Starting phenix.real_space_refine on Sun Mar 10 17:29:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6res_4855/03_2024/6res_4855_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6res_4855/03_2024/6res_4855.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6res_4855/03_2024/6res_4855.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6res_4855/03_2024/6res_4855.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6res_4855/03_2024/6res_4855_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6res_4855/03_2024/6res_4855_updated.pdb" } resolution = 4.3 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= 0.002 sd= 1.020 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 34301 2.51 5 N 9113 2.21 5 O 10174 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 28": "NH1" <-> "NH2" Residue "1 PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 150": "NH1" <-> "NH2" Residue "1 GLU 165": "OE1" <-> "OE2" Residue "1 ASP 172": "OD1" <-> "OD2" Residue "1 ARG 182": "NH1" <-> "NH2" Residue "1 GLU 191": "OE1" <-> "OE2" Residue "1 GLU 212": "OE1" <-> "OE2" Residue "1 GLU 215": "OE1" <-> "OE2" Residue "1 GLU 229": "OE1" <-> "OE2" Residue "1 GLU 255": "OE1" <-> "OE2" Residue "1 ARG 259": "NH1" <-> "NH2" Residue "1 PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 329": "OE1" <-> "OE2" Residue "1 GLU 343": "OE1" <-> "OE2" Residue "1 ARG 359": "NH1" <-> "NH2" Residue "1 GLU 385": "OE1" <-> "OE2" Residue "1 ARG 387": "NH1" <-> "NH2" Residue "1 ARG 434": "NH1" <-> "NH2" Residue "1 ASP 508": "OD1" <-> "OD2" Residue "1 GLU 519": "OE1" <-> "OE2" Residue "1 ASP 539": "OD1" <-> "OD2" Residue "1 ASP 601": "OD1" <-> "OD2" Residue "1 ASP 608": "OD1" <-> "OD2" Residue "1 ARG 609": "NH1" <-> "NH2" Residue "2 GLU 22": "OE1" <-> "OE2" Residue "2 ARG 45": "NH1" <-> "NH2" Residue "2 GLU 53": "OE1" <-> "OE2" Residue "2 GLU 86": "OE1" <-> "OE2" Residue "2 GLU 134": "OE1" <-> "OE2" Residue "2 PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 139": "OE1" <-> "OE2" Residue "2 TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 173": "NH1" <-> "NH2" Residue "2 PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 316": "OD1" <-> "OD2" Residue "2 PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 346": "NH1" <-> "NH2" Residue "2 TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 102": "OD1" <-> "OD2" Residue "3 PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 149": "NH1" <-> "NH2" Residue "3 ASP 154": "OD1" <-> "OD2" Residue "3 ASP 156": "OD1" <-> "OD2" Residue "3 PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 213": "NH1" <-> "NH2" Residue "3 ASP 217": "OD1" <-> "OD2" Residue "3 TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 233": "NH1" <-> "NH2" Residue "3 ARG 242": "NH1" <-> "NH2" Residue "3 PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 257": "NH1" <-> "NH2" Residue "3 PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 21": "OE1" <-> "OE2" Residue "4 TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 GLU 88": "OE1" <-> "OE2" Residue "4 PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 99": "OE1" <-> "OE2" Residue "4 PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 133": "OD1" <-> "OD2" Residue "4 TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 140": "OE1" <-> "OE2" Residue "4 GLU 146": "OE1" <-> "OE2" Residue "4 PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 176": "NH1" <-> "NH2" Residue "4 TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 193": "OE1" <-> "OE2" Residue "4 PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 225": "OE1" <-> "OE2" Residue "4 ARG 232": "NH1" <-> "NH2" Residue "4 ARG 255": "NH1" <-> "NH2" Residue "4 TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 6": "OE1" <-> "OE2" Residue "5 ARG 36": "NH1" <-> "NH2" Residue "5 ARG 50": "NH1" <-> "NH2" Residue "5 ASP 63": "OD1" <-> "OD2" Residue "5 ARG 112": "NH1" <-> "NH2" Residue "5 PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 91": "OD1" <-> "OD2" Residue "6 ASP 102": "OD1" <-> "OD2" Residue "6 PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 47": "OE1" <-> "OE2" Residue "7 ARG 81": "NH1" <-> "NH2" Residue "7 TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 164": "NH1" <-> "NH2" Residue "7 ARG 165": "NH1" <-> "NH2" Residue "7 ARG 166": "NH1" <-> "NH2" Residue "7 PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ARG 13": "NH1" <-> "NH2" Residue "8 ASP 62": "OD1" <-> "OD2" Residue "8 ARG 65": "NH1" <-> "NH2" Residue "8 TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 15": "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 ASP 82": "OD1" <-> "OD2" Residue "A ARG 91": "NH1" <-> "NH2" Residue "C ARG 91": "NH1" <-> "NH2" Residue "E ARG 91": "NH1" <-> "NH2" Residue "G ARG 91": "NH1" <-> "NH2" Residue "G PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 91": "NH1" <-> "NH2" Residue "H GLU 111": "OE1" <-> "OE2" Residue "I GLU 111": "OE1" <-> "OE2" Residue "M ARG 115": "NH1" <-> "NH2" Residue "M ASP 132": "OD1" <-> "OD2" Residue "M ARG 145": "NH1" <-> "NH2" Residue "M PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 232": "NH1" <-> "NH2" Residue "M ARG 239": "NH1" <-> "NH2" Residue "M GLU 288": "OE1" <-> "OE2" Residue "P ASP 68": "OD1" <-> "OD2" Residue "P PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 123": "OE1" <-> "OE2" Residue "P GLU 136": "OE1" <-> "OE2" Residue "P GLU 143": "OE1" <-> "OE2" Residue "P ASP 163": "OD1" <-> "OD2" Residue "P GLU 166": "OE1" <-> "OE2" Residue "P PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 188": "OE1" <-> "OE2" Residue "P PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 206": "NH1" <-> "NH2" Residue "P PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 33": "OE1" <-> "OE2" Residue "Q ARG 42": "NH1" <-> "NH2" Residue "Q PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 48": "NH1" <-> "NH2" Residue "Q TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 174": "OD1" <-> "OD2" Residue "R PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 196": "OE1" <-> "OE2" Residue "S ARG 46": "NH1" <-> "NH2" Residue "S ASP 83": "OD1" <-> "OD2" Residue "S ARG 147": "NH1" <-> "NH2" Residue "S ARG 152": "NH1" <-> "NH2" Residue "S ARG 157": "NH1" <-> "NH2" Residue "S PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 234": "OE1" <-> "OE2" Residue "S ARG 244": "NH1" <-> "NH2" Residue "S ASP 245": "OD1" <-> "OD2" Residue "S TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 47": "OE1" <-> "OE2" Residue "T ARG 49": "NH1" <-> "NH2" Residue "T PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 72": "OE1" <-> "OE2" Residue "T ARG 86": "NH1" <-> "NH2" Residue "T ARG 96": "NH1" <-> "NH2" Residue "T ASP 112": "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 ASP 226": "OD1" <-> "OD2" Residue "T ARG 283": "NH1" <-> "NH2" Residue "T TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 384": "OE1" <-> "OE2" Residue "T PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 418": "NH1" <-> "NH2" Residue "T ARG 429": "NH1" <-> "NH2" Residue "T PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 449": "OE1" <-> "OE2" Residue "T ARG 454": "NH1" <-> "NH2" Residue "T PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 510": "OD1" <-> "OD2" Residue "T GLU 522": "OE1" <-> "OE2" Residue "T ASP 547": "OD1" <-> "OD2" Residue "T ARG 555": "NH1" <-> "NH2" Residue "U ARG 49": "NH1" <-> "NH2" Residue "U PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 72": "OE1" <-> "OE2" Residue "U TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 96": "NH1" <-> "NH2" Residue "U TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 135": "OD1" <-> "OD2" Residue "U ARG 146": "NH1" <-> "NH2" Residue "U ARG 162": "NH1" <-> "NH2" Residue "U ARG 181": "NH1" <-> "NH2" Residue "U ARG 199": "NH1" <-> "NH2" Residue "U GLU 221": "OE1" <-> "OE2" Residue "U ARG 227": "NH1" <-> "NH2" Residue "U ARG 254": "NH1" <-> "NH2" Residue "U PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 283": "NH1" <-> "NH2" Residue "U TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 314": "NH1" <-> "NH2" Residue "U TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 342": "NH1" <-> "NH2" Residue "U ARG 343": "NH1" <-> "NH2" Residue "U PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 364": "NH1" <-> "NH2" Residue "U PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 467": "OD1" <-> "OD2" Residue "U ARG 479": "NH1" <-> "NH2" Residue "U ARG 496": "NH1" <-> "NH2" Residue "U ARG 513": "NH1" <-> "NH2" Residue "U GLU 521": "OE1" <-> "OE2" Residue "U PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 49": "NH1" <-> "NH2" Residue "V PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 181": "NH1" <-> "NH2" Residue "V ARG 217": "NH1" <-> "NH2" Residue "V ARG 220": "NH1" <-> "NH2" Residue "V TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 266": "NH1" <-> "NH2" Residue "V PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 314": "NH1" <-> "NH2" Residue "V ASP 326": "OD1" <-> "OD2" Residue "V ARG 335": "NH1" <-> "NH2" Residue "V ARG 342": "NH1" <-> "NH2" Residue "V ARG 343": "NH1" <-> "NH2" Residue "V PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 360": "NH1" <-> "NH2" Residue "V PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 454": "NH1" <-> "NH2" Residue "V PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 476": "NH1" <-> "NH2" Residue "V GLU 482": "OE1" <-> "OE2" Residue "V ARG 496": "NH1" <-> "NH2" Residue "V TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 513": "NH1" <-> "NH2" Residue "V GLU 521": "OE1" <-> "OE2" Residue "V GLU 553": "OE1" <-> "OE2" Residue "V ARG 555": "NH1" <-> "NH2" Residue "X ASP 49": "OD1" <-> "OD2" Residue "X PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 71": "NH1" <-> "NH2" Residue "X ARG 86": "NH1" <-> "NH2" Residue "X ASP 91": "OD1" <-> "OD2" Residue "X ASP 104": "OD1" <-> "OD2" Residue "X ARG 115": "NH1" <-> "NH2" Residue "X ARG 120": "NH1" <-> "NH2" Residue "X PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 156": "OE1" <-> "OE2" Residue "X TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 258": "NH1" <-> "NH2" Residue "X ASP 279": "OD1" <-> "OD2" Residue "X GLU 296": "OE1" <-> "OE2" Residue "X ASP 317": "OD1" <-> "OD2" Residue "X ARG 366": "NH1" <-> "NH2" Residue "X GLU 370": "OE1" <-> "OE2" Residue "X TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 378": "OD1" <-> "OD2" Residue "X ARG 385": "NH1" <-> "NH2" Residue "X PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 497": "OE1" <-> "OE2" Residue "X ASP 500": "OD1" <-> "OD2" Residue "X ARG 509": "NH1" <-> "NH2" Residue "X GLU 520": "OE1" <-> "OE2" Residue "X GLU 536": "OE1" <-> "OE2" Residue "X GLU 541": "OE1" <-> "OE2" Residue "X GLU 546": "OE1" <-> "OE2" Residue "X GLU 564": "OE1" <-> "OE2" Residue "Y ARG 51": "NH1" <-> "NH2" Residue "Y PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 71": "NH1" <-> "NH2" Residue "Y ARG 86": "NH1" <-> "NH2" Residue "Y ASP 94": "OD1" <-> "OD2" Residue "Y ARG 98": "NH1" <-> "NH2" Residue "Y ARG 120": "NH1" <-> "NH2" Residue "Y GLU 149": "OE1" <-> "OE2" Residue "Y ASP 168": "OD1" <-> "OD2" Residue "Y ARG 216": "NH1" <-> "NH2" Residue "Y GLU 229": "OE1" <-> "OE2" Residue "Y TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 258": "NH1" <-> "NH2" Residue "Y PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 289": "NH1" <-> "NH2" Residue "Y ASP 344": "OD1" <-> "OD2" Residue "Y ASP 345": "OD1" <-> "OD2" Residue "Y PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 385": "NH1" <-> "NH2" Residue "Y ARG 401": "NH1" <-> "NH2" Residue "Y ASP 409": "OD1" <-> "OD2" Residue "Y TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 428": "OE1" <-> "OE2" Residue "Y ASP 429": "OD1" <-> "OD2" Residue "Y ARG 435": "NH1" <-> "NH2" Residue "Y ARG 437": "NH1" <-> "NH2" Residue "Y PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 465": "OD1" <-> "OD2" Residue "Y TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 483": "OE1" <-> "OE2" Residue "Y ARG 509": "NH1" <-> "NH2" Residue "Y GLU 519": "OE1" <-> "OE2" Residue "Y PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 51": "NH1" <-> "NH2" Residue "Z PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 53": "OD1" <-> "OD2" Residue "Z ASP 91": "OD1" <-> "OD2" Residue "Z ASP 104": "OD1" <-> "OD2" Residue "Z GLU 131": "OE1" <-> "OE2" Residue "Z ASP 139": "OD1" <-> "OD2" Residue "Z PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 218": "NH1" <-> "NH2" Residue "Z GLU 219": "OE1" <-> "OE2" Residue "Z ARG 225": "NH1" <-> "NH2" Residue "Z GLU 238": "OE1" <-> "OE2" Residue "Z ARG 239": "NH1" <-> "NH2" Residue "Z GLU 296": "OE1" <-> "OE2" Residue "Z TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 385": "NH1" <-> "NH2" Residue "Z TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 401": "NH1" <-> "NH2" Residue "Z PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 483": "OE1" <-> "OE2" Residue "Z TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 509": "NH1" <-> "NH2" Residue "Z GLU 511": "OE1" <-> "OE2" Residue "Z GLU 519": "OE1" <-> "OE2" Residue "Z GLU 541": "OE1" <-> "OE2" Residue "Z ASP 542": "OD1" <-> "OD2" Residue "Z ASP 548": "OD1" <-> "OD2" Residue "Z PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 53756 Number of models: 1 Model: "" Number of chains: 37 Chain: "0" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 607 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 8, 'TRANS': 72} Chain: "1" Number of atoms: 4661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4661 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 31, 'TRANS': 563} Chain: "2" Number of atoms: 3163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3163 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 17, 'TRANS': 423} Chain: "3" Number of atoms: 1874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1874 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 239} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 7 Chain: "4" Number of atoms: 2177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2177 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 9, 'TRANS': 280} Chain: "5" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 986 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "6" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 926 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "7" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1347 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 5, 'TRANS': 170} Chain: "8" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 692 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 7, 'TRANS': 80} Chain: "9" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 776 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 5, 'TRANS': 91} Chain: "A" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "B" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "C" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain breaks: 1 Chain: "D" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "E" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "F" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "G" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "H" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "I" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "J" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "M" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1640 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "P" Number of atoms: 1532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1532 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 5, 'TRANS': 187} Chain: "Q" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 561 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 5, 'TRANS': 66} Chain: "R" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1303 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 13, 'TRANS': 163} Chain: "S" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2130 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 271} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 3979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3979 Classifications: {'peptide': 523} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Chain: "U" Number of atoms: 3980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3980 Classifications: {'peptide': 523} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Chain: "V" Number of atoms: 3962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3962 Classifications: {'peptide': 520} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 494} Chain: "X" Number of atoms: 4095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4095 Classifications: {'peptide': 539} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 514} Chain: "Y" Number of atoms: 3957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3957 Classifications: {'peptide': 521} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 498} Chain: "Z" Number of atoms: 4115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4115 Classifications: {'peptide': 542} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 517} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 21.54, per 1000 atoms: 0.40 Number of scatterers: 53756 At special positions: 0 Unit cell: (210.6, 136.89, 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 10174 8.00 N 9113 7.00 C 34301 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 16.11 Conformation dependent library (CDL) restraints added in 7.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN M 600 " pdb="ZN ZN M 600 " - pdb=" NE2 HIS M 252 " pdb="ZN ZN M 600 " - pdb=" NE2 HIS M 248 " 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13088 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 295 helices and 31 sheets defined 49.7% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.51 Creating SS restraints... Processing helix chain '0' and resid 5 through 9 Processing helix chain '0' and resid 18 through 25 Processing helix chain '0' and resid 27 through 30 No H-bonds generated for 'chain '0' and resid 27 through 30' Processing helix chain '0' and resid 44 through 48 Processing helix chain '0' and resid 58 through 60 No H-bonds generated for 'chain '0' and resid 58 through 60' Processing helix chain '1' and resid 46 through 69 Processing helix chain '1' and resid 97 through 99 No H-bonds generated for 'chain '1' and resid 97 through 99' Processing helix chain '1' and resid 107 through 141 removed outlier: 3.549A pdb=" N SER 1 125 " --> pdb=" O ALA 1 121 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR 1 135 " --> pdb=" O ALA 1 131 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU 1 136 " --> pdb=" O GLY 1 132 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA 1 139 " --> pdb=" O THR 1 135 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ALA 1 140 " --> pdb=" O GLU 1 136 " (cutoff:3.500A) Processing helix chain '1' and resid 164 through 178 removed outlier: 3.720A pdb=" N LYS 1 173 " --> pdb=" O THR 1 169 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR 1 174 " --> pdb=" O VAL 1 170 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA 1 177 " --> pdb=" O LYS 1 173 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU 1 178 " --> pdb=" O TYR 1 174 " (cutoff:3.500A) Processing helix chain '1' and resid 191 through 203 removed outlier: 3.699A pdb=" N ALA 1 196 " --> pdb=" O GLY 1 192 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE 1 200 " --> pdb=" O ALA 1 196 " (cutoff:3.500A) Processing helix chain '1' and resid 210 through 223 Processing helix chain '1' and resid 242 through 270 removed outlier: 3.513A pdb=" N LYS 1 247 " --> pdb=" O ALA 1 243 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE 1 249 " --> pdb=" O ALA 1 245 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR 1 251 " --> pdb=" O LYS 1 247 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N HIS 1 257 " --> pdb=" O ARG 1 253 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG 1 267 " --> pdb=" O LEU 1 263 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL 1 270 " --> pdb=" O LYS 1 266 " (cutoff:3.500A) Processing helix chain '1' and resid 272 through 276 removed outlier: 3.516A pdb=" N ALA 1 275 " --> pdb=" O PRO 1 272 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE 1 276 " --> pdb=" O GLU 1 273 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 272 through 276' Processing helix chain '1' and resid 279 through 281 No H-bonds generated for 'chain '1' and resid 279 through 281' Processing helix chain '1' and resid 283 through 285 No H-bonds generated for 'chain '1' and resid 283 through 285' Processing helix chain '1' and resid 299 through 304 Processing helix chain '1' and resid 311 through 317 removed outlier: 3.745A pdb=" N LEU 1 315 " --> pdb=" O PHE 1 311 " (cutoff:3.500A) 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: 3.553A pdb=" N GLU 1 343 " --> pdb=" O GLU 1 339 " (cutoff:3.500A) Processing helix chain '1' and resid 354 through 361 Processing helix chain '1' and resid 363 through 365 No H-bonds generated for 'chain '1' and resid 363 through 365' Processing helix chain '1' and resid 376 through 387 removed outlier: 3.620A pdb=" N HIS 1 386 " --> pdb=" O VAL 1 382 " (cutoff:3.500A) Processing helix chain '1' and resid 393 through 416 Processing helix chain '1' and resid 426 through 431 Processing helix chain '1' and resid 436 through 443 removed outlier: 3.504A pdb=" N ASP 1 442 " --> pdb=" O GLN 1 438 " (cutoff:3.500A) Processing helix chain '1' and resid 447 through 457 removed outlier: 3.751A pdb=" N ARG 1 453 " --> pdb=" O ALA 1 449 " (cutoff:3.500A) Processing helix chain '1' and resid 464 through 476 removed outlier: 3.732A pdb=" N THR 1 471 " --> pdb=" O ALA 1 467 " (cutoff:3.500A) Processing helix chain '1' and resid 480 through 482 No H-bonds generated for 'chain '1' and resid 480 through 482' Processing helix chain '1' and resid 486 through 489 No H-bonds generated for 'chain '1' and resid 486 through 489' Processing helix chain '1' and resid 491 through 513 removed outlier: 3.654A pdb=" N GLU 1 501 " --> pdb=" O LEU 1 497 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ASP 1 504 " --> pdb=" O LEU 1 500 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE 1 505 " --> pdb=" O GLU 1 501 " (cutoff:3.500A) Processing helix chain '1' and resid 521 through 533 removed outlier: 4.043A pdb=" N THR 1 526 " --> pdb=" O LEU 1 522 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE 1 529 " --> pdb=" O LEU 1 525 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS 1 530 " --> pdb=" O THR 1 526 " (cutoff:3.500A) Processing helix chain '1' and resid 542 through 548 Processing helix chain '1' and resid 550 through 561 Processing helix chain '1' and resid 567 through 573 Processing helix chain '1' and resid 577 through 587 Processing helix chain '1' and resid 589 through 591 No H-bonds generated for 'chain '1' and resid 589 through 591' Processing helix chain '1' and resid 593 through 606 removed outlier: 3.525A pdb=" N ARG 1 600 " --> pdb=" O ILE 1 596 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS 1 605 " --> pdb=" O ASP 1 601 " (cutoff:3.500A) Processing helix chain '2' and resid 8 through 19 Processing helix chain '2' and resid 26 through 37 removed outlier: 3.560A pdb=" N ASP 2 31 " --> pdb=" O LYS 2 27 " (cutoff:3.500A) Processing helix chain '2' and resid 45 through 55 Processing helix chain '2' and resid 63 through 75 Processing helix chain '2' and resid 81 through 93 removed outlier: 3.541A pdb=" N LEU 2 87 " --> pdb=" O THR 2 83 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N ALA 2 88 " --> pdb=" O VAL 2 84 " (cutoff:3.500A) removed outlier: 4.924A 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 removed outlier: 3.523A pdb=" N GLU 2 108 " --> pdb=" O SER 2 104 " (cutoff:3.500A) Processing helix chain '2' and resid 119 through 130 removed outlier: 3.885A pdb=" N VAL 2 127 " --> pdb=" O LYS 2 123 " (cutoff:3.500A) Processing helix chain '2' and resid 137 through 150 Processing helix chain '2' and resid 156 through 165 removed outlier: 4.097A pdb=" N ALA 2 160 " --> pdb=" O ALA 2 156 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS 2 163 " --> pdb=" O LYS 2 159 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL 2 164 " --> pdb=" O ALA 2 160 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE 2 165 " --> pdb=" O ALA 2 161 " (cutoff:3.500A) Processing helix chain '2' and resid 172 through 185 removed outlier: 3.653A pdb=" N LEU 2 182 " --> pdb=" O ALA 2 178 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA 2 183 " --> pdb=" O LEU 2 179 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS 2 184 " --> pdb=" O TYR 2 180 " (cutoff:3.500A) Processing helix chain '2' and resid 190 through 199 removed outlier: 3.673A pdb=" N ASP 2 194 " --> pdb=" O LYS 2 190 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N SER 2 199 " --> pdb=" O ALA 2 195 " (cutoff:3.500A) Processing helix chain '2' and resid 207 through 220 removed outlier: 3.877A pdb=" N ALA 2 212 " --> pdb=" O SER 2 208 " (cutoff:3.500A) Processing helix chain '2' and resid 228 through 234 Processing helix chain '2' and resid 241 through 253 removed outlier: 3.581A pdb=" N VAL 2 245 " --> pdb=" O PRO 2 241 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N GLU 2 246 " --> pdb=" O ALA 2 242 " (cutoff:3.500A) Processing helix chain '2' and resid 259 through 275 removed outlier: 3.897A pdb=" N VAL 2 268 " --> pdb=" O ALA 2 264 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL 2 269 " --> pdb=" O LEU 2 265 " (cutoff:3.500A) Proline residue: 2 271 - end of helix Processing helix chain '2' and resid 282 through 294 removed outlier: 3.917A pdb=" N HIS 2 289 " --> pdb=" O LEU 2 285 " (cutoff:3.500A) Processing helix chain '2' and resid 301 through 320 removed outlier: 3.577A pdb=" N SER 2 305 " --> pdb=" O ALA 2 301 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE 2 306 " --> pdb=" O ALA 2 302 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA 2 318 " --> pdb=" O ALA 2 314 " (cutoff:3.500A) Processing helix chain '2' and resid 327 through 340 Processing helix chain '2' and resid 346 through 353 Processing helix chain '2' and resid 397 through 407 Processing helix chain '2' and resid 427 through 441 removed outlier: 3.982A pdb=" N VAL 2 441 " --> pdb=" O ALA 2 437 " (cutoff:3.500A) Processing helix chain '3' and resid 78 through 88 removed outlier: 3.743A pdb=" N VAL 3 82 " --> pdb=" O SER 3 78 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN 3 87 " --> pdb=" O SER 3 83 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS 3 88 " --> pdb=" O THR 3 84 " (cutoff:3.500A) Processing helix chain '3' and resid 92 through 95 No H-bonds generated for 'chain '3' and resid 92 through 95' Processing helix chain '3' and resid 103 through 111 removed outlier: 3.574A pdb=" N TRP 3 109 " --> pdb=" O PHE 3 105 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU 3 110 " --> pdb=" O TRP 3 106 " (cutoff:3.500A) Processing helix chain '3' and resid 118 through 128 removed outlier: 3.566A pdb=" N VAL 3 122 " --> pdb=" O LYS 3 118 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS 3 123 " --> pdb=" O ASP 3 119 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA 3 127 " --> pdb=" O LYS 3 123 " (cutoff:3.500A) Processing helix chain '3' and resid 137 through 149 removed outlier: 4.212A pdb=" N ALA 3 146 " --> pdb=" O ASN 3 142 " (cutoff:3.500A) Processing helix chain '3' and resid 155 through 167 removed outlier: 4.317A pdb=" N GLY 3 160 " --> pdb=" O ASP 3 156 " (cutoff:3.500A) Processing helix chain '3' and resid 174 through 186 removed outlier: 4.014A pdb=" N GLN 3 179 " --> pdb=" O GLU 3 175 " (cutoff:3.500A) Processing helix chain '3' and resid 192 through 203 removed outlier: 3.687A pdb=" N THR 3 203 " --> pdb=" O ALA 3 199 " (cutoff:3.500A) Processing helix chain '3' and resid 212 through 214 No H-bonds generated for 'chain '3' and resid 212 through 214' Processing helix chain '3' and resid 216 through 228 removed outlier: 3.598A pdb=" N THR 3 221 " --> pdb=" O ASP 3 217 " (cutoff:3.500A) Processing helix chain '3' and resid 234 through 243 removed outlier: 3.544A pdb=" N THR 3 239 " --> pdb=" O ASP 3 235 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG 3 242 " --> pdb=" O ALA 3 238 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLY 3 243 " --> pdb=" O THR 3 239 " (cutoff:3.500A) Processing helix chain '3' and resid 246 through 250 Processing helix chain '3' and resid 254 through 270 removed outlier: 3.869A pdb=" N ASP 3 259 " --> pdb=" O ALA 3 255 " (cutoff:3.500A) Processing helix chain '3' and resid 276 through 285 removed outlier: 3.528A pdb=" N GLU 3 279 " --> pdb=" O GLU 3 276 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA 3 280 " --> pdb=" O SER 3 277 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY 3 283 " --> pdb=" O ALA 3 280 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA 3 284 " --> pdb=" O VAL 3 281 " (cutoff:3.500A) Processing helix chain '3' and resid 289 through 291 No H-bonds generated for 'chain '3' and resid 289 through 291' Processing helix chain '3' and resid 294 through 311 removed outlier: 3.885A pdb=" N ASN 3 309 " --> pdb=" O VAL 3 305 " (cutoff:3.500A) Processing helix chain '4' and resid 10 through 16 removed outlier: 3.516A pdb=" N PHE 4 14 " --> pdb=" O GLU 4 10 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU 4 15 " --> pdb=" O VAL 4 11 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N SER 4 16 " --> pdb=" O LEU 4 12 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 10 through 16' Processing helix chain '4' and resid 21 through 34 removed outlier: 3.600A pdb=" N SER 4 32 " --> pdb=" O SER 4 28 " (cutoff:3.500A) Processing helix chain '4' and resid 48 through 68 removed outlier: 3.566A pdb=" N ALA 4 60 " --> pdb=" O LYS 4 56 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLN 4 61 " --> pdb=" O TYR 4 57 " (cutoff:3.500A) Proline residue: 4 65 - end of helix removed outlier: 3.534A pdb=" N HIS 4 68 " --> pdb=" O GLU 4 64 " (cutoff:3.500A) Processing helix chain '4' and resid 80 through 96 Processing helix chain '4' and resid 101 through 112 removed outlier: 3.535A pdb=" N VAL 4 105 " --> pdb=" O PRO 4 101 " (cutoff:3.500A) Processing helix chain '4' and resid 119 through 123 Processing helix chain '4' and resid 132 through 148 removed outlier: 3.985A pdb=" N ALA 4 137 " --> pdb=" O ASP 4 133 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU 4 140 " --> pdb=" O ALA 4 136 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL 4 141 " --> pdb=" O ALA 4 137 " (cutoff:3.500A) Processing helix chain '4' and resid 160 through 176 removed outlier: 3.655A pdb=" N PHE 4 165 " --> pdb=" O GLY 4 161 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS 4 168 " --> pdb=" O LYS 4 164 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS 4 170 " --> pdb=" O ALA 4 166 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA 4 171 " --> pdb=" O ALA 4 167 " (cutoff:3.500A) Processing helix chain '4' and resid 180 through 187 removed outlier: 3.585A pdb=" N LEU 4 184 " --> pdb=" O ALA 4 180 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA 4 185 " --> pdb=" O ASP 4 181 " (cutoff:3.500A) Processing helix chain '4' and resid 193 through 235 removed outlier: 4.321A pdb=" N GLU 4 202 " --> pdb=" O LYS 4 198 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR 4 205 " --> pdb=" O LYS 4 201 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER 4 209 " --> pdb=" O THR 4 205 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASP 4 214 " --> pdb=" O ALA 4 210 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA 4 215 " --> pdb=" O TYR 4 211 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA 4 227 " --> pdb=" O GLU 4 223 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG 4 232 " --> pdb=" O SER 4 228 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA 4 235 " --> pdb=" O ASP 4 231 " (cutoff:3.500A) Processing helix chain '4' and resid 238 through 258 removed outlier: 3.829A pdb=" N LYS 4 243 " --> pdb=" O ALA 4 239 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA 4 246 " --> pdb=" O ARG 4 242 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG 4 255 " --> pdb=" O SER 4 251 " (cutoff:3.500A) removed outlier: 4.272A 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 29 removed outlier: 3.741A pdb=" N VAL 5 18 " --> pdb=" O THR 5 14 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL 5 22 " --> pdb=" O VAL 5 18 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU 5 23 " --> pdb=" O ALA 5 19 " (cutoff:3.500A) Processing helix chain '5' and resid 31 through 58 removed outlier: 3.921A pdb=" N LEU 5 40 " --> pdb=" O ARG 5 36 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N HIS 5 41 " --> pdb=" O GLU 5 37 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N LYS 5 49 " --> pdb=" O ALA 5 45 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ARG 5 50 " --> pdb=" O ALA 5 46 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN 5 52 " --> pdb=" O ALA 5 48 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU 5 58 " --> pdb=" O LYS 5 54 " (cutoff:3.500A) Processing helix chain '5' and resid 64 through 67 No H-bonds generated for 'chain '5' and resid 64 through 67' Processing helix chain '5' and resid 73 through 80 removed outlier: 3.562A pdb=" N LEU 5 77 " --> pdb=" O LYS 5 73 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN 5 79 " --> pdb=" O GLN 5 75 " (cutoff:3.500A) Processing helix chain '5' and resid 88 through 105 removed outlier: 3.512A pdb=" N ASN 5 99 " --> pdb=" O MET 5 95 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LYS 5 101 " --> pdb=" O SER 5 97 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL 5 102 " --> pdb=" O ALA 5 98 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA 5 105 " --> pdb=" O LYS 5 101 " (cutoff:3.500A) Processing helix chain '5' and resid 114 through 116 No H-bonds generated for 'chain '5' and resid 114 through 116' Processing helix chain '6' and resid 31 through 40 removed outlier: 3.668A pdb=" N SER 6 38 " --> pdb=" O GLY 6 34 " (cutoff:3.500A) Processing helix chain '6' and resid 51 through 57 Processing helix chain '6' and resid 73 through 93 Processing helix chain '6' and resid 99 through 117 removed outlier: 4.067A pdb=" N VAL 6 107 " --> pdb=" O LEU 6 103 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TRP 6 112 " --> pdb=" O LEU 6 108 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE 6 114 " --> pdb=" O ALA 6 110 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER 6 117 " --> pdb=" O LEU 6 113 " (cutoff:3.500A) Processing helix chain '6' and resid 122 through 130 Processing helix chain '7' and resid 65 through 71 removed outlier: 5.047A pdb=" N GLY 7 71 " --> pdb=" O ARG 7 67 " (cutoff:3.500A) Processing helix chain '7' and resid 84 through 103 removed outlier: 3.844A 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 143 removed outlier: 3.679A pdb=" N LYS 7 128 " --> pdb=" O PRO 7 124 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE 7 130 " --> pdb=" O ASP 7 126 " (cutoff:3.500A) Processing helix chain '7' and resid 147 through 156 removed outlier: 3.953A pdb=" N SER 7 151 " --> pdb=" O ASP 7 148 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ALA 7 154 " --> pdb=" O SER 7 151 " (cutoff:3.500A) Processing helix chain '7' and resid 158 through 162 Processing helix chain '7' and resid 175 through 187 removed outlier: 3.522A pdb=" N THR 7 183 " --> pdb=" O ASP 7 179 " (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 41 through 77 removed outlier: 3.721A pdb=" N TRP 8 45 " --> pdb=" O ILE 8 41 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N TYR 8 46 " --> pdb=" O PRO 8 42 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU 8 47 " --> pdb=" O ARG 8 43 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR 8 54 " --> pdb=" O GLY 8 50 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR 8 56 " --> pdb=" O THR 8 52 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG 8 65 " --> pdb=" O LEU 8 61 " (cutoff:3.500A) Processing helix chain '9' and resid 5 through 16 removed outlier: 3.724A pdb=" N LYS 9 9 " --> pdb=" O SER 9 5 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR 9 14 " --> pdb=" O ALA 9 10 " (cutoff:3.500A) Processing helix chain '9' and resid 20 through 23 No H-bonds generated for 'chain '9' and resid 20 through 23' Processing helix chain '9' and resid 34 through 54 removed outlier: 3.739A pdb=" N LEU 9 39 " --> pdb=" O GLN 9 35 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL 9 42 " --> pdb=" O ALA 9 38 " (cutoff:3.500A) Processing helix chain '9' and resid 83 through 93 Processing helix chain 'A' and resid 55 through 69 removed outlier: 4.443A pdb=" N MET A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N VAL A 62 " --> pdb=" O ALA A 58 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 90 removed outlier: 4.004A pdb=" N ILE A 86 " --> pdb=" O PHE A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 118 removed outlier: 3.970A pdb=" N GLY A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ILE A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 123 No H-bonds generated for 'chain 'A' and resid 120 through 123' Processing helix chain 'B' and resid 55 through 91 removed outlier: 3.591A pdb=" N SER B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS B 60 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N MET B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL B 62 " --> pdb=" O ALA B 58 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N CYS B 66 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N THR B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ILE B 69 " --> pdb=" O GLY B 65 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ALA B 70 " --> pdb=" O CYS B 66 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LEU B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ALA B 72 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLY B 73 " --> pdb=" O ILE B 69 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B 86 " --> pdb=" O PHE B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 116 removed outlier: 5.725A pdb=" N LYS B 97 " --> pdb=" O ASN B 94 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL B 100 " --> pdb=" O LYS B 97 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU B 104 " --> pdb=" O GLY B 101 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU B 105 " --> pdb=" O TYR B 102 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA B 108 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU B 109 " --> pdb=" O GLY B 106 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER B 112 " --> pdb=" O LEU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 124 Processing helix chain 'C' and resid 56 through 65 removed outlier: 4.627A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 89 removed outlier: 3.831A pdb=" N ILE C 86 " --> pdb=" O PHE C 82 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASN C 87 " --> pdb=" O GLY C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 116 removed outlier: 3.619A pdb=" N ALA C 96 " --> pdb=" O PRO C 93 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N LYS C 97 " --> pdb=" O ASN C 94 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LEU C 99 " --> pdb=" O ALA C 96 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL C 100 " --> pdb=" O LYS C 97 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA C 103 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N LEU C 104 " --> pdb=" O GLY C 101 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N PHE C 107 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU C 109 " --> pdb=" O GLY C 106 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU C 111 " --> pdb=" O ALA C 108 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER C 112 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA C 114 " --> pdb=" O GLU C 111 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU C 115 " --> pdb=" O SER C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 123 Processing helix chain 'D' and resid 55 through 91 removed outlier: 4.041A pdb=" N MET D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ILE D 69 " --> pdb=" O GLY D 65 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N ALA D 70 " --> pdb=" O CYS D 66 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N LEU D 71 " --> pdb=" O ALA D 67 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N ALA D 72 " --> pdb=" O THR D 68 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLY D 73 " --> pdb=" O ILE D 69 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLY D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE D 86 " --> pdb=" O PHE D 82 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG D 91 " --> pdb=" O ASN D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 95 No H-bonds generated for 'chain 'D' and resid 93 through 95' Processing helix chain 'D' and resid 99 through 125 removed outlier: 4.231A pdb=" N LEU D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA D 108 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU D 109 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA D 114 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER D 117 " --> pdb=" O ILE D 113 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU D 118 " --> pdb=" O ALA D 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 69 removed outlier: 4.386A pdb=" N MET E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY E 65 " --> pdb=" O MET E 61 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ILE E 69 " --> pdb=" O GLY E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 90 removed outlier: 3.804A pdb=" N ILE E 86 " --> pdb=" O PHE E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 126 removed outlier: 3.690A pdb=" N VAL E 100 " --> pdb=" O ALA E 96 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU E 105 " --> pdb=" O GLY E 101 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU E 109 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N SER E 112 " --> pdb=" O ALA E 108 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ILE E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA E 114 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL E 120 " --> pdb=" O PHE E 116 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE E 122 " --> pdb=" O LEU E 118 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU E 125 " --> pdb=" O VAL E 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 65 removed outlier: 3.514A pdb=" N LYS F 60 " --> pdb=" O LEU F 56 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N MET F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA F 64 " --> pdb=" O LYS F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 91 removed outlier: 3.915A pdb=" N GLY F 73 " --> pdb=" O ALA F 70 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY F 79 " --> pdb=" O ALA F 76 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL F 80 " --> pdb=" O GLY F 77 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE F 82 " --> pdb=" O GLY F 79 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU F 85 " --> pdb=" O PHE F 82 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASN F 87 " --> pdb=" O SER F 84 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY F 88 " --> pdb=" O LEU F 85 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG F 91 " --> pdb=" O GLY F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 123 removed outlier: 3.614A pdb=" N ALA F 96 " --> pdb=" O PRO F 93 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N LYS F 97 " --> pdb=" O ASN F 94 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU F 99 " --> pdb=" O ALA F 96 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL F 100 " --> pdb=" O LYS F 97 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N LEU F 104 " --> pdb=" O GLY F 101 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE F 107 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA F 108 " --> pdb=" O LEU F 105 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU F 111 " --> pdb=" O ALA F 108 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER F 112 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER F 117 " --> pdb=" O ALA F 114 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU F 118 " --> pdb=" O LEU F 115 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU F 119 " --> pdb=" O PHE F 116 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU F 123 " --> pdb=" O VAL F 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 66 removed outlier: 3.660A pdb=" N LYS G 60 " --> pdb=" O LEU G 56 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N MET G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL G 62 " --> pdb=" O ALA G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 91 removed outlier: 4.201A pdb=" N GLY G 73 " --> pdb=" O ALA G 70 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL G 74 " --> pdb=" O LEU G 71 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N MET G 81 " --> pdb=" O LEU G 78 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE G 82 " --> pdb=" O GLY G 79 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU G 85 " --> pdb=" O PHE G 82 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLY G 88 " --> pdb=" O LEU G 85 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA G 89 " --> pdb=" O ILE G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 124 removed outlier: 3.513A pdb=" N ALA G 96 " --> pdb=" O PRO G 93 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LYS G 97 " --> pdb=" O ASN G 94 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL G 100 " --> pdb=" O LYS G 97 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LEU G 104 " --> pdb=" O GLY G 101 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE G 107 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA G 108 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU G 109 " --> pdb=" O GLY G 106 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU G 111 " --> pdb=" O ALA G 108 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE G 113 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA G 114 " --> pdb=" O GLU G 111 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU G 118 " --> pdb=" O LEU G 115 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU G 119 " --> pdb=" O PHE G 116 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE G 122 " --> pdb=" O LEU G 119 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU G 123 " --> pdb=" O VAL G 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 65 removed outlier: 4.148A pdb=" N MET H 61 " --> pdb=" O ALA H 57 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL H 62 " --> pdb=" O ALA H 58 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 91 removed outlier: 3.652A pdb=" N VAL H 74 " --> pdb=" O LEU H 71 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA H 76 " --> pdb=" O GLY H 73 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU H 78 " --> pdb=" O GLY H 75 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL H 80 " --> pdb=" O GLY H 77 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU H 85 " --> pdb=" O PHE H 82 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY H 88 " --> pdb=" O LEU H 85 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG H 91 " --> pdb=" O GLY H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 125 removed outlier: 3.503A pdb=" N VAL H 100 " --> pdb=" O ALA H 96 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ILE H 113 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA H 114 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL H 120 " --> pdb=" O PHE H 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 91 removed outlier: 3.858A pdb=" N SER I 59 " --> pdb=" O VAL I 55 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY I 65 " --> pdb=" O MET I 61 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE I 69 " --> pdb=" O GLY I 65 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ALA I 70 " --> pdb=" O CYS I 66 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N LEU I 71 " --> pdb=" O ALA I 67 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ALA I 72 " --> pdb=" O THR I 68 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLY I 73 " --> pdb=" O ILE I 69 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL I 74 " --> pdb=" O ALA I 70 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY I 79 " --> pdb=" O GLY I 75 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE I 82 " --> pdb=" O LEU I 78 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE I 86 " --> pdb=" O PHE I 82 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN I 87 " --> pdb=" O GLY I 83 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG I 91 " --> pdb=" O ASN I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 126 removed outlier: 4.523A pdb=" N LYS I 97 " --> pdb=" O ASN I 94 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU I 99 " --> pdb=" O ALA I 96 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL I 100 " --> pdb=" O LYS I 97 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N LEU I 104 " --> pdb=" O GLY I 101 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU I 105 " --> pdb=" O TYR I 102 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA I 108 " --> pdb=" O LEU I 105 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N SER I 112 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU I 115 " --> pdb=" O SER I 112 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU I 119 " --> pdb=" O PHE I 116 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE I 122 " --> pdb=" O LEU I 119 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU I 123 " --> pdb=" O VAL I 120 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE I 124 " --> pdb=" O VAL I 121 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU I 125 " --> pdb=" O PHE I 122 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N PHE I 126 " --> pdb=" O LEU I 123 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 91 removed outlier: 3.618A pdb=" N GLY J 63 " --> pdb=" O SER J 59 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA J 64 " --> pdb=" O LYS J 60 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS J 66 " --> pdb=" O VAL J 62 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE J 69 " --> pdb=" O GLY J 65 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ALA J 70 " --> pdb=" O CYS J 66 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N LEU J 71 " --> pdb=" O ALA J 67 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ALA J 72 " --> pdb=" O THR J 68 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLY J 73 " --> pdb=" O ILE J 69 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LEU J 85 " --> pdb=" O MET J 81 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE J 86 " --> pdb=" O PHE J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 123 removed outlier: 4.102A pdb=" N ALA J 96 " --> pdb=" O PRO J 93 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N LYS J 97 " --> pdb=" O ASN J 94 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL J 100 " --> pdb=" O LYS J 97 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU J 104 " --> pdb=" O GLY J 101 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU J 105 " --> pdb=" O TYR J 102 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE J 107 " --> pdb=" O LEU J 104 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR J 110 " --> pdb=" O PHE J 107 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE J 113 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU J 118 " --> pdb=" O LEU J 115 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU J 119 " --> pdb=" O PHE J 116 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL J 121 " --> pdb=" O LEU J 118 " (cutoff:3.500A) Processing helix chain 'M' and resid 105 through 118 Processing helix chain 'M' and resid 135 through 141 Processing helix chain 'M' and resid 148 through 166 removed outlier: 3.604A pdb=" N ILE M 159 " --> pdb=" O PHE M 155 " (cutoff:3.500A) Processing helix chain 'M' and resid 174 through 176 No H-bonds generated for 'chain 'M' and resid 174 through 176' Processing helix chain 'M' and resid 178 through 200 removed outlier: 3.731A pdb=" N SER M 187 " --> pdb=" O GLY M 183 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TRP M 189 " --> pdb=" O GLY M 185 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY M 196 " --> pdb=" O ALA M 192 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR M 200 " --> pdb=" O GLY M 196 " (cutoff:3.500A) Processing helix chain 'M' and resid 221 through 229 Processing helix chain 'M' and resid 232 through 264 removed outlier: 3.778A pdb=" N LEU M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASN M 243 " --> pdb=" O ARG M 239 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLY M 247 " --> pdb=" O ASN M 243 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N HIS M 248 " --> pdb=" O MET M 244 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR M 255 " --> pdb=" O LEU M 251 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ALA M 260 " --> pdb=" O GLY M 256 " (cutoff:3.500A) removed outlier: 4.136A 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: 3.890A pdb=" N GLY M 276 " --> pdb=" O PRO M 272 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU M 294 " --> pdb=" O LEU M 290 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER M 296 " --> pdb=" O ALA M 292 " (cutoff:3.500A) Processing helix chain 'P' and resid 52 through 64 removed outlier: 4.295A pdb=" N LYS P 63 " --> pdb=" O GLN P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 67 through 83 removed outlier: 4.269A pdb=" N ASP P 72 " --> pdb=" O ASP P 68 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU P 73 " --> pdb=" O LYS P 69 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR P 75 " --> pdb=" O GLN P 71 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE P 77 " --> pdb=" O GLU P 73 " (cutoff:3.500A) Processing helix chain 'P' and resid 86 through 89 No H-bonds generated for 'chain 'P' and resid 86 through 89' Processing helix chain 'P' and resid 100 through 108 removed outlier: 3.712A pdb=" N ILE P 105 " --> pdb=" O ARG P 101 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N SER P 107 " --> pdb=" O LYS P 103 " (cutoff:3.500A) Processing helix chain 'P' and resid 116 through 127 removed outlier: 3.585A pdb=" N ALA P 126 " --> pdb=" O PHE P 122 " (cutoff:3.500A) Processing helix chain 'P' and resid 130 through 146 removed outlier: 3.991A pdb=" N LEU P 134 " --> pdb=" O LEU P 131 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU P 135 " --> pdb=" O SER P 132 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU P 136 " --> pdb=" O ALA P 133 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N THR P 138 " --> pdb=" O LEU P 135 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASN P 140 " --> pdb=" O VAL P 137 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU P 142 " --> pdb=" O VAL P 139 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU P 144 " --> pdb=" O TYR P 141 " (cutoff:3.500A) Processing helix chain 'P' and resid 171 through 174 No H-bonds generated for 'chain 'P' and resid 171 through 174' Processing helix chain 'P' and resid 211 through 226 removed outlier: 3.602A pdb=" N GLU P 216 " --> pdb=" O ALA P 212 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU P 225 " --> pdb=" O PHE P 221 " (cutoff:3.500A) Processing helix chain 'Q' and resid 8 through 11 No H-bonds generated for 'chain 'Q' and resid 8 through 11' Processing helix chain 'Q' and resid 16 through 30 removed outlier: 3.728A pdb=" N LEU Q 27 " --> pdb=" O CYS Q 23 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ASN Q 29 " --> pdb=" O ASP Q 25 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL Q 30 " --> pdb=" O LEU Q 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 30 through 40 removed outlier: 3.748A pdb=" N THR R 34 " --> pdb=" O PRO R 30 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N GLU R 35 " --> pdb=" O LYS R 31 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL R 36 " --> pdb=" O GLU R 32 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LYS R 39 " --> pdb=" O GLU R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 53 No H-bonds generated for 'chain 'R' and resid 51 through 53' Processing helix chain 'R' and resid 152 through 154 No H-bonds generated for 'chain 'R' and resid 152 through 154' Processing helix chain 'R' and resid 157 through 167 removed outlier: 4.017A pdb=" N LYS R 161 " --> pdb=" O PRO R 157 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER R 162 " --> pdb=" O ALA R 158 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA R 165 " --> pdb=" O LYS R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 192 removed outlier: 3.514A pdb=" N ALA R 179 " --> pdb=" O GLU R 175 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 69 removed outlier: 3.518A pdb=" N ASN S 52 " --> pdb=" O ARG S 48 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE S 53 " --> pdb=" O ALA S 49 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET S 62 " --> pdb=" O LYS S 58 " (cutoff:3.500A) Processing helix chain 'S' and resid 72 through 78 Processing helix chain 'S' and resid 82 through 89 removed outlier: 4.091A pdb=" N VAL S 86 " --> pdb=" O ASP S 83 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG S 87 " --> pdb=" O PRO S 84 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N PHE S 89 " --> pdb=" O VAL S 86 " (cutoff:3.500A) Processing helix chain 'S' and resid 115 through 130 removed outlier: 3.940A pdb=" N ILE S 119 " --> pdb=" O LEU S 115 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR S 120 " --> pdb=" O ASN S 116 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ARG S 124 " --> pdb=" O THR S 120 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA S 128 " --> pdb=" O ARG S 124 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR S 129 " --> pdb=" O ALA S 125 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR S 130 " --> pdb=" O THR S 126 " (cutoff:3.500A) Processing helix chain 'S' and resid 146 through 149 No H-bonds generated for 'chain 'S' and resid 146 through 149' Processing helix chain 'S' and resid 172 through 182 removed outlier: 3.664A pdb=" N SER S 176 " --> pdb=" O PHE S 172 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU S 177 " --> pdb=" O GLY S 173 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE S 178 " --> pdb=" O GLN S 174 " (cutoff:3.500A) Processing helix chain 'S' and resid 213 through 220 removed outlier: 5.360A pdb=" N LYS S 218 " --> pdb=" O ASP S 214 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N GLN S 219 " --> pdb=" O LEU S 215 " (cutoff:3.500A) Processing helix chain 'S' and resid 227 through 230 No H-bonds generated for 'chain 'S' and resid 227 through 230' Processing helix chain 'S' and resid 239 through 314 removed outlier: 3.754A pdb=" N ARG S 244 " --> pdb=" O SER S 240 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU S 248 " --> pdb=" O ARG S 244 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR S 256 " --> pdb=" O GLY S 252 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA S 268 " --> pdb=" O CYS S 264 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU S 275 " --> pdb=" O MET S 271 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN S 276 " --> pdb=" O SER S 272 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU S 285 " --> pdb=" O ALA S 281 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU S 290 " --> pdb=" O GLY S 286 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS S 295 " --> pdb=" O ASP S 291 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA S 298 " --> pdb=" O ARG S 294 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU S 306 " --> pdb=" O THR S 302 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ILE S 307 " --> pdb=" O GLU S 303 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALA S 313 " --> pdb=" O ALA S 309 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N LEU S 314 " --> pdb=" O GLY S 310 " (cutoff:3.500A) Processing helix chain 'T' and resid 58 through 74 removed outlier: 3.912A pdb=" N ILE T 67 " --> pdb=" O SER T 63 " (cutoff:3.500A) Proline residue: T 68 - end of helix removed outlier: 3.637A pdb=" N TRP T 73 " --> pdb=" O ALA T 69 " (cutoff:3.500A) Processing helix chain 'T' and resid 157 through 159 No H-bonds generated for 'chain 'T' and resid 157 through 159' Processing helix chain 'T' and resid 207 through 210 No H-bonds generated for 'chain 'T' and resid 207 through 210' Processing helix chain 'T' and resid 231 through 248 removed outlier: 4.037A pdb=" N GLU T 247 " --> pdb=" O LYS T 243 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N GLN T 248 " --> pdb=" O ASN T 244 " (cutoff:3.500A) Processing helix chain 'T' and resid 268 through 278 Processing helix chain 'T' and resid 281 through 283 No H-bonds generated for 'chain 'T' and resid 281 through 283' Processing helix chain 'T' and resid 296 through 315 Proline residue: T 303 - end of helix removed outlier: 3.670A pdb=" N TYR T 312 " --> pdb=" O ALA T 308 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE T 313 " --> pdb=" O MET T 309 " (cutoff:3.500A) Processing helix chain 'T' and resid 327 through 340 removed outlier: 3.551A pdb=" N SER T 338 " --> pdb=" O TYR T 334 " (cutoff:3.500A) Processing helix chain 'T' and resid 347 through 349 No H-bonds generated for 'chain 'T' and resid 347 through 349' Processing helix chain 'T' and resid 352 through 362 removed outlier: 4.082A pdb=" N PHE T 355 " --> pdb=" O GLY T 352 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ARG T 360 " --> pdb=" O LEU T 357 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU T 361 " --> pdb=" O HIS T 358 " (cutoff:3.500A) Processing helix chain 'T' and resid 393 through 401 Processing helix chain 'T' and resid 431 through 434 removed outlier: 3.973A pdb=" N ALA T 434 " --> pdb=" O GLY T 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 431 through 434' Processing helix chain 'T' and resid 437 through 459 removed outlier: 4.483A pdb=" N GLN T 441 " --> pdb=" O PRO T 437 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N VAL T 442 " --> pdb=" O GLY T 438 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N THR T 445 " --> pdb=" O GLN T 441 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N LEU T 448 " --> pdb=" O GLY T 444 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL T 456 " --> pdb=" O GLN T 452 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N ALA T 458 " --> pdb=" O ARG T 454 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N PHE T 459 " --> pdb=" O GLU T 455 " (cutoff:3.500A) Processing helix chain 'T' and resid 471 through 480 Processing helix chain 'T' and resid 482 through 484 No H-bonds generated for 'chain 'T' and resid 482 through 484' Processing helix chain 'T' and resid 494 through 505 removed outlier: 3.615A pdb=" N THR T 498 " --> pdb=" O ILE T 494 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL T 499 " --> pdb=" O GLU T 495 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL T 501 " --> pdb=" O GLN T 497 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA T 504 " --> pdb=" O ALA T 500 " (cutoff:3.500A) Processing helix chain 'T' and resid 518 through 521 No H-bonds generated for 'chain 'T' and resid 518 through 521' Processing helix chain 'T' and resid 523 through 526 No H-bonds generated for 'chain 'T' and resid 523 through 526' Processing helix chain 'T' and resid 531 through 539 removed outlier: 3.610A pdb=" N ALA T 538 " --> pdb=" O LYS T 534 " (cutoff:3.500A) Processing helix chain 'T' and resid 547 through 555 Processing helix chain 'U' and resid 42 through 49 Processing helix chain 'U' and resid 59 through 62 No H-bonds generated for 'chain 'U' and resid 59 through 62' Processing helix chain 'U' and resid 65 through 72 Processing helix chain 'U' and resid 74 through 76 No H-bonds generated for 'chain 'U' and resid 74 through 76' Processing helix chain 'U' and resid 192 through 194 No H-bonds generated for 'chain 'U' and resid 192 through 194' Processing helix chain 'U' and resid 207 through 210 No H-bonds generated for 'chain 'U' and resid 207 through 210' Processing helix chain 'U' and resid 231 through 244 Processing helix chain 'U' and resid 266 through 279 removed outlier: 3.682A pdb=" N THR U 279 " --> pdb=" O LEU U 275 " (cutoff:3.500A) Processing helix chain 'U' and resid 281 through 284 Processing helix chain 'U' and resid 296 through 300 Processing helix chain 'U' and resid 302 through 315 removed outlier: 3.803A pdb=" N ALA U 310 " --> pdb=" O GLY U 306 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N TYR U 312 " --> pdb=" O ALA U 308 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) Processing helix chain 'U' and resid 327 through 340 removed outlier: 4.065A pdb=" N MET U 337 " --> pdb=" O ALA U 333 " (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 363 removed outlier: 4.255A pdb=" N PHE U 355 " --> pdb=" O GLY U 352 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU U 357 " --> pdb=" O VAL U 354 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER U 359 " --> pdb=" O TYR U 356 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG U 360 " --> pdb=" O LEU U 357 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU U 361 " --> pdb=" O HIS U 358 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU U 363 " --> pdb=" O ARG U 360 " (cutoff:3.500A) Processing helix chain 'U' and resid 370 through 372 No H-bonds generated for 'chain 'U' and resid 370 through 372' Processing helix chain 'U' and resid 393 through 401 removed outlier: 3.681A pdb=" N ASN U 397 " --> pdb=" O TYR U 393 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER U 400 " --> pdb=" O THR U 396 " (cutoff:3.500A) Processing helix chain 'U' and resid 437 through 456 removed outlier: 3.504A pdb=" N GLN U 441 " --> pdb=" O PRO U 437 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL U 442 " --> pdb=" O GLY U 438 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLY U 444 " --> pdb=" O LYS U 440 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N THR U 445 " --> pdb=" O GLN U 441 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLU U 449 " --> pdb=" O THR U 445 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLU U 455 " --> pdb=" O ALA U 451 " (cutoff:3.500A) Processing helix chain 'U' and resid 466 through 468 No H-bonds generated for 'chain 'U' and resid 466 through 468' Processing helix chain 'U' and resid 472 through 483 removed outlier: 3.749A pdb=" N ARG U 479 " --> pdb=" O GLU U 475 " (cutoff:3.500A) Processing helix chain 'U' and resid 494 through 500 removed outlier: 3.701A pdb=" N VAL U 499 " --> pdb=" O GLU U 495 " (cutoff:3.500A) Processing helix chain 'U' and resid 502 through 505 No H-bonds generated for 'chain 'U' and resid 502 through 505' Processing helix chain 'U' and resid 521 through 527 Processing helix chain 'U' and resid 532 through 539 Processing helix chain 'U' and resid 544 through 556 removed outlier: 3.635A pdb=" N ALA U 548 " --> pdb=" O PRO U 544 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N HIS U 549 " --> pdb=" O ALA U 545 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA U 552 " --> pdb=" O ALA U 548 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU U 554 " --> pdb=" O LEU U 550 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ARG U 555 " --> pdb=" O LYS U 551 " (cutoff:3.500A) Processing helix chain 'V' and resid 59 through 65 removed outlier: 3.852A pdb=" N GLN V 64 " --> pdb=" O GLN V 60 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS V 65 " --> pdb=" O HIS V 61 " (cutoff:3.500A) Processing helix chain 'V' and resid 71 through 73 No H-bonds generated for 'chain 'V' and resid 71 through 73' Processing helix chain 'V' and resid 135 through 137 No H-bonds generated for 'chain 'V' and resid 135 through 137' Processing helix chain 'V' and resid 157 through 159 No H-bonds generated for 'chain 'V' and resid 157 through 159' Processing helix chain 'V' and resid 207 through 212 removed outlier: 3.565A pdb=" N ALA V 211 " --> pdb=" O LYS V 207 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU V 212 " --> pdb=" O ALA V 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 207 through 212' Processing helix chain 'V' and resid 231 through 247 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 278 Processing helix chain 'V' and resid 281 through 284 Processing helix chain 'V' and resid 296 through 315 Proline residue: V 303 - end of helix removed outlier: 3.871A pdb=" N TYR V 312 " --> pdb=" O ALA V 308 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N PHE V 313 " --> pdb=" O MET V 309 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG V 314 " --> pdb=" O ALA V 310 " (cutoff:3.500A) Processing helix chain 'V' and resid 327 through 339 Processing helix chain 'V' and resid 347 through 349 No H-bonds generated for 'chain 'V' and resid 347 through 349' Processing helix chain 'V' and resid 352 through 362 removed outlier: 4.163A pdb=" N PHE V 355 " --> pdb=" O GLY V 352 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU V 357 " --> pdb=" O VAL V 354 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG V 360 " --> pdb=" O LEU V 357 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU V 361 " --> pdb=" O HIS V 358 " (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 395 through 399 removed outlier: 3.527A pdb=" N ILE V 399 " --> pdb=" O ALA V 395 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 395 through 399' Processing helix chain 'V' and resid 410 through 413 No H-bonds generated for 'chain 'V' and resid 410 through 413' Processing helix chain 'V' and resid 439 through 452 removed outlier: 4.715A pdb=" N THR V 445 " --> pdb=" O GLN V 441 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU V 446 " --> pdb=" O VAL V 442 " (cutoff:3.500A) Processing helix chain 'V' and resid 471 through 483 removed outlier: 4.416A pdb=" N ARG V 479 " --> pdb=" O GLU V 475 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU V 482 " --> pdb=" O ALA V 478 " (cutoff:3.500A) Processing helix chain 'V' and resid 494 through 505 removed outlier: 4.093A pdb=" N VAL V 499 " --> pdb=" O GLU V 495 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA V 500 " --> pdb=" O ARG V 496 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA V 504 " --> pdb=" O ALA V 500 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR V 505 " --> pdb=" O VAL V 501 " (cutoff:3.500A) Processing helix chain 'V' and resid 517 through 527 removed outlier: 3.968A pdb=" N GLU V 522 " --> pdb=" O VAL V 518 " (cutoff:3.500A) Processing helix chain 'V' and resid 531 through 539 removed outlier: 3.597A pdb=" N LYS V 537 " --> pdb=" O PHE V 533 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA V 538 " --> pdb=" O LYS V 534 " (cutoff:3.500A) Processing helix chain 'V' and resid 544 through 555 removed outlier: 3.994A pdb=" N ALA V 548 " --> pdb=" O PRO V 544 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N HIS V 549 " --> pdb=" O ALA V 545 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA V 552 " --> pdb=" O ALA V 548 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG V 555 " --> pdb=" O LYS V 551 " (cutoff:3.500A) Processing helix chain 'X' and resid 115 through 117 No H-bonds generated for 'chain 'X' and resid 115 through 117' Processing helix chain 'X' and resid 167 through 170 No H-bonds generated for 'chain 'X' and resid 167 through 170' Processing helix chain 'X' and resid 190 through 200 removed outlier: 3.555A pdb=" N GLU X 195 " --> pdb=" O VAL X 191 " (cutoff:3.500A) Processing helix chain 'X' and resid 218 through 228 removed outlier: 3.911A pdb=" N LEU X 223 " --> pdb=" O GLU X 219 " (cutoff:3.500A) Processing helix chain 'X' and resid 239 through 241 No H-bonds generated for 'chain 'X' and resid 239 through 241' Processing helix chain 'X' and resid 261 through 274 removed outlier: 3.730A pdb=" N VAL X 268 " --> pdb=" O THR X 264 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA X 269 " --> pdb=" O GLY X 265 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP X 274 " --> pdb=" O GLU X 270 " (cutoff:3.500A) Processing helix chain 'X' and resid 287 through 298 removed outlier: 4.147A pdb=" N VAL X 297 " --> pdb=" O ALA X 293 " (cutoff:3.500A) Processing helix chain 'X' and resid 314 through 323 Processing helix chain 'X' and resid 349 through 352 No H-bonds generated for 'chain 'X' and resid 349 through 352' Processing helix chain 'X' and resid 355 through 357 No H-bonds generated for 'chain 'X' and resid 355 through 357' Processing helix chain 'X' and resid 366 through 370 Processing helix chain 'X' and resid 394 through 414 removed outlier: 4.255A pdb=" N VAL X 399 " --> pdb=" O GLU X 395 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA X 400 " --> pdb=" O HIS X 396 " (cutoff:3.500A) Processing helix chain 'X' and resid 416 through 420 removed outlier: 3.841A pdb=" N LEU X 420 " --> pdb=" O ILE X 417 " (cutoff:3.500A) Processing helix chain 'X' and resid 434 through 439 Processing helix chain 'X' and resid 451 through 454 No H-bonds generated for 'chain 'X' and resid 451 through 454' Processing helix chain 'X' and resid 464 through 475 removed outlier: 3.988A pdb=" N SER X 468 " --> pdb=" O ALA X 464 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY X 469 " --> pdb=" O ASP X 465 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL X 473 " --> pdb=" O GLY X 469 " (cutoff:3.500A) Processing helix chain 'X' and resid 484 through 486 No H-bonds generated for 'chain 'X' and resid 484 through 486' Processing helix chain 'X' and resid 492 through 507 removed outlier: 3.744A pdb=" N LYS X 496 " --> pdb=" O ILE X 492 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS X 501 " --> pdb=" O GLU X 497 " (cutoff:3.500A) Processing helix chain 'X' and resid 531 through 533 No H-bonds generated for 'chain 'X' and resid 531 through 533' Processing helix chain 'Y' and resid 115 through 117 No H-bonds generated for 'chain 'Y' and resid 115 through 117' Processing helix chain 'Y' and resid 165 through 169 Processing helix chain 'Y' and resid 189 through 202 Processing helix chain 'Y' and resid 217 through 229 removed outlier: 3.653A pdb=" N GLU Y 226 " --> pdb=" O ASP Y 222 " (cutoff:3.500A) Processing helix chain 'Y' and resid 236 through 241 removed outlier: 4.535A 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 removed outlier: 3.902A pdb=" N PHE Y 272 " --> pdb=" O VAL Y 268 " (cutoff:3.500A) Processing helix chain 'Y' and resid 287 through 300 removed outlier: 3.569A pdb=" N ALA Y 299 " --> pdb=" O SER Y 295 " (cutoff:3.500A) Processing helix chain 'Y' and resid 314 through 324 removed outlier: 3.875A pdb=" N LEU Y 321 " --> pdb=" O ASP Y 317 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG Y 324 " --> pdb=" O GLY Y 320 " (cutoff:3.500A) Processing helix chain 'Y' and resid 342 through 344 No H-bonds generated for 'chain 'Y' and resid 342 through 344' Processing helix chain 'Y' and resid 349 through 356 removed outlier: 3.532A pdb=" N THR Y 353 " --> pdb=" O PRO Y 349 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA Y 356 " --> pdb=" O ALA Y 352 " (cutoff:3.500A) Processing helix chain 'Y' and resid 366 through 371 removed outlier: 3.660A pdb=" N LEU Y 371 " --> pdb=" O SER Y 367 " (cutoff:3.500A) Processing helix chain 'Y' and resid 393 through 417 removed outlier: 3.753A pdb=" N TYR Y 397 " --> pdb=" O GLY Y 393 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR Y 410 " --> pdb=" O VAL Y 406 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS Y 411 " --> pdb=" O LEU Y 407 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASP Y 415 " --> pdb=" O LYS Y 411 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ILE Y 416 " --> pdb=" O ASN Y 412 " (cutoff:3.500A) Processing helix chain 'Y' and resid 428 through 442 removed outlier: 4.337A pdb=" N THR Y 432 " --> pdb=" O GLU Y 428 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N VAL Y 433 " --> pdb=" O ASP Y 429 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS Y 438 " --> pdb=" O ALA Y 434 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG Y 441 " --> pdb=" O ARG Y 437 " (cutoff:3.500A) Processing helix chain 'Y' and resid 464 through 475 removed outlier: 3.530A pdb=" N GLY Y 472 " --> pdb=" O SER Y 468 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL Y 473 " --> pdb=" O GLY Y 469 " (cutoff:3.500A) Processing helix chain 'Y' and resid 483 through 486 Processing helix chain 'Y' and resid 496 through 508 removed outlier: 3.622A pdb=" N ASP Y 505 " --> pdb=" O LYS Y 501 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ILE Y 506 " --> pdb=" O MET Y 502 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ALA Y 507 " --> pdb=" O ALA Y 503 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N SER Y 508 " --> pdb=" O LYS Y 504 " (cutoff:3.500A) Processing helix chain 'Y' and resid 519 through 522 No H-bonds generated for 'chain 'Y' and resid 519 through 522' Processing helix chain 'Y' and resid 527 through 530 No H-bonds generated for 'chain 'Y' and resid 527 through 530' Processing helix chain 'Y' and resid 546 through 554 removed outlier: 3.558A pdb=" N LYS Y 550 " --> pdb=" O GLU Y 546 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA Y 553 " --> pdb=" O PHE Y 549 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU Y 554 " --> pdb=" O LYS Y 550 " (cutoff:3.500A) 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 167 through 170 No H-bonds generated for 'chain 'Z' and resid 167 through 170' Processing helix chain 'Z' and resid 191 through 203 removed outlier: 3.531A pdb=" N ILE Z 197 " --> pdb=" O ILE Z 193 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N LYS Z 202 " --> pdb=" O ASN Z 198 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ALA Z 203 " --> pdb=" O ASN Z 199 " (cutoff:3.500A) Processing helix chain 'Z' and resid 217 through 229 removed outlier: 3.647A pdb=" N LEU Z 223 " --> pdb=" O GLU Z 219 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE Z 228 " --> pdb=" O TYR Z 224 " (cutoff:3.500A) Processing helix chain 'Z' and resid 256 through 273 removed outlier: 4.887A pdb=" N ALA Z 262 " --> pdb=" O ARG Z 258 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LEU Z 263 " --> pdb=" O ALA Z 259 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU Z 266 " --> pdb=" O ALA Z 262 " (cutoff:3.500A) Processing helix chain 'Z' and resid 287 through 297 removed outlier: 3.819A pdb=" N ASN Z 294 " --> pdb=" O THR Z 291 " (cutoff:3.500A) Processing helix chain 'Z' and resid 312 through 324 removed outlier: 4.140A pdb=" N ALA Z 315 " --> pdb=" O PRO Z 312 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR Z 316 " --> pdb=" O THR Z 313 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASP Z 317 " --> pdb=" O LEU Z 314 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU Z 318 " --> pdb=" O ALA Z 315 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN Z 322 " --> pdb=" O GLY Z 319 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N GLU Z 323 " --> pdb=" O GLY Z 320 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG Z 324 " --> pdb=" O LEU Z 321 " (cutoff:3.500A) Processing helix chain 'Z' and resid 349 through 352 No H-bonds generated for 'chain 'Z' and resid 349 through 352' Processing helix chain 'Z' and resid 368 through 371 Processing helix chain 'Z' and resid 394 through 412 removed outlier: 3.969A pdb=" N VAL Z 399 " --> pdb=" O GLU Z 395 " (cutoff:3.500A) Processing helix chain 'Z' and resid 414 through 420 removed outlier: 3.893A pdb=" N ILE Z 419 " --> pdb=" O ASP Z 415 " (cutoff:3.500A) Processing helix chain 'Z' and resid 430 through 442 removed outlier: 3.634A pdb=" N ALA Z 434 " --> pdb=" O LYS Z 430 " (cutoff:3.500A) Processing helix chain 'Z' and resid 450 through 454 removed outlier: 4.139A pdb=" N THR Z 454 " --> pdb=" O GLU Z 451 " (cutoff:3.500A) Processing helix chain 'Z' and resid 463 through 475 removed outlier: 4.070A pdb=" N GLY Z 472 " --> pdb=" O SER Z 468 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N VAL Z 473 " --> pdb=" O GLY Z 469 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU Z 474 " --> pdb=" O PHE Z 470 " (cutoff:3.500A) Processing helix chain 'Z' and resid 483 through 486 removed outlier: 3.739A pdb=" N PHE Z 486 " --> pdb=" O GLU Z 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 483 through 486' Processing helix chain 'Z' and resid 494 through 507 removed outlier: 3.872A pdb=" N LYS Z 498 " --> pdb=" O GLU Z 494 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA Z 499 " --> pdb=" O VAL Z 495 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA Z 503 " --> pdb=" O ALA Z 499 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE Z 506 " --> pdb=" O MET Z 502 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA Z 507 " --> pdb=" O ALA Z 503 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain '2' and resid 368 through 371 removed outlier: 4.324A pdb=" N ILE 2 368 " --> pdb=" O VAL 2 379 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ALA 2 412 " --> pdb=" O LEU 2 378 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N GLN 2 380 " --> pdb=" O ALA 2 412 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ALA 2 414 " --> pdb=" O GLN 2 380 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N VAL 2 382 " --> pdb=" O ALA 2 414 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N VAL 2 416 " --> pdb=" O VAL 2 382 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '7' and resid 36 through 40 removed outlier: 3.728A pdb=" N ASN 7 38 " --> pdb=" O THR 7 49 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU 7 47 " --> pdb=" O ALA 7 40 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA 7 52 " --> pdb=" O ALA 7 55 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ALA 7 55 " --> pdb=" O ALA 7 52 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'R' and resid 72 through 75 removed outlier: 6.912A pdb=" N THR R 142 " --> pdb=" O ASN R 73 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N TYR R 75 " --> pdb=" O THR R 142 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE R 144 " --> pdb=" O TYR R 75 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'R' and resid 96 through 100 removed outlier: 3.506A pdb=" N VAL R 89 " --> pdb=" O VAL R 100 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL R 115 " --> pdb=" O PRO R 92 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU R 125 " --> pdb=" O LEU R 118 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'S' and resid 100 through 102 removed outlier: 6.310A pdb=" N SER S 189 " --> pdb=" O VAL S 101 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA S 208 " --> pdb=" O ILE S 192 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N PHE S 194 " --> pdb=" O THR S 206 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'S' and resid 139 through 142 removed outlier: 3.708A pdb=" N GLN S 159 " --> pdb=" O VAL S 139 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N SER S 141 " --> pdb=" O GLN S 159 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA S 161 " --> pdb=" O SER S 141 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'T' and resid 143 through 145 removed outlier: 6.872A pdb=" N ARG T 96 " --> pdb=" O LEU T 88 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N VAL T 90 " --> pdb=" O ILE T 94 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE T 94 " --> pdb=" O VAL T 90 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU T 107 " --> pdb=" O ALA T 119 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N GLN T 149 " --> pdb=" O LEU T 108 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N CYS T 110 " --> pdb=" O THR T 147 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N THR T 147 " --> pdb=" O CYS T 110 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'T' and resid 152 through 155 Processing sheet with id= I, first strand: chain 'T' and resid 223 through 225 Processing sheet with id= J, first strand: chain 'T' and resid 288 through 290 removed outlier: 3.620A pdb=" N VAL T 288 " --> pdb=" O TYR T 259 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N HIS T 319 " --> pdb=" O TYR T 256 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N VAL T 258 " --> pdb=" O HIS T 319 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LEU T 321 " --> pdb=" O VAL T 258 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N VAL T 260 " --> pdb=" O LEU T 321 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE T 323 " --> pdb=" O VAL T 260 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL T 262 " --> pdb=" O ILE T 323 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ASP T 325 " --> pdb=" O VAL T 262 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N THR T 378 " --> pdb=" O ILE T 322 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N TYR T 324 " --> pdb=" O THR T 378 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N PHE T 380 " --> pdb=" O TYR T 324 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'U' and resid 85 through 91 removed outlier: 3.506A pdb=" N ARG U 86 " --> pdb=" O TYR U 98 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ARG U 96 " --> pdb=" O LEU U 88 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N VAL U 90 " --> pdb=" O ILE U 94 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ILE U 94 " --> pdb=" O VAL U 90 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASN U 121 " --> pdb=" O GLY U 128 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL U 130 " --> pdb=" O ALA U 119 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ALA U 119 " --> pdb=" O VAL U 130 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'U' and resid 152 through 155 removed outlier: 4.094A pdb=" N VAL U 153 " --> pdb=" O SER U 183 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER U 183 " --> pdb=" O VAL U 153 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'U' and resid 404 through 408 removed outlier: 7.963A pdb=" N GLU U 221 " --> pdb=" O LEU U 377 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N ALA U 379 " --> pdb=" O GLU U 221 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE U 223 " --> pdb=" O ALA U 379 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N GLY U 225 " --> pdb=" O PRO U 381 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE U 383 " --> pdb=" O GLY U 225 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL U 262 " --> pdb=" O ASP U 325 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'V' and resid 143 through 145 removed outlier: 3.634A pdb=" N GLY V 85 " --> pdb=" O VAL V 144 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ARG V 96 " --> pdb=" O LEU V 88 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N VAL V 90 " --> pdb=" O ILE V 94 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE V 94 " --> pdb=" O VAL V 90 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL V 130 " --> pdb=" O MET V 118 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'V' and resid 152 through 155 removed outlier: 3.686A pdb=" N SER V 183 " --> pdb=" O VAL V 153 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'V' and resid 404 through 408 Processing sheet with id= Q, first strand: chain 'V' and resid 285 through 290 removed outlier: 9.173A pdb=" N ILE V 286 " --> pdb=" O VAL V 255 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N CYS V 257 " --> pdb=" O ILE V 286 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N VAL V 288 " --> pdb=" O CYS V 257 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TYR V 259 " --> pdb=" O VAL V 288 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ALA V 290 " --> pdb=" O TYR V 259 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ALA V 261 " --> pdb=" O ALA V 290 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N HIS V 319 " --> pdb=" O TYR V 256 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N VAL V 258 " --> pdb=" O HIS V 319 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU V 321 " --> pdb=" O VAL V 258 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N VAL V 260 " --> pdb=" O LEU V 321 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE V 323 " --> pdb=" O VAL V 260 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N VAL V 262 " --> pdb=" O ILE V 323 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N SER V 376 " --> pdb=" O GLY V 320 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ILE V 322 " --> pdb=" O SER V 376 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N THR V 378 " --> pdb=" O ILE V 322 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N TYR V 324 " --> pdb=" O THR V 378 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N PHE V 380 " --> pdb=" O TYR V 324 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'X' and resid 84 through 86 removed outlier: 6.029A pdb=" N ARG X 51 " --> pdb=" O VAL X 40 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N VAL X 40 " --> pdb=" O ARG X 51 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'X' and resid 73 through 75 removed outlier: 3.511A pdb=" N GLU X 64 " --> pdb=" O VAL X 103 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'X' and resid 110 through 112 removed outlier: 3.586A pdb=" N VAL X 111 " --> pdb=" O TRP X 141 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'X' and resid 179 through 181 removed outlier: 6.816A pdb=" N ALA X 360 " --> pdb=" O GLY X 180 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'X' and resid 244 through 249 removed outlier: 6.998A pdb=" N SER X 208 " --> pdb=" O THR X 245 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N VAL X 247 " --> pdb=" O SER X 208 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N PHE X 210 " --> pdb=" O VAL X 247 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N GLY X 249 " --> pdb=" O PHE X 210 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N GLY X 212 " --> pdb=" O GLY X 249 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N PHE X 207 " --> pdb=" O ASP X 279 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU X 281 " --> pdb=" O PHE X 207 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N SER X 332 " --> pdb=" O VAL X 280 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N LEU X 282 " --> pdb=" O SER X 332 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N THR X 334 " --> pdb=" O LEU X 282 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N VAL X 284 " --> pdb=" O THR X 334 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N VAL X 336 " --> pdb=" O VAL X 284 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'X' and resid 559 through 561 Processing sheet with id= X, first strand: chain 'Y' and resid 38 through 44 removed outlier: 6.361A pdb=" N ASP Y 49 " --> pdb=" O SER Y 41 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL Y 43 " --> pdb=" O VAL Y 47 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL Y 47 " --> pdb=" O VAL Y 43 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN Y 78 " --> pdb=" O ARG Y 86 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE Y 88 " --> pdb=" O VAL Y 76 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N VAL Y 76 " --> pdb=" O ILE Y 88 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'Y' and resid 110 through 113 removed outlier: 3.703A pdb=" N TRP Y 141 " --> pdb=" O VAL Y 111 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL Y 113 " --> pdb=" O ASP Y 139 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP Y 139 " --> pdb=" O VAL Y 113 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'Y' and resid 360 through 362 removed outlier: 8.390A pdb=" N ILE Y 179 " --> pdb=" O ILE Y 333 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N SER Y 335 " --> pdb=" O ILE Y 179 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N LEU Y 181 " --> pdb=" O SER Y 335 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLN Y 337 " --> pdb=" O LEU Y 181 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL Y 284 " --> pdb=" O VAL Y 336 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA Y 338 " --> pdb=" O VAL Y 284 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'Z' and resid 39 through 44 removed outlier: 6.473A pdb=" N ASP Z 49 " --> pdb=" O SER Z 41 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N VAL Z 43 " --> pdb=" O VAL Z 47 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL Z 47 " --> pdb=" O VAL Z 43 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL Z 50 " --> pdb=" O VAL Z 85 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN Z 78 " --> pdb=" O ARG Z 86 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ILE Z 88 " --> pdb=" O VAL Z 76 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL Z 76 " --> pdb=" O ILE Z 88 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'Z' and resid 110 through 113 Processing sheet with id= AC, first strand: chain 'Z' and resid 179 through 182 removed outlier: 6.717A pdb=" N ALA Z 360 " --> pdb=" O GLY Z 180 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N PHE Z 182 " --> pdb=" O ALA Z 360 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N THR Z 362 " --> pdb=" O PHE Z 182 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'Z' and resid 244 through 249 removed outlier: 6.669A pdb=" N SER Z 208 " --> pdb=" O THR Z 245 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N VAL Z 247 " --> pdb=" O SER Z 208 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N PHE Z 210 " --> pdb=" O VAL Z 247 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N GLY Z 249 " --> pdb=" O PHE Z 210 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N GLY Z 212 " --> pdb=" O GLY Z 249 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N LEU Z 281 " --> pdb=" O VAL Z 209 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ALA Z 211 " --> pdb=" O LEU Z 281 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N PHE Z 283 " --> pdb=" O ALA Z 211 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL Z 213 " --> pdb=" O PHE Z 283 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ASP Z 285 " --> pdb=" O VAL Z 213 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'Z' and resid 559 through 561 2028 hydrogen bonds defined for protein. 5514 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: 15.93 Time building geometry restraints manager: 17.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 16455 1.34 - 1.46: 8984 1.46 - 1.58: 28980 1.58 - 1.70: 21 1.70 - 1.82: 254 Bond restraints: 54694 Sorted by residual: bond pdb=" C4 ATP U1001 " pdb=" C5 ATP U1001 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.40e+01 bond pdb=" C4 ATP V1001 " pdb=" C5 ATP V1001 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.12e+01 bond pdb=" C4 ATP T1001 " pdb=" C5 ATP T1001 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.41e+01 bond pdb=" C5 ATP T1001 " pdb=" C6 ATP T1001 " ideal model delta sigma weight residual 1.409 1.474 -0.065 1.00e-02 1.00e+04 4.25e+01 bond pdb=" C5 ATP U1001 " pdb=" C6 ATP U1001 " ideal model delta sigma weight residual 1.409 1.474 -0.065 1.00e-02 1.00e+04 4.24e+01 ... (remaining 54689 not shown) Histogram of bond angle deviations from ideal: 99.02 - 106.46: 1450 106.46 - 113.90: 31636 113.90 - 121.35: 28447 121.35 - 128.79: 12387 128.79 - 136.23: 252 Bond angle restraints: 74172 Sorted by residual: angle pdb=" PB ATP V1001 " pdb=" O3B ATP V1001 " pdb=" PG ATP V1001 " ideal model delta sigma weight residual 139.87 119.82 20.05 1.00e+00 1.00e+00 4.02e+02 angle pdb=" PA ATP V1001 " pdb=" O3A ATP V1001 " pdb=" PB ATP V1001 " ideal model delta sigma weight residual 136.83 116.87 19.96 1.00e+00 1.00e+00 3.99e+02 angle pdb=" PB ATP T1001 " pdb=" O3B ATP T1001 " pdb=" PG ATP T1001 " ideal model delta sigma weight residual 139.87 120.14 19.73 1.00e+00 1.00e+00 3.89e+02 angle pdb=" PB ATP U1001 " pdb=" O3B ATP U1001 " pdb=" PG ATP U1001 " ideal model delta sigma weight residual 139.87 121.52 18.35 1.00e+00 1.00e+00 3.37e+02 angle pdb=" PA ATP U1001 " pdb=" O3A ATP U1001 " pdb=" PB ATP U1001 " ideal model delta sigma weight residual 136.83 121.02 15.81 1.00e+00 1.00e+00 2.50e+02 ... (remaining 74167 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.30: 31435 26.30 - 52.60: 1415 52.60 - 78.91: 142 78.91 - 105.21: 36 105.21 - 131.51: 2 Dihedral angle restraints: 33030 sinusoidal: 12669 harmonic: 20361 Sorted by residual: dihedral pdb=" CA ALA X 307 " pdb=" C ALA X 307 " pdb=" N VAL X 308 " pdb=" CA VAL X 308 " ideal model delta harmonic sigma weight residual -180.00 -125.49 -54.51 0 5.00e+00 4.00e-02 1.19e+02 dihedral pdb=" CA ALA Z 307 " pdb=" C ALA Z 307 " pdb=" N VAL Z 308 " pdb=" CA VAL Z 308 " ideal model delta harmonic sigma weight residual -180.00 -131.67 -48.33 0 5.00e+00 4.00e-02 9.34e+01 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 -139.99 -40.01 0 5.00e+00 4.00e-02 6.40e+01 ... (remaining 33027 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 7282 0.074 - 0.148: 1268 0.148 - 0.222: 126 0.222 - 0.296: 11 0.296 - 0.370: 3 Chirality restraints: 8690 Sorted by residual: chirality pdb=" CB ILE T 417 " pdb=" CA ILE T 417 " pdb=" CG1 ILE T 417 " pdb=" CG2 ILE T 417 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" CB VAL 2 41 " pdb=" CA VAL 2 41 " pdb=" CG1 VAL 2 41 " pdb=" CG2 VAL 2 41 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" CB ILE V 542 " pdb=" CA ILE V 542 " pdb=" CG1 ILE V 542 " pdb=" CG2 ILE V 542 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.64e+00 ... (remaining 8687 not shown) Planarity restraints: 9512 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS P 148 " 0.031 2.00e-02 2.50e+03 6.40e-02 4.09e+01 pdb=" C HIS P 148 " -0.111 2.00e-02 2.50e+03 pdb=" O HIS P 148 " 0.042 2.00e-02 2.50e+03 pdb=" N LYS P 149 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA Z 350 " -0.058 5.00e-02 4.00e+02 8.82e-02 1.24e+01 pdb=" N PRO Z 351 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO Z 351 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO Z 351 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL 1 107 " 0.054 5.00e-02 4.00e+02 8.00e-02 1.02e+01 pdb=" N PRO 1 108 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO 1 108 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO 1 108 " 0.045 5.00e-02 4.00e+02 ... (remaining 9509 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.32: 61 2.32 - 2.97: 24866 2.97 - 3.61: 81921 3.61 - 4.26: 127184 4.26 - 4.90: 202616 Nonbonded interactions: 436648 Sorted by model distance: nonbonded pdb=" OG1 THR X 190 " pdb="MG MG X 602 " model vdw 1.680 2.170 nonbonded pdb=" O3B ADP X 601 " pdb="MG MG X 602 " model vdw 1.957 2.170 nonbonded pdb=" O3G ATP U1001 " pdb="MG MG U1002 " model vdw 2.011 2.170 nonbonded pdb=" O LYS X 498 " pdb=" CG MET X 502 " model vdw 2.034 3.440 nonbonded pdb=" O3G ATP V1001 " pdb="MG MG V1002 " model vdw 2.066 2.170 ... (remaining 436643 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 36 through 556) selection = chain 'Y' selection = (chain 'Z' and resid 36 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 group one per residue 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: 0.010 Normalize map: mean=0, sd=1: 3.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 23.400 Check model and map are aligned: 0.670 Set scattering table: 0.410 Process input model: 115.340 Find NCS groups from input model: 2.590 Set up NCS constraints: 0.320 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:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 149.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 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 : 0.006 0.098 54694 Z= 0.410 Angle : 0.955 20.054 74172 Z= 0.544 Chirality : 0.056 0.370 8690 Planarity : 0.007 0.088 9512 Dihedral : 15.076 131.508 19942 Min Nonbonded Distance : 1.680 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.01 % Favored : 93.86 % Rotamer: Outliers : 0.41 % Allowed : 8.04 % Favored : 91.55 % Cbeta Deviations : 0.00 % 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: -5.14 (0.07), residues: 7039 helix: -4.08 (0.04), residues: 3544 sheet: -2.27 (0.20), residues: 550 loop : -2.51 (0.10), residues: 2945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP Z 141 HIS 0.010 0.002 HIS S 250 PHE 0.025 0.002 PHE 3 115 TYR 0.020 0.002 TYR 4 211 ARG 0.008 0.001 ARG Y 273 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1303 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 1280 time to evaluate : 4.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 81 HIS cc_start: 0.4763 (p-80) cc_final: 0.3918 (p-80) REVERT: 1 50 TRP cc_start: 0.8950 (m-10) cc_final: 0.8705 (m-10) REVERT: 1 61 MET cc_start: 0.8474 (tpp) cc_final: 0.7113 (tpp) REVERT: 1 128 LYS cc_start: 0.8607 (ttpp) cc_final: 0.8156 (ttmm) REVERT: 1 263 LEU cc_start: 0.9205 (tt) cc_final: 0.7986 (tt) REVERT: 1 266 LYS cc_start: 0.8547 (mttt) cc_final: 0.8216 (mtmm) REVERT: 1 267 ARG cc_start: 0.8414 (mpt180) cc_final: 0.7735 (mpt180) REVERT: 1 367 GLU cc_start: 0.7123 (mp0) cc_final: 0.6909 (mp0) REVERT: 1 417 LYS cc_start: 0.6350 (pttp) cc_final: 0.5996 (tptm) REVERT: 1 596 ILE cc_start: 0.9558 (pt) cc_final: 0.8753 (mt) REVERT: 2 102 GLN cc_start: 0.8228 (mt0) cc_final: 0.8025 (mt0) REVERT: 2 153 ASN cc_start: 0.8702 (t0) cc_final: 0.7525 (p0) REVERT: 2 367 ASP cc_start: 0.8464 (p0) cc_final: 0.8184 (p0) REVERT: 3 115 PHE cc_start: 0.7320 (t80) cc_final: 0.6405 (m-80) REVERT: 3 142 ASN cc_start: 0.8521 (m-40) cc_final: 0.8120 (m-40) REVERT: 3 154 ASP cc_start: 0.8174 (t70) cc_final: 0.7764 (t0) REVERT: 3 171 LYS cc_start: 0.8502 (mttp) cc_final: 0.8099 (tmtt) REVERT: 3 265 LEU cc_start: 0.9205 (mt) cc_final: 0.8997 (mt) REVERT: 4 12 LEU cc_start: 0.9372 (mt) cc_final: 0.8732 (tp) REVERT: 4 99 GLU cc_start: 0.8562 (mp0) cc_final: 0.8283 (mp0) REVERT: 4 276 GLN cc_start: 0.8952 (mt0) cc_final: 0.8724 (mt0) REVERT: 5 78 GLU cc_start: 0.8278 (pt0) cc_final: 0.7952 (pt0) REVERT: 5 79 ASN cc_start: 0.9034 (m-40) cc_final: 0.8354 (m-40) REVERT: 5 90 GLU cc_start: 0.8920 (tm-30) cc_final: 0.8595 (tm-30) REVERT: 5 94 LYS cc_start: 0.8649 (mttm) cc_final: 0.8220 (mttm) REVERT: 5 103 TYR cc_start: 0.8906 (t80) cc_final: 0.8468 (t80) REVERT: 7 25 ASP cc_start: 0.7555 (m-30) cc_final: 0.6706 (m-30) REVERT: 7 68 LYS cc_start: 0.8730 (mtmt) cc_final: 0.8346 (tmtt) REVERT: 7 113 MET cc_start: 0.8477 (mtt) cc_final: 0.6383 (mtt) REVERT: 7 126 ASP cc_start: 0.8593 (m-30) cc_final: 0.8388 (m-30) REVERT: 7 145 THR cc_start: 0.9405 (p) cc_final: 0.9048 (t) REVERT: 8 62 ASP cc_start: 0.7936 (t70) cc_final: 0.7678 (t70) REVERT: 8 70 LYS cc_start: 0.8678 (tttm) cc_final: 0.8284 (mptt) REVERT: 9 1 MET cc_start: 0.1432 (ptt) cc_final: 0.0117 (mmt) REVERT: 9 94 LYS cc_start: 0.7373 (tptt) cc_final: 0.7018 (tttt) REVERT: A 82 PHE cc_start: 0.6992 (m-10) cc_final: 0.6605 (m-10) REVERT: A 97 LYS cc_start: 0.8400 (mtpp) cc_final: 0.7846 (mtmm) REVERT: B 61 MET cc_start: 0.8363 (mtt) cc_final: 0.8157 (mtm) REVERT: B 113 ILE cc_start: 0.6832 (mm) cc_final: 0.6588 (mm) REVERT: C 61 MET cc_start: 0.7837 (mmt) cc_final: 0.7528 (mmt) REVERT: D 71 LEU cc_start: 0.8490 (mm) cc_final: 0.8190 (tt) REVERT: D 97 LYS cc_start: 0.6992 (mmtm) cc_final: 0.5702 (pttm) REVERT: E 82 PHE cc_start: 0.7662 (m-80) cc_final: 0.7114 (m-80) REVERT: E 98 GLN cc_start: 0.7724 (tt0) cc_final: 0.7250 (tp-100) REVERT: E 113 ILE cc_start: 0.8024 (mm) cc_final: 0.7363 (mm) REVERT: E 118 LEU cc_start: 0.7368 (mt) cc_final: 0.7034 (mp) REVERT: G 69 ILE cc_start: 0.7928 (mm) cc_final: 0.7470 (mm) REVERT: H 69 ILE cc_start: 0.7919 (mt) cc_final: 0.7393 (mm) REVERT: H 85 LEU cc_start: 0.7313 (tp) cc_final: 0.7090 (tp) REVERT: H 97 LYS cc_start: 0.8304 (mmtt) cc_final: 0.7366 (tmtt) REVERT: H 116 PHE cc_start: 0.5825 (m-10) cc_final: 0.5246 (t80) REVERT: I 78 LEU cc_start: 0.7283 (mm) cc_final: 0.7046 (mm) REVERT: M 98 ARG cc_start: 0.7990 (ptp90) cc_final: 0.7581 (ptt180) REVERT: M 168 MET cc_start: 0.7778 (mmt) cc_final: 0.7282 (tpp) REVERT: M 178 LEU cc_start: 0.8974 (tp) cc_final: 0.8583 (tp) REVERT: P 52 GLN cc_start: 0.7401 (pt0) cc_final: 0.7183 (tt0) REVERT: P 71 GLN cc_start: 0.8701 (tt0) cc_final: 0.8446 (tt0) REVERT: P 135 LEU cc_start: 0.8799 (mt) cc_final: 0.8312 (mt) REVERT: P 217 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8652 (tp30) REVERT: Q 19 TYR cc_start: 0.7734 (t80) cc_final: 0.7412 (t80) REVERT: R 97 TYR cc_start: 0.7815 (m-80) cc_final: 0.7219 (m-10) REVERT: S 58 LYS cc_start: 0.8052 (mmtt) cc_final: 0.7576 (ptpp) REVERT: T 65 LYS cc_start: 0.8787 (mttp) cc_final: 0.8248 (tptt) REVERT: T 454 ARG cc_start: 0.8193 (mtm-85) cc_final: 0.6539 (tpp-160) REVERT: U 43 LYS cc_start: 0.7107 (mmtt) cc_final: 0.6421 (ptmt) REVERT: U 152 ASN cc_start: 0.8247 (m-40) cc_final: 0.7922 (t0) REVERT: U 291 THR cc_start: 0.8739 (t) cc_final: 0.8499 (p) REVERT: U 304 TYR cc_start: 0.8031 (m-80) cc_final: 0.7803 (m-80) REVERT: U 337 MET cc_start: 0.7822 (mtm) cc_final: 0.7553 (mtm) REVERT: U 399 ILE cc_start: 0.7583 (pt) cc_final: 0.7307 (pt) REVERT: V 45 LEU cc_start: 0.8201 (pt) cc_final: 0.7907 (tp) REVERT: V 112 ASP cc_start: 0.7686 (p0) cc_final: 0.7144 (m-30) REVERT: V 243 LYS cc_start: 0.8212 (tmtt) cc_final: 0.7997 (tttp) REVERT: V 251 LYS cc_start: 0.6849 (ttpt) cc_final: 0.6537 (ptpp) REVERT: V 483 MET cc_start: 0.8442 (tpp) cc_final: 0.8234 (tpt) REVERT: X 219 GLU cc_start: 0.8154 (pt0) cc_final: 0.7773 (pt0) REVERT: X 235 LEU cc_start: 0.7614 (mp) cc_final: 0.7166 (tt) REVERT: X 241 ASN cc_start: 0.7029 (p0) cc_final: 0.6752 (p0) REVERT: X 244 CYS cc_start: 0.6013 (m) cc_final: 0.5810 (m) REVERT: X 294 ASN cc_start: 0.7174 (m110) cc_final: 0.6741 (m110) REVERT: X 325 ILE cc_start: 0.8537 (mt) cc_final: 0.8038 (tp) REVERT: X 438 LYS cc_start: 0.6294 (mttm) cc_final: 0.6084 (mmtp) REVERT: X 502 MET cc_start: 0.5385 (mtp) cc_final: 0.5101 (mtp) REVERT: X 563 GLU cc_start: 0.5831 (mp0) cc_final: 0.5482 (tp30) REVERT: Y 127 GLU cc_start: 0.8019 (mp0) cc_final: 0.7792 (pm20) REVERT: Y 266 LEU cc_start: 0.9004 (tt) cc_final: 0.8726 (tp) REVERT: Y 282 LEU cc_start: 0.9169 (tp) cc_final: 0.8920 (tp) REVERT: Y 285 ASP cc_start: 0.7860 (t0) cc_final: 0.7609 (t0) REVERT: Y 502 MET cc_start: 0.7048 (mtp) cc_final: 0.6604 (tpt) REVERT: Z 65 VAL cc_start: 0.7934 (p) cc_final: 0.7697 (p) REVERT: Z 219 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7880 (tp30) REVERT: Z 477 LYS cc_start: 0.8541 (mtpt) cc_final: 0.8187 (ttmm) outliers start: 23 outliers final: 6 residues processed: 1301 average time/residue: 0.5534 time to fit residues: 1189.3959 Evaluate side-chains 836 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 830 time to evaluate : 4.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 589 optimal weight: 7.9990 chunk 529 optimal weight: 10.0000 chunk 293 optimal weight: 5.9990 chunk 180 optimal weight: 10.0000 chunk 356 optimal weight: 5.9990 chunk 282 optimal weight: 2.9990 chunk 547 optimal weight: 6.9990 chunk 211 optimal weight: 6.9990 chunk 332 optimal weight: 20.0000 chunk 407 optimal weight: 4.9990 chunk 633 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 60 GLN 1 65 GLN 1 285 GLN ** 1 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 477 GLN 1 587 ASN 1 606 ASN 2 68 ASN 2 122 ASN 2 289 HIS 3 97 ASN 3 142 ASN 3 189 HIS 3 206 ASN ** 3 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 95 GLN 5 25 HIS 5 29 GLN 5 109 GLN 7 106 GLN 7 156 GLN ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 184 ASN ** 8 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 98 GLN B 87 ASN C 98 GLN G 98 GLN ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 243 ASN P 66 GLN ** P 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 219 ASN P 223 ASN Q 21 ASN ** Q 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 43 GLN R 53 ASN R 83 GLN S 52 ASN S 219 GLN T 83 HIS T 104 GLN T 241 HIS T 405 GLN T 461 GLN U 83 HIS U 123 GLN U 140 GLN U 228 GLN U 242 GLN ** U 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 278 GLN U 319 HIS U 386 GLN U 441 GLN ** U 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 549 HIS V 104 GLN V 123 GLN V 149 GLN ** V 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 299 GLN V 422 ASN V 435 GLN ** V 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 157 GLN ** X 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 294 ASN ** X 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 390 ASN X 448 GLN Y 78 GLN Y 83 ASN Y 100 GLN Y 198 ASN Y 278 GLN Y 294 ASN Y 398 ASN Y 404 GLN Z 199 ASN ** Z 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 357 HIS Z 388 ASN Total number of N/Q/H flips: 70 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 54694 Z= 0.375 Angle : 0.756 11.966 74172 Z= 0.395 Chirality : 0.046 0.243 8690 Planarity : 0.006 0.103 9512 Dihedral : 7.272 115.468 7671 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.27 % Favored : 93.61 % Rotamer: Outliers : 0.05 % Allowed : 6.32 % Favored : 93.63 % 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: -3.34 (0.09), residues: 7039 helix: -2.29 (0.07), residues: 3545 sheet: -1.87 (0.21), residues: 546 loop : -1.99 (0.11), residues: 2948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP Z 141 HIS 0.008 0.001 HIS V 61 PHE 0.031 0.002 PHE V 313 TYR 0.030 0.002 TYR V 356 ARG 0.008 0.001 ARG 2 187 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1029 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1026 time to evaluate : 4.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 72 LYS cc_start: 0.8069 (mptt) cc_final: 0.7862 (mmtp) REVERT: 0 81 HIS cc_start: 0.4712 (p-80) cc_final: 0.3913 (p-80) REVERT: 1 61 MET cc_start: 0.8358 (tpp) cc_final: 0.6743 (tpp) REVERT: 1 128 LYS cc_start: 0.8536 (ttpp) cc_final: 0.8110 (ttmm) REVERT: 1 297 TYR cc_start: 0.9081 (m-80) cc_final: 0.8800 (m-80) REVERT: 1 381 ARG cc_start: 0.8134 (mtt90) cc_final: 0.7832 (mtt90) REVERT: 1 417 LYS cc_start: 0.6385 (pttp) cc_final: 0.6106 (tptm) REVERT: 1 538 ILE cc_start: 0.9162 (mm) cc_final: 0.8922 (mm) REVERT: 1 588 LEU cc_start: 0.9150 (mt) cc_final: 0.8906 (tt) REVERT: 2 153 ASN cc_start: 0.8848 (t0) cc_final: 0.8580 (t0) REVERT: 2 322 ARG cc_start: 0.8339 (ttm170) cc_final: 0.7195 (mtt-85) REVERT: 3 108 TYR cc_start: 0.8158 (t80) cc_final: 0.7946 (t80) REVERT: 3 115 PHE cc_start: 0.7574 (t80) cc_final: 0.6553 (m-80) REVERT: 3 171 LYS cc_start: 0.8567 (mttp) cc_final: 0.7900 (tmtt) REVERT: 3 177 LEU cc_start: 0.9284 (mp) cc_final: 0.8976 (mp) REVERT: 3 217 ASP cc_start: 0.7993 (p0) cc_final: 0.7744 (p0) REVERT: 3 265 LEU cc_start: 0.9420 (mt) cc_final: 0.9190 (mt) REVERT: 4 99 GLU cc_start: 0.8397 (mp0) cc_final: 0.8186 (mp0) REVERT: 5 78 GLU cc_start: 0.8261 (pt0) cc_final: 0.7941 (tt0) REVERT: 5 79 ASN cc_start: 0.9171 (m-40) cc_final: 0.8318 (t0) REVERT: 5 103 TYR cc_start: 0.9030 (t80) cc_final: 0.8485 (t80) REVERT: 6 113 LEU cc_start: 0.9164 (mp) cc_final: 0.8527 (tp) REVERT: 7 68 LYS cc_start: 0.8767 (mtmt) cc_final: 0.8244 (tmtt) REVERT: 7 109 ASP cc_start: 0.8953 (t0) cc_final: 0.8750 (t0) REVERT: 7 113 MET cc_start: 0.8388 (mtt) cc_final: 0.5776 (mtt) REVERT: 7 145 THR cc_start: 0.9246 (p) cc_final: 0.8820 (t) REVERT: 8 54 THR cc_start: 0.9635 (p) cc_final: 0.9430 (t) REVERT: 8 62 ASP cc_start: 0.7601 (t70) cc_final: 0.7371 (t70) REVERT: 8 70 LYS cc_start: 0.8770 (tttm) cc_final: 0.8273 (mptt) REVERT: 9 1 MET cc_start: 0.1224 (ptt) cc_final: -0.0026 (mmt) REVERT: 9 4 THR cc_start: 0.6834 (m) cc_final: 0.6611 (m) REVERT: 9 7 LEU cc_start: 0.8473 (pp) cc_final: 0.8220 (mm) REVERT: 9 94 LYS cc_start: 0.7599 (tptt) cc_final: 0.7103 (tttt) REVERT: A 97 LYS cc_start: 0.8446 (mtpp) cc_final: 0.7888 (mtmm) REVERT: D 71 LEU cc_start: 0.8562 (mm) cc_final: 0.8149 (tt) REVERT: D 97 LYS cc_start: 0.7053 (mmtm) cc_final: 0.5814 (pptt) REVERT: E 98 GLN cc_start: 0.7693 (tt0) cc_final: 0.7270 (tp40) REVERT: F 69 ILE cc_start: 0.7856 (mt) cc_final: 0.7652 (mt) REVERT: H 97 LYS cc_start: 0.8255 (mmtt) cc_final: 0.7230 (tttt) REVERT: H 116 PHE cc_start: 0.5671 (m-10) cc_final: 0.5053 (t80) REVERT: M 98 ARG cc_start: 0.8056 (ptp90) cc_final: 0.7627 (ptt180) REVERT: M 232 ARG cc_start: 0.8424 (mtm180) cc_final: 0.7648 (mtm180) REVERT: M 244 MET cc_start: 0.8736 (mmm) cc_final: 0.8528 (mmm) REVERT: M 250 LEU cc_start: 0.8903 (tt) cc_final: 0.8702 (tt) REVERT: M 277 VAL cc_start: 0.9010 (p) cc_final: 0.8732 (t) REVERT: P 135 LEU cc_start: 0.8658 (mt) cc_final: 0.8341 (mt) REVERT: P 217 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8403 (tp30) REVERT: R 97 TYR cc_start: 0.7656 (m-80) cc_final: 0.7233 (m-10) REVERT: S 271 MET cc_start: 0.8103 (ttm) cc_final: 0.7726 (ttt) REVERT: S 307 ILE cc_start: 0.9097 (mm) cc_final: 0.8721 (mt) REVERT: T 65 LYS cc_start: 0.8735 (mttp) cc_final: 0.8296 (tptt) REVERT: T 72 GLU cc_start: 0.8202 (pt0) cc_final: 0.7504 (tm-30) REVERT: T 169 GLN cc_start: 0.7670 (mp10) cc_final: 0.7315 (mp10) REVERT: T 447 LYS cc_start: 0.7979 (mtmm) cc_final: 0.7436 (mttm) REVERT: U 43 LYS cc_start: 0.6935 (mmtt) cc_final: 0.6460 (ptmt) REVERT: U 152 ASN cc_start: 0.8048 (m-40) cc_final: 0.7793 (t0) REVERT: U 203 PHE cc_start: 0.6636 (m-80) cc_final: 0.6396 (m-80) REVERT: U 291 THR cc_start: 0.8871 (t) cc_final: 0.8536 (p) REVERT: V 45 LEU cc_start: 0.8165 (pt) cc_final: 0.7800 (tp) REVERT: V 112 ASP cc_start: 0.7899 (p0) cc_final: 0.6975 (m-30) REVERT: V 243 LYS cc_start: 0.8232 (tmtt) cc_final: 0.8031 (tttp) REVERT: X 174 GLN cc_start: 0.7042 (tt0) cc_final: 0.6540 (mm-40) REVERT: X 219 GLU cc_start: 0.8190 (pt0) cc_final: 0.7936 (pt0) REVERT: X 326 THR cc_start: 0.7869 (p) cc_final: 0.7635 (p) REVERT: X 438 LYS cc_start: 0.6114 (mttm) cc_final: 0.5864 (mmtp) REVERT: Y 194 MET cc_start: 0.7457 (mtm) cc_final: 0.6861 (mtt) REVERT: Y 323 GLU cc_start: 0.8480 (mm-30) cc_final: 0.8244 (mm-30) REVERT: Y 422 MET cc_start: 0.4331 (mmt) cc_final: 0.3891 (tpp) REVERT: Y 502 MET cc_start: 0.7296 (mtp) cc_final: 0.6699 (tpt) REVERT: Z 169 LEU cc_start: 0.9068 (tp) cc_final: 0.8835 (tt) REVERT: Z 477 LYS cc_start: 0.8609 (mtpt) cc_final: 0.8316 (mtpp) outliers start: 3 outliers final: 1 residues processed: 1029 average time/residue: 0.5116 time to fit residues: 886.7347 Evaluate side-chains 756 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 755 time to evaluate : 4.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 352 optimal weight: 0.6980 chunk 196 optimal weight: 4.9990 chunk 527 optimal weight: 9.9990 chunk 431 optimal weight: 5.9990 chunk 174 optimal weight: 4.9990 chunk 635 optimal weight: 0.9990 chunk 685 optimal weight: 2.9990 chunk 565 optimal weight: 1.9990 chunk 629 optimal weight: 8.9990 chunk 216 optimal weight: 0.0010 chunk 509 optimal weight: 6.9990 overall best weight: 1.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 60 GLN ** 1 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 104 ASN 7 60 GLN ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN G 98 GLN I 92 ASN J 87 ASN M 243 ASN P 71 GLN ** P 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 40 GLN R 154 GLN T 358 HIS ** U 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 264 GLN U 278 GLN ** U 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 139 HIS ** V 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 221 ASN ** X 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 294 ASN ** X 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 79 HIS Y 153 GLN Y 278 GLN ** Z 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 294 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 54694 Z= 0.184 Angle : 0.604 9.998 74172 Z= 0.310 Chirality : 0.043 0.207 8690 Planarity : 0.005 0.075 9512 Dihedral : 6.553 96.885 7671 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.83 % Favored : 95.06 % Rotamer: Outliers : 0.05 % Allowed : 4.42 % Favored : 95.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.09), residues: 7039 helix: -1.41 (0.08), residues: 3559 sheet: -1.53 (0.22), residues: 539 loop : -1.70 (0.11), residues: 2941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP 7 107 HIS 0.007 0.001 HIS V 61 PHE 0.027 0.002 PHE A 116 TYR 0.020 0.001 TYR 4 211 ARG 0.008 0.000 ARG 1 253 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1101 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1098 time to evaluate : 4.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 72 LYS cc_start: 0.7988 (mptt) cc_final: 0.7420 (mttt) REVERT: 0 81 HIS cc_start: 0.4775 (p-80) cc_final: 0.4009 (p-80) REVERT: 1 61 MET cc_start: 0.8436 (tpp) cc_final: 0.6877 (tpp) REVERT: 1 128 LYS cc_start: 0.8417 (ttpp) cc_final: 0.7984 (ttmm) REVERT: 1 297 TYR cc_start: 0.9008 (m-80) cc_final: 0.8780 (m-80) REVERT: 1 381 ARG cc_start: 0.8067 (mtt90) cc_final: 0.7673 (ttm170) REVERT: 1 417 LYS cc_start: 0.6328 (pttp) cc_final: 0.6082 (tptm) REVERT: 1 505 ILE cc_start: 0.8925 (mt) cc_final: 0.8703 (mm) REVERT: 1 538 ILE cc_start: 0.9106 (mm) cc_final: 0.8859 (mm) REVERT: 2 153 ASN cc_start: 0.8802 (t0) cc_final: 0.8492 (t0) REVERT: 2 246 GLU cc_start: 0.7554 (mp0) cc_final: 0.7249 (mp0) REVERT: 3 115 PHE cc_start: 0.7737 (t80) cc_final: 0.6493 (m-80) REVERT: 3 157 LEU cc_start: 0.8708 (tp) cc_final: 0.8249 (tt) REVERT: 3 260 THR cc_start: 0.9225 (m) cc_final: 0.8829 (m) REVERT: 4 57 TYR cc_start: 0.8267 (m-80) cc_final: 0.7871 (m-80) REVERT: 4 99 GLU cc_start: 0.8472 (mp0) cc_final: 0.8178 (mp0) REVERT: 5 78 GLU cc_start: 0.7826 (pt0) cc_final: 0.7486 (tt0) REVERT: 5 79 ASN cc_start: 0.9124 (m-40) cc_final: 0.8385 (t0) REVERT: 5 103 TYR cc_start: 0.8937 (t80) cc_final: 0.8410 (t80) REVERT: 5 115 ILE cc_start: 0.8820 (tp) cc_final: 0.8582 (tp) REVERT: 6 36 ILE cc_start: 0.9059 (mm) cc_final: 0.8458 (mm) REVERT: 6 113 LEU cc_start: 0.9066 (mp) cc_final: 0.8470 (tt) REVERT: 7 68 LYS cc_start: 0.8639 (mtmt) cc_final: 0.8177 (tmtt) REVERT: 7 113 MET cc_start: 0.8391 (mtt) cc_final: 0.5836 (mtt) REVERT: 8 64 LEU cc_start: 0.8742 (mt) cc_final: 0.8043 (tt) REVERT: 8 70 LYS cc_start: 0.8690 (tttm) cc_final: 0.8194 (mptt) REVERT: 9 7 LEU cc_start: 0.8507 (pp) cc_final: 0.8180 (mm) REVERT: 9 14 TYR cc_start: 0.8344 (t80) cc_final: 0.8041 (t80) REVERT: 9 46 MET cc_start: 0.7403 (mmt) cc_final: 0.7134 (mmt) REVERT: 9 89 MET cc_start: 0.7866 (ptp) cc_final: 0.7664 (ptp) REVERT: 9 94 LYS cc_start: 0.7484 (tptt) cc_final: 0.7126 (tttt) REVERT: A 61 MET cc_start: 0.5423 (ttm) cc_final: 0.4651 (ttp) REVERT: A 97 LYS cc_start: 0.8389 (mtpp) cc_final: 0.7817 (mtmm) REVERT: B 113 ILE cc_start: 0.6165 (mm) cc_final: 0.5951 (mm) REVERT: B 124 ILE cc_start: 0.5432 (mm) cc_final: 0.5050 (mm) REVERT: D 71 LEU cc_start: 0.8472 (mm) cc_final: 0.8116 (tt) REVERT: D 97 LYS cc_start: 0.7112 (mmtm) cc_final: 0.6020 (pttm) REVERT: E 98 GLN cc_start: 0.7398 (tt0) cc_final: 0.7085 (tp40) REVERT: H 97 LYS cc_start: 0.7950 (mmtt) cc_final: 0.6931 (tttt) REVERT: H 116 PHE cc_start: 0.5437 (m-10) cc_final: 0.5065 (t80) REVERT: I 56 LEU cc_start: 0.7949 (tp) cc_final: 0.7363 (tp) REVERT: I 78 LEU cc_start: 0.7576 (mp) cc_final: 0.7356 (mp) REVERT: M 98 ARG cc_start: 0.7996 (ptp90) cc_final: 0.7629 (ptt180) REVERT: M 180 PHE cc_start: 0.8846 (t80) cc_final: 0.8514 (t80) REVERT: M 232 ARG cc_start: 0.8347 (mtm180) cc_final: 0.7772 (mtm180) REVERT: M 244 MET cc_start: 0.8641 (mmm) cc_final: 0.8250 (mmm) REVERT: P 52 GLN cc_start: 0.7652 (pt0) cc_final: 0.7445 (tt0) REVERT: P 135 LEU cc_start: 0.8682 (mt) cc_final: 0.8170 (mt) REVERT: P 217 GLU cc_start: 0.8810 (mm-30) cc_final: 0.8365 (tp30) REVERT: Q 19 TYR cc_start: 0.7488 (t80) cc_final: 0.7069 (t80) REVERT: Q 43 GLN cc_start: 0.6359 (mt0) cc_final: 0.5641 (mm-40) REVERT: Q 63 TYR cc_start: 0.8447 (m-80) cc_final: 0.8200 (m-80) REVERT: R 97 TYR cc_start: 0.7478 (m-80) cc_final: 0.6981 (m-10) REVERT: S 89 PHE cc_start: 0.7235 (m-10) cc_final: 0.6449 (m-10) REVERT: S 271 MET cc_start: 0.8758 (ttm) cc_final: 0.8363 (ttt) REVERT: S 307 ILE cc_start: 0.8966 (mm) cc_final: 0.8617 (mt) REVERT: S 312 SER cc_start: 0.7631 (p) cc_final: 0.7378 (p) REVERT: T 65 LYS cc_start: 0.8714 (mttp) cc_final: 0.8252 (tptt) REVERT: T 72 GLU cc_start: 0.8150 (pt0) cc_final: 0.7446 (tm-30) REVERT: T 169 GLN cc_start: 0.7639 (mp10) cc_final: 0.7305 (mp10) REVERT: T 447 LYS cc_start: 0.7969 (mttp) cc_final: 0.7090 (tttt) REVERT: T 454 ARG cc_start: 0.8218 (mtm-85) cc_final: 0.6625 (tpp-160) REVERT: U 152 ASN cc_start: 0.8069 (m-40) cc_final: 0.7800 (t0) REVERT: U 231 LYS cc_start: 0.8493 (mtmm) cc_final: 0.8111 (mtmm) REVERT: U 291 THR cc_start: 0.8775 (t) cc_final: 0.8536 (p) REVERT: U 360 ARG cc_start: 0.7831 (ptt-90) cc_final: 0.7618 (ptt90) REVERT: U 414 TYR cc_start: 0.5918 (m-80) cc_final: 0.5242 (m-10) REVERT: V 45 LEU cc_start: 0.8212 (pt) cc_final: 0.7843 (tp) REVERT: V 112 ASP cc_start: 0.7947 (p0) cc_final: 0.6811 (m-30) REVERT: V 165 ASP cc_start: 0.7987 (p0) cc_final: 0.7719 (p0) REVERT: V 243 LYS cc_start: 0.8228 (tmtt) cc_final: 0.7910 (tttp) REVERT: V 244 ASN cc_start: 0.7573 (m-40) cc_final: 0.6831 (t0) REVERT: V 298 LEU cc_start: 0.8695 (mt) cc_final: 0.8119 (mp) REVERT: X 174 GLN cc_start: 0.7148 (tt0) cc_final: 0.6516 (mm-40) REVERT: X 196 LEU cc_start: 0.8152 (tp) cc_final: 0.7919 (tp) REVERT: X 219 GLU cc_start: 0.8024 (pt0) cc_final: 0.7506 (pt0) REVERT: X 386 MET cc_start: 0.5717 (tpp) cc_final: 0.5395 (tpp) REVERT: X 564 GLU cc_start: 0.6232 (mp0) cc_final: 0.5552 (mp0) REVERT: Y 153 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7823 (mt0) REVERT: Y 194 MET cc_start: 0.7276 (mtm) cc_final: 0.6972 (mtt) REVERT: Y 323 GLU cc_start: 0.8459 (mm-30) cc_final: 0.7939 (mm-30) REVERT: Y 502 MET cc_start: 0.7179 (mtp) cc_final: 0.6627 (tpt) REVERT: Z 90 MET cc_start: 0.8879 (mmm) cc_final: 0.8602 (mmm) REVERT: Z 477 LYS cc_start: 0.8526 (mtpt) cc_final: 0.8221 (mtpp) outliers start: 3 outliers final: 1 residues processed: 1100 average time/residue: 0.5156 time to fit residues: 954.1562 Evaluate side-chains 785 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 783 time to evaluate : 4.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 627 optimal weight: 0.0000 chunk 477 optimal weight: 20.0000 chunk 329 optimal weight: 9.9990 chunk 70 optimal weight: 0.0870 chunk 303 optimal weight: 6.9990 chunk 426 optimal weight: 6.9990 chunk 637 optimal weight: 20.0000 chunk 674 optimal weight: 9.9990 chunk 332 optimal weight: 9.9990 chunk 603 optimal weight: 6.9990 chunk 181 optimal weight: 2.9990 overall best weight: 3.4168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 60 GLN ** 3 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 74 ASN 7 106 GLN ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN F 98 GLN J 87 ASN J 98 GLN ** M 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 243 ASN ** P 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 154 GLN T 358 HIS ** U 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 228 GLN U 278 GLN ** U 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 149 GLN V 253 GLN ** V 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 157 GLN ** X 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 294 ASN ** X 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 78 GLN Y 278 GLN Y 322 GLN Y 337 GLN Z 337 GLN Z 390 ASN Z 448 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 54694 Z= 0.268 Angle : 0.645 11.244 74172 Z= 0.328 Chirality : 0.044 0.194 8690 Planarity : 0.005 0.057 9512 Dihedral : 6.425 79.633 7671 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.34 % Favored : 93.55 % Rotamer: Outliers : 0.02 % Allowed : 3.98 % Favored : 96.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.10), residues: 7039 helix: -1.04 (0.08), residues: 3572 sheet: -1.52 (0.21), residues: 551 loop : -1.56 (0.11), residues: 2916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP 7 107 HIS 0.007 0.001 HIS T 83 PHE 0.033 0.002 PHE 6 116 TYR 0.022 0.002 TYR T 356 ARG 0.019 0.001 ARG V 418 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1005 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1004 time to evaluate : 4.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 72 LYS cc_start: 0.8060 (mptt) cc_final: 0.7592 (mttt) REVERT: 0 81 HIS cc_start: 0.4761 (p-80) cc_final: 0.4025 (p-80) REVERT: 1 128 LYS cc_start: 0.8453 (ttpp) cc_final: 0.8062 (ttmm) REVERT: 1 269 LEU cc_start: 0.9271 (tp) cc_final: 0.9014 (tp) REVERT: 1 381 ARG cc_start: 0.8056 (mtt90) cc_final: 0.7663 (ttm170) REVERT: 1 417 LYS cc_start: 0.6449 (pttp) cc_final: 0.6082 (tptm) REVERT: 1 456 LYS cc_start: 0.8346 (tmtt) cc_final: 0.8065 (mptt) REVERT: 2 14 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7638 (mm-30) REVERT: 2 153 ASN cc_start: 0.8785 (t0) cc_final: 0.8462 (t0) REVERT: 3 115 PHE cc_start: 0.7808 (t80) cc_final: 0.6526 (m-80) REVERT: 3 217 ASP cc_start: 0.8006 (p0) cc_final: 0.7673 (p0) REVERT: 4 252 LEU cc_start: 0.9093 (mm) cc_final: 0.8763 (mm) REVERT: 5 9 GLN cc_start: 0.8221 (tm-30) cc_final: 0.7971 (tm-30) REVERT: 5 79 ASN cc_start: 0.9146 (m-40) cc_final: 0.8651 (m-40) REVERT: 5 103 TYR cc_start: 0.9002 (t80) cc_final: 0.8675 (t80) REVERT: 5 115 ILE cc_start: 0.8863 (tp) cc_final: 0.8629 (tp) REVERT: 5 116 TRP cc_start: 0.7782 (m100) cc_final: 0.7529 (m100) REVERT: 6 36 ILE cc_start: 0.8968 (mm) cc_final: 0.8115 (mm) REVERT: 6 113 LEU cc_start: 0.9154 (mp) cc_final: 0.8687 (tp) REVERT: 7 68 LYS cc_start: 0.8682 (mtmt) cc_final: 0.8279 (tmtt) REVERT: 7 113 MET cc_start: 0.8769 (mtt) cc_final: 0.8459 (mtt) REVERT: 7 145 THR cc_start: 0.9136 (p) cc_final: 0.8816 (t) REVERT: 8 62 ASP cc_start: 0.7898 (t0) cc_final: 0.7613 (t70) REVERT: 8 64 LEU cc_start: 0.8713 (mt) cc_final: 0.8069 (tt) REVERT: 8 70 LYS cc_start: 0.8695 (tttm) cc_final: 0.8208 (mptt) REVERT: 9 46 MET cc_start: 0.7467 (mmt) cc_final: 0.7238 (mmt) REVERT: 9 94 LYS cc_start: 0.7577 (tptt) cc_final: 0.7157 (tttt) REVERT: A 61 MET cc_start: 0.5781 (ttm) cc_final: 0.5485 (ttm) REVERT: A 97 LYS cc_start: 0.8451 (mtpp) cc_final: 0.7852 (mtmm) REVERT: D 97 LYS cc_start: 0.7210 (mmtm) cc_final: 0.6190 (pptt) REVERT: D 122 PHE cc_start: 0.6287 (m-10) cc_final: 0.5869 (t80) REVERT: E 61 MET cc_start: 0.7570 (ptm) cc_final: 0.7332 (ptm) REVERT: E 94 ASN cc_start: 0.6604 (t0) cc_final: 0.6372 (t0) REVERT: E 98 GLN cc_start: 0.7574 (tt0) cc_final: 0.7104 (tp40) REVERT: H 97 LYS cc_start: 0.8004 (mmtt) cc_final: 0.7003 (tmtt) REVERT: H 116 PHE cc_start: 0.5362 (m-10) cc_final: 0.5007 (t80) REVERT: M 98 ARG cc_start: 0.8123 (ptp90) cc_final: 0.7699 (ptt180) REVERT: M 180 PHE cc_start: 0.8838 (t80) cc_final: 0.8389 (t80) REVERT: M 244 MET cc_start: 0.8711 (mmm) cc_final: 0.8460 (mmm) REVERT: M 324 LYS cc_start: 0.5693 (pttt) cc_final: 0.5139 (mmmm) REVERT: P 135 LEU cc_start: 0.8699 (mt) cc_final: 0.8185 (mt) REVERT: P 217 GLU cc_start: 0.8852 (mm-30) cc_final: 0.8471 (tp30) REVERT: Q 19 TYR cc_start: 0.7528 (t80) cc_final: 0.7138 (t80) REVERT: Q 43 GLN cc_start: 0.6099 (mt0) cc_final: 0.5711 (mm-40) REVERT: Q 63 TYR cc_start: 0.8608 (m-80) cc_final: 0.8319 (m-80) REVERT: R 97 TYR cc_start: 0.7545 (m-80) cc_final: 0.7039 (m-10) REVERT: S 274 MET cc_start: 0.6986 (mmt) cc_final: 0.6339 (mmp) REVERT: S 307 ILE cc_start: 0.8976 (mm) cc_final: 0.8668 (mt) REVERT: T 65 LYS cc_start: 0.8810 (mttp) cc_final: 0.8371 (tptt) REVERT: T 72 GLU cc_start: 0.8272 (pt0) cc_final: 0.7496 (tm-30) REVERT: T 169 GLN cc_start: 0.7720 (mp10) cc_final: 0.7500 (mp10) REVERT: T 337 MET cc_start: 0.8437 (mpp) cc_final: 0.7846 (mmp) REVERT: T 447 LYS cc_start: 0.7937 (mttp) cc_final: 0.7247 (tppt) REVERT: U 152 ASN cc_start: 0.8019 (m-40) cc_final: 0.7706 (t0) REVERT: V 45 LEU cc_start: 0.8177 (pt) cc_final: 0.7844 (tp) REVERT: V 165 ASP cc_start: 0.7986 (p0) cc_final: 0.7773 (p0) REVERT: V 243 LYS cc_start: 0.8299 (tmtt) cc_final: 0.7855 (tttp) REVERT: V 244 ASN cc_start: 0.7747 (m-40) cc_final: 0.7029 (t0) REVERT: X 174 GLN cc_start: 0.7057 (tt0) cc_final: 0.6545 (mm-40) REVERT: X 219 GLU cc_start: 0.8175 (pt0) cc_final: 0.7790 (pt0) REVERT: X 244 CYS cc_start: 0.7082 (t) cc_final: 0.6868 (t) REVERT: X 386 MET cc_start: 0.5778 (tpp) cc_final: 0.5029 (tpt) REVERT: X 488 MET cc_start: 0.4612 (mmm) cc_final: 0.2538 (ttp) REVERT: X 564 GLU cc_start: 0.6377 (mp0) cc_final: 0.5737 (mp0) REVERT: Y 194 MET cc_start: 0.7347 (mtm) cc_final: 0.6885 (mtt) REVERT: Y 227 MET cc_start: 0.6453 (ptp) cc_final: 0.6198 (ptp) REVERT: Y 323 GLU cc_start: 0.8433 (mm-30) cc_final: 0.7880 (mm-30) REVERT: Y 502 MET cc_start: 0.7161 (mtp) cc_final: 0.6458 (tpt) REVERT: Z 90 MET cc_start: 0.8929 (mmm) cc_final: 0.8557 (mmm) REVERT: Z 386 MET cc_start: 0.8640 (mmm) cc_final: 0.8350 (mmm) REVERT: Z 477 LYS cc_start: 0.8556 (mtpt) cc_final: 0.8121 (mtpp) outliers start: 1 outliers final: 1 residues processed: 1005 average time/residue: 0.5041 time to fit residues: 859.6861 Evaluate side-chains 740 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 739 time to evaluate : 4.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 561 optimal weight: 0.6980 chunk 382 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 502 optimal weight: 2.9990 chunk 278 optimal weight: 6.9990 chunk 575 optimal weight: 10.0000 chunk 466 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 344 optimal weight: 10.0000 chunk 605 optimal weight: 8.9990 chunk 170 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 60 GLN ** 3 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 104 ASN ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 98 GLN J 98 GLN ** M 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 243 ASN ** P 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 358 HIS ** U 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 278 GLN ** U 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 149 GLN ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 221 ASN ** X 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 294 ASN ** X 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 78 GLN Y 79 HIS Y 153 GLN Y 278 GLN ** Y 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 398 ASN ** Z 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 390 ASN Z 574 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 54694 Z= 0.209 Angle : 0.599 10.834 74172 Z= 0.305 Chirality : 0.043 0.275 8690 Planarity : 0.004 0.055 9512 Dihedral : 6.192 85.098 7671 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.34 % Favored : 94.56 % Rotamer: Outliers : 0.05 % Allowed : 2.79 % Favored : 97.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.10), residues: 7039 helix: -0.78 (0.09), residues: 3566 sheet: -1.36 (0.22), residues: 549 loop : -1.41 (0.12), residues: 2924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP 6 99 HIS 0.005 0.001 HIS 5 91 PHE 0.022 0.002 PHE S 194 TYR 0.020 0.001 TYR M 289 ARG 0.007 0.000 ARG 1 267 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1021 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1018 time to evaluate : 4.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 72 LYS cc_start: 0.7990 (mptt) cc_final: 0.7488 (mttt) REVERT: 0 81 HIS cc_start: 0.4800 (p-80) cc_final: 0.4002 (p-80) REVERT: 1 128 LYS cc_start: 0.8416 (ttpp) cc_final: 0.8074 (ttmm) REVERT: 1 269 LEU cc_start: 0.9236 (tp) cc_final: 0.8860 (tt) REVERT: 1 381 ARG cc_start: 0.8077 (mtt90) cc_final: 0.7744 (ttm170) REVERT: 1 417 LYS cc_start: 0.6399 (pttp) cc_final: 0.6087 (tptm) REVERT: 1 538 ILE cc_start: 0.9078 (mm) cc_final: 0.8827 (mm) REVERT: 1 551 LEU cc_start: 0.9407 (mm) cc_final: 0.8888 (mm) REVERT: 2 153 ASN cc_start: 0.8768 (t0) cc_final: 0.8400 (t0) REVERT: 2 367 ASP cc_start: 0.8220 (p0) cc_final: 0.7983 (p0) REVERT: 3 115 PHE cc_start: 0.7811 (t80) cc_final: 0.6421 (m-80) REVERT: 3 157 LEU cc_start: 0.8639 (tp) cc_final: 0.8417 (tt) REVERT: 3 217 ASP cc_start: 0.7977 (p0) cc_final: 0.7671 (p0) REVERT: 4 252 LEU cc_start: 0.9104 (mm) cc_final: 0.8734 (mm) REVERT: 5 9 GLN cc_start: 0.8260 (tm-30) cc_final: 0.7973 (tm-30) REVERT: 5 79 ASN cc_start: 0.9066 (m-40) cc_final: 0.8405 (t0) REVERT: 5 103 TYR cc_start: 0.8895 (t80) cc_final: 0.8468 (t80) REVERT: 5 115 ILE cc_start: 0.8868 (tp) cc_final: 0.8650 (tp) REVERT: 5 116 TRP cc_start: 0.7723 (m100) cc_final: 0.7494 (m100) REVERT: 6 36 ILE cc_start: 0.8942 (mm) cc_final: 0.8068 (mm) REVERT: 6 113 LEU cc_start: 0.9103 (mp) cc_final: 0.8479 (tp) REVERT: 7 68 LYS cc_start: 0.8698 (mtmt) cc_final: 0.8243 (tmtt) REVERT: 7 112 THR cc_start: 0.9587 (p) cc_final: 0.9043 (t) REVERT: 7 113 MET cc_start: 0.8682 (mtt) cc_final: 0.8230 (mtt) REVERT: 7 140 LEU cc_start: 0.9019 (mt) cc_final: 0.8423 (mt) REVERT: 8 62 ASP cc_start: 0.7781 (t0) cc_final: 0.7484 (t70) REVERT: 8 64 LEU cc_start: 0.8764 (mt) cc_final: 0.8416 (tt) REVERT: 8 70 LYS cc_start: 0.8665 (tttm) cc_final: 0.8280 (tptt) REVERT: 9 27 ASN cc_start: 0.7058 (t0) cc_final: 0.6821 (m-40) REVERT: 9 46 MET cc_start: 0.7533 (mmt) cc_final: 0.7293 (mmt) REVERT: 9 94 LYS cc_start: 0.7573 (tptt) cc_final: 0.7132 (tttt) REVERT: A 61 MET cc_start: 0.5344 (ttm) cc_final: 0.4597 (tpp) REVERT: A 97 LYS cc_start: 0.8441 (mtpp) cc_final: 0.7838 (mtmm) REVERT: D 97 LYS cc_start: 0.7161 (mmtm) cc_final: 0.6202 (pttm) REVERT: D 122 PHE cc_start: 0.6242 (m-10) cc_final: 0.5836 (t80) REVERT: E 98 GLN cc_start: 0.7657 (tt0) cc_final: 0.7124 (tp40) REVERT: G 62 VAL cc_start: 0.7297 (t) cc_final: 0.7082 (t) REVERT: H 97 LYS cc_start: 0.7880 (mmtt) cc_final: 0.6831 (tttt) REVERT: H 116 PHE cc_start: 0.5224 (m-10) cc_final: 0.4980 (t80) REVERT: I 78 LEU cc_start: 0.7574 (mp) cc_final: 0.7202 (mp) REVERT: M 98 ARG cc_start: 0.8161 (ptp90) cc_final: 0.7734 (ptt180) REVERT: M 172 GLU cc_start: 0.7426 (pt0) cc_final: 0.7096 (tt0) REVERT: M 244 MET cc_start: 0.8704 (mmm) cc_final: 0.8426 (mmm) REVERT: M 324 LYS cc_start: 0.5816 (pttt) cc_final: 0.5185 (mmmm) REVERT: P 135 LEU cc_start: 0.8709 (mt) cc_final: 0.8231 (mt) REVERT: P 217 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8383 (tp30) REVERT: Q 19 TYR cc_start: 0.7374 (t80) cc_final: 0.6958 (t80) REVERT: Q 43 GLN cc_start: 0.6165 (mt0) cc_final: 0.5624 (mm-40) REVERT: R 97 TYR cc_start: 0.7485 (m-80) cc_final: 0.6967 (m-10) REVERT: S 89 PHE cc_start: 0.7365 (m-80) cc_final: 0.6575 (m-80) REVERT: S 307 ILE cc_start: 0.8935 (mm) cc_final: 0.8645 (mt) REVERT: T 72 GLU cc_start: 0.8277 (pt0) cc_final: 0.7482 (tm-30) REVERT: T 169 GLN cc_start: 0.7684 (mp10) cc_final: 0.7318 (mp10) REVERT: T 337 MET cc_start: 0.8322 (mpp) cc_final: 0.7800 (mmp) REVERT: T 415 LYS cc_start: 0.7287 (mmmt) cc_final: 0.6964 (tptt) REVERT: T 447 LYS cc_start: 0.7997 (mttp) cc_final: 0.7066 (tttt) REVERT: U 152 ASN cc_start: 0.8055 (m-40) cc_final: 0.7798 (t0) REVERT: U 304 TYR cc_start: 0.7991 (m-10) cc_final: 0.7747 (m-10) REVERT: U 414 TYR cc_start: 0.5927 (m-80) cc_final: 0.5257 (m-10) REVERT: V 45 LEU cc_start: 0.8167 (pt) cc_final: 0.7854 (tp) REVERT: V 61 HIS cc_start: 0.6848 (t70) cc_final: 0.6425 (t70) REVERT: V 243 LYS cc_start: 0.8151 (tmtt) cc_final: 0.7946 (tmmt) REVERT: V 244 ASN cc_start: 0.7667 (m-40) cc_final: 0.7214 (t0) REVERT: V 298 LEU cc_start: 0.8811 (mt) cc_final: 0.8185 (mp) REVERT: V 360 ARG cc_start: 0.7827 (ptt180) cc_final: 0.7282 (ptt180) REVERT: X 174 GLN cc_start: 0.6905 (tt0) cc_final: 0.6390 (mm-40) REVERT: X 219 GLU cc_start: 0.8150 (pt0) cc_final: 0.7925 (pt0) REVERT: X 244 CYS cc_start: 0.7412 (t) cc_final: 0.7049 (t) REVERT: X 386 MET cc_start: 0.5767 (tpp) cc_final: 0.4984 (tpt) REVERT: X 484 MET cc_start: 0.6428 (ppp) cc_final: 0.6137 (ppp) REVERT: Y 323 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7789 (mm-30) REVERT: Y 502 MET cc_start: 0.7192 (mtp) cc_final: 0.6578 (tpt) REVERT: Z 41 SER cc_start: 0.7820 (p) cc_final: 0.7606 (p) REVERT: Z 466 THR cc_start: 0.8607 (p) cc_final: 0.8335 (p) REVERT: Z 477 LYS cc_start: 0.8471 (mtpt) cc_final: 0.8195 (mtpp) outliers start: 3 outliers final: 1 residues processed: 1021 average time/residue: 0.4948 time to fit residues: 862.3537 Evaluate side-chains 748 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 747 time to evaluate : 4.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 226 optimal weight: 1.9990 chunk 607 optimal weight: 5.9990 chunk 133 optimal weight: 6.9990 chunk 396 optimal weight: 9.9990 chunk 166 optimal weight: 4.9990 chunk 675 optimal weight: 0.0370 chunk 560 optimal weight: 10.0000 chunk 312 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 223 optimal weight: 7.9990 chunk 354 optimal weight: 20.0000 overall best weight: 3.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 60 GLN 1 316 ASN 2 122 ASN ** 3 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 106 GLN ** 7 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 98 GLN J 87 ASN J 98 GLN ** M 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 243 ASN ** P 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 40 GLN Q 43 GLN S 293 ASN T 61 HIS T 405 GLN T 452 GLN ** U 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 278 GLN ** U 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 149 GLN ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 221 ASN ** X 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 294 ASN ** X 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 78 GLN ** Y 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 278 GLN ** Y 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 390 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 54694 Z= 0.291 Angle : 0.651 11.407 74172 Z= 0.331 Chirality : 0.044 0.221 8690 Planarity : 0.004 0.054 9512 Dihedral : 6.221 88.283 7671 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.92 % Favored : 92.97 % Rotamer: Outliers : 0.02 % Allowed : 3.09 % Favored : 96.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.10), residues: 7039 helix: -0.67 (0.08), residues: 3598 sheet: -1.40 (0.22), residues: 563 loop : -1.39 (0.12), residues: 2878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP M 189 HIS 0.009 0.001 HIS Y 79 PHE 0.036 0.002 PHE E 116 TYR 0.027 0.002 TYR S 158 ARG 0.014 0.001 ARG 2 322 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 967 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 966 time to evaluate : 4.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 72 LYS cc_start: 0.8004 (mptt) cc_final: 0.7545 (mttt) REVERT: 0 81 HIS cc_start: 0.4819 (p-80) cc_final: 0.4041 (p-80) REVERT: 1 128 LYS cc_start: 0.8486 (ttpp) cc_final: 0.8108 (ttmm) REVERT: 1 269 LEU cc_start: 0.9302 (tp) cc_final: 0.8933 (tt) REVERT: 1 381 ARG cc_start: 0.8122 (mtt90) cc_final: 0.7718 (ttm170) REVERT: 1 417 LYS cc_start: 0.6455 (pttp) cc_final: 0.6064 (tptm) REVERT: 1 538 ILE cc_start: 0.9132 (mm) cc_final: 0.8925 (mm) REVERT: 1 551 LEU cc_start: 0.9446 (mm) cc_final: 0.8764 (mm) REVERT: 2 153 ASN cc_start: 0.8780 (t0) cc_final: 0.8453 (t0) REVERT: 3 115 PHE cc_start: 0.7801 (t80) cc_final: 0.6403 (m-80) REVERT: 3 171 LYS cc_start: 0.7164 (tmtt) cc_final: 0.6910 (tmtt) REVERT: 3 205 CYS cc_start: 0.8887 (m) cc_final: 0.8630 (m) REVERT: 3 217 ASP cc_start: 0.7994 (p0) cc_final: 0.7735 (p0) REVERT: 4 252 LEU cc_start: 0.9039 (mm) cc_final: 0.8778 (mm) REVERT: 5 9 GLN cc_start: 0.8220 (tm-30) cc_final: 0.7891 (tm-30) REVERT: 5 78 GLU cc_start: 0.7891 (pt0) cc_final: 0.7580 (tt0) REVERT: 5 79 ASN cc_start: 0.9224 (m-40) cc_final: 0.8506 (t0) REVERT: 5 103 TYR cc_start: 0.9034 (t80) cc_final: 0.8740 (t80) REVERT: 5 115 ILE cc_start: 0.8894 (tp) cc_final: 0.8678 (tp) REVERT: 5 116 TRP cc_start: 0.7838 (m100) cc_final: 0.7539 (m100) REVERT: 6 36 ILE cc_start: 0.9000 (mm) cc_final: 0.8060 (mm) REVERT: 6 113 LEU cc_start: 0.9197 (mp) cc_final: 0.8529 (tt) REVERT: 7 68 LYS cc_start: 0.8736 (mtmt) cc_final: 0.8259 (tmtt) REVERT: 7 113 MET cc_start: 0.8629 (mtt) cc_final: 0.8238 (mtt) REVERT: 7 140 LEU cc_start: 0.8983 (mt) cc_final: 0.8477 (mt) REVERT: 7 145 THR cc_start: 0.9038 (p) cc_final: 0.8781 (t) REVERT: 8 62 ASP cc_start: 0.7823 (t0) cc_final: 0.7499 (t70) REVERT: 8 64 LEU cc_start: 0.8818 (mt) cc_final: 0.8447 (tt) REVERT: 8 70 LYS cc_start: 0.8662 (tttm) cc_final: 0.8296 (tptt) REVERT: 9 27 ASN cc_start: 0.7072 (t0) cc_final: 0.6796 (m-40) REVERT: 9 88 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7600 (mm-30) REVERT: 9 94 LYS cc_start: 0.7613 (tptt) cc_final: 0.7165 (tttt) REVERT: A 61 MET cc_start: 0.5398 (ttm) cc_final: 0.4854 (ttp) REVERT: A 97 LYS cc_start: 0.8485 (mtpp) cc_final: 0.7990 (mtmm) REVERT: B 61 MET cc_start: 0.7662 (mtm) cc_final: 0.7441 (mtm) REVERT: B 94 ASN cc_start: 0.4566 (p0) cc_final: 0.4145 (m-40) REVERT: D 71 LEU cc_start: 0.8528 (mm) cc_final: 0.8088 (tt) REVERT: D 97 LYS cc_start: 0.7055 (mmtm) cc_final: 0.6281 (pptt) REVERT: D 122 PHE cc_start: 0.6245 (m-10) cc_final: 0.5839 (t80) REVERT: E 82 PHE cc_start: 0.7786 (m-10) cc_final: 0.7586 (m-80) REVERT: E 94 ASN cc_start: 0.6659 (t0) cc_final: 0.6377 (t0) REVERT: E 98 GLN cc_start: 0.7619 (tt0) cc_final: 0.7102 (tp40) REVERT: H 97 LYS cc_start: 0.7923 (mmtt) cc_final: 0.6891 (tttt) REVERT: H 116 PHE cc_start: 0.5220 (m-10) cc_final: 0.4964 (t80) REVERT: I 56 LEU cc_start: 0.7777 (tp) cc_final: 0.7544 (tp) REVERT: M 98 ARG cc_start: 0.8226 (ptp90) cc_final: 0.7743 (ptt180) REVERT: M 101 LYS cc_start: 0.9320 (tmmt) cc_final: 0.9085 (ttpp) REVERT: M 244 MET cc_start: 0.8781 (mmm) cc_final: 0.8449 (mmm) REVERT: P 135 LEU cc_start: 0.8733 (mt) cc_final: 0.8222 (mt) REVERT: P 217 GLU cc_start: 0.8916 (mm-30) cc_final: 0.8397 (tp30) REVERT: Q 19 TYR cc_start: 0.7380 (t80) cc_final: 0.6970 (t80) REVERT: Q 43 GLN cc_start: 0.6256 (mt0) cc_final: 0.5692 (mm-40) REVERT: R 33 PHE cc_start: 0.5769 (t80) cc_final: 0.5520 (t80) REVERT: R 97 TYR cc_start: 0.7573 (m-80) cc_final: 0.7133 (m-10) REVERT: S 166 TYR cc_start: 0.7580 (m-80) cc_final: 0.7373 (m-80) REVERT: S 307 ILE cc_start: 0.8958 (mm) cc_final: 0.8694 (mt) REVERT: T 72 GLU cc_start: 0.8266 (pt0) cc_final: 0.7419 (tm-30) REVERT: T 447 LYS cc_start: 0.7979 (mttp) cc_final: 0.7285 (tppt) REVERT: U 152 ASN cc_start: 0.8024 (m-40) cc_final: 0.7663 (t0) REVERT: U 262 VAL cc_start: 0.9074 (t) cc_final: 0.8867 (t) REVERT: V 45 LEU cc_start: 0.8167 (pt) cc_final: 0.7801 (tp) REVERT: V 243 LYS cc_start: 0.8195 (tmtt) cc_final: 0.7945 (tmmt) REVERT: V 244 ASN cc_start: 0.7760 (m-40) cc_final: 0.7277 (t0) REVERT: X 110 LYS cc_start: 0.7484 (mmpt) cc_final: 0.6823 (tptt) REVERT: X 174 GLN cc_start: 0.7009 (tt0) cc_final: 0.6432 (mm-40) REVERT: X 314 LEU cc_start: 0.8125 (pt) cc_final: 0.7834 (pt) REVERT: X 336 VAL cc_start: 0.8710 (t) cc_final: 0.8219 (t) REVERT: X 386 MET cc_start: 0.5891 (tpp) cc_final: 0.4870 (tpt) REVERT: X 474 LEU cc_start: 0.7451 (mm) cc_final: 0.7191 (mt) REVERT: X 484 MET cc_start: 0.6452 (ppp) cc_final: 0.6207 (ppp) REVERT: Y 227 MET cc_start: 0.6882 (ptt) cc_final: 0.6596 (ptt) REVERT: Y 232 VAL cc_start: 0.8717 (t) cc_final: 0.8038 (t) REVERT: Y 323 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7683 (mm-30) REVERT: Y 502 MET cc_start: 0.7341 (mtp) cc_final: 0.6724 (tpt) REVERT: Z 386 MET cc_start: 0.8344 (mmm) cc_final: 0.8011 (mmm) REVERT: Z 477 LYS cc_start: 0.8520 (mtpt) cc_final: 0.8014 (mtpp) REVERT: Z 478 TYR cc_start: 0.8153 (m-80) cc_final: 0.7788 (m-10) outliers start: 1 outliers final: 1 residues processed: 967 average time/residue: 0.4860 time to fit residues: 805.2149 Evaluate side-chains 729 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 728 time to evaluate : 4.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 651 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 384 optimal weight: 0.8980 chunk 493 optimal weight: 2.9990 chunk 382 optimal weight: 3.9990 chunk 568 optimal weight: 0.9990 chunk 377 optimal weight: 3.9990 chunk 672 optimal weight: 5.9990 chunk 421 optimal weight: 5.9990 chunk 410 optimal weight: 0.0970 chunk 310 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 60 GLN 1 386 HIS 1 531 HIS 1 587 ASN ** 1 590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 243 GLN ** 3 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 123 HIS ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 98 GLN J 98 GLN ** M 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 243 ASN ** P 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 358 HIS T 405 GLN ** U 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 278 GLN U 486 GLN ** U 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 64 GLN V 149 GLN ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 68 HIS X 198 ASN X 221 ASN ** X 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 294 ASN ** X 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 78 GLN ** Y 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 278 GLN ** Y 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 68 HIS Z 221 ASN ** Z 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 390 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 54694 Z= 0.169 Angle : 0.591 12.415 74172 Z= 0.299 Chirality : 0.043 0.322 8690 Planarity : 0.004 0.055 9512 Dihedral : 5.931 84.300 7671 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.59 % Favored : 95.31 % Rotamer: Outliers : 0.04 % Allowed : 1.72 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.10), residues: 7039 helix: -0.48 (0.09), residues: 3631 sheet: -1.29 (0.22), residues: 555 loop : -1.31 (0.12), residues: 2853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP M 189 HIS 0.006 0.001 HIS Y 79 PHE 0.030 0.002 PHE S 92 TYR 0.022 0.001 TYR 8 73 ARG 0.007 0.000 ARG 1 267 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1040 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1038 time to evaluate : 4.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 72 LYS cc_start: 0.7875 (mptt) cc_final: 0.7338 (mttt) REVERT: 0 81 HIS cc_start: 0.4900 (p-80) cc_final: 0.4075 (p-80) REVERT: 1 61 MET cc_start: 0.7507 (mmt) cc_final: 0.7219 (mmt) REVERT: 1 128 LYS cc_start: 0.8388 (ttpp) cc_final: 0.8043 (ttmm) REVERT: 1 269 LEU cc_start: 0.9192 (tp) cc_final: 0.8899 (tt) REVERT: 1 381 ARG cc_start: 0.8006 (mtt90) cc_final: 0.7701 (ttm170) REVERT: 1 417 LYS cc_start: 0.6353 (pttp) cc_final: 0.6035 (tptm) REVERT: 1 538 ILE cc_start: 0.9086 (mm) cc_final: 0.8859 (mm) REVERT: 1 551 LEU cc_start: 0.9321 (mm) cc_final: 0.8903 (mm) REVERT: 2 153 ASN cc_start: 0.8722 (t0) cc_final: 0.8368 (t0) REVERT: 2 439 LYS cc_start: 0.8895 (mmtp) cc_final: 0.8382 (tptp) REVERT: 3 115 PHE cc_start: 0.7811 (t80) cc_final: 0.6355 (m-80) REVERT: 3 157 LEU cc_start: 0.8617 (tp) cc_final: 0.8348 (tt) REVERT: 3 217 ASP cc_start: 0.7854 (p0) cc_final: 0.7521 (p0) REVERT: 4 252 LEU cc_start: 0.8994 (mm) cc_final: 0.8711 (mm) REVERT: 4 276 GLN cc_start: 0.9215 (mt0) cc_final: 0.8840 (mp10) REVERT: 5 9 GLN cc_start: 0.8170 (tm-30) cc_final: 0.7859 (tm-30) REVERT: 5 11 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8280 (tm-30) REVERT: 5 78 GLU cc_start: 0.7793 (pt0) cc_final: 0.7489 (tt0) REVERT: 5 79 ASN cc_start: 0.9170 (m-40) cc_final: 0.8405 (t0) REVERT: 5 103 TYR cc_start: 0.8827 (t80) cc_final: 0.8525 (t80) REVERT: 5 116 TRP cc_start: 0.7680 (m100) cc_final: 0.7475 (m100) REVERT: 6 36 ILE cc_start: 0.8891 (mm) cc_final: 0.8201 (mm) REVERT: 6 74 GLN cc_start: 0.8124 (mt0) cc_final: 0.7914 (mm-40) REVERT: 7 68 LYS cc_start: 0.8678 (mtmt) cc_final: 0.8259 (tmtt) REVERT: 7 112 THR cc_start: 0.9552 (p) cc_final: 0.9065 (t) REVERT: 7 113 MET cc_start: 0.8710 (mtt) cc_final: 0.7930 (mtt) REVERT: 7 140 LEU cc_start: 0.8981 (mt) cc_final: 0.8279 (mt) REVERT: 8 62 ASP cc_start: 0.7686 (t0) cc_final: 0.7383 (t70) REVERT: 8 64 LEU cc_start: 0.8708 (mt) cc_final: 0.8392 (tt) REVERT: 8 70 LYS cc_start: 0.8655 (tttm) cc_final: 0.8268 (tptt) REVERT: 9 27 ASN cc_start: 0.7196 (t0) cc_final: 0.6820 (m-40) REVERT: 9 88 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7578 (mm-30) REVERT: 9 94 LYS cc_start: 0.7586 (tptt) cc_final: 0.7138 (tttt) REVERT: A 61 MET cc_start: 0.5400 (ttm) cc_final: 0.4914 (ttp) REVERT: A 97 LYS cc_start: 0.8472 (mtpp) cc_final: 0.7854 (mtmm) REVERT: C 61 MET cc_start: 0.8006 (mmm) cc_final: 0.7724 (mmp) REVERT: D 60 LYS cc_start: 0.6378 (mttp) cc_final: 0.6116 (pttp) REVERT: D 71 LEU cc_start: 0.8432 (mm) cc_final: 0.8062 (tt) REVERT: D 97 LYS cc_start: 0.7016 (mmtm) cc_final: 0.6263 (pttp) REVERT: D 122 PHE cc_start: 0.6175 (m-10) cc_final: 0.5834 (t80) REVERT: E 94 ASN cc_start: 0.6673 (t0) cc_final: 0.6420 (t0) REVERT: E 98 GLN cc_start: 0.7687 (tt0) cc_final: 0.7112 (tp40) REVERT: G 62 VAL cc_start: 0.7255 (t) cc_final: 0.7020 (t) REVERT: H 82 PHE cc_start: 0.7904 (m-10) cc_final: 0.7649 (m-10) REVERT: H 97 LYS cc_start: 0.7682 (mmtt) cc_final: 0.6764 (tttt) REVERT: H 116 PHE cc_start: 0.5309 (m-10) cc_final: 0.5086 (t80) REVERT: I 56 LEU cc_start: 0.7934 (tp) cc_final: 0.7477 (tp) REVERT: J 87 ASN cc_start: 0.7308 (t0) cc_final: 0.7006 (t0) REVERT: M 98 ARG cc_start: 0.8166 (ptp90) cc_final: 0.7764 (ptt180) REVERT: M 172 GLU cc_start: 0.7464 (pt0) cc_final: 0.7193 (tt0) REVERT: M 244 MET cc_start: 0.8785 (mmm) cc_final: 0.8471 (mmm) REVERT: P 77 PHE cc_start: 0.8348 (m-80) cc_final: 0.7892 (m-80) REVERT: P 135 LEU cc_start: 0.8691 (mt) cc_final: 0.8430 (mt) REVERT: P 217 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8276 (tp30) REVERT: Q 19 TYR cc_start: 0.7287 (t80) cc_final: 0.6913 (t80) REVERT: Q 31 LEU cc_start: 0.7936 (mt) cc_final: 0.7130 (tt) REVERT: Q 43 GLN cc_start: 0.6251 (mt0) cc_final: 0.5654 (mm-40) REVERT: Q 65 LEU cc_start: 0.8546 (mt) cc_final: 0.8256 (tt) REVERT: R 97 TYR cc_start: 0.7328 (m-80) cc_final: 0.6851 (m-10) REVERT: S 89 PHE cc_start: 0.7049 (m-80) cc_final: 0.6615 (m-80) REVERT: S 241 ASP cc_start: 0.8198 (p0) cc_final: 0.6148 (t70) REVERT: T 72 GLU cc_start: 0.8197 (pt0) cc_final: 0.7491 (tm-30) REVERT: T 169 GLN cc_start: 0.7666 (mp10) cc_final: 0.7251 (mp10) REVERT: T 415 LYS cc_start: 0.7116 (mmmt) cc_final: 0.6780 (tptt) REVERT: T 447 LYS cc_start: 0.7899 (mttp) cc_final: 0.7069 (tttt) REVERT: U 152 ASN cc_start: 0.8035 (m-40) cc_final: 0.7711 (t0) REVERT: U 414 TYR cc_start: 0.6033 (m-80) cc_final: 0.5296 (m-10) REVERT: U 474 LEU cc_start: 0.7893 (tp) cc_final: 0.7416 (pp) REVERT: V 243 LYS cc_start: 0.8089 (tmtt) cc_final: 0.7876 (tmmt) REVERT: V 244 ASN cc_start: 0.7580 (m-40) cc_final: 0.7122 (t0) REVERT: X 110 LYS cc_start: 0.7434 (mmpt) cc_final: 0.6824 (tptt) REVERT: X 174 GLN cc_start: 0.6915 (tt0) cc_final: 0.6377 (mm-40) REVERT: X 241 ASN cc_start: 0.7259 (p0) cc_final: 0.6989 (p0) REVERT: X 386 MET cc_start: 0.5737 (tpp) cc_final: 0.4763 (tpt) REVERT: X 484 MET cc_start: 0.6482 (ppp) cc_final: 0.6242 (ppp) REVERT: X 488 MET cc_start: 0.3944 (mmm) cc_final: 0.2827 (tmm) REVERT: X 564 GLU cc_start: 0.6171 (mp0) cc_final: 0.5688 (mp0) REVERT: Y 323 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7518 (mm-30) REVERT: Y 502 MET cc_start: 0.7285 (mtp) cc_final: 0.6719 (tpt) REVERT: Z 122 MET cc_start: 0.7816 (mmp) cc_final: 0.7591 (mmp) REVERT: Z 386 MET cc_start: 0.8321 (mmm) cc_final: 0.8026 (mmm) REVERT: Z 423 ASP cc_start: 0.7809 (m-30) cc_final: 0.7368 (m-30) REVERT: Z 466 THR cc_start: 0.8558 (p) cc_final: 0.8317 (p) REVERT: Z 477 LYS cc_start: 0.8472 (mtpt) cc_final: 0.8178 (mtpp) REVERT: Z 478 TYR cc_start: 0.8118 (m-80) cc_final: 0.7870 (m-10) outliers start: 2 outliers final: 0 residues processed: 1039 average time/residue: 0.5042 time to fit residues: 890.1157 Evaluate side-chains 766 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 766 time to evaluate : 4.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 416 optimal weight: 3.9990 chunk 268 optimal weight: 10.0000 chunk 401 optimal weight: 6.9990 chunk 202 optimal weight: 0.8980 chunk 132 optimal weight: 20.0000 chunk 130 optimal weight: 0.9990 chunk 427 optimal weight: 9.9990 chunk 458 optimal weight: 3.9990 chunk 332 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 528 optimal weight: 0.7980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 60 GLN 1 51 ASN 1 587 ASN 2 243 GLN 3 309 ASN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 106 GLN ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 98 GLN ** M 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 243 ASN ** P 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 40 GLN ** S 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 405 GLN ** T 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 278 GLN U 486 GLN ** U 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 61 HIS V 149 GLN ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 221 ASN ** X 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 78 GLN ** Y 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 278 GLN ** Y 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 390 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 54694 Z= 0.194 Angle : 0.591 11.805 74172 Z= 0.299 Chirality : 0.043 0.175 8690 Planarity : 0.004 0.054 9512 Dihedral : 5.859 87.830 7671 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.54 % Favored : 94.36 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.10), residues: 7039 helix: -0.35 (0.09), residues: 3625 sheet: -1.28 (0.22), residues: 551 loop : -1.22 (0.12), residues: 2863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP M 189 HIS 0.007 0.001 HIS V 61 PHE 0.028 0.002 PHE C 116 TYR 0.029 0.001 TYR M 306 ARG 0.022 0.000 ARG M 232 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 999 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 999 time to evaluate : 4.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 72 LYS cc_start: 0.7874 (mptt) cc_final: 0.7427 (mttt) REVERT: 0 81 HIS cc_start: 0.4864 (p-80) cc_final: 0.4078 (p-80) REVERT: 1 128 LYS cc_start: 0.8428 (ttpp) cc_final: 0.8046 (ttmm) REVERT: 1 267 ARG cc_start: 0.8302 (mpt180) cc_final: 0.8053 (mpt180) REVERT: 1 269 LEU cc_start: 0.9213 (tp) cc_final: 0.8921 (tt) REVERT: 1 381 ARG cc_start: 0.8049 (mtt90) cc_final: 0.7712 (ttm170) REVERT: 1 417 LYS cc_start: 0.6349 (pttp) cc_final: 0.6036 (tptm) REVERT: 1 538 ILE cc_start: 0.9102 (mm) cc_final: 0.8870 (mm) REVERT: 1 551 LEU cc_start: 0.9417 (mm) cc_final: 0.9001 (mm) REVERT: 2 46 ARG cc_start: 0.8446 (tpm170) cc_final: 0.8013 (tpt-90) REVERT: 2 79 GLU cc_start: 0.6586 (tt0) cc_final: 0.6375 (tt0) REVERT: 2 153 ASN cc_start: 0.8721 (t0) cc_final: 0.8408 (t0) REVERT: 2 238 ASP cc_start: 0.6091 (m-30) cc_final: 0.4984 (t0) REVERT: 2 439 LYS cc_start: 0.8910 (mmtp) cc_final: 0.8408 (tptp) REVERT: 3 115 PHE cc_start: 0.7690 (t80) cc_final: 0.6345 (m-80) REVERT: 3 157 LEU cc_start: 0.8545 (tp) cc_final: 0.8324 (tt) REVERT: 3 194 PHE cc_start: 0.8977 (t80) cc_final: 0.8771 (t80) REVERT: 3 217 ASP cc_start: 0.7840 (p0) cc_final: 0.7562 (p0) REVERT: 3 223 LEU cc_start: 0.8884 (mt) cc_final: 0.8627 (mt) REVERT: 3 260 THR cc_start: 0.9144 (m) cc_final: 0.8880 (m) REVERT: 4 252 LEU cc_start: 0.9014 (mm) cc_final: 0.8696 (mm) REVERT: 4 276 GLN cc_start: 0.9305 (mt0) cc_final: 0.8823 (mp10) REVERT: 5 9 GLN cc_start: 0.8183 (tm-30) cc_final: 0.7822 (tm-30) REVERT: 5 78 GLU cc_start: 0.7839 (pt0) cc_final: 0.7581 (tt0) REVERT: 5 79 ASN cc_start: 0.9172 (m-40) cc_final: 0.8670 (m-40) REVERT: 5 94 LYS cc_start: 0.8919 (mttm) cc_final: 0.8664 (mttp) REVERT: 5 103 TYR cc_start: 0.8853 (t80) cc_final: 0.8597 (t80) REVERT: 5 116 TRP cc_start: 0.7739 (m100) cc_final: 0.7469 (m100) REVERT: 6 36 ILE cc_start: 0.8878 (mm) cc_final: 0.8152 (mm) REVERT: 6 74 GLN cc_start: 0.8211 (mt0) cc_final: 0.7960 (mm-40) REVERT: 7 68 LYS cc_start: 0.8694 (mtmt) cc_final: 0.7637 (tmtt) REVERT: 7 104 LEU cc_start: 0.9291 (mt) cc_final: 0.8796 (tt) REVERT: 7 112 THR cc_start: 0.9520 (p) cc_final: 0.9106 (t) REVERT: 7 113 MET cc_start: 0.8659 (mtt) cc_final: 0.7987 (mtt) REVERT: 7 140 LEU cc_start: 0.8921 (mt) cc_final: 0.8175 (mt) REVERT: 8 62 ASP cc_start: 0.7765 (t0) cc_final: 0.7446 (t70) REVERT: 8 64 LEU cc_start: 0.8713 (mt) cc_final: 0.8395 (tt) REVERT: 8 70 LYS cc_start: 0.8652 (tttm) cc_final: 0.8257 (tptt) REVERT: 9 26 LEU cc_start: 0.8237 (mm) cc_final: 0.7924 (mm) REVERT: 9 27 ASN cc_start: 0.7184 (t0) cc_final: 0.6844 (m-40) REVERT: 9 88 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7618 (mm-30) REVERT: 9 94 LYS cc_start: 0.7651 (tptt) cc_final: 0.7155 (tttt) REVERT: A 61 MET cc_start: 0.5395 (ttm) cc_final: 0.4898 (ttp) REVERT: A 97 LYS cc_start: 0.8453 (mtpp) cc_final: 0.7846 (mtmm) REVERT: C 61 MET cc_start: 0.7983 (mmm) cc_final: 0.7400 (mmp) REVERT: D 71 LEU cc_start: 0.8409 (mm) cc_final: 0.8078 (tt) REVERT: D 97 LYS cc_start: 0.7038 (mmtm) cc_final: 0.6273 (pttp) REVERT: D 122 PHE cc_start: 0.6243 (m-10) cc_final: 0.5869 (t80) REVERT: E 61 MET cc_start: 0.8056 (ptp) cc_final: 0.6585 (ptp) REVERT: E 98 GLN cc_start: 0.7658 (tt0) cc_final: 0.7043 (tp40) REVERT: H 97 LYS cc_start: 0.7751 (mmtt) cc_final: 0.6771 (tttt) REVERT: H 116 PHE cc_start: 0.5414 (m-10) cc_final: 0.5007 (t80) REVERT: J 87 ASN cc_start: 0.7347 (t0) cc_final: 0.7076 (t0) REVERT: M 98 ARG cc_start: 0.8257 (ptp90) cc_final: 0.7771 (ptt180) REVERT: M 244 MET cc_start: 0.8785 (mmm) cc_final: 0.8442 (mmm) REVERT: M 302 LEU cc_start: 0.9090 (mm) cc_final: 0.8848 (mm) REVERT: P 135 LEU cc_start: 0.8711 (mt) cc_final: 0.8472 (mt) REVERT: P 208 ASP cc_start: 0.8021 (t0) cc_final: 0.7725 (t0) REVERT: P 217 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8473 (tp30) REVERT: Q 19 TYR cc_start: 0.7341 (t80) cc_final: 0.6945 (t80) REVERT: Q 31 LEU cc_start: 0.7801 (mt) cc_final: 0.7008 (tt) REVERT: Q 43 GLN cc_start: 0.6254 (mt0) cc_final: 0.5444 (mm-40) REVERT: Q 65 LEU cc_start: 0.8531 (mt) cc_final: 0.8265 (tt) REVERT: R 33 PHE cc_start: 0.5299 (t80) cc_final: 0.5012 (t80) REVERT: R 97 TYR cc_start: 0.7424 (m-80) cc_final: 0.6926 (m-10) REVERT: S 58 LYS cc_start: 0.8116 (mmtt) cc_final: 0.7462 (ptpp) REVERT: S 89 PHE cc_start: 0.7124 (m-80) cc_final: 0.6325 (m-80) REVERT: T 72 GLU cc_start: 0.8117 (pt0) cc_final: 0.7460 (tm-30) REVERT: T 169 GLN cc_start: 0.7694 (mp10) cc_final: 0.7283 (mp10) REVERT: T 415 LYS cc_start: 0.7129 (mmmt) cc_final: 0.6770 (tptt) REVERT: T 447 LYS cc_start: 0.7933 (mttp) cc_final: 0.7124 (tttt) REVERT: U 414 TYR cc_start: 0.6018 (m-80) cc_final: 0.5301 (m-10) REVERT: U 474 LEU cc_start: 0.7794 (tp) cc_final: 0.7400 (pp) REVERT: V 165 ASP cc_start: 0.7982 (p0) cc_final: 0.7775 (p0) REVERT: V 243 LYS cc_start: 0.8091 (tmtt) cc_final: 0.7848 (tmmt) REVERT: V 244 ASN cc_start: 0.7593 (m-40) cc_final: 0.6972 (t0) REVERT: X 110 LYS cc_start: 0.7463 (mmpt) cc_final: 0.6848 (tptt) REVERT: X 174 GLN cc_start: 0.6870 (tt0) cc_final: 0.6252 (mm-40) REVERT: X 209 VAL cc_start: 0.7473 (p) cc_final: 0.7133 (p) REVERT: X 241 ASN cc_start: 0.7311 (p0) cc_final: 0.7034 (p0) REVERT: X 386 MET cc_start: 0.5708 (tpp) cc_final: 0.5330 (tpt) REVERT: X 488 MET cc_start: 0.4076 (mmm) cc_final: 0.2799 (tmm) REVERT: X 564 GLU cc_start: 0.6177 (mp0) cc_final: 0.5727 (mp0) REVERT: Y 323 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7480 (mm-30) REVERT: Y 502 MET cc_start: 0.7313 (mtp) cc_final: 0.6693 (tpt) REVERT: Z 386 MET cc_start: 0.8207 (mmm) cc_final: 0.7937 (mmm) REVERT: Z 477 LYS cc_start: 0.8441 (mtpt) cc_final: 0.8048 (mtpp) REVERT: Z 478 TYR cc_start: 0.8122 (m-80) cc_final: 0.7850 (m-10) outliers start: 0 outliers final: 0 residues processed: 999 average time/residue: 0.4951 time to fit residues: 844.3916 Evaluate side-chains 748 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 748 time to evaluate : 4.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 611 optimal weight: 0.0570 chunk 644 optimal weight: 10.0000 chunk 588 optimal weight: 5.9990 chunk 626 optimal weight: 9.9990 chunk 377 optimal weight: 0.9990 chunk 273 optimal weight: 6.9990 chunk 492 optimal weight: 7.9990 chunk 192 optimal weight: 10.0000 chunk 566 optimal weight: 0.8980 chunk 592 optimal weight: 7.9990 chunk 624 optimal weight: 3.9990 overall best weight: 2.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 60 GLN ** 1 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 122 ASN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 109 GLN ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 98 GLN ** M 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 278 GLN U 486 GLN ** U 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 149 GLN ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 221 ASN ** X 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 78 GLN Y 278 GLN Y 337 GLN ** Z 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 390 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 54694 Z= 0.220 Angle : 0.627 15.602 74172 Z= 0.314 Chirality : 0.043 0.237 8690 Planarity : 0.004 0.056 9512 Dihedral : 5.841 79.978 7671 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.77 % Favored : 94.13 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.10), residues: 7039 helix: -0.30 (0.09), residues: 3619 sheet: -1.24 (0.22), residues: 541 loop : -1.20 (0.12), residues: 2879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP M 189 HIS 0.008 0.001 HIS Y 79 PHE 0.048 0.002 PHE M 231 TYR 0.030 0.001 TYR T 356 ARG 0.011 0.000 ARG M 232 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 989 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 989 time to evaluate : 4.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 12 PHE cc_start: 0.7163 (t80) cc_final: 0.6702 (t80) REVERT: 0 72 LYS cc_start: 0.7910 (mptt) cc_final: 0.7493 (mttt) REVERT: 0 81 HIS cc_start: 0.4805 (p-80) cc_final: 0.3995 (p-80) REVERT: 1 128 LYS cc_start: 0.8414 (ttpp) cc_final: 0.8053 (ttmm) REVERT: 1 267 ARG cc_start: 0.8351 (mpt180) cc_final: 0.8141 (mpt180) REVERT: 1 269 LEU cc_start: 0.9259 (tp) cc_final: 0.8962 (tt) REVERT: 1 381 ARG cc_start: 0.8058 (mtt90) cc_final: 0.7691 (ttm170) REVERT: 1 417 LYS cc_start: 0.6336 (pttp) cc_final: 0.6016 (tptm) REVERT: 1 538 ILE cc_start: 0.9081 (mm) cc_final: 0.8831 (mm) REVERT: 1 549 ASP cc_start: 0.8379 (t70) cc_final: 0.8035 (p0) REVERT: 1 551 LEU cc_start: 0.9386 (mm) cc_final: 0.9135 (mm) REVERT: 2 46 ARG cc_start: 0.8545 (tpm170) cc_final: 0.7947 (tpt-90) REVERT: 2 79 GLU cc_start: 0.6744 (tt0) cc_final: 0.6444 (tt0) REVERT: 2 153 ASN cc_start: 0.8723 (t0) cc_final: 0.8465 (t0) REVERT: 2 238 ASP cc_start: 0.6138 (m-30) cc_final: 0.5065 (t0) REVERT: 2 439 LYS cc_start: 0.8938 (mmtp) cc_final: 0.8428 (tptp) REVERT: 3 115 PHE cc_start: 0.7714 (t80) cc_final: 0.6328 (m-80) REVERT: 3 139 ASP cc_start: 0.8676 (m-30) cc_final: 0.8450 (m-30) REVERT: 3 157 LEU cc_start: 0.8576 (tp) cc_final: 0.8323 (tt) REVERT: 3 217 ASP cc_start: 0.7935 (p0) cc_final: 0.7621 (p0) REVERT: 3 223 LEU cc_start: 0.8879 (mt) cc_final: 0.8622 (mt) REVERT: 4 57 TYR cc_start: 0.8299 (m-80) cc_final: 0.8013 (m-80) REVERT: 4 140 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8167 (mm-30) REVERT: 4 252 LEU cc_start: 0.9052 (mm) cc_final: 0.8685 (mm) REVERT: 4 276 GLN cc_start: 0.9291 (mt0) cc_final: 0.8814 (mp10) REVERT: 5 9 GLN cc_start: 0.8186 (tm-30) cc_final: 0.7826 (tm-30) REVERT: 5 78 GLU cc_start: 0.7841 (pt0) cc_final: 0.7574 (tt0) REVERT: 5 79 ASN cc_start: 0.9177 (m-40) cc_final: 0.8697 (m-40) REVERT: 5 103 TYR cc_start: 0.8888 (t80) cc_final: 0.8577 (t80) REVERT: 5 116 TRP cc_start: 0.7792 (m100) cc_final: 0.7530 (m100) REVERT: 6 28 GLU cc_start: 0.7848 (tt0) cc_final: 0.7321 (tm-30) REVERT: 6 36 ILE cc_start: 0.8861 (mm) cc_final: 0.8107 (mm) REVERT: 6 74 GLN cc_start: 0.8283 (mt0) cc_final: 0.7970 (mm-40) REVERT: 7 68 LYS cc_start: 0.8722 (mtmt) cc_final: 0.7650 (tmtt) REVERT: 7 104 LEU cc_start: 0.9231 (mt) cc_final: 0.8731 (tt) REVERT: 7 113 MET cc_start: 0.8731 (mtt) cc_final: 0.7180 (mtt) REVERT: 7 140 LEU cc_start: 0.8976 (mt) cc_final: 0.8302 (mt) REVERT: 8 62 ASP cc_start: 0.7715 (t0) cc_final: 0.7414 (t70) REVERT: 8 64 LEU cc_start: 0.8687 (mt) cc_final: 0.8383 (tt) REVERT: 8 70 LYS cc_start: 0.8643 (tttm) cc_final: 0.8243 (tptt) REVERT: 9 26 LEU cc_start: 0.8445 (mm) cc_final: 0.8141 (mm) REVERT: 9 27 ASN cc_start: 0.7181 (t0) cc_final: 0.6822 (m-40) REVERT: 9 59 PHE cc_start: 0.7477 (p90) cc_final: 0.7144 (p90) REVERT: 9 88 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7635 (mm-30) REVERT: 9 94 LYS cc_start: 0.7629 (tptt) cc_final: 0.7203 (tttt) REVERT: A 61 MET cc_start: 0.5486 (ttm) cc_final: 0.4925 (ttp) REVERT: A 97 LYS cc_start: 0.8398 (mtpp) cc_final: 0.7843 (mtmm) REVERT: B 61 MET cc_start: 0.7610 (mtm) cc_final: 0.7265 (mtm) REVERT: B 81 MET cc_start: 0.8198 (tmm) cc_final: 0.7908 (tmm) REVERT: D 71 LEU cc_start: 0.8451 (mm) cc_final: 0.8030 (tt) REVERT: D 97 LYS cc_start: 0.6958 (mmtm) cc_final: 0.6231 (pttp) REVERT: D 122 PHE cc_start: 0.6156 (m-10) cc_final: 0.5885 (t80) REVERT: E 61 MET cc_start: 0.7787 (ptp) cc_final: 0.7315 (ptp) REVERT: E 98 GLN cc_start: 0.7605 (tt0) cc_final: 0.7061 (tp40) REVERT: G 62 VAL cc_start: 0.7164 (t) cc_final: 0.6872 (t) REVERT: G 74 VAL cc_start: 0.8415 (t) cc_final: 0.8089 (p) REVERT: H 97 LYS cc_start: 0.7761 (mmtt) cc_final: 0.6770 (tttt) REVERT: H 116 PHE cc_start: 0.5337 (m-10) cc_final: 0.5077 (t80) REVERT: J 87 ASN cc_start: 0.7519 (t0) cc_final: 0.7227 (t0) REVERT: M 98 ARG cc_start: 0.8235 (ptp90) cc_final: 0.7790 (ptt180) REVERT: M 101 LYS cc_start: 0.9301 (tmmt) cc_final: 0.9083 (ttpp) REVERT: M 244 MET cc_start: 0.8814 (mmm) cc_final: 0.8526 (mmm) REVERT: M 306 TYR cc_start: 0.8277 (m-80) cc_final: 0.7782 (m-10) REVERT: M 311 ASN cc_start: 0.7767 (t0) cc_final: 0.7441 (t0) REVERT: P 135 LEU cc_start: 0.8721 (mt) cc_final: 0.8170 (mt) REVERT: P 217 GLU cc_start: 0.8919 (mm-30) cc_final: 0.8510 (tp30) REVERT: Q 19 TYR cc_start: 0.7364 (t80) cc_final: 0.6954 (t80) REVERT: Q 43 GLN cc_start: 0.6255 (mt0) cc_final: 0.5464 (mm-40) REVERT: R 97 TYR cc_start: 0.7448 (m-80) cc_final: 0.6965 (m-10) REVERT: S 58 LYS cc_start: 0.8132 (mmtt) cc_final: 0.7643 (ptpt) REVERT: S 89 PHE cc_start: 0.7150 (m-80) cc_final: 0.6854 (m-80) REVERT: S 241 ASP cc_start: 0.8239 (p0) cc_final: 0.6176 (t70) REVERT: T 72 GLU cc_start: 0.8205 (pt0) cc_final: 0.7477 (tm-30) REVERT: T 169 GLN cc_start: 0.7692 (mp10) cc_final: 0.7306 (mp10) REVERT: T 415 LYS cc_start: 0.7130 (mmmt) cc_final: 0.6852 (tptt) REVERT: T 447 LYS cc_start: 0.7984 (mttp) cc_final: 0.7191 (tttt) REVERT: U 152 ASN cc_start: 0.8392 (m-40) cc_final: 0.7612 (m110) REVERT: U 414 TYR cc_start: 0.6026 (m-80) cc_final: 0.5384 (m-10) REVERT: U 474 LEU cc_start: 0.7797 (tp) cc_final: 0.7396 (pp) REVERT: V 45 LEU cc_start: 0.8180 (pt) cc_final: 0.7789 (tp) REVERT: V 243 LYS cc_start: 0.8297 (tmtt) cc_final: 0.8056 (tmmt) REVERT: V 244 ASN cc_start: 0.7727 (m-40) cc_final: 0.7381 (t0) REVERT: X 174 GLN cc_start: 0.6764 (tt0) cc_final: 0.6173 (mt0) REVERT: X 241 ASN cc_start: 0.7327 (p0) cc_final: 0.7070 (p0) REVERT: X 340 TYR cc_start: 0.6447 (t80) cc_final: 0.6028 (t80) REVERT: X 386 MET cc_start: 0.5744 (tpp) cc_final: 0.5520 (tpt) REVERT: X 488 MET cc_start: 0.4237 (mmm) cc_final: 0.2622 (ttp) REVERT: X 564 GLU cc_start: 0.6137 (mp0) cc_final: 0.5713 (mp0) REVERT: Y 323 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7723 (mm-30) REVERT: Y 488 MET cc_start: 0.7851 (mmt) cc_final: 0.7470 (mmm) REVERT: Y 502 MET cc_start: 0.7197 (mtp) cc_final: 0.6586 (tpt) REVERT: Z 41 SER cc_start: 0.7754 (p) cc_final: 0.7524 (p) REVERT: Z 122 MET cc_start: 0.7489 (mmp) cc_final: 0.7217 (mmp) REVERT: Z 466 THR cc_start: 0.8514 (p) cc_final: 0.8271 (p) REVERT: Z 477 LYS cc_start: 0.8458 (mtpt) cc_final: 0.8064 (mtpp) REVERT: Z 478 TYR cc_start: 0.8116 (m-80) cc_final: 0.7865 (m-10) outliers start: 0 outliers final: 0 residues processed: 989 average time/residue: 0.4934 time to fit residues: 835.0036 Evaluate side-chains 736 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 736 time to evaluate : 4.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 411 optimal weight: 10.0000 chunk 662 optimal weight: 10.0000 chunk 404 optimal weight: 0.9990 chunk 314 optimal weight: 2.9990 chunk 460 optimal weight: 6.9990 chunk 695 optimal weight: 6.9990 chunk 640 optimal weight: 7.9990 chunk 553 optimal weight: 0.9980 chunk 57 optimal weight: 6.9990 chunk 427 optimal weight: 8.9990 chunk 339 optimal weight: 0.3980 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 60 GLN ** 1 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 122 ASN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 109 GLN 7 60 GLN 7 106 GLN ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 98 GLN ** M 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 243 ASN ** P 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 40 GLN ** S 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 278 GLN U 486 GLN ** U 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 149 GLN ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 221 ASN ** X 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 78 GLN Y 278 GLN ** Z 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 390 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 54694 Z= 0.228 Angle : 0.620 9.451 74172 Z= 0.312 Chirality : 0.044 0.286 8690 Planarity : 0.004 0.074 9512 Dihedral : 5.808 81.246 7671 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.92 % Favored : 93.98 % Rotamer: Outliers : 0.02 % Allowed : 0.53 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.10), residues: 7039 helix: -0.24 (0.09), residues: 3623 sheet: -1.30 (0.22), residues: 547 loop : -1.21 (0.12), residues: 2869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP 8 45 HIS 0.008 0.001 HIS Y 79 PHE 0.033 0.002 PHE B 82 TYR 0.034 0.001 TYR X 397 ARG 0.007 0.000 ARG U 364 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 980 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 979 time to evaluate : 4.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 72 LYS cc_start: 0.7916 (mptt) cc_final: 0.7495 (mttt) REVERT: 0 81 HIS cc_start: 0.5110 (p-80) cc_final: 0.4254 (p-80) REVERT: 1 61 MET cc_start: 0.7180 (tpp) cc_final: 0.6967 (tpp) REVERT: 1 128 LYS cc_start: 0.8424 (ttpp) cc_final: 0.8053 (ttmm) REVERT: 1 269 LEU cc_start: 0.9222 (tp) cc_final: 0.8974 (tt) REVERT: 1 381 ARG cc_start: 0.8058 (mtt90) cc_final: 0.7216 (ttm170) REVERT: 1 417 LYS cc_start: 0.6343 (pttp) cc_final: 0.6032 (tptm) REVERT: 1 538 ILE cc_start: 0.9026 (mm) cc_final: 0.8799 (mm) REVERT: 1 549 ASP cc_start: 0.8392 (t70) cc_final: 0.8126 (p0) REVERT: 1 551 LEU cc_start: 0.9330 (mm) cc_final: 0.9051 (mm) REVERT: 2 21 ARG cc_start: 0.7831 (mtm-85) cc_final: 0.7510 (mtm-85) REVERT: 2 153 ASN cc_start: 0.8734 (t0) cc_final: 0.8388 (t0) REVERT: 2 238 ASP cc_start: 0.6187 (m-30) cc_final: 0.5076 (t0) REVERT: 2 439 LYS cc_start: 0.8931 (mmtp) cc_final: 0.8430 (tptp) REVERT: 3 115 PHE cc_start: 0.7634 (t80) cc_final: 0.6349 (m-80) REVERT: 3 157 LEU cc_start: 0.8595 (tp) cc_final: 0.8368 (tt) REVERT: 3 209 LEU cc_start: 0.8771 (mp) cc_final: 0.8550 (mp) REVERT: 3 217 ASP cc_start: 0.7910 (p0) cc_final: 0.7595 (p0) REVERT: 3 223 LEU cc_start: 0.8879 (mt) cc_final: 0.8608 (mt) REVERT: 4 57 TYR cc_start: 0.8350 (m-80) cc_final: 0.8063 (m-80) REVERT: 4 140 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8175 (mm-30) REVERT: 4 252 LEU cc_start: 0.9040 (mm) cc_final: 0.8658 (mm) REVERT: 4 276 GLN cc_start: 0.9289 (mt0) cc_final: 0.8753 (mp10) REVERT: 5 9 GLN cc_start: 0.8263 (tm-30) cc_final: 0.7888 (tm-30) REVERT: 5 10 GLN cc_start: 0.9044 (tm-30) cc_final: 0.8477 (tm-30) REVERT: 5 78 GLU cc_start: 0.7906 (pt0) cc_final: 0.7606 (tt0) REVERT: 5 79 ASN cc_start: 0.9326 (m-40) cc_final: 0.8749 (m-40) REVERT: 5 103 TYR cc_start: 0.8846 (t80) cc_final: 0.8562 (t80) REVERT: 5 116 TRP cc_start: 0.7795 (m100) cc_final: 0.7503 (m100) REVERT: 6 28 GLU cc_start: 0.7834 (tt0) cc_final: 0.7231 (tm-30) REVERT: 6 36 ILE cc_start: 0.8838 (mm) cc_final: 0.8169 (mm) REVERT: 6 74 GLN cc_start: 0.8257 (mt0) cc_final: 0.8011 (mm-40) REVERT: 7 68 LYS cc_start: 0.8735 (mtmt) cc_final: 0.7647 (tmtt) REVERT: 7 104 LEU cc_start: 0.9254 (mt) cc_final: 0.8723 (tt) REVERT: 7 113 MET cc_start: 0.8301 (mtt) cc_final: 0.7273 (mtt) REVERT: 7 140 LEU cc_start: 0.8962 (mt) cc_final: 0.8278 (mt) REVERT: 8 62 ASP cc_start: 0.7714 (t0) cc_final: 0.7405 (t70) REVERT: 8 64 LEU cc_start: 0.8696 (mt) cc_final: 0.8396 (tt) REVERT: 8 70 LYS cc_start: 0.8633 (tttm) cc_final: 0.8228 (tptt) REVERT: 9 26 LEU cc_start: 0.8486 (mm) cc_final: 0.8159 (mm) REVERT: 9 27 ASN cc_start: 0.7185 (t0) cc_final: 0.6706 (m-40) REVERT: 9 59 PHE cc_start: 0.7413 (p90) cc_final: 0.7030 (p90) REVERT: 9 88 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7712 (mm-30) REVERT: 9 94 LYS cc_start: 0.7650 (tptt) cc_final: 0.7205 (tttt) REVERT: A 61 MET cc_start: 0.5563 (ttm) cc_final: 0.4971 (ttp) REVERT: A 97 LYS cc_start: 0.8405 (mtpp) cc_final: 0.7859 (mtmm) REVERT: B 81 MET cc_start: 0.8199 (tmm) cc_final: 0.7756 (tmm) REVERT: D 61 MET cc_start: 0.5626 (ppp) cc_final: 0.4978 (ppp) REVERT: D 71 LEU cc_start: 0.8365 (mm) cc_final: 0.7993 (tt) REVERT: D 97 LYS cc_start: 0.6882 (mmtm) cc_final: 0.6245 (pptt) REVERT: D 122 PHE cc_start: 0.6142 (m-10) cc_final: 0.5903 (t80) REVERT: E 61 MET cc_start: 0.7746 (ptp) cc_final: 0.7240 (ptp) REVERT: E 98 GLN cc_start: 0.7676 (tt0) cc_final: 0.7067 (tp40) REVERT: H 97 LYS cc_start: 0.7777 (mmtt) cc_final: 0.6805 (tttt) REVERT: H 116 PHE cc_start: 0.5340 (m-10) cc_final: 0.5119 (t80) REVERT: M 98 ARG cc_start: 0.8233 (ptp90) cc_final: 0.7780 (ptt180) REVERT: M 101 LYS cc_start: 0.9281 (tmmt) cc_final: 0.9035 (ttpp) REVERT: M 244 MET cc_start: 0.8835 (mmm) cc_final: 0.8498 (mmm) REVERT: P 135 LEU cc_start: 0.8701 (mt) cc_final: 0.8441 (mt) REVERT: P 217 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8451 (tp30) REVERT: Q 19 TYR cc_start: 0.7329 (t80) cc_final: 0.7027 (t80) REVERT: R 73 ASN cc_start: 0.5961 (m-40) cc_final: 0.5754 (m-40) REVERT: R 97 TYR cc_start: 0.7441 (m-80) cc_final: 0.6957 (m-10) REVERT: S 58 LYS cc_start: 0.8122 (mmtt) cc_final: 0.7615 (ptpt) REVERT: S 89 PHE cc_start: 0.7061 (m-80) cc_final: 0.6745 (m-80) REVERT: S 209 THR cc_start: 0.8163 (p) cc_final: 0.7906 (t) REVERT: S 241 ASP cc_start: 0.8257 (p0) cc_final: 0.6196 (t70) REVERT: T 72 GLU cc_start: 0.8230 (pt0) cc_final: 0.7486 (tm-30) REVERT: T 169 GLN cc_start: 0.7668 (mp10) cc_final: 0.7270 (mp10) REVERT: T 415 LYS cc_start: 0.7169 (mmmt) cc_final: 0.6874 (tptt) REVERT: T 447 LYS cc_start: 0.8018 (mttp) cc_final: 0.7187 (tttt) REVERT: U 152 ASN cc_start: 0.8406 (m-40) cc_final: 0.7585 (m110) REVERT: U 414 TYR cc_start: 0.5932 (m-80) cc_final: 0.5254 (m-10) REVERT: U 474 LEU cc_start: 0.7843 (tp) cc_final: 0.7415 (pp) REVERT: V 243 LYS cc_start: 0.8277 (tmtt) cc_final: 0.7965 (tmmt) REVERT: V 244 ASN cc_start: 0.7662 (m-40) cc_final: 0.7038 (t0) REVERT: X 110 LYS cc_start: 0.8001 (mptt) cc_final: 0.6820 (tptt) REVERT: X 174 GLN cc_start: 0.6903 (tt0) cc_final: 0.6178 (mt0) REVERT: X 241 ASN cc_start: 0.7370 (p0) cc_final: 0.7090 (p0) REVERT: X 340 TYR cc_start: 0.6432 (t80) cc_final: 0.6054 (t80) REVERT: X 386 MET cc_start: 0.5779 (tpp) cc_final: 0.5551 (tpt) REVERT: X 488 MET cc_start: 0.4567 (mmm) cc_final: 0.2923 (ttp) REVERT: X 564 GLU cc_start: 0.6135 (mp0) cc_final: 0.5794 (mp0) REVERT: Y 323 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7667 (mm-30) REVERT: Y 488 MET cc_start: 0.7883 (mmt) cc_final: 0.7480 (mmm) REVERT: Y 502 MET cc_start: 0.7221 (mtp) cc_final: 0.6570 (tpt) REVERT: Z 477 LYS cc_start: 0.8466 (mtpt) cc_final: 0.8055 (mtpp) REVERT: Z 478 TYR cc_start: 0.8122 (m-80) cc_final: 0.7854 (m-10) outliers start: 1 outliers final: 0 residues processed: 979 average time/residue: 0.4895 time to fit residues: 822.4800 Evaluate side-chains 730 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 730 time to evaluate : 4.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 439 optimal weight: 0.9980 chunk 589 optimal weight: 20.0000 chunk 169 optimal weight: 3.9990 chunk 510 optimal weight: 0.1980 chunk 81 optimal weight: 9.9990 chunk 153 optimal weight: 1.9990 chunk 554 optimal weight: 10.0000 chunk 232 optimal weight: 6.9990 chunk 569 optimal weight: 6.9990 chunk 70 optimal weight: 0.0980 chunk 102 optimal weight: 20.0000 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 60 GLN ** 1 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 184 ASN E 94 ASN J 98 GLN ** M 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 243 ASN ** P 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 271 GLN ** U 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 278 GLN U 486 GLN ** U 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 61 HIS V 149 GLN ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 157 GLN X 221 ASN ** X 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 78 GLN ** Y 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 390 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.111000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.098037 restraints weight = 152622.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.098284 restraints weight = 131673.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.098430 restraints weight = 109442.656| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 54694 Z= 0.186 Angle : 0.597 8.898 74172 Z= 0.300 Chirality : 0.043 0.297 8690 Planarity : 0.004 0.057 9512 Dihedral : 5.626 79.015 7671 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.19 % Favored : 94.72 % Rotamer: Outliers : 0.02 % Allowed : 0.37 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.10), residues: 7039 helix: -0.08 (0.09), residues: 3596 sheet: -1.20 (0.22), residues: 532 loop : -1.14 (0.12), residues: 2911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.092 0.002 TRP M 117 HIS 0.014 0.001 HIS V 61 PHE 0.030 0.001 PHE M 231 TYR 0.066 0.001 TYR U 356 ARG 0.010 0.000 ARG 1 267 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13151.56 seconds wall clock time: 231 minutes 49.29 seconds (13909.29 seconds total)