 2 405 " (cutoff:3.500A) Processing helix chain '2' and resid 418 through 423 removed outlier: 4.473A pdb=" N ALA 2 423 " --> pdb=" O ASN 2 419 " (cutoff:3.500A) Processing helix chain '2' and resid 427 through 441 removed outlier: 3.581A pdb=" N VAL 2 441 " --> pdb=" O ALA 2 437 " (cutoff:3.500A) Processing helix chain '3' and resid 78 through 86 Processing helix chain '3' and resid 92 through 95 No H-bonds generated for 'chain '3' and resid 92 through 95' Processing helix chain '3' and resid 103 through 113 removed outlier: 3.555A pdb=" N SER 3 111 " --> pdb=" O SER 3 107 " (cutoff:3.500A) Processing helix chain '3' and resid 120 through 127 removed outlier: 3.844A pdb=" N ALA 3 127 " --> pdb=" O LYS 3 123 " (cutoff:3.500A) Processing helix chain '3' and resid 132 through 134 No H-bonds generated for 'chain '3' and resid 132 through 134' Processing helix chain '3' and resid 137 through 149 Processing helix chain '3' and resid 155 through 165 removed outlier: 3.753A pdb=" N GLY 3 160 " --> pdb=" O ASP 3 156 " (cutoff:3.500A) 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 184 removed outlier: 4.111A pdb=" N GLN 3 179 " --> pdb=" O GLU 3 175 " (cutoff:3.500A) Processing helix chain '3' and resid 192 through 203 Processing helix chain '3' and resid 216 through 227 removed outlier: 4.153A pdb=" N THR 3 221 " --> pdb=" O ASP 3 217 " (cutoff:3.500A) Processing helix chain '3' and resid 234 through 242 removed outlier: 3.841A pdb=" N ARG 3 242 " --> pdb=" O ALA 3 238 " (cutoff:3.500A) Processing helix chain '3' and resid 246 through 250 Processing helix chain '3' and resid 254 through 270 removed outlier: 3.562A pdb=" N LYS 3 258 " --> pdb=" O ALA 3 254 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA 3 267 " --> pdb=" O SER 3 263 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN 3 269 " --> pdb=" O LEU 3 265 " (cutoff:3.500A) Processing helix chain '3' and resid 276 through 278 No H-bonds generated for 'chain '3' and resid 276 through 278' Processing helix chain '3' and resid 294 through 311 removed outlier: 3.588A pdb=" N ASN 3 309 " --> pdb=" O VAL 3 305 " (cutoff:3.500A) Processing helix chain '4' and resid 10 through 13 No H-bonds generated for 'chain '4' and resid 10 through 13' Processing helix chain '4' and resid 20 through 34 removed outlier: 3.901A pdb=" N ALA 4 25 " --> pdb=" O GLU 4 21 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER 4 28 " --> pdb=" O THR 4 24 " (cutoff:3.500A) Processing helix chain '4' and resid 48 through 67 removed outlier: 3.521A pdb=" N ALA 4 60 " --> pdb=" O LYS 4 56 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLN 4 61 " --> pdb=" O TYR 4 57 " (cutoff:3.500A) removed outlier: 3.535A 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: 3.819A pdb=" N VAL 4 141 " --> pdb=" O ALA 4 137 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA 4 147 " --> pdb=" O SER 4 143 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLU 4 148 " --> pdb=" O SER 4 144 " (cutoff:3.500A) Processing helix chain '4' and resid 160 through 176 removed outlier: 3.997A pdb=" N LYS 4 168 " --> pdb=" O LYS 4 164 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS 4 170 " --> pdb=" O ALA 4 166 " (cutoff:3.500A) removed outlier: 3.762A 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 231 removed outlier: 3.548A pdb=" N LYS 4 198 " --> pdb=" O ASP 4 194 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL 4 199 " --> pdb=" O ALA 4 195 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU 4 202 " --> pdb=" O LYS 4 198 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N THR 4 205 " --> pdb=" O LYS 4 201 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TRP 4 206 " --> pdb=" O GLU 4 202 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA 4 213 " --> pdb=" O SER 4 209 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA 4 221 " --> pdb=" O ALA 4 217 " (cutoff:3.500A) Processing helix chain '4' and resid 238 through 258 removed outlier: 3.603A pdb=" N ALA 4 256 " --> pdb=" O LEU 4 252 " (cutoff:3.500A) Processing helix chain '4' and resid 263 through 284 Processing helix chain '5' and resid 8 through 28 Processing helix chain '5' and resid 31 through 46 removed outlier: 3.529A pdb=" N ARG 5 36 " --> pdb=" O PRO 5 32 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU 5 37 " --> pdb=" O THR 5 33 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N HIS 5 41 " --> pdb=" O GLU 5 37 " (cutoff:3.500A) Processing helix chain '5' and resid 48 through 58 removed outlier: 3.539A pdb=" N ASN 5 52 " --> pdb=" O ALA 5 48 " (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 89 through 105 removed outlier: 3.572A pdb=" N SER 5 97 " --> pdb=" O GLU 5 93 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LYS 5 101 " --> pdb=" O SER 5 97 " (cutoff:3.500A) Processing helix chain '6' and resid 31 through 40 Processing helix chain '6' and resid 49 through 55 removed outlier: 4.294A pdb=" N LYS 6 52 " --> pdb=" O SER 6 49 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR 6 53 " --> pdb=" O SER 6 50 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE 6 54 " --> pdb=" O LEU 6 51 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS 6 55 " --> pdb=" O LYS 6 52 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 49 through 55' Processing helix chain '6' and resid 73 through 93 Processing helix chain '6' and resid 99 through 117 removed outlier: 3.932A pdb=" N ASN 6 106 " --> pdb=" O ASP 6 102 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL 6 107 " --> pdb=" O LEU 6 103 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU 6 108 " --> pdb=" O ASN 6 104 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TRP 6 112 " --> pdb=" O LEU 6 108 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER 6 117 " --> pdb=" O LEU 6 113 " (cutoff:3.500A) Processing helix chain '6' and resid 122 through 129 Processing helix chain '6' and resid 134 through 137 No H-bonds generated for 'chain '6' and resid 134 through 137' Processing helix chain '7' and resid 63 through 66 No H-bonds generated for 'chain '7' and resid 63 through 66' 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: 3.892A pdb=" N GLU 7 99 " --> pdb=" O SER 7 95 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU 7 103 " --> pdb=" O GLU 7 99 " (cutoff:3.500A) Processing helix chain '7' and resid 110 through 113 Processing helix chain '7' and resid 116 through 119 No H-bonds generated for 'chain '7' and resid 116 through 119' Processing helix chain '7' and resid 124 through 144 removed outlier: 3.568A pdb=" N PHE 7 130 " --> pdb=" O ASP 7 126 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR 7 138 " --> pdb=" O ALA 7 134 " (cutoff:3.500A) Processing helix chain '7' and resid 147 through 149 No H-bonds generated for 'chain '7' and resid 147 through 149' Processing helix chain '7' and resid 151 through 165 removed outlier: 3.633A pdb=" N SER 7 155 " --> pdb=" O SER 7 151 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLN 7 156 " --> pdb=" O ALA 7 152 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL 7 157 " --> pdb=" O LEU 7 153 " (cutoff:3.500A) Proline residue: 7 159 - end of helix removed outlier: 3.591A pdb=" N ARG 7 164 " --> pdb=" O ASN 7 160 " (cutoff:3.500A) Processing helix chain '7' and resid 175 through 186 removed outlier: 3.576A pdb=" N ASN 7 184 " --> pdb=" O GLY 7 180 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE 7 185 " --> pdb=" O ALA 7 181 " (cutoff:3.500A) Processing helix chain '8' and resid 27 through 30 No H-bonds generated for 'chain '8' and resid 27 through 30' Processing helix chain '8' and resid 32 through 38 Processing helix chain '8' and resid 40 through 79 removed outlier: 3.764A pdb=" N TRP 8 45 " --> pdb=" O ILE 8 41 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TYR 8 46 " --> pdb=" O PRO 8 42 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LEU 8 47 " --> pdb=" O ARG 8 43 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA 8 76 " --> pdb=" O ALA 8 72 " (cutoff:3.500A) removed outlier: 4.569A 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 37 through 56 removed outlier: 4.025A pdb=" N VAL 9 42 " --> pdb=" O ALA 9 38 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASN 9 56 " --> pdb=" O LEU 9 52 " (cutoff:3.500A) Processing helix chain '9' and resid 83 through 96 removed outlier: 3.739A pdb=" N GLU 9 88 " --> pdb=" O ALA 9 84 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS 9 91 " --> pdb=" O LEU 9 87 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU 9 92 " --> pdb=" O GLU 9 88 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER 9 96 " --> pdb=" O GLU 9 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 91 removed outlier: 3.593A pdb=" N MET A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR A 68 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ALA A 70 " --> pdb=" O CYS A 66 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N LEU A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ALA A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLY A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A 74 " --> pdb=" O ALA A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 124 removed outlier: 3.793A pdb=" N GLY A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU A 105 " --> pdb=" O GLY A 101 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU A 109 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ILE A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 91 removed outlier: 3.802A pdb=" N MET B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE B 69 " --> pdb=" O GLY B 65 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N ALA B 70 " --> pdb=" O CYS B 66 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N LEU B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ALA B 72 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLY B 73 " --> pdb=" O ILE B 69 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE B 86 " --> pdb=" O PHE B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 95 No H-bonds generated for 'chain 'B' and resid 93 through 95' Processing helix chain 'B' and resid 98 through 125 removed outlier: 3.502A pdb=" N LEU B 105 " --> pdb=" O GLY B 101 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER B 112 " --> pdb=" O ALA B 108 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ILE B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA B 114 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU B 119 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL B 120 " --> pdb=" O PHE B 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 65 removed outlier: 3.653A pdb=" N LYS C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 91 removed outlier: 3.657A pdb=" N GLY C 73 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL C 74 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LEU C 78 " --> pdb=" O GLY C 75 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE C 82 " --> pdb=" O GLY C 79 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU C 85 " --> pdb=" O PHE C 82 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASN C 87 " --> pdb=" O SER C 84 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA C 89 " --> pdb=" O ILE C 86 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG C 91 " --> pdb=" O GLY C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 125 removed outlier: 3.501A pdb=" N ALA C 96 " --> pdb=" O PRO C 93 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N LYS C 97 " --> pdb=" O ASN C 94 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU C 99 " --> pdb=" O ALA C 96 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL C 100 " --> pdb=" O LYS C 97 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU C 104 " --> pdb=" O GLY C 101 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU C 105 " --> pdb=" O TYR C 102 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE C 107 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU C 111 " --> pdb=" O ALA C 108 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER C 112 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA C 114 " --> pdb=" O GLU C 111 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU C 115 " --> pdb=" O SER C 112 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER C 117 " --> pdb=" O ALA C 114 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU C 118 " --> pdb=" O LEU C 115 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU C 119 " --> pdb=" O PHE C 116 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL C 121 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE C 124 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU C 125 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 65 removed outlier: 4.473A pdb=" N MET D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 89 removed outlier: 3.611A pdb=" N ALA D 72 " --> pdb=" O ILE D 69 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY D 73 " --> pdb=" O ALA D 70 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL D 74 " --> pdb=" O LEU D 71 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY D 77 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU D 78 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL D 80 " --> pdb=" O GLY D 77 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N MET D 81 " --> pdb=" O LEU D 78 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE D 82 " --> pdb=" O GLY D 79 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLY D 83 " --> pdb=" O VAL D 80 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN D 87 " --> pdb=" O SER D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 125 removed outlier: 4.645A pdb=" N LYS D 97 " --> pdb=" O ASN D 94 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU D 99 " --> pdb=" O ALA D 96 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL D 100 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N LEU D 104 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU D 105 " --> pdb=" O TYR D 102 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE D 107 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA D 108 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR D 110 " --> pdb=" O PHE D 107 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU D 111 " --> pdb=" O ALA D 108 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER D 112 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE D 116 " --> pdb=" O ILE D 113 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N SER D 117 " --> pdb=" O ALA D 114 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU D 119 " --> pdb=" O PHE D 116 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL D 121 " --> pdb=" O LEU D 118 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE D 122 " --> pdb=" O LEU D 119 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE D 124 " --> pdb=" O VAL D 121 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU D 125 " --> pdb=" O PHE D 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 91 removed outlier: 3.536A pdb=" N LYS E 60 " --> pdb=" O LEU E 56 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N MET E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE E 69 " --> pdb=" O GLY E 65 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N ALA E 70 " --> pdb=" O CYS E 66 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N LEU E 71 " --> pdb=" O ALA E 67 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ALA E 72 " --> pdb=" O THR E 68 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLY E 73 " --> pdb=" O ILE E 69 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL E 74 " --> pdb=" O ALA E 70 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY E 79 " --> pdb=" O GLY E 75 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE E 86 " --> pdb=" O PHE E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 124 removed outlier: 3.748A pdb=" N VAL E 100 " --> pdb=" O ALA E 96 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY E 101 " --> pdb=" O LYS E 97 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ILE E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA E 114 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL E 120 " --> pdb=" O PHE E 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 91 removed outlier: 4.128A pdb=" N MET F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL F 62 " --> pdb=" O ALA F 58 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE F 69 " --> pdb=" O GLY F 65 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ALA F 70 " --> pdb=" O CYS F 66 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N LEU F 71 " --> pdb=" O ALA F 67 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ALA F 72 " --> pdb=" O THR F 68 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLY F 73 " --> pdb=" O ILE F 69 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL F 74 " --> pdb=" O ALA F 70 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY F 79 " --> pdb=" O GLY F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 124 removed outlier: 3.791A pdb=" N GLY F 101 " --> pdb=" O LYS F 97 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR F 102 " --> pdb=" O GLN F 98 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ILE F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA F 114 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL F 120 " --> pdb=" O PHE F 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 91 removed outlier: 4.112A pdb=" N MET G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL G 62 " --> pdb=" O ALA G 58 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE G 69 " --> pdb=" O GLY G 65 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ALA G 70 " --> pdb=" O CYS G 66 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N LEU G 71 " --> pdb=" O ALA G 67 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ALA G 72 " --> pdb=" O THR G 68 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY G 73 " --> pdb=" O ILE G 69 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY G 79 " --> pdb=" O GLY G 75 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE G 86 " --> pdb=" O PHE G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 125 removed outlier: 3.647A pdb=" N ALA G 96 " --> pdb=" O PRO G 93 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N LYS G 97 " --> pdb=" O ASN G 94 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL G 100 " --> pdb=" O LYS G 97 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LEU G 104 " --> pdb=" O GLY G 101 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU G 105 " --> pdb=" O TYR G 102 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE G 107 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA G 108 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU G 109 " --> pdb=" O GLY G 106 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU G 111 " --> pdb=" O ALA G 108 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER G 112 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU G 118 " --> pdb=" O LEU G 115 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU G 119 " --> pdb=" O PHE G 116 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL G 121 " --> pdb=" O LEU G 118 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU G 123 " --> pdb=" O VAL G 120 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU G 125 " --> pdb=" O PHE G 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 91 removed outlier: 3.849A pdb=" N MET H 61 " --> pdb=" O ALA H 57 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL H 62 " --> pdb=" O ALA H 58 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY H 65 " --> pdb=" O MET H 61 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE H 69 " --> pdb=" O GLY H 65 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ALA H 70 " --> pdb=" O CYS H 66 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N LEU H 71 " --> pdb=" O ALA H 67 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ALA H 72 " --> pdb=" O THR H 68 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLY H 73 " --> pdb=" O ILE H 69 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY H 79 " --> pdb=" O GLY H 75 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE H 86 " --> pdb=" O PHE H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 125 removed outlier: 3.796A pdb=" N GLY H 101 " --> pdb=" O LYS H 97 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA H 108 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ILE H 113 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA H 114 " --> pdb=" O THR H 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 91 removed outlier: 4.217A pdb=" N MET I 61 " --> pdb=" O ALA I 57 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL I 62 " --> pdb=" O ALA I 58 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR I 68 " --> pdb=" O ALA I 64 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE I 69 " --> pdb=" O GLY I 65 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ALA I 70 " --> pdb=" O CYS I 66 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N LEU I 71 " --> pdb=" O ALA I 67 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ALA I 72 " --> pdb=" O THR I 68 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLY I 73 " --> pdb=" O ILE I 69 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE I 86 " --> pdb=" O PHE I 82 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG I 91 " --> pdb=" O ASN I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 110 removed outlier: 5.266A pdb=" N LYS I 97 " --> pdb=" O ASN I 94 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL I 100 " --> pdb=" O LYS I 97 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA I 103 " --> pdb=" O VAL I 100 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU I 104 " --> pdb=" O GLY I 101 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU I 105 " --> pdb=" O TYR I 102 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE I 107 " --> pdb=" O LEU I 104 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA I 108 " --> pdb=" O LEU I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 112 through 125 removed outlier: 3.526A pdb=" N VAL I 120 " --> pdb=" O PHE I 116 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 91 removed outlier: 4.045A pdb=" N MET J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA J 64 " --> pdb=" O LYS J 60 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY J 65 " --> pdb=" O MET J 61 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR J 68 " --> pdb=" O ALA J 64 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE J 69 " --> pdb=" O GLY J 65 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ALA J 70 " --> pdb=" O CYS J 66 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N LEU J 71 " --> pdb=" O ALA J 67 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ALA J 72 " --> pdb=" O THR J 68 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLY J 73 " --> pdb=" O ILE J 69 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE J 86 " --> pdb=" O PHE J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 126 removed outlier: 4.301A pdb=" N SER J 112 " --> pdb=" O ALA J 108 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE J 113 " --> pdb=" O LEU J 109 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA J 114 " --> pdb=" O THR J 110 " (cutoff:3.500A) Processing helix chain 'M' and resid 105 through 117 Processing helix chain 'M' and resid 135 through 144 Processing helix chain 'M' and resid 148 through 165 removed outlier: 3.654A pdb=" N THR M 153 " --> pdb=" O GLY M 149 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N CYS M 162 " --> pdb=" O THR M 158 " (cutoff:3.500A) Processing helix chain 'M' and resid 174 through 176 No H-bonds generated for 'chain 'M' and resid 174 through 176' Processing helix chain 'M' and resid 178 through 198 removed outlier: 3.526A pdb=" N SER M 187 " --> pdb=" O GLY M 183 " (cutoff:3.500A) Processing helix chain 'M' and resid 222 through 264 removed outlier: 3.519A pdb=" N SER M 228 " --> pdb=" O LEU M 224 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ARG M 232 " --> pdb=" O SER M 228 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ALA M 233 " --> pdb=" O TYR M 229 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL M 234 " --> pdb=" O THR M 230 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLY M 237 " --> pdb=" O ALA M 233 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY M 247 " --> pdb=" O ASN M 243 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N HIS M 248 " --> pdb=" O MET M 244 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU M 250 " --> pdb=" O ALA M 246 " (cutoff:3.500A) removed outlier: 3.740A 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: 3.600A pdb=" N VAL M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N CYS M 278 " --> pdb=" O THR M 274 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU M 280 " --> pdb=" O GLY M 276 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU M 290 " --> pdb=" O GLY M 286 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER M 296 " --> pdb=" O ALA M 292 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER M 300 " --> pdb=" O SER M 296 " (cutoff:3.500A) Processing helix chain 'P' and resid 51 through 63 Processing helix chain 'P' and resid 69 through 83 Processing helix chain 'P' and resid 85 through 92 removed outlier: 4.069A pdb=" N LEU P 90 " --> pdb=" O GLU P 86 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALA P 91 " --> pdb=" O LEU P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 98 through 108 removed outlier: 3.511A pdb=" N ILE P 105 " --> pdb=" O ARG P 101 " (cutoff:3.500A) Processing helix chain 'P' and resid 116 through 127 Processing helix chain 'P' and resid 131 through 146 removed outlier: 3.875A pdb=" N LEU P 135 " --> pdb=" O SER P 132 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N THR P 138 " --> pdb=" O LEU P 135 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL P 139 " --> pdb=" O GLU P 136 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU P 142 " --> pdb=" O VAL P 139 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU P 143 " --> pdb=" O ASN P 140 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU P 144 " --> pdb=" O TYR P 141 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU P 146 " --> pdb=" O GLU P 143 " (cutoff:3.500A) Processing helix chain 'P' and resid 166 through 176 removed outlier: 5.134A pdb=" N LYS P 176 " --> pdb=" O LYS P 172 " (cutoff:3.500A) Processing helix chain 'P' and resid 211 through 226 removed outlier: 3.647A pdb=" N GLU P 216 " --> pdb=" O ALA P 212 " (cutoff:3.500A) Processing helix chain 'Q' and resid 16 through 30 removed outlier: 3.579A pdb=" N ASN Q 29 " --> pdb=" O ASP Q 25 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N VAL Q 30 " --> pdb=" O LEU Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 33 through 39 removed outlier: 3.573A pdb=" N ALA Q 37 " --> pdb=" O GLU Q 33 " (cutoff:3.500A) removed outlier: 3.889A 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 40 removed outlier: 3.629A pdb=" N THR R 34 " --> pdb=" O PRO R 30 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLU R 35 " --> pdb=" O LYS R 31 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL R 36 " --> pdb=" O GLU R 32 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS R 39 " --> pdb=" O GLU R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 54 Processing helix chain 'R' and resid 160 through 169 removed outlier: 4.120A pdb=" N ALA R 166 " --> pdb=" O SER R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 192 removed outlier: 3.619A pdb=" N LEU R 187 " --> pdb=" O ALA R 183 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 88 removed outlier: 3.617A pdb=" N ARG S 48 " --> pdb=" O LYS S 44 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS S 55 " --> pdb=" O LYS S 51 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS S 58 " --> pdb=" O GLY S 54 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN S 70 " --> pdb=" O SER S 66 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE S 73 " --> pdb=" O LYS S 69 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ALA S 74 " --> pdb=" O ASN S 70 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU S 76 " --> pdb=" O GLN S 72 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLN S 77 " --> pdb=" O ILE S 73 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY S 80 " --> pdb=" O GLU S 76 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N LEU S 81 " --> pdb=" O GLN S 77 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N VAL S 82 " --> pdb=" O SER S 78 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ASP S 83 " --> pdb=" O ARG S 79 " (cutoff:3.500A) Proline residue: S 84 - end of helix Processing helix chain 'S' and resid 116 through 127 removed outlier: 3.803A pdb=" N THR S 120 " --> pdb=" O ASN S 116 " (cutoff:3.500A) Processing helix chain 'S' and resid 144 through 150 removed outlier: 4.047A pdb=" N GLN S 149 " --> pdb=" O LYS S 145 " (cutoff:3.500A) Processing helix chain 'S' and resid 172 through 184 removed outlier: 3.643A pdb=" N LEU S 182 " --> pdb=" O ILE S 178 " (cutoff:3.500A) Processing helix chain 'S' and resid 213 through 220 removed outlier: 5.927A pdb=" N LYS S 218 " --> pdb=" O ASP S 214 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N GLN S 219 " --> pdb=" O LEU S 215 " (cutoff:3.500A) Processing helix chain 'S' and resid 239 through 273 removed outlier: 3.823A pdb=" N ARG S 244 " --> pdb=" O SER S 240 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP S 245 " --> pdb=" O ASP S 241 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN S 263 " --> pdb=" O MET S 259 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N CYS S 264 " --> pdb=" O LEU S 260 " (cutoff:3.500A) Processing helix chain 'S' and resid 275 through 312 removed outlier: 3.555A pdb=" N LYS S 279 " --> pdb=" O GLU S 275 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP S 291 " --> pdb=" O LYS S 287 " (cutoff:3.500A) Processing helix chain 'T' and resid 58 through 75 removed outlier: 3.833A pdb=" N ILE T 67 " --> pdb=" O SER T 63 " (cutoff:3.500A) Proline residue: T 68 - end of helix removed outlier: 5.254A pdb=" N GLU T 72 " --> pdb=" O PRO T 68 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TRP T 73 " --> pdb=" O ALA T 69 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU T 74 " --> pdb=" O VAL T 70 " (cutoff:3.500A) Processing helix chain 'T' and resid 135 through 137 No H-bonds generated for 'chain 'T' and resid 135 through 137' Processing helix chain 'T' and resid 157 through 159 No H-bonds generated for 'chain 'T' and resid 157 through 159' Processing helix chain 'T' and resid 192 through 194 No H-bonds generated for 'chain 'T' and resid 192 through 194' Processing helix chain 'T' and resid 207 through 212 Processing helix chain 'T' and resid 231 through 246 removed outlier: 3.542A pdb=" N ASN T 244 " --> pdb=" O ILE T 240 " (cutoff:3.500A) Processing helix chain 'T' and resid 266 through 279 Processing helix chain 'T' and resid 281 through 283 No H-bonds generated for 'chain 'T' and resid 281 through 283' Processing helix chain 'T' and resid 296 through 315 Proline residue: T 303 - end of helix removed outlier: 4.319A pdb=" N PHE T 313 " --> pdb=" O MET T 309 " (cutoff:3.500A) Processing helix chain 'T' and resid 328 through 340 removed outlier: 3.631A 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 354 through 362 removed outlier: 3.878A pdb=" N HIS T 358 " --> pdb=" O VAL T 354 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU T 361 " --> pdb=" O LEU T 357 " (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 431 through 434 Processing helix chain 'T' and resid 437 through 459 removed outlier: 3.684A pdb=" N GLN T 441 " --> pdb=" O PRO T 437 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY T 444 " --> pdb=" O LYS T 440 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N THR T 445 " --> pdb=" O GLN T 441 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU T 446 " --> pdb=" O VAL T 442 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE T 459 " --> pdb=" O GLU T 455 " (cutoff:3.500A) Processing helix chain 'T' and resid 470 through 484 removed outlier: 3.620A pdb=" N ARG T 479 " --> pdb=" O GLU T 475 " (cutoff:3.500A) Processing helix chain 'T' and resid 494 through 505 removed outlier: 3.915A pdb=" N ALA T 500 " --> pdb=" O ARG T 496 " (cutoff:3.500A) Processing helix chain 'T' and resid 517 through 527 removed outlier: 3.582A pdb=" N GLU T 522 " --> pdb=" O VAL T 518 " (cutoff:3.500A) Processing helix chain 'T' and resid 531 through 539 Processing helix chain 'T' and resid 544 through 555 removed outlier: 3.568A pdb=" N ALA T 548 " --> pdb=" O PRO T 544 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N HIS T 549 " --> pdb=" O ALA T 545 " (cutoff:3.500A) 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 66 through 72 Processing helix chain 'U' and resid 135 through 137 No H-bonds generated for 'chain 'U' and resid 135 through 137' Processing helix chain 'U' and resid 207 through 212 Processing helix chain 'U' and resid 231 through 246 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 314 Proline residue: U 303 - end of helix removed outlier: 3.559A pdb=" N TYR U 312 " --> pdb=" O ALA U 308 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N PHE U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) Processing helix chain 'U' and resid 327 through 340 removed outlier: 3.877A 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: 4.536A pdb=" N PHE U 355 " --> pdb=" O GLY U 352 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR U 356 " --> pdb=" O ASP U 353 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU U 357 " --> pdb=" O VAL U 354 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER U 359 " --> pdb=" O TYR U 356 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ARG U 360 " --> pdb=" O LEU U 357 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU U 362 " --> pdb=" O SER U 359 " (cutoff:3.500A) removed outlier: 4.580A 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 456 removed outlier: 4.252A pdb=" N VAL U 442 " --> pdb=" O GLY U 438 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY U 444 " --> pdb=" O LYS U 440 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N THR U 445 " --> pdb=" O GLN U 441 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU U 448 " --> pdb=" O GLY U 444 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA U 451 " --> pdb=" O LYS U 447 " (cutoff:3.500A) Processing helix chain 'U' and resid 470 through 484 removed outlier: 3.742A pdb=" N ALA U 478 " --> pdb=" O LEU U 474 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU U 482 " --> pdb=" O ALA U 478 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET U 483 " --> pdb=" O ARG U 479 " (cutoff:3.500A) Processing helix chain 'U' and resid 494 through 505 removed outlier: 3.690A pdb=" N VAL U 499 " --> pdb=" O GLU U 495 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA U 500 " --> pdb=" O ARG U 496 " (cutoff:3.500A) Processing helix chain 'U' and resid 517 through 527 removed outlier: 3.609A pdb=" N GLU U 522 " --> pdb=" O VAL U 518 " (cutoff:3.500A) Processing helix chain 'U' and resid 532 through 539 removed outlier: 3.501A pdb=" N ASN U 539 " --> pdb=" O ILE U 535 " (cutoff:3.500A) Processing helix chain 'U' and resid 544 through 553 Processing helix chain 'V' and resid 45 through 48 Processing helix chain 'V' and resid 58 through 66 removed outlier: 3.853A pdb=" N GLN V 64 " --> pdb=" O GLN V 60 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS V 65 " --> pdb=" O HIS V 61 " (cutoff:3.500A) 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 248 removed outlier: 3.553A pdb=" N GLN V 242 " --> pdb=" O ALA V 238 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS V 243 " --> pdb=" O ILE V 239 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLU V 247 " --> pdb=" O LYS V 243 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLN V 248 " --> pdb=" O ASN V 244 " (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 283 No H-bonds generated for 'chain 'V' and resid 281 through 283' Processing helix chain 'V' and resid 296 through 315 Proline residue: V 303 - end of helix removed outlier: 3.562A pdb=" N TYR V 312 " --> pdb=" O ALA V 308 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N PHE V 313 " --> pdb=" O MET V 309 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG V 314 " --> pdb=" O ALA V 310 " (cutoff:3.500A) Processing helix chain 'V' and resid 328 through 340 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: 4.347A pdb=" N PHE V 355 " --> pdb=" O GLY V 352 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR V 356 " --> pdb=" O ASP V 353 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU V 357 " --> pdb=" O VAL V 354 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER V 359 " --> pdb=" O TYR V 356 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ARG V 360 " --> pdb=" O LEU V 357 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU V 362 " --> pdb=" O SER V 359 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU V 363 " --> pdb=" O ARG V 360 " (cutoff:3.500A) Processing helix chain 'V' and resid 370 through 372 No H-bonds generated for 'chain 'V' and resid 370 through 372' Processing helix chain 'V' and resid 393 through 401 Processing helix chain 'V' and resid 410 through 414 removed outlier: 3.616A pdb=" N TYR V 414 " --> pdb=" O THR V 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 410 through 414' Processing helix chain 'V' and resid 431 through 434 removed outlier: 3.585A 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: 3.990A pdb=" N GLY V 444 " --> pdb=" O LYS V 440 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N THR V 445 " --> pdb=" O GLN V 441 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU V 455 " --> pdb=" O ALA V 451 " (cutoff:3.500A) Processing helix chain 'V' and resid 470 through 483 removed outlier: 3.513A pdb=" N GLU V 475 " --> pdb=" O GLN V 471 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA V 478 " --> pdb=" O LEU V 474 " (cutoff:3.500A) Processing helix chain 'V' and resid 494 through 505 removed outlier: 3.663A pdb=" N ALA V 504 " --> pdb=" O ALA V 500 " (cutoff:3.500A) Processing helix chain 'V' and resid 514 through 516 No H-bonds generated for 'chain 'V' and resid 514 through 516' Processing helix chain 'V' and resid 518 through 525 removed outlier: 3.847A pdb=" N GLU V 522 " --> pdb=" O VAL V 518 " (cutoff:3.500A) Processing helix chain 'V' and resid 532 through 539 removed outlier: 3.543A 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 150 through 152 No H-bonds generated for 'chain 'X' and resid 150 through 152' Processing helix chain 'X' and resid 165 through 170 Processing helix chain 'X' and resid 189 through 203 Processing helix chain 'X' and resid 217 through 230 Processing helix chain 'X' and resid 236 through 241 removed outlier: 4.766A 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: 3.675A 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 324 removed outlier: 4.411A pdb=" N ARG X 324 " --> pdb=" O GLY X 320 " (cutoff:3.500A) Processing helix chain 'X' and resid 342 through 344 No H-bonds generated for 'chain 'X' and resid 342 through 344' Processing helix chain 'X' and resid 349 through 356 removed outlier: 3.864A pdb=" N ALA X 356 " --> pdb=" O ALA X 352 " (cutoff:3.500A) Processing helix chain 'X' and resid 366 through 370 Processing helix chain 'X' and resid 389 through 392 No H-bonds generated for 'chain 'X' and resid 389 through 392' Processing helix chain 'X' and resid 394 through 412 removed outlier: 3.546A pdb=" N VAL X 399 " --> pdb=" O GLU X 395 " (cutoff:3.500A) Processing helix chain 'X' and resid 414 through 417 No H-bonds generated for 'chain 'X' and resid 414 through 417' Processing helix chain 'X' and resid 428 through 442 removed outlier: 3.758A pdb=" N THR X 432 " --> pdb=" O GLU X 428 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA X 436 " --> pdb=" O THR X 432 " (cutoff:3.500A) Processing helix chain 'X' and resid 450 through 454 removed outlier: 4.047A pdb=" N THR X 454 " --> pdb=" O GLU X 451 " (cutoff:3.500A) Processing helix chain 'X' and resid 463 through 474 removed outlier: 3.501A pdb=" N SER X 468 " --> pdb=" O ALA X 464 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL X 473 " --> pdb=" O GLY X 469 " (cutoff:3.500A) Processing helix chain 'X' and resid 483 through 485 No H-bonds generated for 'chain 'X' and resid 483 through 485' Processing helix chain 'X' and resid 493 through 502 removed outlier: 4.084A pdb=" N GLU X 497 " --> pdb=" O LYS X 493 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS X 501 " --> pdb=" O GLU X 497 " (cutoff:3.500A) Processing helix chain 'X' and resid 504 through 506 No H-bonds generated for 'chain 'X' and resid 504 through 506' Processing helix chain 'X' and resid 527 through 533 removed outlier: 3.557A pdb=" N SER X 532 " --> pdb=" O ASP X 528 " (cutoff:3.500A) 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 150 through 152 No H-bonds generated for 'chain 'Y' and resid 150 through 152' Processing helix chain 'Y' and resid 165 through 170 Processing helix chain 'Y' and resid 191 through 202 removed outlier: 4.068A pdb=" N LYS Y 202 " --> pdb=" O ASN Y 198 " (cutoff:3.500A) Processing helix chain 'Y' and resid 217 through 229 Processing helix chain 'Y' and resid 236 through 241 removed outlier: 3.885A pdb=" N ARG Y 239 " --> pdb=" O GLY Y 236 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N GLY Y 240 " --> pdb=" O ALA Y 237 " (cutoff:3.500A) Processing helix chain 'Y' and resid 255 through 258 No H-bonds generated for 'chain 'Y' and resid 255 through 258' Processing helix chain 'Y' and resid 261 through 274 Processing helix chain 'Y' and resid 288 through 300 removed outlier: 3.792A pdb=" N ALA Y 299 " --> pdb=" O SER Y 295 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU Y 300 " --> pdb=" O GLU Y 296 " (cutoff:3.500A) 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: 3.656A pdb=" N THR Y 354 " --> pdb=" O ALA Y 350 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ALA Y 356 " --> pdb=" O ALA Y 352 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N HIS Y 357 " --> pdb=" O THR Y 353 " (cutoff:3.500A) Processing helix chain 'Y' and resid 366 through 371 removed outlier: 3.775A pdb=" N LEU Y 371 " --> pdb=" O SER Y 367 " (cutoff:3.500A) Processing helix chain 'Y' and resid 394 through 412 Processing helix chain 'Y' and resid 414 through 419 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 442 removed outlier: 3.625A pdb=" N THR Y 432 " --> pdb=" O GLU Y 428 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA Y 434 " --> pdb=" O LYS Y 430 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG Y 441 " --> pdb=" O ARG Y 437 " (cutoff:3.500A) Processing helix chain 'Y' and resid 451 through 454 No H-bonds generated for 'chain 'Y' and resid 451 through 454' Processing helix chain 'Y' and resid 463 through 475 removed outlier: 3.798A pdb=" N VAL Y 473 " --> pdb=" O GLY Y 469 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU Y 474 " --> pdb=" O PHE Y 470 " (cutoff:3.500A) Processing helix chain 'Y' and resid 484 through 486 No H-bonds generated for 'chain 'Y' and resid 484 through 486' Processing helix chain 'Y' and resid 492 through 505 removed outlier: 3.839A pdb=" N LYS Y 496 " --> pdb=" O ILE Y 492 " (cutoff:3.500A) Processing helix chain 'Y' and resid 527 through 532 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 199 Processing helix chain 'Z' and resid 217 through 229 Processing helix chain 'Z' and resid 236 through 241 removed outlier: 3.618A pdb=" N ARG Z 239 " --> pdb=" O GLY Z 236 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N GLY Z 240 " --> pdb=" O ALA Z 237 " (cutoff:3.500A) Processing helix chain 'Z' and resid 255 through 274 removed outlier: 3.546A pdb=" N ARG Z 260 " --> pdb=" O GLY Z 256 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ALA Z 262 " --> pdb=" O ARG Z 258 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N LEU Z 263 " --> pdb=" O ALA Z 259 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA Z 269 " --> pdb=" O GLY Z 265 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE Z 272 " --> pdb=" O VAL Z 268 " (cutoff:3.500A) Processing helix chain 'Z' and resid 288 through 298 removed outlier: 3.865A pdb=" N VAL Z 297 " --> pdb=" O ALA Z 293 " (cutoff:3.500A) Processing helix chain 'Z' and resid 314 through 324 removed outlier: 4.362A 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 357 removed outlier: 3.780A pdb=" N THR Z 354 " --> pdb=" O ALA Z 350 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ALA Z 356 " --> pdb=" O ALA Z 352 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N HIS Z 357 " --> pdb=" O THR Z 353 " (cutoff:3.500A) Processing helix chain 'Z' and resid 366 through 370 Processing helix chain 'Z' and resid 385 through 387 No H-bonds generated for 'chain 'Z' and resid 385 through 387' Processing helix chain 'Z' and resid 389 through 392 No H-bonds generated for 'chain 'Z' and resid 389 through 392' Processing helix chain 'Z' and resid 394 through 413 removed outlier: 3.686A pdb=" N VAL Z 399 " --> pdb=" O GLU Z 395 " (cutoff:3.500A) Processing helix chain 'Z' and resid 431 through 443 removed outlier: 3.743A pdb=" N LYS Z 438 " --> pdb=" O ALA Z 434 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG Z 441 " --> pdb=" O ARG Z 437 " (cutoff:3.500A) Processing helix chain 'Z' and resid 463 through 475 removed outlier: 3.812A pdb=" N VAL Z 473 " --> pdb=" O GLY Z 469 " (cutoff:3.500A) Processing helix chain 'Z' and resid 483 through 485 No H-bonds generated for 'chain 'Z' and resid 483 through 485' Processing helix chain 'Z' and resid 492 through 508 removed outlier: 4.092A pdb=" N LYS Z 501 " --> pdb=" O GLU Z 497 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA Z 503 " --> pdb=" O ALA Z 499 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALA Z 507 " --> pdb=" O ALA Z 503 " (cutoff:3.500A) Processing helix chain 'Z' and resid 527 through 533 removed outlier: 3.956A pdb=" N VAL Z 531 " --> pdb=" O LEU Z 527 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N SER Z 532 " --> pdb=" O ASP Z 528 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain '1' and resid 183 through 185 removed outlier: 4.352A pdb=" N VAL 1 226 " --> pdb=" O ALA 1 185 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '2' and resid 369 through 372 Processing sheet with id= C, first strand: chain '7' and resid 36 through 41 Processing sheet with id= D, first strand: chain 'P' and resid 188 through 190 removed outlier: 6.771A pdb=" N VAL P 156 " --> pdb=" O LYS P 189 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'R' and resid 72 through 75 removed outlier: 6.943A pdb=" N THR R 142 " --> pdb=" O ASN R 73 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N TYR R 75 " --> pdb=" O THR R 142 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE R 144 " --> pdb=" O TYR R 75 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'R' and resid 97 through 100 removed outlier: 3.679A pdb=" N THR R 88 " --> pdb=" O HIS R 119 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL R 115 " --> pdb=" O PRO R 92 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'S' and resid 203 through 211 removed outlier: 5.215A pdb=" N ASN S 195 " --> pdb=" O VAL S 105 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ASP S 136 " --> pdb=" O SER S 100 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N VAL S 102 " --> pdb=" O ASP S 136 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL S 138 " --> pdb=" O VAL S 102 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ALA S 104 " --> pdb=" O VAL S 138 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL S 140 " --> pdb=" O ALA S 104 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N SER S 141 " --> pdb=" O GLN S 159 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ALA S 161 " --> pdb=" O SER S 141 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'T' and resid 94 through 97 removed outlier: 6.810A pdb=" N VAL T 130 " --> pdb=" O ALA T 119 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ALA T 119 " --> pdb=" O VAL T 130 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N PHE T 132 " --> pdb=" O GLY T 117 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N GLY T 117 " --> pdb=" O PHE T 132 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'T' and resid 152 through 155 Processing sheet with id= J, first strand: chain 'T' and resid 404 through 408 removed outlier: 3.782A pdb=" N LEU T 222 " --> pdb=" O GLY T 404 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'T' and resid 285 through 290 removed outlier: 8.900A pdb=" N ILE T 286 " --> pdb=" O VAL T 255 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N CYS T 257 " --> pdb=" O ILE T 286 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N VAL T 288 " --> pdb=" O CYS T 257 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYR T 259 " --> pdb=" O VAL T 288 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ALA T 290 " --> pdb=" O TYR T 259 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ALA T 261 " --> pdb=" O ALA T 290 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N HIS T 319 " --> pdb=" O TYR T 256 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N VAL T 258 " --> pdb=" O HIS T 319 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU T 321 " --> pdb=" O VAL T 258 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N VAL T 260 " --> pdb=" O LEU T 321 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ILE T 323 " --> pdb=" O VAL T 260 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL T 262 " --> pdb=" O ILE T 323 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ASP T 325 " --> pdb=" O VAL T 262 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N SER T 376 " --> pdb=" O GLY T 320 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ILE T 322 " --> pdb=" O SER T 376 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N THR T 378 " --> pdb=" O ILE T 322 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N TYR T 324 " --> pdb=" O THR T 378 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N PHE T 380 " --> pdb=" O TYR T 324 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'U' and resid 85 through 91 removed outlier: 6.725A pdb=" N ARG U 96 " --> pdb=" O LEU U 88 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL U 90 " --> pdb=" O ILE U 94 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE U 94 " --> pdb=" O VAL U 90 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN U 121 " --> pdb=" O GLY U 128 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL U 130 " --> pdb=" O ALA U 119 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ALA U 119 " --> pdb=" O VAL U 130 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'U' and resid 152 through 155 Processing sheet with id= N, first strand: chain 'U' and resid 163 through 165 removed outlier: 8.241A pdb=" N THR U 164 " --> pdb=" O THR U 285 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N MET U 287 " --> pdb=" O THR U 164 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N ILE U 286 " --> pdb=" O VAL U 255 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N CYS U 257 " --> pdb=" O ILE U 286 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N VAL U 288 " --> pdb=" O CYS U 257 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N TYR U 259 " --> pdb=" O VAL U 288 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ALA U 290 " --> pdb=" O TYR U 259 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ALA U 261 " --> pdb=" O ALA U 290 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N HIS U 319 " --> pdb=" O TYR U 256 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N VAL U 258 " --> pdb=" O HIS U 319 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU U 321 " --> pdb=" O VAL U 258 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N VAL U 260 " --> pdb=" O LEU U 321 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ILE U 323 " --> pdb=" O VAL U 260 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL U 262 " --> pdb=" O ILE U 323 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ASP U 325 " --> pdb=" O VAL U 262 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLN U 264 " --> pdb=" O ASP U 325 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N SER U 376 " --> pdb=" O GLY U 320 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ILE U 322 " --> pdb=" O SER U 376 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N THR U 378 " --> pdb=" O ILE U 322 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N TYR U 324 " --> pdb=" O THR U 378 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N PHE U 380 " --> pdb=" O TYR U 324 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'U' and resid 405 through 408 removed outlier: 6.579A pdb=" N LEU U 222 " --> pdb=" O ILE U 406 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N LEU U 408 " --> pdb=" O LEU U 222 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ILE U 224 " --> pdb=" O LEU U 408 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'U' and resid 107 through 111 removed outlier: 4.691A pdb=" N GLN U 149 " --> pdb=" O LEU U 108 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N CYS U 110 " --> pdb=" O THR U 147 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N THR U 147 " --> pdb=" O CYS U 110 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'V' and resid 143 through 145 removed outlier: 6.512A pdb=" N ARG V 96 " --> pdb=" O LEU V 88 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL V 90 " --> pdb=" O ILE V 94 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE V 94 " --> pdb=" O VAL V 90 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL V 130 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ALA V 119 " --> pdb=" O VAL V 130 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU V 107 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N GLN V 149 " --> pdb=" O LEU V 108 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N CYS V 110 " --> pdb=" O THR V 147 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N THR V 147 " --> pdb=" O CYS V 110 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'V' and resid 152 through 155 Processing sheet with id= S, first strand: chain 'V' and resid 404 through 407 Processing sheet with id= T, first strand: chain 'V' and resid 286 through 290 removed outlier: 6.683A pdb=" N HIS V 319 " --> pdb=" O TYR V 256 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N VAL V 258 " --> pdb=" O HIS V 319 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LEU V 321 " --> pdb=" O VAL V 258 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N VAL V 260 " --> pdb=" O LEU V 321 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE V 323 " --> pdb=" O VAL V 260 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL V 262 " --> pdb=" O ILE V 323 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ASP V 325 " --> pdb=" O VAL V 262 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N SER V 376 " --> pdb=" O GLY V 320 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ILE V 322 " --> pdb=" O SER V 376 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N THR V 378 " --> pdb=" O ILE V 322 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N TYR V 324 " --> pdb=" O THR V 378 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N PHE V 380 " --> pdb=" O TYR V 324 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'X' and resid 38 through 44 removed outlier: 6.346A pdb=" N ASP X 49 " --> pdb=" O SER X 41 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N VAL X 43 " --> pdb=" O VAL X 47 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL X 47 " --> pdb=" O VAL X 43 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ILE X 88 " --> pdb=" O VAL X 76 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N VAL X 76 " --> pdb=" O ILE X 88 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'X' and resid 110 through 113 Processing sheet with id= W, first strand: chain 'X' and resid 244 through 250 removed outlier: 7.052A pdb=" N SER X 208 " --> pdb=" O THR X 245 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N VAL X 247 " --> pdb=" O SER X 208 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N PHE X 210 " --> pdb=" O VAL X 247 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N GLY X 249 " --> pdb=" O PHE X 210 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N GLY X 212 " --> pdb=" O GLY X 249 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N VAL X 209 " --> pdb=" O ASP X 279 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N LEU X 281 " --> pdb=" O VAL X 209 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ALA X 211 " --> pdb=" O LEU X 281 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N PHE X 283 " --> pdb=" O ALA X 211 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL X 213 " --> pdb=" O PHE X 283 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ASP X 285 " --> pdb=" O VAL X 213 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N GLU X 215 " --> pdb=" O ASP X 285 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N SER X 332 " --> pdb=" O VAL X 280 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N LEU X 282 " --> pdb=" O SER X 332 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N THR X 334 " --> pdb=" O LEU X 282 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N VAL X 284 " --> pdb=" O THR X 334 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL X 336 " --> pdb=" O VAL X 284 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLY X 180 " --> pdb=" O ASP X 359 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N THR X 361 " --> pdb=" O GLY X 180 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N PHE X 182 " --> pdb=" O THR X 361 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N VAL X 363 " --> pdb=" O PHE X 182 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'X' and resid 559 through 561 Processing sheet with id= Y, first strand: chain 'Y' and resid 37 through 39 removed outlier: 6.544A pdb=" N ARG Y 86 " --> pdb=" O ALA Y 77 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N HIS Y 79 " --> pdb=" O THR Y 84 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR Y 84 " --> pdb=" O HIS Y 79 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N ARG Y 51 " --> pdb=" O VAL Y 40 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N VAL Y 40 " --> pdb=" O ARG Y 51 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'Y' and resid 110 through 113 Processing sheet with id= AA, first strand: chain 'Y' and resid 360 through 363 removed outlier: 7.321A pdb=" N ILE Y 179 " --> pdb=" O ILE Y 333 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N SER Y 335 " --> pdb=" O ILE Y 179 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N LEU Y 181 " --> pdb=" O SER Y 335 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN Y 337 " --> pdb=" O LEU Y 181 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N GLY Y 183 " --> pdb=" O GLN Y 337 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N VAL Y 339 " --> pdb=" O GLY Y 183 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N PHE Y 207 " --> pdb=" O LEU Y 281 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N PHE Y 283 " --> pdb=" O PHE Y 207 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL Y 209 " --> pdb=" O PHE Y 283 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ASP Y 285 " --> pdb=" O VAL Y 209 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ALA Y 211 " --> pdb=" O ASP Y 285 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'Z' and resid 38 through 44 removed outlier: 6.523A pdb=" N ASP Z 49 " --> pdb=" O SER Z 41 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N VAL Z 43 " --> pdb=" O VAL Z 47 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL Z 47 " --> pdb=" O VAL Z 43 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ILE Z 88 " --> pdb=" O VAL Z 76 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N VAL Z 76 " --> pdb=" O ILE Z 88 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'Z' and resid 110 through 113 Processing sheet with id= AD, first strand: chain 'Z' and resid 360 through 363 removed outlier: 7.355A pdb=" N ILE Z 179 " --> pdb=" O ILE Z 333 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N SER Z 335 " --> pdb=" O ILE Z 179 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N LEU Z 181 " --> pdb=" O SER Z 335 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLN Z 337 " --> pdb=" O LEU Z 181 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N GLY Z 183 " --> pdb=" O GLN Z 337 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N VAL Z 339 " --> pdb=" O GLY Z 183 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'Z' and resid 559 through 561 2208 hydrogen bonds defined for protein. 6282 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: 15.24 Time building geometry restraints manager: 17.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 12302 1.33 - 1.45: 10859 1.45 - 1.57: 31248 1.57 - 1.69: 21 1.69 - 1.81: 254 Bond restraints: 54684 Sorted by residual: 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 4.84e+01 bond pdb=" C4 ATP T1001 " pdb=" C5 ATP T1001 " ideal model delta sigma weight residual 1.388 1.457 -0.069 1.00e-02 1.00e+04 4.72e+01 bond pdb=" C4 ATP V1001 " pdb=" C5 ATP V1001 " ideal model delta sigma weight residual 1.388 1.454 -0.066 1.00e-02 1.00e+04 4.36e+01 bond pdb=" C5 ATP T1001 " pdb=" C6 ATP T1001 " ideal model delta sigma weight residual 1.409 1.467 -0.058 1.00e-02 1.00e+04 3.42e+01 bond pdb=" C5 ATP U1001 " pdb=" C6 ATP U1001 " ideal model delta sigma weight residual 1.409 1.467 -0.058 1.00e-02 1.00e+04 3.39e+01 ... (remaining 54679 not shown) Histogram of bond angle deviations from ideal: 92.35 - 101.15: 96 101.15 - 109.94: 10431 109.94 - 118.73: 33829 118.73 - 127.52: 29365 127.52 - 136.32: 434 Bond angle restraints: 74155 Sorted by residual: angle pdb=" PB ATP U1001 " pdb=" O3B ATP U1001 " pdb=" PG ATP U1001 " ideal model delta sigma weight residual 139.87 119.60 20.27 1.00e+00 1.00e+00 4.11e+02 angle pdb=" PB ATP T1001 " pdb=" O3B ATP T1001 " pdb=" PG ATP T1001 " ideal model delta sigma weight residual 139.87 122.39 17.48 1.00e+00 1.00e+00 3.06e+02 angle pdb=" PA ATP T1001 " pdb=" O3A ATP T1001 " pdb=" PB ATP T1001 " ideal model delta sigma weight residual 136.83 122.62 14.21 1.00e+00 1.00e+00 2.02e+02 angle pdb=" PB ATP V1001 " pdb=" O3B ATP V1001 " pdb=" PG ATP V1001 " ideal model delta sigma weight residual 139.87 128.05 11.82 1.00e+00 1.00e+00 1.40e+02 angle pdb=" PA ATP U1001 " pdb=" O3A ATP U1001 " pdb=" PB ATP U1001 " ideal model delta sigma weight residual 136.83 126.82 10.01 1.00e+00 1.00e+00 1.00e+02 ... (remaining 74150 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.65: 32088 30.65 - 61.31: 857 61.31 - 91.96: 75 91.96 - 122.62: 2 122.62 - 153.27: 1 Dihedral angle restraints: 33023 sinusoidal: 12667 harmonic: 20356 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 -123.63 -56.37 0 5.00e+00 4.00e-02 1.27e+02 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 -132.66 -47.34 0 5.00e+00 4.00e-02 8.96e+01 dihedral pdb=" CA SER S 212 " pdb=" C SER S 212 " pdb=" N PRO S 213 " pdb=" CA PRO S 213 " ideal model delta harmonic sigma weight residual -180.00 -137.60 -42.40 0 5.00e+00 4.00e-02 7.19e+01 ... (remaining 33020 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 6913 0.077 - 0.155: 1596 0.155 - 0.232: 160 0.232 - 0.309: 17 0.309 - 0.386: 3 Chirality restraints: 8689 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 2.26 0.39 2.00e-01 2.50e+01 3.73e+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 -2.27 -0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" CA ASP S 83 " pdb=" N ASP S 83 " pdb=" C ASP S 83 " pdb=" CB ASP S 83 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.26e+00 ... (remaining 8686 not shown) Planarity restraints: 9508 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA Z 503 " 0.030 2.00e-02 2.50e+03 5.94e-02 3.53e+01 pdb=" C ALA Z 503 " -0.103 2.00e-02 2.50e+03 pdb=" O ALA Z 503 " 0.038 2.00e-02 2.50e+03 pdb=" N LYS Z 504 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA X 307 " 0.016 2.00e-02 2.50e+03 3.15e-02 9.90e+00 pdb=" C ALA X 307 " -0.054 2.00e-02 2.50e+03 pdb=" O ALA X 307 " 0.020 2.00e-02 2.50e+03 pdb=" N VAL X 308 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU 2 299 " 0.050 5.00e-02 4.00e+02 7.55e-02 9.12e+00 pdb=" N PRO 2 300 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO 2 300 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO 2 300 " 0.041 5.00e-02 4.00e+02 ... (remaining 9505 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 272 2.47 - 3.08: 33578 3.08 - 3.69: 85158 3.69 - 4.29: 131603 4.29 - 4.90: 213193 Nonbonded interactions: 463804 Sorted by model distance: nonbonded pdb=" O GLN Q 49 " pdb=" N LYS Q 61 " model vdw 1.864 2.520 nonbonded pdb=" O3B ADP Y 601 " pdb="MG MG Y 602 " model vdw 2.040 2.170 nonbonded pdb=" OG1 THR U 232 " pdb="MG MG U1002 " model vdw 2.041 2.170 nonbonded pdb=" OG1 THR Y 190 " pdb="MG MG Y 602 " model vdw 2.045 2.170 nonbonded pdb=" O2B ATP V1001 " pdb="MG MG V1002 " model vdw 2.050 2.170 ... (remaining 463799 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = (chain 'T' and (resid 43 through 562 or resid 1001 through 1002)) selection = (chain 'U' and (resid 43 through 561 or (resid 562 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1001 through 1002)) selection = (chain 'V' and (resid 43 through 561 or (resid 562 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1001 through 1002)) } ncs_group { reference = (chain 'X' and resid 37 through 556) selection = (chain 'Y' and resid 37 through 556) selection = (chain 'Z' and resid 37 through 556) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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: 4.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 23.550 Check model and map are aligned: 0.640 Set scattering table: 0.370 Process input model: 111.490 Find NCS groups from input model: 2.660 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:2.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 145.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 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 : 0.013 0.117 54684 Z= 0.846 Angle : 1.069 20.275 74155 Z= 0.601 Chirality : 0.065 0.386 8689 Planarity : 0.008 0.075 9508 Dihedral : 13.979 153.270 19937 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.17 % Favored : 94.64 % Rotamer: Outliers : 0.41 % Allowed : 6.80 % Favored : 92.79 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.34 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.20 (0.07), residues: 7034 helix: -4.31 (0.04), residues: 3811 sheet: -1.56 (0.19), residues: 686 loop : -2.13 (0.10), residues: 2537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP Z 141 HIS 0.015 0.002 HIS 4 233 PHE 0.029 0.003 PHE S 249 TYR 0.030 0.003 TYR 7 119 ARG 0.013 0.001 ARG T 347 *********************** 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 865 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 842 time to evaluate : 4.535 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 41 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7360 (pm20) REVERT: 1 242 LYS cc_start: 0.8201 (tttt) cc_final: 0.7746 (mmtm) REVERT: 2 68 ASN cc_start: 0.8985 (m110) cc_final: 0.8352 (m110) REVERT: 2 101 VAL cc_start: 0.8427 (p) cc_final: 0.8094 (t) REVERT: 2 119 GLU cc_start: 0.8032 (pt0) cc_final: 0.7820 (pt0) REVERT: 2 173 ARG cc_start: 0.7204 (tmm160) cc_final: 0.7002 (ttp-110) REVERT: 2 233 LYS cc_start: 0.7768 (ttmm) cc_final: 0.7454 (ttmt) REVERT: 2 346 ARG cc_start: 0.7575 (mtm-85) cc_final: 0.7369 (mtm-85) REVERT: 3 132 VAL cc_start: 0.8804 (p) cc_final: 0.8600 (t) REVERT: 3 185 ASP cc_start: 0.8108 (t70) cc_final: 0.7849 (t70) REVERT: 4 91 ASN cc_start: 0.8484 (m-40) cc_final: 0.8209 (m-40) REVERT: 4 133 ASP cc_start: 0.8426 (t0) cc_final: 0.8103 (t70) REVERT: 7 47 GLU cc_start: 0.7016 (mm-30) cc_final: 0.6775 (mp0) REVERT: 7 135 ASP cc_start: 0.8573 (m-30) cc_final: 0.8165 (m-30) REVERT: 8 38 LYS cc_start: 0.8983 (mttt) cc_final: 0.8526 (mtpp) REVERT: 9 12 GLU cc_start: 0.8345 (tt0) cc_final: 0.8107 (tt0) REVERT: 9 68 MET cc_start: 0.8079 (mtt) cc_final: 0.7845 (mtm) REVERT: 9 80 GLN cc_start: 0.8483 (tp40) cc_final: 0.8197 (mm-40) REVERT: A 97 LYS cc_start: 0.8150 (tptp) cc_final: 0.7680 (mmtp) REVERT: B 60 LYS cc_start: 0.8798 (mtpp) cc_final: 0.8564 (mttt) REVERT: B 81 MET cc_start: 0.7671 (ttp) cc_final: 0.7444 (ttp) REVERT: E 92 ASN cc_start: 0.8760 (p0) cc_final: 0.8490 (p0) REVERT: E 126 PHE cc_start: 0.7880 (m-80) cc_final: 0.7578 (m-80) REVERT: G 98 GLN cc_start: 0.8744 (tt0) cc_final: 0.8368 (tt0) REVERT: H 81 MET cc_start: 0.8764 (ttp) cc_final: 0.8530 (ttp) REVERT: I 97 LYS cc_start: 0.8330 (mmmt) cc_final: 0.8073 (mmmt) REVERT: M 199 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7899 (mmtt) REVERT: P 68 ASP cc_start: 0.7466 (t70) cc_final: 0.7205 (t0) REVERT: S 215 LEU cc_start: 0.5678 (OUTLIER) cc_final: 0.5407 (pp) REVERT: S 271 MET cc_start: 0.7638 (ttp) cc_final: 0.7410 (ttt) REVERT: T 101 LYS cc_start: 0.7977 (mmmt) cc_final: 0.7695 (mmmt) REVERT: T 287 MET cc_start: 0.8548 (tpp) cc_final: 0.8316 (tpp) REVERT: T 452 GLN cc_start: 0.7466 (mt0) cc_final: 0.7149 (mt0) REVERT: T 496 ARG cc_start: 0.7782 (mtt-85) cc_final: 0.7441 (mtt180) REVERT: T 537 LYS cc_start: 0.8385 (tptt) cc_final: 0.7896 (ttpp) REVERT: U 309 MET cc_start: 0.8865 (mtt) cc_final: 0.8634 (mtt) REVERT: U 521 GLU cc_start: 0.7152 (pt0) cc_final: 0.6934 (tt0) REVERT: V 52 LYS cc_start: 0.7877 (mmpt) cc_final: 0.7660 (mmmt) REVERT: V 101 LYS cc_start: 0.8476 (mmtp) cc_final: 0.8244 (mmmt) REVERT: V 135 ASP cc_start: 0.7820 (p0) cc_final: 0.7592 (p0) REVERT: V 473 VAL cc_start: 0.7580 (m) cc_final: 0.7281 (p) REVERT: V 483 MET cc_start: 0.7486 (tpp) cc_final: 0.7104 (tpp) REVERT: X 227 MET cc_start: 0.8686 (mtt) cc_final: 0.8365 (mtt) REVERT: X 493 LYS cc_start: 0.7982 (tmmt) cc_final: 0.7598 (mtmm) REVERT: Y 528 ASP cc_start: 0.6772 (t0) cc_final: 0.6312 (t0) REVERT: Z 90 MET cc_start: 0.8945 (mmp) cc_final: 0.8742 (mmt) REVERT: Z 317 ASP cc_start: 0.7476 (m-30) cc_final: 0.7088 (m-30) REVERT: Z 405 LYS cc_start: 0.8693 (tptt) cc_final: 0.8393 (tptm) outliers start: 23 outliers final: 8 residues processed: 863 average time/residue: 0.5620 time to fit residues: 783.7024 Evaluate side-chains 633 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 623 time to evaluate : 4.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 256 VAL Chi-restraints excluded: chain 2 residue 78 VAL Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain M residue 199 LYS Chi-restraints excluded: chain S residue 215 LEU Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 185 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain Y residue 308 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 697 random chunks: chunk 588 optimal weight: 10.0000 chunk 528 optimal weight: 3.9990 chunk 293 optimal weight: 0.6980 chunk 180 optimal weight: 1.9990 chunk 356 optimal weight: 0.9980 chunk 282 optimal weight: 1.9990 chunk 546 optimal weight: 0.9990 chunk 211 optimal weight: 0.8980 chunk 332 optimal weight: 0.7980 chunk 406 optimal weight: 0.6980 chunk 632 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 44 ASN 1 65 GLN 1 100 GLN 1 257 HIS 1 285 GLN 1 298 GLN 1 316 ASN 1 423 ASN 1 482 ASN 1 531 HIS 1 587 ASN 1 590 HIS 2 40 GLN 2 68 ASN ** 2 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 122 ASN 2 243 GLN 2 289 HIS 2 380 GLN 3 189 HIS 3 206 ASN 3 229 ASN 4 135 ASN 4 240 GLN 5 29 GLN 5 107 ASN 6 40 ASN 6 74 GLN 7 86 HIS 7 98 ASN 7 123 HIS ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 184 ASN ** 8 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 94 ASN A 98 GLN B 87 ASN B 94 ASN C 94 ASN D 98 GLN G 94 ASN G 98 GLN H 94 ASN H 98 GLN M 120 GLN M 163 ASN P 52 GLN P 223 ASN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 38 ASN R 66 HIS R 85 GLN R 137 HIS R 154 GLN ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 98 ASN ** S 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 262 ASN S 267 HIS T 152 ASN T 264 GLN T 358 HIS T 386 GLN T 435 GLN T 441 GLN T 539 ASN U 149 GLN U 152 ASN U 246 ASN U 248 GLN U 264 GLN U 271 GLN U 319 HIS U 386 GLN U 515 GLN U 527 GLN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 61 HIS V 64 GLN ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 126 HIS V 139 HIS V 149 GLN V 242 GLN V 271 GLN V 386 GLN V 405 GLN V 471 GLN V 486 GLN ** V 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 497 GLN X 199 ASN X 278 GLN X 294 ASN Y 174 GLN Y 199 ASN Y 278 GLN ** Y 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 174 GLN ** Z 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 398 ASN Z 408 GLN Total number of N/Q/H flips: 91 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 54684 Z= 0.187 Angle : 0.580 11.974 74155 Z= 0.303 Chirality : 0.042 0.253 8689 Planarity : 0.005 0.057 9508 Dihedral : 6.842 130.852 7685 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.48 % Favored : 96.37 % Rotamer: Outliers : 1.39 % Allowed : 9.93 % Favored : 88.69 % 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: -3.14 (0.09), residues: 7034 helix: -2.32 (0.07), residues: 3832 sheet: -1.19 (0.20), residues: 656 loop : -1.58 (0.11), residues: 2546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP 4 206 HIS 0.008 0.001 HIS V 61 PHE 0.021 0.001 PHE U 508 TYR 0.031 0.001 TYR 4 211 ARG 0.006 0.000 ARG 1 387 *********************** 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 816 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 738 time to evaluate : 4.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 41 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7302 (pm20) REVERT: 1 69 ASP cc_start: 0.7587 (m-30) cc_final: 0.6877 (m-30) REVERT: 1 232 LYS cc_start: 0.8415 (mmmt) cc_final: 0.8162 (mmmm) REVERT: 2 233 LYS cc_start: 0.7775 (ttmm) cc_final: 0.7429 (ttmt) REVERT: 4 133 ASP cc_start: 0.8170 (t0) cc_final: 0.7869 (t70) REVERT: 7 67 ARG cc_start: 0.8274 (mmm-85) cc_final: 0.8026 (mmm-85) REVERT: 8 38 LYS cc_start: 0.8882 (mttt) cc_final: 0.8503 (mtpp) REVERT: 8 66 ASP cc_start: 0.8071 (t70) cc_final: 0.7704 (t0) REVERT: 9 9 LYS cc_start: 0.8506 (mtmt) cc_final: 0.8180 (mtmm) REVERT: 9 12 GLU cc_start: 0.8348 (tt0) cc_final: 0.8132 (tt0) REVERT: 9 80 GLN cc_start: 0.8487 (tp40) cc_final: 0.8007 (mm-40) REVERT: B 60 LYS cc_start: 0.8444 (mtpp) cc_final: 0.8204 (mttt) REVERT: D 119 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.6923 (mt) REVERT: H 81 MET cc_start: 0.8336 (ttp) cc_final: 0.7958 (ttt) REVERT: I 92 ASN cc_start: 0.8504 (p0) cc_final: 0.7933 (p0) REVERT: P 68 ASP cc_start: 0.7582 (t70) cc_final: 0.7284 (t0) REVERT: S 215 LEU cc_start: 0.5270 (OUTLIER) cc_final: 0.5039 (pp) REVERT: S 271 MET cc_start: 0.7584 (ttp) cc_final: 0.7300 (ttt) REVERT: T 447 LYS cc_start: 0.7617 (ptpt) cc_final: 0.7397 (mtmt) REVERT: T 537 LYS cc_start: 0.8300 (tptt) cc_final: 0.7675 (ttpp) REVERT: T 546 LEU cc_start: 0.8620 (tp) cc_final: 0.8344 (tp) REVERT: U 46 ASP cc_start: 0.7641 (m-30) cc_final: 0.7411 (m-30) REVERT: U 309 MET cc_start: 0.8720 (mtt) cc_final: 0.8514 (mtt) REVERT: V 52 LYS cc_start: 0.7896 (mmpt) cc_final: 0.7626 (mmmt) REVERT: V 521 GLU cc_start: 0.7142 (tt0) cc_final: 0.6642 (tt0) REVERT: X 227 MET cc_start: 0.8678 (mtt) cc_final: 0.8449 (mtt) REVERT: X 493 LYS cc_start: 0.7968 (tmmt) cc_final: 0.7595 (mtmm) REVERT: X 524 ILE cc_start: 0.4753 (OUTLIER) cc_final: 0.4370 (tp) REVERT: Y 422 MET cc_start: 0.8042 (mmm) cc_final: 0.7788 (tpp) REVERT: Y 528 ASP cc_start: 0.6880 (t0) cc_final: 0.6543 (t0) REVERT: Z 90 MET cc_start: 0.8803 (mmp) cc_final: 0.8449 (mmp) REVERT: Z 227 MET cc_start: 0.8706 (mtp) cc_final: 0.8479 (mtp) REVERT: Z 398 ASN cc_start: 0.8807 (m-40) cc_final: 0.8163 (m-40) REVERT: Z 405 LYS cc_start: 0.8417 (tptt) cc_final: 0.8097 (tptm) outliers start: 78 outliers final: 45 residues processed: 795 average time/residue: 0.5660 time to fit residues: 746.5211 Evaluate side-chains 654 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 606 time to evaluate : 4.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 1 residue 42 SER Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 308 ASN Chi-restraints excluded: chain 1 residue 367 GLU Chi-restraints excluded: chain 1 residue 512 LEU Chi-restraints excluded: chain 1 residue 578 ASP Chi-restraints excluded: chain 2 residue 78 VAL Chi-restraints excluded: chain 2 residue 97 SER Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 3 residue 297 LEU Chi-restraints excluded: chain 3 residue 308 GLU Chi-restraints excluded: chain 6 residue 52 LYS Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 9 residue 7 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain S residue 88 LEU Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 215 LEU Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 185 VAL Chi-restraints excluded: chain T residue 472 TYR Chi-restraints excluded: chain T residue 473 VAL Chi-restraints excluded: chain U residue 63 SER Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 427 VAL Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain X residue 49 ASP Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 359 ASP Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain Y residue 69 SER Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 367 SER Chi-restraints excluded: chain Y residue 381 ASP Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Z residue 325 ILE Chi-restraints excluded: chain Z residue 367 SER Chi-restraints excluded: chain Z residue 415 ASP Chi-restraints excluded: chain Z residue 534 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 697 random chunks: chunk 351 optimal weight: 7.9990 chunk 196 optimal weight: 0.5980 chunk 526 optimal weight: 4.9990 chunk 431 optimal weight: 8.9990 chunk 174 optimal weight: 0.8980 chunk 634 optimal weight: 0.2980 chunk 685 optimal weight: 7.9990 chunk 564 optimal weight: 4.9990 chunk 628 optimal weight: 3.9990 chunk 216 optimal weight: 4.9990 chunk 508 optimal weight: 3.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 44 ASN 0 48 ASN ** 1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 423 ASN 1 562 ASN 2 44 ASN ** 2 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 111 GLN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 26 HIS C 98 GLN D 87 ASN G 98 GLN P 52 GLN ** P 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 85 GLN ** R 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 529 ASN ** U 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 61 HIS ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 244 ASN ** V 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 204 HIS ** Y 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 412 ASN Z 100 GLN Z 412 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 54684 Z= 0.326 Angle : 0.599 13.568 74155 Z= 0.308 Chirality : 0.044 0.206 8689 Planarity : 0.005 0.052 9508 Dihedral : 6.622 118.172 7676 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.34 % Favored : 95.54 % Rotamer: Outliers : 2.29 % Allowed : 11.79 % Favored : 85.92 % 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: -1.98 (0.09), residues: 7034 helix: -1.20 (0.08), residues: 3844 sheet: -1.00 (0.20), residues: 645 loop : -1.30 (0.12), residues: 2545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP U 73 HIS 0.008 0.001 HIS 7 123 PHE 0.018 0.002 PHE P 122 TYR 0.029 0.002 TYR 4 211 ARG 0.005 0.000 ARG 1 387 *********************** 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 757 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 628 time to evaluate : 4.602 Fit side-chains REVERT: 0 41 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7326 (pm20) REVERT: 1 69 ASP cc_start: 0.7537 (m-30) cc_final: 0.6792 (m-30) REVERT: 1 101 ASN cc_start: 0.8548 (t0) cc_final: 0.8314 (t0) REVERT: 1 232 LYS cc_start: 0.8414 (mmmt) cc_final: 0.8186 (mmmm) REVERT: 2 44 ASN cc_start: 0.8551 (t0) cc_final: 0.8228 (t0) REVERT: 2 74 ASN cc_start: 0.8983 (t0) cc_final: 0.8770 (t0) REVERT: 2 233 LYS cc_start: 0.7807 (ttmm) cc_final: 0.7507 (tppt) REVERT: 2 422 GLU cc_start: 0.7447 (tp30) cc_final: 0.6880 (tp30) REVERT: 4 133 ASP cc_start: 0.8243 (t0) cc_final: 0.7897 (t70) REVERT: 8 38 LYS cc_start: 0.8881 (mttt) cc_final: 0.8503 (mtpp) REVERT: 9 80 GLN cc_start: 0.8478 (tp40) cc_final: 0.8191 (mm-40) REVERT: B 60 LYS cc_start: 0.8556 (mtpp) cc_final: 0.8300 (mttt) REVERT: C 102 TYR cc_start: 0.7546 (m-80) cc_final: 0.7280 (m-80) REVERT: D 98 GLN cc_start: 0.7593 (OUTLIER) cc_final: 0.7357 (tt0) REVERT: D 107 PHE cc_start: 0.8728 (t80) cc_final: 0.8394 (t80) REVERT: H 81 MET cc_start: 0.8441 (ttp) cc_final: 0.7982 (ttt) REVERT: H 111 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.6878 (mm-30) REVERT: I 92 ASN cc_start: 0.8495 (p0) cc_final: 0.7918 (p0) REVERT: P 68 ASP cc_start: 0.7503 (t70) cc_final: 0.7218 (t0) REVERT: S 215 LEU cc_start: 0.5304 (OUTLIER) cc_final: 0.5102 (pp) REVERT: S 271 MET cc_start: 0.7635 (ttp) cc_final: 0.7324 (ttt) REVERT: T 228 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7932 (mt0) REVERT: T 537 LYS cc_start: 0.8367 (tptt) cc_final: 0.7844 (ttpp) REVERT: T 546 LEU cc_start: 0.8418 (tp) cc_final: 0.8041 (tp) REVERT: V 86 ARG cc_start: 0.8292 (mtm-85) cc_final: 0.7994 (mtm110) REVERT: V 483 MET cc_start: 0.7597 (tpp) cc_final: 0.7094 (tpp) REVERT: V 521 GLU cc_start: 0.7275 (tt0) cc_final: 0.6811 (tt0) REVERT: X 227 MET cc_start: 0.8753 (mtt) cc_final: 0.8541 (mtt) REVERT: X 493 LYS cc_start: 0.7849 (tmmt) cc_final: 0.7528 (mtmm) REVERT: X 524 ILE cc_start: 0.4720 (OUTLIER) cc_final: 0.4310 (tp) REVERT: Y 422 MET cc_start: 0.8031 (mmm) cc_final: 0.7751 (tpp) REVERT: Y 495 VAL cc_start: 0.8817 (m) cc_final: 0.8488 (t) REVERT: Y 528 ASP cc_start: 0.6873 (t0) cc_final: 0.6553 (t0) REVERT: Z 227 MET cc_start: 0.8690 (mtp) cc_final: 0.8425 (mtp) REVERT: Z 398 ASN cc_start: 0.8797 (m-40) cc_final: 0.8126 (m110) outliers start: 129 outliers final: 84 residues processed: 725 average time/residue: 0.5390 time to fit residues: 650.2889 Evaluate side-chains 671 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 582 time to evaluate : 4.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 1 residue 42 SER Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 256 VAL Chi-restraints excluded: chain 1 residue 367 GLU Chi-restraints excluded: chain 1 residue 475 GLU Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 41 VAL Chi-restraints excluded: chain 2 residue 78 VAL Chi-restraints excluded: chain 2 residue 97 SER Chi-restraints excluded: chain 2 residue 155 VAL Chi-restraints excluded: chain 2 residue 366 LEU Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 3 residue 297 LEU Chi-restraints excluded: chain 3 residue 311 LEU Chi-restraints excluded: chain 4 residue 122 VAL Chi-restraints excluded: chain 6 residue 52 LYS Chi-restraints excluded: chain 6 residue 84 SER Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 23 LEU Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 6 VAL Chi-restraints excluded: chain 9 residue 7 LEU Chi-restraints excluded: chain 9 residue 65 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 69 ILE Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain M residue 234 VAL Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 139 ASN Chi-restraints excluded: chain S residue 83 ASP Chi-restraints excluded: chain S residue 88 LEU Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 215 LEU Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 185 VAL Chi-restraints excluded: chain T residue 228 GLN Chi-restraints excluded: chain T residue 300 PHE Chi-restraints excluded: chain T residue 472 TYR Chi-restraints excluded: chain T residue 473 VAL Chi-restraints excluded: chain U residue 63 SER Chi-restraints excluded: chain U residue 70 VAL Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 197 SER Chi-restraints excluded: chain U residue 470 THR Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain V residue 209 VAL Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 549 HIS Chi-restraints excluded: chain X residue 49 ASP Chi-restraints excluded: chain X residue 298 SER Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain Y residue 69 SER Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 367 SER Chi-restraints excluded: chain Y residue 381 ASP Chi-restraints excluded: chain Y residue 466 THR Chi-restraints excluded: chain Y residue 504 LYS Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Z residue 151 THR Chi-restraints excluded: chain Z residue 242 SER Chi-restraints excluded: chain Z residue 325 ILE Chi-restraints excluded: chain Z residue 367 SER Chi-restraints excluded: chain Z residue 414 GLN Chi-restraints excluded: chain Z residue 534 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 697 random chunks: chunk 626 optimal weight: 1.9990 chunk 476 optimal weight: 8.9990 chunk 329 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 302 optimal weight: 2.9990 chunk 425 optimal weight: 0.0670 chunk 636 optimal weight: 3.9990 chunk 673 optimal weight: 2.9990 chunk 332 optimal weight: 3.9990 chunk 603 optimal weight: 0.0870 chunk 181 optimal weight: 1.9990 overall best weight: 1.0300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 44 ASN ** 1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 423 ASN ** 2 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 ASN G 98 GLN P 52 GLN ** P 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 85 GLN R 139 ASN ** S 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 241 HIS U 152 ASN ** U 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 515 GLN ** U 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 61 HIS V 471 GLN ** V 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 204 HIS ** Y 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 54684 Z= 0.200 Angle : 0.531 12.054 74155 Z= 0.272 Chirality : 0.041 0.193 8689 Planarity : 0.004 0.052 9508 Dihedral : 6.238 105.158 7676 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.47 % Favored : 96.42 % Rotamer: Outliers : 2.36 % Allowed : 12.89 % Favored : 84.75 % 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: -1.24 (0.10), residues: 7034 helix: -0.52 (0.08), residues: 3843 sheet: -0.81 (0.21), residues: 638 loop : -1.05 (0.12), residues: 2553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP 9 73 HIS 0.005 0.001 HIS U 61 PHE 0.020 0.001 PHE B 107 TYR 0.028 0.001 TYR 4 211 ARG 0.004 0.000 ARG X 51 *********************** 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 778 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 645 time to evaluate : 4.519 Fit side-chains revert: symmetry clash REVERT: 0 37 LYS cc_start: 0.8694 (tmtt) cc_final: 0.8454 (tmtt) REVERT: 0 41 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7340 (pm20) REVERT: 1 69 ASP cc_start: 0.7463 (m-30) cc_final: 0.6802 (m-30) REVERT: 1 101 ASN cc_start: 0.8521 (t0) cc_final: 0.8303 (t0) REVERT: 1 232 LYS cc_start: 0.8403 (mmmt) cc_final: 0.8184 (mmmm) REVERT: 1 456 LYS cc_start: 0.7952 (ttpt) cc_final: 0.7664 (tptt) REVERT: 2 74 ASN cc_start: 0.8888 (t0) cc_final: 0.8625 (t0) REVERT: 2 422 GLU cc_start: 0.7406 (tp30) cc_final: 0.6755 (tp30) REVERT: 4 133 ASP cc_start: 0.8195 (t0) cc_final: 0.7834 (t70) REVERT: 7 67 ARG cc_start: 0.8297 (mmm-85) cc_final: 0.8030 (mmm-85) REVERT: 8 38 LYS cc_start: 0.8858 (mttt) cc_final: 0.8474 (mtpp) REVERT: 9 92 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6584 (mp0) REVERT: B 60 LYS cc_start: 0.8545 (mtpp) cc_final: 0.8289 (mttt) REVERT: C 102 TYR cc_start: 0.7494 (m-80) cc_final: 0.7101 (m-80) REVERT: C 116 PHE cc_start: 0.7623 (m-10) cc_final: 0.7410 (m-10) REVERT: D 107 PHE cc_start: 0.8701 (t80) cc_final: 0.8323 (t80) REVERT: E 102 TYR cc_start: 0.6542 (m-80) cc_final: 0.6114 (m-80) REVERT: H 81 MET cc_start: 0.8446 (ttp) cc_final: 0.7998 (ttt) REVERT: I 92 ASN cc_start: 0.8440 (p0) cc_final: 0.7504 (p0) REVERT: P 68 ASP cc_start: 0.7527 (t70) cc_final: 0.7216 (t0) REVERT: S 271 MET cc_start: 0.7635 (ttp) cc_final: 0.7298 (ttt) REVERT: T 228 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7787 (mt0) REVERT: T 537 LYS cc_start: 0.8313 (tptt) cc_final: 0.7810 (ttpp) REVERT: V 86 ARG cc_start: 0.8270 (mtm-85) cc_final: 0.8028 (mtm110) REVERT: V 287 MET cc_start: 0.8196 (OUTLIER) cc_final: 0.7873 (tpp) REVERT: X 227 MET cc_start: 0.8742 (mtt) cc_final: 0.8514 (mtt) REVERT: X 524 ILE cc_start: 0.4708 (OUTLIER) cc_final: 0.4315 (tp) REVERT: Y 337 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.8209 (pt0) REVERT: Y 422 MET cc_start: 0.7950 (mmm) cc_final: 0.7676 (tpp) REVERT: Y 495 VAL cc_start: 0.8777 (m) cc_final: 0.8464 (t) REVERT: Y 528 ASP cc_start: 0.6796 (t0) cc_final: 0.6457 (t0) REVERT: Z 227 MET cc_start: 0.8664 (mtp) cc_final: 0.8386 (mtp) REVERT: Z 398 ASN cc_start: 0.8856 (m-40) cc_final: 0.8239 (m110) outliers start: 133 outliers final: 83 residues processed: 740 average time/residue: 0.5374 time to fit residues: 662.2869 Evaluate side-chains 680 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 592 time to evaluate : 4.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 1 residue 92 TYR Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 256 VAL Chi-restraints excluded: chain 1 residue 335 VAL Chi-restraints excluded: chain 1 residue 367 GLU Chi-restraints excluded: chain 1 residue 374 LEU Chi-restraints excluded: chain 1 residue 475 GLU Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 41 VAL Chi-restraints excluded: chain 2 residue 78 VAL Chi-restraints excluded: chain 2 residue 97 SER Chi-restraints excluded: chain 2 residue 127 VAL Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 3 residue 297 LEU Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 4 residue 122 VAL Chi-restraints excluded: chain 4 residue 181 ASP Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 52 LYS Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 84 SER Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 23 LEU Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 6 VAL Chi-restraints excluded: chain 9 residue 7 LEU Chi-restraints excluded: chain 9 residue 52 LEU Chi-restraints excluded: chain 9 residue 65 THR Chi-restraints excluded: chain 9 residue 92 GLU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain J residue 59 SER Chi-restraints excluded: chain J residue 69 ILE Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain M residue 234 VAL Chi-restraints excluded: chain M residue 261 LEU Chi-restraints excluded: chain P residue 163 ASP Chi-restraints excluded: chain P residue 204 ASP Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 82 SER Chi-restraints excluded: chain R residue 139 ASN Chi-restraints excluded: chain S residue 83 ASP Chi-restraints excluded: chain S residue 88 LEU Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain T residue 122 LEU Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 185 VAL Chi-restraints excluded: chain T residue 228 GLN Chi-restraints excluded: chain T residue 300 PHE Chi-restraints excluded: chain T residue 456 VAL Chi-restraints excluded: chain T residue 472 TYR Chi-restraints excluded: chain U residue 63 SER Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 427 VAL Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 287 MET Chi-restraints excluded: chain X residue 298 SER Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain Y residue 69 SER Chi-restraints excluded: chain Y residue 122 MET Chi-restraints excluded: chain Y residue 226 GLU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 337 GLN Chi-restraints excluded: chain Y residue 367 SER Chi-restraints excluded: chain Y residue 381 ASP Chi-restraints excluded: chain Y residue 466 THR Chi-restraints excluded: chain Y residue 504 LYS Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Z residue 242 SER Chi-restraints excluded: chain Z residue 325 ILE Chi-restraints excluded: chain Z residue 414 GLN Chi-restraints excluded: chain Z residue 415 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 697 random chunks: chunk 561 optimal weight: 0.8980 chunk 382 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 501 optimal weight: 0.3980 chunk 277 optimal weight: 0.8980 chunk 574 optimal weight: 4.9990 chunk 465 optimal weight: 0.4980 chunk 0 optimal weight: 2.9990 chunk 344 optimal weight: 5.9990 chunk 604 optimal weight: 6.9990 chunk 170 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 44 ASN ** 1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 423 ASN ** 2 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 80 GLN P 52 GLN ** P 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 85 GLN ** S 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 152 ASN ** U 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 515 GLN ** U 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 61 HIS V 278 GLN ** V 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 204 HIS ** 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: 0.8013 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 54684 Z= 0.161 Angle : 0.507 11.146 74155 Z= 0.259 Chirality : 0.041 0.187 8689 Planarity : 0.004 0.053 9508 Dihedral : 5.928 92.625 7672 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.55 % Favored : 96.33 % Rotamer: Outliers : 2.22 % Allowed : 13.82 % Favored : 83.96 % 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: -0.73 (0.10), residues: 7034 helix: -0.04 (0.09), residues: 3847 sheet: -0.76 (0.20), residues: 661 loop : -0.88 (0.12), residues: 2526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP 9 73 HIS 0.005 0.001 HIS V 61 PHE 0.015 0.001 PHE P 122 TYR 0.027 0.001 TYR 4 211 ARG 0.004 0.000 ARG 2 319 *********************** 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 768 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 643 time to evaluate : 4.573 Fit side-chains REVERT: 0 37 LYS cc_start: 0.8658 (tmtt) cc_final: 0.8411 (tmtt) REVERT: 0 41 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7344 (pm20) REVERT: 1 69 ASP cc_start: 0.7461 (m-30) cc_final: 0.6760 (m-30) REVERT: 1 101 ASN cc_start: 0.8490 (t0) cc_final: 0.8275 (t0) REVERT: 1 232 LYS cc_start: 0.8376 (mmmt) cc_final: 0.8167 (mmmm) REVERT: 2 74 ASN cc_start: 0.8871 (t0) cc_final: 0.8567 (t0) REVERT: 4 133 ASP cc_start: 0.8093 (t0) cc_final: 0.7726 (t70) REVERT: 4 220 LYS cc_start: 0.8000 (mptt) cc_final: 0.7487 (mmmt) REVERT: 8 38 LYS cc_start: 0.8833 (mttt) cc_final: 0.8404 (mtpp) REVERT: 9 80 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.8151 (mm-40) REVERT: 9 92 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6516 (mp0) REVERT: B 60 LYS cc_start: 0.8536 (mtpp) cc_final: 0.8292 (mttt) REVERT: D 107 PHE cc_start: 0.8700 (t80) cc_final: 0.8339 (t80) REVERT: D 119 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.6955 (mt) REVERT: E 102 TYR cc_start: 0.6488 (m-80) cc_final: 0.6086 (m-80) REVERT: H 81 MET cc_start: 0.8438 (ttp) cc_final: 0.7988 (ttt) REVERT: I 92 ASN cc_start: 0.8413 (p0) cc_final: 0.7501 (p0) REVERT: P 68 ASP cc_start: 0.7569 (t70) cc_final: 0.7331 (t0) REVERT: S 212 SER cc_start: 0.8275 (t) cc_final: 0.7994 (p) REVERT: S 271 MET cc_start: 0.7729 (ttp) cc_final: 0.7414 (ttt) REVERT: T 228 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7853 (mt0) REVERT: T 439 MET cc_start: 0.8793 (mmt) cc_final: 0.8519 (tpt) REVERT: T 537 LYS cc_start: 0.8316 (tptt) cc_final: 0.7881 (ttpp) REVERT: U 46 ASP cc_start: 0.7593 (m-30) cc_final: 0.7355 (m-30) REVERT: U 227 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7372 (ptt90) REVERT: V 52 LYS cc_start: 0.7596 (mmmt) cc_final: 0.7215 (mmtm) REVERT: V 86 ARG cc_start: 0.8244 (mtm-85) cc_final: 0.8031 (mtm110) REVERT: V 287 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.7840 (tpp) REVERT: X 227 MET cc_start: 0.8682 (mtt) cc_final: 0.8463 (mtt) REVERT: X 524 ILE cc_start: 0.4732 (OUTLIER) cc_final: 0.4367 (tp) REVERT: X 535 LYS cc_start: 0.7171 (mttp) cc_final: 0.6730 (mtpt) REVERT: Y 337 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.8169 (pt0) REVERT: Y 422 MET cc_start: 0.7895 (mmm) cc_final: 0.7491 (tpp) REVERT: Y 495 VAL cc_start: 0.8657 (m) cc_final: 0.8367 (t) REVERT: Y 528 ASP cc_start: 0.6769 (t0) cc_final: 0.6441 (t0) REVERT: Z 227 MET cc_start: 0.8647 (mtp) cc_final: 0.8377 (mtp) REVERT: Z 398 ASN cc_start: 0.8824 (m-40) cc_final: 0.8231 (m110) outliers start: 125 outliers final: 89 residues processed: 731 average time/residue: 0.5387 time to fit residues: 653.5344 Evaluate side-chains 685 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 588 time to evaluate : 4.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 1 residue 92 TYR Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 335 VAL Chi-restraints excluded: chain 1 residue 374 LEU Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 475 GLU Chi-restraints excluded: chain 1 residue 512 LEU Chi-restraints excluded: chain 1 residue 578 ASP Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 41 VAL Chi-restraints excluded: chain 2 residue 78 VAL Chi-restraints excluded: chain 2 residue 97 SER Chi-restraints excluded: chain 2 residue 119 GLU Chi-restraints excluded: chain 2 residue 229 VAL Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 3 residue 297 LEU Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 4 residue 181 ASP Chi-restraints excluded: chain 4 residue 255 ARG Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain 6 residue 84 SER Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 23 LEU Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 6 VAL Chi-restraints excluded: chain 9 residue 3 VAL Chi-restraints excluded: chain 9 residue 7 LEU Chi-restraints excluded: chain 9 residue 52 LEU Chi-restraints excluded: chain 9 residue 65 THR Chi-restraints excluded: chain 9 residue 80 GLN Chi-restraints excluded: chain 9 residue 92 GLU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain H residue 92 ASN Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain J residue 59 SER Chi-restraints excluded: chain J residue 69 ILE Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain M residue 234 VAL Chi-restraints excluded: chain M residue 261 LEU Chi-restraints excluded: chain M residue 323 VAL Chi-restraints excluded: chain P residue 163 ASP Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain S residue 83 ASP Chi-restraints excluded: chain S residue 88 LEU Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 122 LEU Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 185 VAL Chi-restraints excluded: chain T residue 228 GLN Chi-restraints excluded: chain T residue 300 PHE Chi-restraints excluded: chain T residue 456 VAL Chi-restraints excluded: chain T residue 472 TYR Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 227 ARG Chi-restraints excluded: chain U residue 354 VAL Chi-restraints excluded: chain U residue 427 VAL Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 287 MET Chi-restraints excluded: chain V residue 354 VAL Chi-restraints excluded: chain V residue 474 LEU Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 298 SER Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain X residue 533 GLU Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain Y residue 69 SER Chi-restraints excluded: chain Y residue 122 MET Chi-restraints excluded: chain Y residue 226 GLU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 337 GLN Chi-restraints excluded: chain Y residue 367 SER Chi-restraints excluded: chain Y residue 381 ASP Chi-restraints excluded: chain Y residue 504 LYS Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Z residue 151 THR Chi-restraints excluded: chain Z residue 242 SER Chi-restraints excluded: chain Z residue 414 GLN Chi-restraints excluded: chain Z residue 415 ASP Chi-restraints excluded: chain Z residue 531 VAL 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: 2.9990 chunk 133 optimal weight: 5.9990 chunk 395 optimal weight: 3.9990 chunk 166 optimal weight: 0.5980 chunk 674 optimal weight: 2.9990 chunk 559 optimal weight: 8.9990 chunk 312 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 223 optimal weight: 5.9990 chunk 354 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 44 ASN ** 1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 52 GLN P 223 ASN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 85 GLN R 154 GLN ** S 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 152 ASN ** U 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 515 GLN ** U 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 61 HIS V 179 ASN V 471 GLN ** V 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 204 HIS ** Y 388 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: 0.8049 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 54684 Z= 0.274 Angle : 0.551 11.970 74155 Z= 0.281 Chirality : 0.043 0.195 8689 Planarity : 0.004 0.051 9508 Dihedral : 6.037 97.623 7672 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.99 % Favored : 95.88 % Rotamer: Outliers : 2.68 % Allowed : 14.33 % Favored : 82.99 % 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: -0.58 (0.10), residues: 7034 helix: 0.09 (0.09), residues: 3840 sheet: -0.68 (0.20), residues: 643 loop : -0.84 (0.12), residues: 2551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 9 73 HIS 0.007 0.001 HIS U 61 PHE 0.019 0.001 PHE 3 115 TYR 0.026 0.001 TYR 4 211 ARG 0.004 0.000 ARG X 51 *********************** 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 760 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 609 time to evaluate : 4.533 Fit side-chains REVERT: 0 37 LYS cc_start: 0.8701 (tmtt) cc_final: 0.8452 (tmtt) REVERT: 0 41 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7331 (pm20) REVERT: 1 69 ASP cc_start: 0.7430 (m-30) cc_final: 0.6771 (m-30) REVERT: 1 101 ASN cc_start: 0.8532 (t0) cc_final: 0.8321 (t0) REVERT: 1 232 LYS cc_start: 0.8386 (mmmt) cc_final: 0.8168 (mmmm) REVERT: 2 74 ASN cc_start: 0.8916 (t0) cc_final: 0.8626 (t0) REVERT: 2 422 GLU cc_start: 0.7349 (tp30) cc_final: 0.6623 (tp30) REVERT: 4 133 ASP cc_start: 0.8126 (t0) cc_final: 0.7757 (t70) REVERT: 4 140 GLU cc_start: 0.7781 (tp30) cc_final: 0.7475 (tt0) REVERT: 8 38 LYS cc_start: 0.8808 (mttt) cc_final: 0.8405 (mtpp) REVERT: 9 80 GLN cc_start: 0.8370 (mm-40) cc_final: 0.8128 (mm-40) REVERT: 9 92 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.6529 (mp0) REVERT: B 60 LYS cc_start: 0.8612 (mtpp) cc_final: 0.8337 (mttt) REVERT: C 102 TYR cc_start: 0.7467 (m-80) cc_final: 0.7002 (m-80) REVERT: E 102 TYR cc_start: 0.6665 (m-80) cc_final: 0.6222 (m-80) REVERT: G 61 MET cc_start: 0.7634 (mmt) cc_final: 0.7029 (mmt) REVERT: H 81 MET cc_start: 0.8481 (ttp) cc_final: 0.8040 (ttt) REVERT: H 111 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.6855 (mm-30) REVERT: I 92 ASN cc_start: 0.8448 (OUTLIER) cc_final: 0.7549 (p0) REVERT: P 68 ASP cc_start: 0.7496 (t70) cc_final: 0.7170 (t0) REVERT: S 212 SER cc_start: 0.8361 (t) cc_final: 0.8029 (p) REVERT: S 271 MET cc_start: 0.7721 (ttp) cc_final: 0.7408 (ttt) REVERT: T 72 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.6628 (mp0) REVERT: T 228 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.7987 (mt0) REVERT: T 537 LYS cc_start: 0.8268 (tptt) cc_final: 0.7859 (ttpp) REVERT: U 227 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7402 (ptt90) REVERT: U 357 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8357 (tp) REVERT: V 52 LYS cc_start: 0.7655 (mmmt) cc_final: 0.7256 (mmtm) REVERT: V 86 ARG cc_start: 0.8282 (mtm-85) cc_final: 0.8003 (mtm110) REVERT: V 546 LEU cc_start: 0.6989 (OUTLIER) cc_final: 0.6725 (tt) REVERT: X 227 MET cc_start: 0.8759 (mtt) cc_final: 0.8528 (mtt) REVERT: X 524 ILE cc_start: 0.4582 (OUTLIER) cc_final: 0.4207 (tp) REVERT: X 535 LYS cc_start: 0.7199 (mttp) cc_final: 0.6746 (mtpt) REVERT: Y 337 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.8203 (pt0) REVERT: Y 422 MET cc_start: 0.7932 (mmm) cc_final: 0.7508 (tpp) REVERT: Y 495 VAL cc_start: 0.8731 (m) cc_final: 0.8462 (t) REVERT: Y 528 ASP cc_start: 0.6708 (t0) cc_final: 0.6386 (t0) REVERT: Z 395 GLU cc_start: 0.6763 (OUTLIER) cc_final: 0.6276 (pp20) REVERT: Z 398 ASN cc_start: 0.8821 (m-40) cc_final: 0.8299 (m-40) outliers start: 151 outliers final: 117 residues processed: 724 average time/residue: 0.5647 time to fit residues: 682.6988 Evaluate side-chains 713 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 585 time to evaluate : 4.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 0 residue 43 SER Chi-restraints excluded: chain 1 residue 42 SER Chi-restraints excluded: chain 1 residue 92 TYR Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 256 VAL Chi-restraints excluded: chain 1 residue 335 VAL Chi-restraints excluded: chain 1 residue 367 GLU Chi-restraints excluded: chain 1 residue 374 LEU Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 475 GLU Chi-restraints excluded: chain 1 residue 494 SER Chi-restraints excluded: chain 1 residue 578 ASP Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 41 VAL Chi-restraints excluded: chain 2 residue 78 VAL Chi-restraints excluded: chain 2 residue 97 SER Chi-restraints excluded: chain 2 residue 119 GLU Chi-restraints excluded: chain 2 residue 127 VAL Chi-restraints excluded: chain 2 residue 174 THR Chi-restraints excluded: chain 2 residue 229 VAL Chi-restraints excluded: chain 2 residue 290 VAL Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 3 residue 297 LEU Chi-restraints excluded: chain 3 residue 311 LEU Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 4 residue 122 VAL Chi-restraints excluded: chain 4 residue 150 ASN Chi-restraints excluded: chain 4 residue 181 ASP Chi-restraints excluded: chain 5 residue 110 SER Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 52 LYS Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 84 SER Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 23 LEU Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 6 VAL Chi-restraints excluded: chain 9 residue 3 VAL Chi-restraints excluded: chain 9 residue 7 LEU Chi-restraints excluded: chain 9 residue 65 THR Chi-restraints excluded: chain 9 residue 92 GLU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 92 ASN Chi-restraints excluded: chain J residue 59 SER Chi-restraints excluded: chain J residue 69 ILE Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain M residue 234 VAL Chi-restraints excluded: chain M residue 261 LEU Chi-restraints excluded: chain M residue 290 LEU Chi-restraints excluded: chain M residue 296 SER Chi-restraints excluded: chain M residue 323 VAL Chi-restraints excluded: chain P residue 163 ASP Chi-restraints excluded: chain P residue 223 ASN Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 82 SER Chi-restraints excluded: chain R residue 112 LYS Chi-restraints excluded: chain S residue 83 ASP Chi-restraints excluded: chain S residue 88 LEU Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain T residue 72 GLU Chi-restraints excluded: chain T residue 74 GLU Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 122 LEU Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 185 VAL Chi-restraints excluded: chain T residue 228 GLN Chi-restraints excluded: chain T residue 300 PHE Chi-restraints excluded: chain T residue 456 VAL Chi-restraints excluded: chain T residue 472 TYR Chi-restraints excluded: chain U residue 63 SER Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 197 SER Chi-restraints excluded: chain U residue 227 ARG Chi-restraints excluded: chain U residue 354 VAL Chi-restraints excluded: chain U residue 357 LEU Chi-restraints excluded: chain U residue 427 VAL Chi-restraints excluded: chain U residue 517 ILE Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain V residue 89 SER Chi-restraints excluded: chain V residue 209 VAL Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 287 MET Chi-restraints excluded: chain V residue 354 VAL Chi-restraints excluded: chain V residue 474 LEU Chi-restraints excluded: chain V residue 546 LEU Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 298 SER Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain X residue 533 GLU Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain Y residue 69 SER Chi-restraints excluded: chain Y residue 226 GLU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 337 GLN Chi-restraints excluded: chain Y residue 367 SER Chi-restraints excluded: chain Y residue 381 ASP Chi-restraints excluded: chain Y residue 416 ILE Chi-restraints excluded: chain Y residue 466 THR Chi-restraints excluded: chain Y residue 504 LYS Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Z residue 151 THR Chi-restraints excluded: chain Z residue 242 SER Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 325 ILE Chi-restraints excluded: chain Z residue 367 SER Chi-restraints excluded: chain Z residue 395 GLU Chi-restraints excluded: chain Z residue 414 GLN Chi-restraints excluded: chain Z residue 415 ASP Chi-restraints excluded: chain Z residue 531 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 697 random chunks: chunk 650 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 384 optimal weight: 3.9990 chunk 492 optimal weight: 0.9980 chunk 381 optimal weight: 2.9990 chunk 567 optimal weight: 2.9990 chunk 376 optimal weight: 1.9990 chunk 671 optimal weight: 0.7980 chunk 420 optimal weight: 0.9980 chunk 409 optimal weight: 0.8980 chunk 310 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 44 ASN ** 1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 52 GLN P 65 ASN P 66 GLN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 64 GLN R 73 ASN R 85 GLN ** S 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 152 ASN ** U 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 515 GLN ** U 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 61 HIS V 471 GLN ** V 488 GLN ** 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: 0.8019 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 54684 Z= 0.177 Angle : 0.510 11.572 74155 Z= 0.259 Chirality : 0.041 0.188 8689 Planarity : 0.004 0.051 9508 Dihedral : 5.795 93.643 7672 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.58 % Favored : 96.30 % Rotamer: Outliers : 2.65 % Allowed : 14.65 % Favored : 82.70 % 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: -0.29 (0.10), residues: 7034 helix: 0.33 (0.09), residues: 3845 sheet: -0.61 (0.20), residues: 650 loop : -0.72 (0.12), residues: 2539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 9 73 HIS 0.009 0.001 HIS U 61 PHE 0.022 0.001 PHE D 107 TYR 0.026 0.001 TYR 4 211 ARG 0.004 0.000 ARG T 479 *********************** 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 772 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 623 time to evaluate : 4.499 Fit side-chains REVERT: 0 37 LYS cc_start: 0.8670 (tmtt) cc_final: 0.8440 (tmtt) REVERT: 0 41 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7341 (pm20) REVERT: 1 69 ASP cc_start: 0.7436 (m-30) cc_final: 0.6742 (m-30) REVERT: 1 101 ASN cc_start: 0.8453 (t0) cc_final: 0.8230 (t0) REVERT: 2 74 ASN cc_start: 0.8863 (t0) cc_final: 0.8555 (t0) REVERT: 4 220 LYS cc_start: 0.7986 (mptt) cc_final: 0.7482 (mmmt) REVERT: 8 38 LYS cc_start: 0.8788 (mttt) cc_final: 0.8382 (mtpp) REVERT: 9 80 GLN cc_start: 0.8415 (mm-40) cc_final: 0.8152 (mm-40) REVERT: 9 92 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6438 (mp0) REVERT: B 60 LYS cc_start: 0.8556 (mtpp) cc_final: 0.8303 (mttt) REVERT: D 119 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.6891 (mt) REVERT: E 102 TYR cc_start: 0.6632 (m-80) cc_final: 0.6220 (m-80) REVERT: G 61 MET cc_start: 0.7564 (mmt) cc_final: 0.7031 (mmt) REVERT: H 81 MET cc_start: 0.8430 (ttp) cc_final: 0.7974 (ttt) REVERT: I 92 ASN cc_start: 0.8426 (OUTLIER) cc_final: 0.7520 (p0) REVERT: P 68 ASP cc_start: 0.7536 (t70) cc_final: 0.7238 (t0) REVERT: P 205 ARG cc_start: 0.8158 (ptt-90) cc_final: 0.7948 (ptt-90) REVERT: R 112 LYS cc_start: 0.9147 (OUTLIER) cc_final: 0.8795 (mtmm) REVERT: S 212 SER cc_start: 0.8358 (t) cc_final: 0.8051 (p) REVERT: S 271 MET cc_start: 0.7743 (ttp) cc_final: 0.7442 (ttt) REVERT: T 72 GLU cc_start: 0.7034 (OUTLIER) cc_final: 0.6592 (mp0) REVERT: T 101 LYS cc_start: 0.7841 (mmmt) cc_final: 0.7638 (mmmt) REVERT: T 228 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7874 (mt0) REVERT: T 439 MET cc_start: 0.8805 (mmt) cc_final: 0.8520 (tpt) REVERT: T 537 LYS cc_start: 0.8286 (tptt) cc_final: 0.7912 (ttpp) REVERT: U 227 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.7395 (ptt90) REVERT: V 52 LYS cc_start: 0.7634 (mmmt) cc_final: 0.7249 (mmtm) REVERT: V 86 ARG cc_start: 0.8244 (mtm-85) cc_final: 0.8015 (mtm110) REVERT: V 287 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7934 (tpp) REVERT: V 546 LEU cc_start: 0.7073 (OUTLIER) cc_final: 0.6745 (tt) REVERT: X 227 MET cc_start: 0.8733 (mtt) cc_final: 0.8522 (mtt) REVERT: X 524 ILE cc_start: 0.4540 (OUTLIER) cc_final: 0.4186 (tp) REVERT: X 535 LYS cc_start: 0.7152 (mttp) cc_final: 0.6699 (mtpt) REVERT: Y 337 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.8183 (pt0) REVERT: Y 422 MET cc_start: 0.7933 (mmm) cc_final: 0.7570 (tpp) REVERT: Y 495 VAL cc_start: 0.8622 (m) cc_final: 0.8340 (t) REVERT: Y 528 ASP cc_start: 0.6820 (t0) cc_final: 0.6523 (t0) REVERT: Z 395 GLU cc_start: 0.6748 (OUTLIER) cc_final: 0.6257 (pp20) REVERT: Z 398 ASN cc_start: 0.8782 (m-40) cc_final: 0.8280 (m-40) outliers start: 149 outliers final: 110 residues processed: 730 average time/residue: 0.5393 time to fit residues: 654.2887 Evaluate side-chains 712 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 590 time to evaluate : 4.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 0 residue 43 SER Chi-restraints excluded: chain 1 residue 92 TYR Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 256 VAL Chi-restraints excluded: chain 1 residue 335 VAL Chi-restraints excluded: chain 1 residue 367 GLU Chi-restraints excluded: chain 1 residue 374 LEU Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 475 GLU Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 41 VAL Chi-restraints excluded: chain 2 residue 78 VAL Chi-restraints excluded: chain 2 residue 97 SER Chi-restraints excluded: chain 2 residue 119 GLU Chi-restraints excluded: chain 2 residue 174 THR Chi-restraints excluded: chain 2 residue 229 VAL Chi-restraints excluded: chain 2 residue 290 VAL Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 3 residue 297 LEU Chi-restraints excluded: chain 3 residue 311 LEU Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 4 residue 122 VAL Chi-restraints excluded: chain 4 residue 181 ASP Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 52 LYS Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 84 SER Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 23 LEU Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 6 VAL Chi-restraints excluded: chain 9 residue 3 VAL Chi-restraints excluded: chain 9 residue 7 LEU Chi-restraints excluded: chain 9 residue 52 LEU Chi-restraints excluded: chain 9 residue 92 GLU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain H residue 92 ASN Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 92 ASN Chi-restraints excluded: chain J residue 59 SER Chi-restraints excluded: chain J residue 69 ILE Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain M residue 148 ILE Chi-restraints excluded: chain M residue 182 THR Chi-restraints excluded: chain M residue 234 VAL Chi-restraints excluded: chain M residue 261 LEU Chi-restraints excluded: chain M residue 290 LEU Chi-restraints excluded: chain M residue 323 VAL Chi-restraints excluded: chain P residue 163 ASP Chi-restraints excluded: chain P residue 223 ASN Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 82 SER Chi-restraints excluded: chain R residue 112 LYS Chi-restraints excluded: chain S residue 83 ASP Chi-restraints excluded: chain S residue 88 LEU Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain T residue 72 GLU Chi-restraints excluded: chain T residue 74 GLU Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 122 LEU Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 185 VAL Chi-restraints excluded: chain T residue 228 GLN Chi-restraints excluded: chain T residue 300 PHE Chi-restraints excluded: chain T residue 456 VAL Chi-restraints excluded: chain T residue 472 TYR Chi-restraints excluded: chain U residue 63 SER Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 197 SER Chi-restraints excluded: chain U residue 227 ARG Chi-restraints excluded: chain U residue 354 VAL Chi-restraints excluded: chain U residue 427 VAL Chi-restraints excluded: chain U residue 470 THR Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain U residue 517 ILE Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain V residue 89 SER Chi-restraints excluded: chain V residue 209 VAL Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 287 MET Chi-restraints excluded: chain V residue 354 VAL Chi-restraints excluded: chain V residue 474 LEU Chi-restraints excluded: chain V residue 546 LEU Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 298 SER Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain X residue 533 GLU Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain Y residue 69 SER Chi-restraints excluded: chain Y residue 226 GLU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 337 GLN Chi-restraints excluded: chain Y residue 367 SER Chi-restraints excluded: chain Y residue 381 ASP Chi-restraints excluded: chain Y residue 466 THR Chi-restraints excluded: chain Y residue 504 LYS Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Z residue 151 THR Chi-restraints excluded: chain Z residue 242 SER Chi-restraints excluded: chain Z residue 325 ILE Chi-restraints excluded: chain Z residue 367 SER Chi-restraints excluded: chain Z residue 395 GLU Chi-restraints excluded: chain Z residue 414 GLN Chi-restraints excluded: chain Z residue 415 ASP Chi-restraints excluded: chain Z residue 531 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 697 random chunks: chunk 415 optimal weight: 0.7980 chunk 268 optimal weight: 0.0060 chunk 401 optimal weight: 5.9990 chunk 202 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 427 optimal weight: 0.9980 chunk 457 optimal weight: 2.9990 chunk 332 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 528 optimal weight: 5.9990 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 44 ASN ** 1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 ASN P 52 GLN P 66 GLN P 223 ASN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 64 GLN R 85 GLN ** S 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 515 GLN ** U 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 61 HIS V 471 GLN ** V 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 388 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: 0.8030 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 54684 Z= 0.214 Angle : 0.527 11.459 74155 Z= 0.268 Chirality : 0.042 0.212 8689 Planarity : 0.004 0.051 9508 Dihedral : 5.769 93.142 7672 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.85 % Favored : 96.03 % Rotamer: Outliers : 2.72 % Allowed : 15.01 % Favored : 82.28 % 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: -0.17 (0.10), residues: 7034 helix: 0.44 (0.09), residues: 3841 sheet: -0.56 (0.21), residues: 650 loop : -0.68 (0.12), residues: 2543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 9 73 HIS 0.005 0.001 HIS 4 233 PHE 0.021 0.001 PHE D 107 TYR 0.026 0.001 TYR 4 211 ARG 0.004 0.000 ARG 2 319 *********************** 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 758 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 605 time to evaluate : 4.713 Fit side-chains REVERT: 0 37 LYS cc_start: 0.8677 (tmtt) cc_final: 0.8452 (tmtt) REVERT: 0 41 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7340 (pm20) REVERT: 1 69 ASP cc_start: 0.7390 (m-30) cc_final: 0.6695 (m-30) REVERT: 1 101 ASN cc_start: 0.8462 (t0) cc_final: 0.8247 (t0) REVERT: 2 74 ASN cc_start: 0.8875 (t0) cc_final: 0.8563 (t0) REVERT: 4 140 GLU cc_start: 0.7736 (tp30) cc_final: 0.7435 (tt0) REVERT: 4 220 LYS cc_start: 0.8006 (mptt) cc_final: 0.7496 (mmmt) REVERT: 8 38 LYS cc_start: 0.8788 (mttt) cc_final: 0.8384 (mtpp) REVERT: 9 80 GLN cc_start: 0.8458 (mm-40) cc_final: 0.8177 (mm-40) REVERT: 9 92 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6448 (mp0) REVERT: B 60 LYS cc_start: 0.8624 (mtpp) cc_final: 0.8366 (mttt) REVERT: D 119 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.6886 (mt) REVERT: E 102 TYR cc_start: 0.6616 (m-80) cc_final: 0.6192 (m-80) REVERT: H 81 MET cc_start: 0.8445 (ttp) cc_final: 0.8001 (ttt) REVERT: H 111 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.6860 (mm-30) REVERT: I 92 ASN cc_start: 0.8452 (OUTLIER) cc_final: 0.7545 (p0) REVERT: P 68 ASP cc_start: 0.7544 (t70) cc_final: 0.7267 (t0) REVERT: P 205 ARG cc_start: 0.8154 (ptt-90) cc_final: 0.7923 (ptt-90) REVERT: R 112 LYS cc_start: 0.9147 (OUTLIER) cc_final: 0.8800 (mtmm) REVERT: S 212 SER cc_start: 0.8385 (t) cc_final: 0.8065 (p) REVERT: S 271 MET cc_start: 0.7749 (ttp) cc_final: 0.7432 (ttt) REVERT: T 72 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.6563 (mp0) REVERT: T 228 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7946 (mt0) REVERT: T 439 MET cc_start: 0.8824 (mmt) cc_final: 0.8528 (tpt) REVERT: T 537 LYS cc_start: 0.8296 (tptt) cc_final: 0.7908 (ttpp) REVERT: U 227 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7411 (ptt90) REVERT: V 52 LYS cc_start: 0.7629 (mmmt) cc_final: 0.7254 (mmtm) REVERT: V 86 ARG cc_start: 0.8254 (mtm-85) cc_final: 0.8010 (mtm110) REVERT: V 546 LEU cc_start: 0.7077 (OUTLIER) cc_final: 0.6721 (tt) REVERT: V 549 HIS cc_start: 0.7069 (OUTLIER) cc_final: 0.5804 (m-70) REVERT: X 227 MET cc_start: 0.8749 (mtt) cc_final: 0.8522 (mtt) REVERT: X 524 ILE cc_start: 0.4488 (OUTLIER) cc_final: 0.4135 (tp) REVERT: X 535 LYS cc_start: 0.7151 (mttp) cc_final: 0.6699 (mtpt) REVERT: Y 337 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.8197 (pt0) REVERT: Y 422 MET cc_start: 0.7968 (mmm) cc_final: 0.7691 (tpp) REVERT: Y 495 VAL cc_start: 0.8625 (m) cc_final: 0.8343 (t) REVERT: Z 395 GLU cc_start: 0.6757 (OUTLIER) cc_final: 0.6259 (pp20) REVERT: Z 398 ASN cc_start: 0.8776 (m-40) cc_final: 0.8285 (m-40) outliers start: 153 outliers final: 121 residues processed: 713 average time/residue: 0.5505 time to fit residues: 652.9079 Evaluate side-chains 723 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 589 time to evaluate : 4.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 0 residue 43 SER Chi-restraints excluded: chain 1 residue 42 SER Chi-restraints excluded: chain 1 residue 92 TYR Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 256 VAL Chi-restraints excluded: chain 1 residue 335 VAL Chi-restraints excluded: chain 1 residue 367 GLU Chi-restraints excluded: chain 1 residue 374 LEU Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 475 GLU Chi-restraints excluded: chain 1 residue 578 ASP Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 41 VAL Chi-restraints excluded: chain 2 residue 78 VAL Chi-restraints excluded: chain 2 residue 119 GLU Chi-restraints excluded: chain 2 residue 174 THR Chi-restraints excluded: chain 2 residue 229 VAL Chi-restraints excluded: chain 2 residue 290 VAL Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 3 residue 297 LEU Chi-restraints excluded: chain 3 residue 311 LEU Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 4 residue 122 VAL Chi-restraints excluded: chain 4 residue 150 ASN Chi-restraints excluded: chain 4 residue 181 ASP Chi-restraints excluded: chain 5 residue 106 LEU Chi-restraints excluded: chain 5 residue 109 GLN Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 52 LYS Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 84 SER Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 23 LEU Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 6 VAL Chi-restraints excluded: chain 8 residue 82 THR Chi-restraints excluded: chain 9 residue 3 VAL Chi-restraints excluded: chain 9 residue 7 LEU Chi-restraints excluded: chain 9 residue 52 LEU Chi-restraints excluded: chain 9 residue 65 THR Chi-restraints excluded: chain 9 residue 92 GLU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain H residue 92 ASN Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 92 ASN Chi-restraints excluded: chain J residue 59 SER Chi-restraints excluded: chain J residue 69 ILE Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain M residue 182 THR Chi-restraints excluded: chain M residue 234 VAL Chi-restraints excluded: chain M residue 261 LEU Chi-restraints excluded: chain M residue 290 LEU Chi-restraints excluded: chain M residue 323 VAL Chi-restraints excluded: chain P residue 163 ASP Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 64 GLN Chi-restraints excluded: chain R residue 82 SER Chi-restraints excluded: chain R residue 112 LYS Chi-restraints excluded: chain S residue 83 ASP Chi-restraints excluded: chain S residue 88 LEU Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain T residue 72 GLU Chi-restraints excluded: chain T residue 74 GLU Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 122 LEU Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 185 VAL Chi-restraints excluded: chain T residue 228 GLN Chi-restraints excluded: chain T residue 300 PHE Chi-restraints excluded: chain T residue 456 VAL Chi-restraints excluded: chain T residue 472 TYR Chi-restraints excluded: chain U residue 63 SER Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 197 SER Chi-restraints excluded: chain U residue 227 ARG Chi-restraints excluded: chain U residue 354 VAL Chi-restraints excluded: chain U residue 427 VAL Chi-restraints excluded: chain U residue 470 THR Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain U residue 517 ILE Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain V residue 89 SER Chi-restraints excluded: chain V residue 209 VAL Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 354 VAL Chi-restraints excluded: chain V residue 474 LEU Chi-restraints excluded: chain V residue 515 GLN Chi-restraints excluded: chain V residue 546 LEU Chi-restraints excluded: chain V residue 549 HIS Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 298 SER Chi-restraints excluded: chain X residue 318 LEU Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain X residue 533 GLU Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain Y residue 69 SER Chi-restraints excluded: chain Y residue 122 MET Chi-restraints excluded: chain Y residue 226 GLU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 337 GLN Chi-restraints excluded: chain Y residue 367 SER Chi-restraints excluded: chain Y residue 381 ASP Chi-restraints excluded: chain Y residue 466 THR Chi-restraints excluded: chain Y residue 504 LYS Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Y residue 524 ILE Chi-restraints excluded: chain Y residue 538 VAL Chi-restraints excluded: chain Z residue 151 THR Chi-restraints excluded: chain Z residue 242 SER Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 325 ILE Chi-restraints excluded: chain Z residue 367 SER Chi-restraints excluded: chain Z residue 395 GLU Chi-restraints excluded: chain Z residue 414 GLN Chi-restraints excluded: chain Z residue 415 ASP Chi-restraints excluded: chain Z residue 531 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 697 random chunks: chunk 611 optimal weight: 2.9990 chunk 643 optimal weight: 4.9990 chunk 587 optimal weight: 10.0000 chunk 626 optimal weight: 1.9990 chunk 376 optimal weight: 5.9990 chunk 272 optimal weight: 7.9990 chunk 491 optimal weight: 0.9980 chunk 192 optimal weight: 10.0000 chunk 565 optimal weight: 0.6980 chunk 592 optimal weight: 1.9990 chunk 623 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 44 ASN ** 1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 52 GLN ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 52 GLN P 66 GLN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 64 GLN R 85 GLN ** S 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 515 GLN ** U 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 61 HIS V 179 ASN V 471 GLN ** V 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 388 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: 0.8035 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 54684 Z= 0.236 Angle : 0.538 12.843 74155 Z= 0.273 Chirality : 0.042 0.230 8689 Planarity : 0.004 0.050 9508 Dihedral : 5.793 94.187 7671 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.85 % Favored : 96.03 % Rotamer: Outliers : 2.68 % Allowed : 14.99 % Favored : 82.33 % 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: -0.14 (0.10), residues: 7034 helix: 0.47 (0.09), residues: 3844 sheet: -0.60 (0.20), residues: 663 loop : -0.65 (0.12), residues: 2527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 9 73 HIS 0.006 0.001 HIS 4 233 PHE 0.029 0.001 PHE D 107 TYR 0.026 0.001 TYR 4 211 ARG 0.004 0.000 ARG A 91 *********************** 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 752 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 601 time to evaluate : 4.581 Fit side-chains REVERT: 0 37 LYS cc_start: 0.8680 (tmtt) cc_final: 0.8466 (tmtt) REVERT: 0 41 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7336 (pm20) REVERT: 1 69 ASP cc_start: 0.7414 (m-30) cc_final: 0.6743 (m-30) REVERT: 1 101 ASN cc_start: 0.8478 (t0) cc_final: 0.8269 (t0) REVERT: 4 140 GLU cc_start: 0.7731 (tp30) cc_final: 0.7428 (tt0) REVERT: 4 220 LYS cc_start: 0.8054 (mptt) cc_final: 0.7530 (mmmt) REVERT: 8 38 LYS cc_start: 0.8790 (mttt) cc_final: 0.8389 (mtpp) REVERT: 9 80 GLN cc_start: 0.8460 (mm-40) cc_final: 0.8188 (mm-40) REVERT: 9 92 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6446 (mp0) REVERT: D 98 GLN cc_start: 0.7559 (OUTLIER) cc_final: 0.7137 (tt0) REVERT: E 102 TYR cc_start: 0.6612 (m-80) cc_final: 0.6178 (m-80) REVERT: G 61 MET cc_start: 0.7308 (mmm) cc_final: 0.6996 (mmt) REVERT: H 81 MET cc_start: 0.8452 (ttp) cc_final: 0.8008 (ttt) REVERT: H 111 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.6859 (mm-30) REVERT: I 92 ASN cc_start: 0.8462 (OUTLIER) cc_final: 0.7555 (p0) REVERT: P 68 ASP cc_start: 0.7529 (t70) cc_final: 0.7222 (t0) REVERT: P 205 ARG cc_start: 0.8155 (ptt-90) cc_final: 0.7919 (ptt-90) REVERT: R 112 LYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8779 (mtmm) REVERT: S 212 SER cc_start: 0.8404 (t) cc_final: 0.8093 (p) REVERT: S 271 MET cc_start: 0.7750 (ttp) cc_final: 0.7432 (ttt) REVERT: T 72 GLU cc_start: 0.7037 (OUTLIER) cc_final: 0.6593 (mp0) REVERT: T 228 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7959 (mt0) REVERT: T 439 MET cc_start: 0.8813 (mmt) cc_final: 0.8521 (tpt) REVERT: T 537 LYS cc_start: 0.8305 (tptt) cc_final: 0.7912 (ttpp) REVERT: U 227 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7412 (ptt90) REVERT: V 52 LYS cc_start: 0.7635 (mmmt) cc_final: 0.7263 (mmtm) REVERT: V 86 ARG cc_start: 0.8282 (mtm-85) cc_final: 0.8031 (mtm110) REVERT: V 546 LEU cc_start: 0.7046 (OUTLIER) cc_final: 0.6665 (tt) REVERT: V 549 HIS cc_start: 0.6978 (OUTLIER) cc_final: 0.5729 (m-70) REVERT: X 227 MET cc_start: 0.8754 (mtt) cc_final: 0.8532 (mtt) REVERT: X 524 ILE cc_start: 0.4490 (OUTLIER) cc_final: 0.4148 (tp) REVERT: X 535 LYS cc_start: 0.7152 (mttp) cc_final: 0.6696 (mtpt) REVERT: Y 337 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.8184 (pt0) REVERT: Y 422 MET cc_start: 0.7958 (mmm) cc_final: 0.7701 (tpp) REVERT: Y 495 VAL cc_start: 0.8626 (m) cc_final: 0.8345 (t) REVERT: Z 395 GLU cc_start: 0.6653 (OUTLIER) cc_final: 0.6144 (pp20) REVERT: Z 398 ASN cc_start: 0.8773 (m-40) cc_final: 0.8281 (m-40) outliers start: 151 outliers final: 126 residues processed: 704 average time/residue: 0.5503 time to fit residues: 643.4101 Evaluate side-chains 726 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 587 time to evaluate : 4.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 0 residue 43 SER Chi-restraints excluded: chain 1 residue 42 SER Chi-restraints excluded: chain 1 residue 92 TYR Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 256 VAL Chi-restraints excluded: chain 1 residue 335 VAL Chi-restraints excluded: chain 1 residue 367 GLU Chi-restraints excluded: chain 1 residue 374 LEU Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 475 GLU Chi-restraints excluded: chain 1 residue 494 SER Chi-restraints excluded: chain 1 residue 578 ASP Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 41 VAL Chi-restraints excluded: chain 2 residue 78 VAL Chi-restraints excluded: chain 2 residue 97 SER Chi-restraints excluded: chain 2 residue 119 GLU Chi-restraints excluded: chain 2 residue 174 THR Chi-restraints excluded: chain 2 residue 229 VAL Chi-restraints excluded: chain 2 residue 290 VAL Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 3 residue 116 THR Chi-restraints excluded: chain 3 residue 297 LEU Chi-restraints excluded: chain 3 residue 311 LEU Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 4 residue 122 VAL Chi-restraints excluded: chain 4 residue 150 ASN Chi-restraints excluded: chain 4 residue 181 ASP Chi-restraints excluded: chain 5 residue 106 LEU Chi-restraints excluded: chain 5 residue 109 GLN Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 52 LYS Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 84 SER Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 23 LEU Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 6 VAL Chi-restraints excluded: chain 8 residue 82 THR Chi-restraints excluded: chain 9 residue 3 VAL Chi-restraints excluded: chain 9 residue 7 LEU Chi-restraints excluded: chain 9 residue 52 LEU Chi-restraints excluded: chain 9 residue 65 THR Chi-restraints excluded: chain 9 residue 92 GLU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain H residue 92 ASN Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 92 ASN Chi-restraints excluded: chain J residue 59 SER Chi-restraints excluded: chain J residue 69 ILE Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain M residue 148 ILE Chi-restraints excluded: chain M residue 182 THR Chi-restraints excluded: chain M residue 234 VAL Chi-restraints excluded: chain M residue 261 LEU Chi-restraints excluded: chain M residue 290 LEU Chi-restraints excluded: chain M residue 323 VAL Chi-restraints excluded: chain P residue 163 ASP Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 82 SER Chi-restraints excluded: chain R residue 112 LYS Chi-restraints excluded: chain S residue 83 ASP Chi-restraints excluded: chain S residue 88 LEU Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 72 GLU Chi-restraints excluded: chain T residue 74 GLU Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 122 LEU Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 185 VAL Chi-restraints excluded: chain T residue 228 GLN Chi-restraints excluded: chain T residue 456 VAL Chi-restraints excluded: chain T residue 472 TYR Chi-restraints excluded: chain U residue 63 SER Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 197 SER Chi-restraints excluded: chain U residue 227 ARG Chi-restraints excluded: chain U residue 354 VAL Chi-restraints excluded: chain U residue 427 VAL Chi-restraints excluded: chain U residue 470 THR Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain U residue 517 ILE Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain V residue 89 SER Chi-restraints excluded: chain V residue 209 VAL Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 354 VAL Chi-restraints excluded: chain V residue 474 LEU Chi-restraints excluded: chain V residue 515 GLN Chi-restraints excluded: chain V residue 546 LEU Chi-restraints excluded: chain V residue 549 HIS Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 298 SER Chi-restraints excluded: chain X residue 318 LEU Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain X residue 533 GLU Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain Y residue 69 SER Chi-restraints excluded: chain Y residue 122 MET Chi-restraints excluded: chain Y residue 226 GLU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 337 GLN Chi-restraints excluded: chain Y residue 367 SER Chi-restraints excluded: chain Y residue 381 ASP Chi-restraints excluded: chain Y residue 466 THR Chi-restraints excluded: chain Y residue 504 LYS Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Y residue 524 ILE Chi-restraints excluded: chain Y residue 538 VAL Chi-restraints excluded: chain Z residue 151 THR Chi-restraints excluded: chain Z residue 242 SER Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 325 ILE Chi-restraints excluded: chain Z residue 367 SER Chi-restraints excluded: chain Z residue 390 ASN Chi-restraints excluded: chain Z residue 395 GLU Chi-restraints excluded: chain Z residue 414 GLN Chi-restraints excluded: chain Z residue 415 ASP Chi-restraints excluded: chain Z residue 531 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 697 random chunks: chunk 411 optimal weight: 0.6980 chunk 661 optimal weight: 3.9990 chunk 404 optimal weight: 0.7980 chunk 314 optimal weight: 4.9990 chunk 460 optimal weight: 1.9990 chunk 694 optimal weight: 5.9990 chunk 639 optimal weight: 1.9990 chunk 552 optimal weight: 0.0670 chunk 57 optimal weight: 0.8980 chunk 427 optimal weight: 1.9990 chunk 339 optimal weight: 20.0000 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 44 ASN ** 1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 ASN P 52 GLN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 85 GLN ** S 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 515 GLN ** U 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 61 HIS V 471 GLN ** V 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 54684 Z= 0.183 Angle : 0.518 12.903 74155 Z= 0.262 Chirality : 0.041 0.187 8689 Planarity : 0.004 0.051 9508 Dihedral : 5.648 93.877 7671 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.65 % Favored : 96.23 % Rotamer: Outliers : 2.42 % Allowed : 15.25 % Favored : 82.33 % 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: 0.62 (0.09), residues: 3845 sheet: -0.56 (0.20), residues: 665 loop : -0.60 (0.13), residues: 2524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 9 73 HIS 0.005 0.001 HIS 4 233 PHE 0.029 0.001 PHE D 107 TYR 0.026 0.001 TYR 4 211 ARG 0.004 0.000 ARG 2 319 ********************** 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 739 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 603 time to evaluate : 4.490 Fit side-chains REVERT: 0 41 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7351 (pm20) REVERT: 1 101 ASN cc_start: 0.8460 (t0) cc_final: 0.8260 (t0) REVERT: 4 220 LYS cc_start: 0.7994 (mptt) cc_final: 0.7478 (mmmt) REVERT: 8 38 LYS cc_start: 0.8778 (mttt) cc_final: 0.8380 (mtpp) REVERT: 9 80 GLN cc_start: 0.8488 (mm-40) cc_final: 0.8234 (mm-40) REVERT: 9 92 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6441 (mp0) REVERT: B 60 LYS cc_start: 0.8525 (mttt) cc_final: 0.8297 (mmmt) REVERT: E 102 TYR cc_start: 0.6553 (m-80) cc_final: 0.6265 (m-80) REVERT: G 61 MET cc_start: 0.7303 (mmm) cc_final: 0.7018 (mmt) REVERT: H 81 MET cc_start: 0.8428 (ttp) cc_final: 0.7982 (ttt) REVERT: I 92 ASN cc_start: 0.8437 (OUTLIER) cc_final: 0.7552 (p0) REVERT: M 270 MET cc_start: 0.5777 (tpp) cc_final: 0.5565 (ttm) REVERT: P 68 ASP cc_start: 0.7606 (t70) cc_final: 0.7289 (t0) REVERT: R 112 LYS cc_start: 0.9126 (OUTLIER) cc_final: 0.8777 (mtmm) REVERT: S 212 SER cc_start: 0.8384 (t) cc_final: 0.8077 (p) REVERT: S 271 MET cc_start: 0.7768 (ttp) cc_final: 0.7453 (ttt) REVERT: T 72 GLU cc_start: 0.6969 (OUTLIER) cc_final: 0.6528 (mp0) REVERT: T 228 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.7977 (mt0) REVERT: T 439 MET cc_start: 0.8812 (mmt) cc_final: 0.8510 (tpt) REVERT: T 537 LYS cc_start: 0.8285 (tptt) cc_final: 0.7905 (ttpp) REVERT: U 227 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7392 (ptt90) REVERT: V 52 LYS cc_start: 0.7643 (mmmt) cc_final: 0.7286 (mmtm) REVERT: V 86 ARG cc_start: 0.8242 (mtm-85) cc_final: 0.8010 (mtm110) REVERT: V 546 LEU cc_start: 0.6983 (OUTLIER) cc_final: 0.6581 (tt) REVERT: V 549 HIS cc_start: 0.7051 (OUTLIER) cc_final: 0.5842 (m-70) REVERT: X 227 MET cc_start: 0.8733 (mtt) cc_final: 0.8523 (mtt) REVERT: X 524 ILE cc_start: 0.4523 (OUTLIER) cc_final: 0.4167 (tp) REVERT: X 535 LYS cc_start: 0.7144 (mttp) cc_final: 0.6689 (mtpt) REVERT: Y 337 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.8177 (pt0) REVERT: Y 422 MET cc_start: 0.7913 (mmm) cc_final: 0.7666 (tpp) REVERT: Y 495 VAL cc_start: 0.8608 (m) cc_final: 0.8331 (t) REVERT: Z 395 GLU cc_start: 0.6591 (OUTLIER) cc_final: 0.6097 (pp20) REVERT: Z 398 ASN cc_start: 0.8751 (m-40) cc_final: 0.8268 (m-40) REVERT: Z 563 GLU cc_start: 0.7492 (mm-30) cc_final: 0.7274 (mm-30) outliers start: 136 outliers final: 120 residues processed: 697 average time/residue: 0.5386 time to fit residues: 624.4507 Evaluate side-chains 719 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 588 time to evaluate : 4.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 0 residue 43 SER Chi-restraints excluded: chain 1 residue 42 SER Chi-restraints excluded: chain 1 residue 92 TYR Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 256 VAL Chi-restraints excluded: chain 1 residue 335 VAL Chi-restraints excluded: chain 1 residue 367 GLU Chi-restraints excluded: chain 1 residue 374 LEU Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 475 GLU Chi-restraints excluded: chain 1 residue 494 SER Chi-restraints excluded: chain 1 residue 578 ASP Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 41 VAL Chi-restraints excluded: chain 2 residue 78 VAL Chi-restraints excluded: chain 2 residue 119 GLU Chi-restraints excluded: chain 2 residue 174 THR Chi-restraints excluded: chain 2 residue 229 VAL Chi-restraints excluded: chain 2 residue 290 VAL Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 3 residue 297 LEU Chi-restraints excluded: chain 3 residue 311 LEU Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 4 residue 122 VAL Chi-restraints excluded: chain 4 residue 150 ASN Chi-restraints excluded: chain 4 residue 181 ASP Chi-restraints excluded: chain 5 residue 106 LEU Chi-restraints excluded: chain 5 residue 109 GLN Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 84 SER Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 23 LEU Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 6 VAL Chi-restraints excluded: chain 9 residue 3 VAL Chi-restraints excluded: chain 9 residue 7 LEU Chi-restraints excluded: chain 9 residue 52 LEU Chi-restraints excluded: chain 9 residue 65 THR Chi-restraints excluded: chain 9 residue 92 GLU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain H residue 92 ASN Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 92 ASN Chi-restraints excluded: chain J residue 59 SER Chi-restraints excluded: chain J residue 69 ILE Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain M residue 148 ILE Chi-restraints excluded: chain M residue 182 THR Chi-restraints excluded: chain M residue 234 VAL Chi-restraints excluded: chain M residue 261 LEU Chi-restraints excluded: chain M residue 290 LEU Chi-restraints excluded: chain M residue 296 SER Chi-restraints excluded: chain M residue 323 VAL Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 82 SER Chi-restraints excluded: chain R residue 112 LYS Chi-restraints excluded: chain S residue 83 ASP Chi-restraints excluded: chain S residue 88 LEU Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain T residue 72 GLU Chi-restraints excluded: chain T residue 74 GLU Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 122 LEU Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 185 VAL Chi-restraints excluded: chain T residue 228 GLN Chi-restraints excluded: chain T residue 456 VAL Chi-restraints excluded: chain T residue 472 TYR Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 197 SER Chi-restraints excluded: chain U residue 227 ARG Chi-restraints excluded: chain U residue 354 VAL Chi-restraints excluded: chain U residue 427 VAL Chi-restraints excluded: chain U residue 470 THR Chi-restraints excluded: chain U residue 492 ILE Chi-restraints excluded: chain U residue 517 ILE Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain V residue 89 SER Chi-restraints excluded: chain V residue 209 VAL Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 354 VAL Chi-restraints excluded: chain V residue 474 LEU Chi-restraints excluded: chain V residue 515 GLN Chi-restraints excluded: chain V residue 546 LEU Chi-restraints excluded: chain V residue 549 HIS Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 298 SER Chi-restraints excluded: chain X residue 318 LEU Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain X residue 533 GLU Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain Y residue 69 SER Chi-restraints excluded: chain Y residue 122 MET Chi-restraints excluded: chain Y residue 226 GLU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 337 GLN Chi-restraints excluded: chain Y residue 367 SER Chi-restraints excluded: chain Y residue 381 ASP Chi-restraints excluded: chain Y residue 466 THR Chi-restraints excluded: chain Y residue 504 LYS Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Y residue 524 ILE Chi-restraints excluded: chain Y residue 538 VAL Chi-restraints excluded: chain Z residue 151 THR Chi-restraints excluded: chain Z residue 242 SER Chi-restraints excluded: chain Z residue 325 ILE Chi-restraints excluded: chain Z residue 367 SER Chi-restraints excluded: chain Z residue 390 ASN Chi-restraints excluded: chain Z residue 395 GLU Chi-restraints excluded: chain Z residue 414 GLN Chi-restraints excluded: chain Z residue 415 ASP Chi-restraints excluded: chain Z residue 531 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 697 random chunks: chunk 439 optimal weight: 0.9990 chunk 589 optimal weight: 0.9990 chunk 169 optimal weight: 0.9990 chunk 509 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 153 optimal weight: 6.9990 chunk 553 optimal weight: 6.9990 chunk 231 optimal weight: 4.9990 chunk 568 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 44 ASN ** 1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 52 GLN ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 52 GLN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 85 GLN ** S 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 515 GLN ** U 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 61 HIS V 149 GLN ** V 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.135029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.106350 restraints weight = 72742.000| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.84 r_work: 0.2922 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.126 54684 Z= 0.239 Angle : 0.592 59.199 74155 Z= 0.316 Chirality : 0.042 0.378 8689 Planarity : 0.004 0.051 9508 Dihedral : 5.652 93.911 7671 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.70 % Favored : 96.19 % Rotamer: Outliers : 2.59 % Allowed : 15.27 % Favored : 82.13 % Cbeta Deviations : 0.02 % 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: 0.03 (0.10), residues: 7034 helix: 0.62 (0.09), residues: 3839 sheet: -0.55 (0.20), residues: 665 loop : -0.60 (0.13), residues: 2530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 9 73 HIS 0.008 0.001 HIS U 61 PHE 0.026 0.001 PHE D 107 TYR 0.026 0.001 TYR 4 211 ARG 0.004 0.000 ARG 2 319 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12055.35 seconds wall clock time: 213 minutes 10.28 seconds (12790.28 seconds total)