Starting phenix.real_space_refine on Sun Mar 10 17:36:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ref_4852/03_2024/6ref_4852_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ref_4852/03_2024/6ref_4852.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ref_4852/03_2024/6ref_4852.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ref_4852/03_2024/6ref_4852.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ref_4852/03_2024/6ref_4852_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ref_4852/03_2024/6ref_4852_updated.pdb" } resolution = 3.3 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= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 13 5.49 5 Mg 5 5.21 5 S 149 5.16 5 C 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 "0 ASP 59": "OD1" <-> "OD2" Residue "1 TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 28": "NH1" <-> "NH2" Residue "1 PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 69": "OD1" <-> "OD2" Residue "1 ASP 91": "OD1" <-> "OD2" Residue "1 ARG 150": "NH1" <-> "NH2" Residue "1 GLU 165": "OE1" <-> "OE2" Residue "1 ASP 172": "OD1" <-> "OD2" Residue "1 ARG 182": "NH1" <-> "NH2" Residue "1 ASP 199": "OD1" <-> "OD2" Residue "1 GLU 215": "OE1" <-> "OE2" Residue "1 ARG 259": "NH1" <-> "NH2" Residue "1 ASP 283": "OD1" <-> "OD2" Residue "1 PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 329": "OE1" <-> "OE2" Residue "1 GLU 332": "OE1" <-> "OE2" Residue "1 GLU 339": "OE1" <-> "OE2" Residue "1 GLU 341": "OE1" <-> "OE2" Residue "1 GLU 350": "OE1" <-> "OE2" Residue "1 ASP 353": "OD1" <-> "OD2" Residue "1 GLU 355": "OE1" <-> "OE2" Residue "1 ARG 359": "NH1" <-> "NH2" Residue "1 ARG 387": "NH1" <-> "NH2" Residue "1 GLU 409": "OE1" <-> "OE2" Residue "1 TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 425": "OD1" <-> "OD2" Residue "1 ARG 434": "NH1" <-> "NH2" Residue "1 GLU 457": "OE1" <-> "OE2" Residue "1 ASP 479": "OD1" <-> "OD2" Residue "1 GLU 496": "OE1" <-> "OE2" Residue "1 GLU 501": "OE1" <-> "OE2" Residue "1 GLU 513": "OE1" <-> "OE2" Residue "1 ASP 601": "OD1" <-> "OD2" Residue "1 ARG 609": "NH1" <-> "NH2" Residue "2 ASP 7": "OD1" <-> "OD2" Residue "2 ASP 16": "OD1" <-> "OD2" Residue "2 ARG 45": "NH1" <-> "NH2" Residue "2 GLU 86": "OE1" <-> "OE2" Residue "2 GLU 134": "OE1" <-> "OE2" Residue "2 TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 173": "NH1" <-> "NH2" Residue "2 PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 225": "OE1" <-> "OE2" Residue "2 PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 278": "OD1" <-> "OD2" Residue "2 PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 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 PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 149": "NH1" <-> "NH2" Residue "3 ASP 154": "OD1" <-> "OD2" Residue "3 ASP 156": "OD1" <-> "OD2" Residue "3 PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 175": "OE1" <-> "OE2" Residue "3 PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 213": "NH1" <-> "NH2" Residue "3 TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 233": "NH1" <-> "NH2" Residue "3 ARG 242": "NH1" <-> "NH2" Residue "3 ARG 257": "NH1" <-> "NH2" Residue "3 PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 276": "OE1" <-> "OE2" Residue "3 GLU 291": "OE1" <-> "OE2" Residue "3 TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 314": "OE1" <-> "OE2" Residue "3 GLU 320": "OE1" <-> "OE2" Residue "4 TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 45": "OD1" <-> "OD2" 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 TYR 134": "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 GLU 202": "OE1" <-> "OE2" Residue "4 PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 218": "OE1" <-> "OE2" Residue "4 GLU 225": "OE1" <-> "OE2" Residue "4 ASP 231": "OD1" <-> "OD2" Residue "4 ARG 232": "NH1" <-> "NH2" Residue "4 GLU 244": "OE1" <-> "OE2" Residue "4 ARG 255": "NH1" <-> "NH2" Residue "4 TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 36": "NH1" <-> "NH2" Residue "5 ARG 50": "NH1" <-> "NH2" Residue "5 ARG 112": "NH1" <-> "NH2" Residue "5 PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 81": "NH1" <-> "NH2" Residue "7 TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 109": "OD1" <-> "OD2" Residue "7 PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 164": "NH1" <-> "NH2" Residue "7 ARG 165": "NH1" <-> "NH2" Residue "7 ARG 166": "NH1" <-> "NH2" Residue "7 ASP 179": "OD1" <-> "OD2" Residue "7 PHE 185": "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 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ASP 17": "OD1" <-> "OD2" Residue "9 ARG 28": "NH1" <-> "NH2" Residue "9 ARG 40": "NH1" <-> "NH2" Residue "9 PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 91": "NH1" <-> "NH2" Residue "A GLU 111": "OE1" <-> "OE2" Residue "A PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 111": "OE1" <-> "OE2" Residue "C ARG 91": "NH1" <-> "NH2" Residue "E ARG 91": "NH1" <-> "NH2" Residue "F GLU 111": "OE1" <-> "OE2" Residue "G ARG 91": "NH1" <-> "NH2" Residue "G GLU 111": "OE1" <-> "OE2" 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 PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 136": "OE1" <-> "OE2" Residue "P GLU 143": "OE1" <-> "OE2" Residue "P TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 160": "OE1" <-> "OE2" Residue "P PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 191": "OD1" <-> "OD2" Residue "P PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 206": "NH1" <-> "NH2" Residue "P PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 42": "NH1" <-> "NH2" Residue "Q ARG 48": "NH1" <-> "NH2" Residue "Q TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 23": "OE1" <-> "OE2" Residue "R PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 68": "OD1" <-> "OD2" Residue "R ASP 95": "OD1" <-> "OD2" Residue "R ASP 143": "OD1" <-> "OD2" Residue "R ASP 156": "OD1" <-> "OD2" Residue "R PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 46": "NH1" <-> "NH2" Residue "S ASP 91": "OD1" <-> "OD2" Residue "S TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 147": "NH1" <-> "NH2" Residue "S ARG 152": "NH1" <-> "NH2" Residue "S ARG 157": "NH1" <-> "NH2" Residue "S PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 214": "OD1" <-> "OD2" Residue "S ASP 232": "OD1" <-> "OD2" Residue "S ASP 241": "OD1" <-> "OD2" Residue "S ARG 244": "NH1" <-> "NH2" Residue "S TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 306": "OE1" <-> "OE2" Residue "T ASP 46": "OD1" <-> "OD2" Residue "T ARG 49": "NH1" <-> "NH2" Residue "T ARG 86": "NH1" <-> "NH2" Residue "T ARG 96": "NH1" <-> "NH2" Residue "T ASP 112": "OD1" <-> "OD2" Residue "T TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 162": "NH1" <-> "NH2" Residue "T ASP 172": "OD1" <-> "OD2" Residue "T GLU 186": "OE1" <-> "OE2" Residue "T ARG 195": "NH1" <-> "NH2" Residue "T ARG 199": "NH1" <-> "NH2" Residue "T PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 247": "OE1" <-> "OE2" Residue "T TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 283": "NH1" <-> "NH2" Residue "T TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 418": "NH1" <-> "NH2" Residue "T ARG 429": "NH1" <-> "NH2" Residue "T PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 454": "NH1" <-> "NH2" Residue "T GLU 455": "OE1" <-> "OE2" Residue "T PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 516": "OD1" <-> "OD2" Residue "T ARG 555": "NH1" <-> "NH2" Residue "U ASP 46": "OD1" <-> "OD2" Residue "U ARG 49": "NH1" <-> "NH2" Residue "U PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 96": "NH1" <-> "NH2" Residue "U TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 135": "OD1" <-> "OD2" Residue "U TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 146": "NH1" <-> "NH2" Residue "U ARG 162": "NH1" <-> "NH2" Residue "U ARG 181": "NH1" <-> "NH2" Residue "U ARG 199": "NH1" <-> "NH2" Residue "U ARG 227": "NH1" <-> "NH2" Residue "U ARG 254": "NH1" <-> "NH2" Residue "U TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 283": "NH1" <-> "NH2" Residue "U TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 311": "OE1" <-> "OE2" Residue "U PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 314": "NH1" <-> "NH2" Residue "U ARG 342": "NH1" <-> "NH2" Residue "U ARG 343": "NH1" <-> "NH2" Residue "U ARG 364": "NH1" <-> "NH2" Residue "U PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 409": "OE1" <-> "OE2" Residue "U GLU 411": "OE1" <-> "OE2" Residue "U PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 454": "NH1" <-> "NH2" Residue "U PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 479": "NH1" <-> "NH2" Residue "U ARG 496": "NH1" <-> "NH2" Residue "U TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 510": "OD1" <-> "OD2" Residue "U ARG 513": "NH1" <-> "NH2" Residue "U GLU 521": "OE1" <-> "OE2" Residue "U PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 47": "OE1" <-> "OE2" Residue "V ARG 49": "NH1" <-> "NH2" Residue "V PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 142": "OD1" <-> "OD2" Residue "V TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 181": "NH1" <-> "NH2" Residue "V 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 TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 314": "NH1" <-> "NH2" Residue "V ARG 335": "NH1" <-> "NH2" Residue "V ARG 342": "NH1" <-> "NH2" Residue "V ARG 343": "NH1" <-> "NH2" Residue "V ARG 360": "NH1" <-> "NH2" Residue "V PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 403": "OD1" <-> "OD2" Residue "V PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 454": "NH1" <-> "NH2" Residue "V ASP 467": "OD1" <-> "OD2" Residue "V ARG 476": "NH1" <-> "NH2" Residue "V ARG 496": "NH1" <-> "NH2" Residue "V TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 513": "NH1" <-> "NH2" Residue "V ARG 555": "NH1" <-> "NH2" Residue "X TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 71": "NH1" <-> "NH2" Residue "X ARG 86": "NH1" <-> "NH2" Residue "X ASP 104": "OD1" <-> "OD2" Residue "X ARG 115": "NH1" <-> "NH2" Residue "X ARG 120": "NH1" <-> "NH2" Residue "X ASP 136": "OD1" <-> "OD2" Residue "X ASP 139": "OD1" <-> "OD2" Residue "X PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 168": "OD1" <-> "OD2" Residue "X TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 215": "OE1" <-> "OE2" Residue "X GLU 253": "OE1" <-> "OE2" Residue "X ARG 258": "NH1" <-> "NH2" Residue "X GLU 270": "OE1" <-> "OE2" Residue "X TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 462": "OD1" <-> "OD2" Residue "X PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 479": "OD1" <-> "OD2" Residue "X TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 505": "OD1" <-> "OD2" Residue "X ARG 509": "NH1" <-> "NH2" Residue "X GLU 520": "OE1" <-> "OE2" Residue "X GLU 533": "OE1" <-> "OE2" Residue "X ASP 542": "OD1" <-> "OD2" Residue "X ASP 543": "OD1" <-> "OD2" Residue "Y TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 49": "OD1" <-> "OD2" Residue "Y ARG 51": "NH1" <-> "NH2" Residue "Y GLU 55": "OE1" <-> "OE2" Residue "Y GLU 66": "OE1" <-> "OE2" 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 PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 216": "NH1" <-> "NH2" Residue "Y GLU 226": "OE1" <-> "OE2" Residue "Y ARG 258": "NH1" <-> "NH2" Residue "Y PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 289": "NH1" <-> "NH2" 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 TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 435": "NH1" <-> "NH2" Residue "Y ARG 437": "NH1" <-> "NH2" Residue "Y PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 497": "OE1" <-> "OE2" Residue "Y ASP 500": "OD1" <-> "OD2" Residue "Y ASP 505": "OD1" <-> "OD2" Residue "Y ARG 509": "NH1" <-> "NH2" Residue "Y ASP 528": "OD1" <-> "OD2" Residue "Y ASP 542": "OD1" <-> "OD2" Residue "Y GLU 546": "OE1" <-> "OE2" Residue "Y PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 49": "OD1" <-> "OD2" Residue "Z ARG 51": "NH1" <-> "NH2" Residue "Z ASP 82": "OD1" <-> "OD2" Residue "Z GLU 131": "OE1" <-> "OE2" Residue "Z PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 182": "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 TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 296": "OE1" <-> "OE2" Residue "Z TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 378": "OD1" <-> "OD2" Residue "Z ARG 385": "NH1" <-> "NH2" Residue "Z TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 401": "NH1" <-> "NH2" Residue "Z ASP 415": "OD1" <-> "OD2" Residue "Z PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 509": "NH1" <-> "NH2" Residue "Z ASP 513": "OD1" <-> "OD2" Residue "Z ASP 528": "OD1" <-> "OD2" Residue "Z GLU 541": "OE1" <-> "OE2" Residue "Z ASP 542": "OD1" <-> "OD2" Residue "Z ASP 543": "OD1" <-> "OD2" Residue "Z GLU 547": "OE1" <-> "OE2" Residue "Z PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 552": "OE1" <-> "OE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 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: 20.55, per 1000 atoms: 0.38 Number of scatterers: 53756 At special positions: 0 Unit cell: (211.653, 134.784, 263.25, 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: 15.58 Conformation dependent library (CDL) restraints added in 7.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN M 600 " pdb="ZN ZN M 600 " - pdb=" NE2 HIS M 248 " pdb="ZN ZN M 600 " - pdb=" NE2 HIS M 252 " 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: 293 helices and 31 sheets defined 52.2% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.75 Creating SS restraints... Processing helix chain '0' and resid 4 through 7 No H-bonds generated for 'chain '0' and resid 4 through 7' Processing helix chain '0' and resid 18 through 29 Processing helix chain '0' and resid 44 through 49 Processing helix chain '0' and resid 52 through 55 No H-bonds generated for 'chain '0' and resid 52 through 55' Processing helix chain '1' and resid 46 through 71 Processing helix chain '1' and resid 107 through 141 removed outlier: 3.823A pdb=" N ALA 1 140 " --> pdb=" O GLU 1 136 " (cutoff:3.500A) Processing helix chain '1' and resid 164 through 177 removed outlier: 3.999A pdb=" N THR 1 169 " --> pdb=" O GLU 1 165 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA 1 177 " --> pdb=" O LYS 1 173 " (cutoff:3.500A) Processing helix chain '1' and resid 191 through 204 removed outlier: 3.540A pdb=" N ALA 1 196 " --> pdb=" O GLY 1 192 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL 1 204 " --> pdb=" O PHE 1 200 " (cutoff:3.500A) Processing helix chain '1' and resid 207 through 223 removed outlier: 5.217A pdb=" N SER 1 211 " --> pdb=" O LYS 1 208 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL 1 213 " --> pdb=" O ALA 1 210 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU 1 223 " --> pdb=" O SER 1 220 " (cutoff:3.500A) Processing helix chain '1' and resid 242 through 270 Processing helix chain '1' and resid 272 through 276 removed outlier: 3.755A pdb=" N ALA 1 275 " --> pdb=" O PRO 1 272 " (cutoff:3.500A) Processing helix chain '1' and resid 283 through 285 No H-bonds generated for 'chain '1' and resid 283 through 285' Processing helix chain '1' and resid 290 through 292 No H-bonds generated for 'chain '1' and resid 290 through 292' Processing helix chain '1' and resid 298 through 306 removed outlier: 4.214A pdb=" N GLN 1 306 " --> pdb=" O SER 1 302 " (cutoff:3.500A) Processing helix chain '1' and resid 311 through 316 Processing helix chain '1' and resid 324 through 326 No H-bonds generated for 'chain '1' and resid 324 through 326' Processing helix chain '1' and resid 331 through 333 No H-bonds generated for 'chain '1' and resid 331 through 333' Processing helix chain '1' and resid 339 through 352 Processing helix chain '1' and resid 354 through 361 Processing helix chain '1' and resid 363 through 366 Processing helix chain '1' and resid 376 through 387 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 445 removed outlier: 3.759A pdb=" N LYS 1 445 " --> pdb=" O PHE 1 441 " (cutoff:3.500A) Processing helix chain '1' and resid 447 through 459 Processing helix chain '1' and resid 464 through 477 Processing helix chain '1' and resid 480 through 482 No H-bonds generated for 'chain '1' and resid 480 through 482' Processing helix chain '1' and resid 486 through 489 No H-bonds generated for 'chain '1' and resid 486 through 489' Processing helix chain '1' and resid 491 through 515 removed outlier: 3.690A pdb=" N GLU 1 496 " --> pdb=" O GLN 1 492 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU 1 501 " --> pdb=" O LEU 1 497 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASP 1 504 " --> pdb=" O LEU 1 500 " (cutoff:3.500A) Processing helix chain '1' and resid 519 through 535 Processing helix chain '1' and resid 542 through 548 Processing helix chain '1' and resid 550 through 561 Processing helix chain '1' and resid 567 through 573 Processing helix chain '1' and resid 577 through 587 Processing helix chain '1' and resid 589 through 591 No H-bonds generated for 'chain '1' and resid 589 through 591' Processing helix chain '1' and resid 593 through 605 Processing helix chain '2' and resid 8 through 18 Processing helix chain '2' and resid 26 through 37 Processing helix chain '2' and resid 45 through 56 Processing helix chain '2' and resid 63 through 75 Processing helix chain '2' and resid 81 through 93 removed outlier: 3.549A pdb=" N LEU 2 87 " --> pdb=" O THR 2 83 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA 2 88 " --> pdb=" O VAL 2 84 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N GLY 2 89 " --> pdb=" O ALA 2 85 " (cutoff:3.500A) Proline residue: 2 90 - end of helix Processing helix chain '2' and resid 100 through 112 Processing helix chain '2' and resid 118 through 130 removed outlier: 3.843A pdb=" N VAL 2 127 " --> pdb=" O LYS 2 123 " (cutoff:3.500A) Processing helix chain '2' and resid 137 through 149 Processing helix chain '2' and resid 155 through 167 removed outlier: 3.611A pdb=" N VAL 2 164 " --> pdb=" O ALA 2 160 " (cutoff:3.500A) Processing helix chain '2' and resid 172 through 185 Processing helix chain '2' and resid 190 through 198 removed outlier: 3.691A pdb=" N ALA 2 195 " --> pdb=" O ALA 2 191 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS 2 198 " --> pdb=" O ASP 2 194 " (cutoff:3.500A) Processing helix chain '2' and resid 207 through 220 Processing helix chain '2' and resid 228 through 234 Processing helix chain '2' and resid 241 through 254 removed outlier: 3.628A pdb=" N GLU 2 246 " --> pdb=" O ALA 2 242 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER 2 254 " --> pdb=" O GLY 2 250 " (cutoff:3.500A) Processing helix chain '2' and resid 259 through 275 removed outlier: 3.523A pdb=" N VAL 2 268 " --> pdb=" O ALA 2 264 " (cutoff:3.500A) Proline residue: 2 271 - end of helix Processing helix chain '2' and resid 277 through 279 No H-bonds generated for 'chain '2' and resid 277 through 279' Processing helix chain '2' and resid 282 through 295 Processing helix chain '2' and resid 303 through 320 removed outlier: 3.555A pdb=" N GLY 2 312 " --> pdb=" O ALA 2 308 " (cutoff:3.500A) Processing helix chain '2' and resid 326 through 340 Processing helix chain '2' and resid 346 through 353 Processing helix chain '2' and resid 397 through 406 Processing helix chain '2' and resid 418 through 421 No H-bonds generated for 'chain '2' and resid 418 through 421' Processing helix chain '2' and resid 427 through 441 removed outlier: 3.825A pdb=" N VAL 2 441 " --> pdb=" O ALA 2 437 " (cutoff:3.500A) Processing helix chain '3' and resid 78 through 86 Processing helix chain '3' and resid 95 through 98 No H-bonds generated for 'chain '3' and resid 95 through 98' Processing helix chain '3' and resid 103 through 112 Processing helix chain '3' and resid 118 through 126 removed outlier: 4.128A pdb=" N LYS 3 123 " --> pdb=" O ASP 3 119 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU 3 126 " --> pdb=" O VAL 3 122 " (cutoff:3.500A) Processing helix chain '3' and resid 129 through 131 No H-bonds generated for 'chain '3' and resid 129 through 131' Processing helix chain '3' and resid 137 through 149 Processing helix chain '3' and resid 155 through 167 Processing helix chain '3' and resid 174 through 186 removed outlier: 4.064A pdb=" N GLN 3 179 " --> pdb=" O GLU 3 175 " (cutoff:3.500A) Processing helix chain '3' and resid 192 through 204 Processing helix chain '3' and resid 216 through 228 removed outlier: 4.073A pdb=" N THR 3 221 " --> pdb=" O ASP 3 217 " (cutoff:3.500A) Processing helix chain '3' and resid 234 through 243 removed outlier: 3.757A pdb=" N ARG 3 242 " --> pdb=" O ALA 3 238 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLY 3 243 " --> pdb=" O THR 3 239 " (cutoff:3.500A) Processing helix chain '3' and resid 246 through 250 Processing helix chain '3' and resid 254 through 271 Processing helix chain '3' and resid 276 through 285 removed outlier: 3.893A pdb=" N GLU 3 279 " --> pdb=" O GLU 3 276 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA 3 280 " --> pdb=" O SER 3 277 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE 3 282 " --> pdb=" O GLU 3 279 " (cutoff:3.500A) removed outlier: 3.921A 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: 3.658A pdb=" N VAL 3 303 " --> pdb=" O GLU 3 299 " (cutoff:3.500A) Processing helix chain '4' and resid 10 through 13 No H-bonds generated for 'chain '4' and resid 10 through 13' Processing helix chain '4' and resid 20 through 34 removed outlier: 3.663A pdb=" N ALA 4 25 " --> pdb=" O GLU 4 21 " (cutoff:3.500A) Processing helix chain '4' and resid 48 through 67 removed outlier: 4.153A pdb=" N GLN 4 61 " --> pdb=" O TYR 4 57 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL 4 62 " --> pdb=" O LEU 4 58 " (cutoff:3.500A) Proline residue: 4 65 - end of helix Processing helix chain '4' and resid 80 through 96 Processing helix chain '4' and resid 101 through 112 Processing helix chain '4' and resid 119 through 125 Processing helix chain '4' and resid 132 through 149 removed outlier: 3.829A pdb=" N ALA 4 137 " --> pdb=" O ASP 4 133 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL 4 141 " --> pdb=" O ALA 4 137 " (cutoff:3.500A) Processing helix chain '4' and resid 160 through 176 removed outlier: 4.248A pdb=" N LYS 4 168 " --> pdb=" O LYS 4 164 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA 4 171 " --> pdb=" O ALA 4 167 " (cutoff:3.500A) Processing helix chain '4' and resid 180 through 188 Processing helix chain '4' and resid 193 through 233 removed outlier: 4.001A pdb=" N GLU 4 202 " --> pdb=" O LYS 4 198 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N THR 4 205 " --> pdb=" O LYS 4 201 " (cutoff:3.500A) Processing helix chain '4' and resid 238 through 257 removed outlier: 3.514A pdb=" N ALA 4 256 " --> pdb=" O LEU 4 252 " (cutoff:3.500A) Processing helix chain '4' and resid 263 through 284 Processing helix chain '5' and resid 8 through 58 removed outlier: 5.273A pdb=" N LEU 5 31 " --> pdb=" O ASP 5 27 " (cutoff:3.500A) Proline residue: 5 32 - end of helix removed outlier: 3.708A pdb=" N GLU 5 37 " --> pdb=" O THR 5 33 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N HIS 5 41 " --> pdb=" O GLU 5 37 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N LYS 5 49 " --> pdb=" O ALA 5 45 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ARG 5 50 " --> pdb=" O ALA 5 46 " (cutoff:3.500A) Processing helix chain '5' and resid 73 through 80 Processing helix chain '5' and resid 88 through 105 removed outlier: 3.972A pdb=" N LEU 5 92 " --> pdb=" O PRO 5 88 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LYS 5 101 " --> pdb=" O SER 5 97 " (cutoff:3.500A) Processing helix chain '5' and resid 115 through 118 No H-bonds generated for 'chain '5' and resid 115 through 118' Processing helix chain '6' and resid 31 through 40 Processing helix chain '6' and resid 49 through 57 removed outlier: 4.296A pdb=" N LYS 6 52 " --> pdb=" O SER 6 49 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N THR 6 53 " --> pdb=" O SER 6 50 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA 6 56 " --> pdb=" O THR 6 53 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN 6 57 " --> pdb=" O ILE 6 54 " (cutoff:3.500A) Processing helix chain '6' and resid 73 through 93 Processing helix chain '6' and resid 99 through 119 removed outlier: 3.649A pdb=" N VAL 6 107 " --> pdb=" O LEU 6 103 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TRP 6 112 " --> pdb=" O LEU 6 108 " (cutoff:3.500A) Processing helix chain '6' and resid 122 through 130 Processing helix chain '6' and resid 134 through 137 No H-bonds generated for 'chain '6' and resid 134 through 137' Processing helix chain '7' and resid 63 through 66 No H-bonds generated for 'chain '7' and resid 63 through 66' Processing helix chain '7' and resid 84 through 103 removed outlier: 3.554A pdb=" N GLU 7 99 " --> pdb=" O SER 7 95 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU 7 103 " --> pdb=" O GLU 7 99 " (cutoff:3.500A) Processing helix chain '7' and resid 111 through 113 No H-bonds generated for 'chain '7' and resid 111 through 113' Processing helix chain '7' and resid 116 through 119 No H-bonds generated for 'chain '7' and resid 116 through 119' Processing helix chain '7' and resid 124 through 144 Processing helix chain '7' and resid 147 through 164 removed outlier: 3.671A pdb=" N LEU 7 150 " --> pdb=" O PHE 7 147 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N SER 7 151 " --> pdb=" O ASP 7 148 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ALA 7 154 " --> pdb=" O SER 7 151 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER 7 155 " --> pdb=" O ALA 7 152 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL 7 157 " --> pdb=" O ALA 7 154 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL 7 158 " --> pdb=" O SER 7 155 " (cutoff:3.500A) Proline residue: 7 159 - end of helix Processing helix chain '7' and resid 175 through 186 Processing helix chain '8' and resid 27 through 30 No H-bonds generated for 'chain '8' and resid 27 through 30' Processing helix chain '8' and resid 32 through 38 Processing helix chain '8' and resid 40 through 43 No H-bonds generated for 'chain '8' and resid 40 through 43' Processing helix chain '8' and resid 45 through 79 removed outlier: 3.803A pdb=" N ALA 8 76 " --> pdb=" O ALA 8 72 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ALA 8 79 " --> pdb=" O GLU 8 75 " (cutoff:3.500A) Processing helix chain '9' and resid 6 through 16 Processing helix chain '9' and resid 20 through 23 No H-bonds generated for 'chain '9' and resid 20 through 23' Processing helix chain '9' and resid 33 through 54 removed outlier: 3.971A pdb=" N ALA 9 38 " --> pdb=" O GLY 9 34 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N VAL 9 42 " --> pdb=" O ALA 9 38 " (cutoff:3.500A) Processing helix chain '9' and resid 83 through 93 removed outlier: 3.520A pdb=" N GLU 9 88 " --> pdb=" O ALA 9 84 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU 9 92 " --> pdb=" O GLU 9 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 66 removed outlier: 4.055A pdb=" N MET A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL A 62 " --> pdb=" O ALA A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 91 removed outlier: 4.112A pdb=" N GLY A 73 " --> pdb=" O ALA A 70 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL A 74 " --> pdb=" O LEU A 71 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE A 82 " --> pdb=" O GLY A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 125 removed outlier: 3.617A pdb=" N ALA A 96 " --> pdb=" O PRO A 93 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N LYS A 97 " --> pdb=" O ASN A 94 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL A 100 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N SER A 112 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU A 119 " --> pdb=" O PHE A 116 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE A 122 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU A 125 " --> pdb=" O PHE A 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 91 removed outlier: 3.932A pdb=" N THR B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ILE B 69 " --> pdb=" O GLY B 65 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ALA B 70 " --> pdb=" O CYS B 66 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N LEU B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ALA B 72 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY B 73 " --> pdb=" O ILE B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 125 removed outlier: 3.543A pdb=" N ALA B 96 " --> pdb=" O PRO B 93 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N LYS B 97 " --> pdb=" O ASN B 94 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY B 106 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER B 112 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER B 117 " --> pdb=" O ALA B 114 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU B 119 " --> pdb=" O PHE B 116 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL B 121 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE B 124 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU B 125 " --> pdb=" O PHE B 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 91 removed outlier: 4.113A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE C 69 " --> pdb=" O GLY C 65 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ALA C 70 " --> pdb=" O CYS C 66 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N LEU C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ALA C 72 " --> pdb=" O THR C 68 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLY C 73 " --> pdb=" O ILE C 69 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 126 removed outlier: 4.053A pdb=" N ILE C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL C 120 " --> pdb=" O PHE C 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 91 removed outlier: 3.942A pdb=" N MET D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ILE D 69 " --> pdb=" O GLY D 65 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ALA D 70 " --> pdb=" O CYS D 66 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N LEU D 71 " --> pdb=" O ALA D 67 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ALA D 72 " --> pdb=" O THR D 68 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLY D 73 " --> pdb=" O ILE D 69 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 126 removed outlier: 3.659A pdb=" N ALA D 96 " --> pdb=" O PRO D 93 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N LYS D 97 " --> pdb=" O ASN D 94 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU D 104 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N SER D 112 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU D 119 " --> pdb=" O PHE D 116 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU D 125 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N PHE D 126 " --> pdb=" O LEU D 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 91 removed outlier: 4.453A pdb=" N MET E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ILE E 69 " --> pdb=" O GLY E 65 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ALA E 70 " --> pdb=" O CYS E 66 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N LEU E 71 " --> pdb=" O ALA E 67 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ALA E 72 " --> pdb=" O THR E 68 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLY E 73 " --> pdb=" O ILE E 69 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL E 74 " --> pdb=" O ALA E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 126 removed outlier: 3.929A pdb=" N ALA E 96 " --> pdb=" O PRO E 93 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N LYS E 97 " --> pdb=" O ASN E 94 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA E 108 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N GLU E 111 " --> pdb=" O ALA E 108 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N SER E 112 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU E 118 " --> pdb=" O LEU E 115 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU E 125 " --> pdb=" O PHE E 122 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N PHE E 126 " --> pdb=" O LEU E 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 91 removed outlier: 3.749A pdb=" N MET F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ILE F 69 " --> pdb=" O GLY F 65 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ALA F 70 " --> pdb=" O CYS F 66 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N LEU F 71 " --> pdb=" O ALA F 67 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ALA F 72 " --> pdb=" O THR F 68 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLY F 73 " --> pdb=" O ILE F 69 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL F 74 " --> pdb=" O ALA F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 125 removed outlier: 3.631A pdb=" N GLY F 101 " --> pdb=" O LYS F 97 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER F 112 " --> pdb=" O ALA F 108 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ILE F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA F 114 " --> pdb=" O THR F 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 91 removed outlier: 4.013A pdb=" N MET G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL G 62 " --> pdb=" O ALA G 58 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ILE G 69 " --> pdb=" O GLY G 65 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N ALA G 70 " --> pdb=" O CYS G 66 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N LEU G 71 " --> pdb=" O ALA G 67 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ALA G 72 " --> pdb=" O THR G 68 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLY G 73 " --> pdb=" O ILE G 69 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 110 removed outlier: 3.564A pdb=" N ALA G 96 " --> pdb=" O PRO G 93 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LYS G 97 " --> pdb=" O ASN G 94 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU G 104 " --> pdb=" O GLY G 101 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR G 110 " --> pdb=" O PHE G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 125 removed outlier: 3.589A pdb=" N SER G 117 " --> pdb=" O ILE G 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 91 removed outlier: 3.823A pdb=" N MET H 61 " --> pdb=" O ALA H 57 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL H 62 " --> pdb=" O ALA H 58 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE H 69 " --> pdb=" O GLY H 65 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ALA H 70 " --> pdb=" O CYS H 66 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N LEU H 71 " --> pdb=" O ALA H 67 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ALA H 72 " --> pdb=" O THR H 68 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLY H 73 " --> pdb=" O ILE H 69 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL H 74 " --> pdb=" O ALA H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 125 removed outlier: 5.310A pdb=" N LYS H 97 " --> pdb=" O ASN H 94 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLU H 111 " --> pdb=" O ALA H 108 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER H 112 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU H 119 " --> pdb=" O PHE H 116 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE H 124 " --> pdb=" O VAL H 121 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU H 125 " --> pdb=" O PHE H 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 91 removed outlier: 3.895A pdb=" N GLY I 65 " --> pdb=" O MET I 61 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE I 69 " --> pdb=" O GLY I 65 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N ALA I 70 " --> pdb=" O CYS I 66 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N LEU I 71 " --> pdb=" O ALA I 67 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ALA I 72 " --> pdb=" O THR I 68 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLY I 73 " --> pdb=" O ILE I 69 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL I 74 " --> pdb=" O ALA I 70 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY I 79 " --> pdb=" O GLY I 75 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 95 No H-bonds generated for 'chain 'I' and resid 93 through 95' Processing helix chain 'I' and resid 98 through 123 removed outlier: 3.505A pdb=" N LEU I 105 " --> pdb=" O GLY I 101 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE I 113 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL I 120 " --> pdb=" O PHE I 116 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 91 removed outlier: 3.803A pdb=" N MET J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N CYS J 66 " --> pdb=" O VAL J 62 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ILE J 69 " --> pdb=" O GLY J 65 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ALA J 70 " --> pdb=" O CYS J 66 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N LEU J 71 " --> pdb=" O ALA J 67 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ALA J 72 " --> pdb=" O THR J 68 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLY J 73 " --> pdb=" O ILE J 69 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE J 86 " --> pdb=" O PHE J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 95 No H-bonds generated for 'chain 'J' and resid 93 through 95' Processing helix chain 'J' and resid 98 through 125 removed outlier: 4.105A pdb=" N ILE J 113 " --> pdb=" O LEU J 109 " (cutoff:3.500A) Processing helix chain 'M' and resid 105 through 118 Processing helix chain 'M' and resid 135 through 143 Processing helix chain 'M' and resid 148 through 167 removed outlier: 3.981A pdb=" N GLY M 166 " --> pdb=" O CYS M 162 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU M 167 " --> pdb=" O ASN M 163 " (cutoff:3.500A) Processing helix chain 'M' and resid 174 through 176 No H-bonds generated for 'chain 'M' and resid 174 through 176' Processing helix chain 'M' and resid 178 through 200 removed outlier: 3.858A 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 231 through 257 removed outlier: 4.112A pdb=" N GLY M 237 " --> pdb=" O ALA M 233 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLY M 247 " --> pdb=" O ASN M 243 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N HIS M 248 " --> pdb=" O MET M 244 " (cutoff:3.500A) Processing helix chain 'M' and resid 259 through 264 Processing helix chain 'M' and resid 271 through 310 removed outlier: 3.715A pdb=" N VAL M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU M 280 " --> pdb=" O GLY M 276 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER M 296 " --> pdb=" O ALA M 292 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N PHE M 310 " --> pdb=" O TYR M 306 " (cutoff:3.500A) Processing helix chain 'P' and resid 52 through 63 removed outlier: 3.583A pdb=" N LYS P 63 " --> pdb=" O GLN P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 67 through 83 removed outlier: 3.936A pdb=" N ASP P 72 " --> pdb=" O ASP P 68 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLU P 73 " --> pdb=" O LYS P 69 " (cutoff:3.500A) Processing helix chain 'P' and resid 89 through 92 No H-bonds generated for 'chain 'P' and resid 89 through 92' Processing helix chain 'P' and resid 98 through 108 Processing helix chain 'P' and resid 116 through 125 removed outlier: 3.759A pdb=" N ALA P 124 " --> pdb=" O LYS P 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 131 through 146 removed outlier: 3.823A pdb=" N LEU P 135 " --> pdb=" O SER P 132 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N THR P 138 " --> pdb=" O LEU P 135 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN P 140 " --> pdb=" O VAL P 137 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU P 146 " --> pdb=" O GLU P 143 " (cutoff:3.500A) Processing helix chain 'P' and resid 164 through 177 removed outlier: 3.815A pdb=" N VAL P 168 " --> pdb=" O LYS P 164 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS P 172 " --> pdb=" O VAL P 168 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N LYS P 176 " --> pdb=" O LYS P 172 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N PHE P 177 " --> pdb=" O LYS P 173 " (cutoff:3.500A) Processing helix chain 'P' and resid 211 through 228 removed outlier: 3.612A pdb=" N GLU P 216 " --> pdb=" O ALA P 212 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS P 224 " --> pdb=" O ASN P 220 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL P 226 " --> pdb=" O VAL P 222 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU P 227 " --> pdb=" O ASN P 223 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER P 228 " --> pdb=" O LYS P 224 " (cutoff:3.500A) Processing helix chain 'Q' and resid 16 through 30 removed outlier: 4.280A pdb=" N VAL Q 30 " --> pdb=" O LEU Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 33 through 37 Processing helix chain 'R' and resid 30 through 40 removed outlier: 4.147A pdb=" N GLU R 35 " --> pdb=" O LYS R 31 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL R 36 " --> pdb=" O GLU R 32 " (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 158 through 168 removed outlier: 3.791A pdb=" N SER R 162 " --> pdb=" O ALA R 158 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 195 Processing helix chain 'S' and resid 42 through 78 removed outlier: 3.672A pdb=" N ASN S 52 " --> pdb=" O ARG S 48 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET S 62 " --> pdb=" O LYS S 58 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ILE S 73 " --> pdb=" O LYS S 69 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ALA S 74 " --> pdb=" O ASN S 70 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL S 75 " --> pdb=" O ALA S 71 " (cutoff:3.500A) Processing helix chain 'S' and resid 81 through 88 removed outlier: 4.464A pdb=" N PHE S 85 " --> pdb=" O LEU S 81 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL S 86 " --> pdb=" O VAL S 82 " (cutoff:3.500A) Processing helix chain 'S' and resid 118 through 129 removed outlier: 3.760A pdb=" N THR S 129 " --> pdb=" O ALA S 125 " (cutoff:3.500A) Processing helix chain 'S' and resid 147 through 150 No H-bonds generated for 'chain 'S' and resid 147 through 150' Processing helix chain 'S' and resid 172 through 182 Processing helix chain 'S' and resid 213 through 216 No H-bonds generated for 'chain 'S' and resid 213 through 216' Processing helix chain 'S' and resid 239 through 314 removed outlier: 3.753A pdb=" N ARG S 244 " --> pdb=" O SER S 240 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER S 272 " --> pdb=" O ALA S 268 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU S 275 " --> pdb=" O MET S 271 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU S 285 " --> pdb=" O ALA S 281 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA S 313 " --> pdb=" O ALA S 309 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU S 314 " --> pdb=" O GLY S 310 " (cutoff:3.500A) Processing helix chain 'T' and resid 58 through 75 removed outlier: 3.678A pdb=" N LYS T 65 " --> pdb=" O HIS T 61 " (cutoff:3.500A) Proline residue: T 68 - end of helix removed outlier: 4.107A pdb=" N GLU T 72 " --> pdb=" O PRO T 68 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TRP T 73 " --> pdb=" O ALA T 69 " (cutoff:3.500A) Processing helix chain 'T' and resid 135 through 137 No H-bonds generated for 'chain 'T' and resid 135 through 137' Processing helix chain 'T' and resid 157 through 159 No H-bonds generated for 'chain 'T' and resid 157 through 159' Processing helix chain 'T' and resid 207 through 211 Processing helix chain 'T' and resid 231 through 247 removed outlier: 3.774A pdb=" N GLU T 247 " --> pdb=" O LYS T 243 " (cutoff:3.500A) Processing helix chain 'T' and resid 268 through 279 removed outlier: 3.585A pdb=" N VAL T 273 " --> pdb=" O VAL T 269 " (cutoff:3.500A) Processing helix chain 'T' and resid 281 through 283 No H-bonds generated for 'chain 'T' and resid 281 through 283' Processing helix chain 'T' and resid 296 through 315 Proline residue: T 303 - end of helix removed outlier: 4.156A pdb=" N PHE T 313 " --> pdb=" O MET T 309 " (cutoff:3.500A) Processing helix chain 'T' and resid 327 through 340 removed outlier: 3.769A pdb=" N VAL T 332 " --> pdb=" O SER T 328 " (cutoff:3.500A) Processing helix chain 'T' and resid 347 through 349 No H-bonds generated for 'chain 'T' and resid 347 through 349' Processing helix chain 'T' and resid 354 through 364 removed outlier: 4.262A pdb=" N ARG T 364 " --> pdb=" O ARG T 360 " (cutoff:3.500A) Processing helix chain 'T' and resid 393 through 401 Processing helix chain 'T' and resid 410 through 414 removed outlier: 3.574A pdb=" N TYR T 414 " --> pdb=" O THR T 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 410 through 414' Processing helix chain 'T' and resid 431 through 434 Processing helix chain 'T' and resid 437 through 440 No H-bonds generated for 'chain 'T' and resid 437 through 440' Processing helix chain 'T' and resid 443 through 455 removed outlier: 3.621A pdb=" N LEU T 448 " --> pdb=" O GLY T 444 " (cutoff:3.500A) Processing helix chain 'T' and resid 459 through 461 No H-bonds generated for 'chain 'T' and resid 459 through 461' Processing helix chain 'T' and resid 470 through 483 removed outlier: 3.781A pdb=" N ALA T 478 " --> pdb=" O LEU T 474 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU T 482 " --> pdb=" O ALA T 478 " (cutoff:3.500A) Processing helix chain 'T' and resid 494 through 505 removed outlier: 3.659A pdb=" N ALA T 504 " --> pdb=" O ALA T 500 " (cutoff:3.500A) Processing helix chain 'T' and resid 523 through 527 Processing helix chain 'T' and resid 531 through 539 Processing helix chain 'T' and resid 547 through 555 Processing helix chain 'U' and resid 42 through 49 removed outlier: 4.332A pdb=" N ARG U 49 " --> pdb=" O LEU U 45 " (cutoff:3.500A) Processing helix chain 'U' and resid 59 through 73 removed outlier: 4.459A pdb=" N GLN U 64 " --> pdb=" O GLN U 60 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS U 65 " --> pdb=" O HIS U 61 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ILE U 67 " --> pdb=" O SER U 63 " (cutoff:3.500A) Proline residue: U 68 - end of helix removed outlier: 3.865A pdb=" N GLU U 72 " --> pdb=" O PRO U 68 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TRP U 73 " --> pdb=" O ALA U 69 " (cutoff:3.500A) Processing helix chain 'U' and resid 135 through 137 No H-bonds generated for 'chain 'U' and resid 135 through 137' Processing helix chain 'U' and resid 157 through 159 No H-bonds generated for 'chain 'U' and resid 157 through 159' Processing helix chain 'U' and resid 207 through 212 Processing helix chain 'U' and resid 231 through 246 Processing helix chain 'U' and resid 266 through 278 Processing helix chain 'U' and resid 281 through 283 No H-bonds generated for 'chain 'U' and resid 281 through 283' Processing helix chain 'U' and resid 296 through 315 Proline residue: U 303 - end of helix removed outlier: 3.787A pdb=" N TYR U 312 " --> pdb=" O ALA U 308 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N PHE U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) Processing helix chain 'U' and resid 327 through 340 removed outlier: 3.660A pdb=" N VAL U 332 " --> pdb=" O SER U 328 " (cutoff:3.500A) Processing helix chain 'U' and resid 347 through 349 No H-bonds generated for 'chain 'U' and resid 347 through 349' Processing helix chain 'U' and resid 352 through 364 removed outlier: 4.305A pdb=" N PHE U 355 " --> pdb=" O GLY U 352 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU U 357 " --> pdb=" O VAL U 354 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ARG U 360 " --> pdb=" O LEU U 357 " (cutoff:3.500A) removed outlier: 4.501A 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 Processing helix chain 'U' and resid 410 through 413 No H-bonds generated for 'chain 'U' and resid 410 through 413' Processing helix chain 'U' and resid 437 through 459 removed outlier: 3.560A pdb=" N GLN U 441 " --> pdb=" O PRO U 437 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL U 442 " --> pdb=" O GLY U 438 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY U 444 " --> pdb=" O LYS U 440 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N THR U 445 " --> pdb=" O GLN U 441 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU U 446 " --> pdb=" O VAL U 442 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA U 451 " --> pdb=" O LYS U 447 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL U 456 " --> pdb=" O GLN U 452 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA U 458 " --> pdb=" O ARG U 454 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N PHE U 459 " --> pdb=" O GLU U 455 " (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 470 through 483 removed outlier: 3.677A pdb=" N LEU U 474 " --> pdb=" O THR U 470 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ARG U 479 " --> pdb=" O GLU U 475 " (cutoff:3.500A) Processing helix chain 'U' and resid 494 through 500 removed outlier: 3.604A pdb=" N ALA U 500 " --> pdb=" O ARG U 496 " (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 517 through 527 removed outlier: 3.938A pdb=" N GLU U 522 " --> pdb=" O VAL U 518 " (cutoff:3.500A) Processing helix chain 'U' and resid 531 through 539 Processing helix chain 'U' and resid 546 through 553 Processing helix chain 'V' and resid 46 through 48 No H-bonds generated for 'chain 'V' and resid 46 through 48' Processing helix chain 'V' and resid 58 through 66 removed outlier: 3.750A pdb=" N LYS V 65 " --> pdb=" O HIS V 61 " (cutoff:3.500A) Processing helix chain 'V' and resid 135 through 137 No H-bonds generated for 'chain 'V' and resid 135 through 137' Processing helix chain 'V' and resid 157 through 159 No H-bonds generated for 'chain 'V' and resid 157 through 159' Processing helix chain 'V' and resid 207 through 212 Processing helix chain 'V' and resid 231 through 246 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: 4.264A pdb=" N PHE V 313 " --> pdb=" O MET V 309 " (cutoff:3.500A) Processing helix chain 'V' and resid 327 through 340 Processing helix chain 'V' and resid 347 through 349 No H-bonds generated for 'chain 'V' and resid 347 through 349' Processing helix chain 'V' and resid 352 through 364 removed outlier: 4.387A pdb=" N PHE V 355 " --> pdb=" O GLY V 352 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR V 356 " --> pdb=" O ASP V 353 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU V 357 " --> pdb=" O VAL V 354 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ARG V 360 " --> pdb=" O LEU V 357 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU V 362 " --> pdb=" O SER V 359 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU V 363 " --> pdb=" O ARG V 360 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG V 364 " --> pdb=" O LEU V 361 " (cutoff:3.500A) Processing helix chain 'V' and resid 370 through 372 No H-bonds generated for 'chain 'V' and resid 370 through 372' Processing helix chain 'V' and resid 393 through 399 Processing helix chain 'V' and resid 410 through 414 removed outlier: 3.825A pdb=" N TYR V 414 " --> pdb=" O THR V 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 410 through 414' Processing helix chain 'V' and resid 439 through 453 removed outlier: 4.087A pdb=" N GLY V 444 " --> pdb=" O LYS V 440 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N THR V 445 " --> pdb=" O GLN V 441 " (cutoff:3.500A) Processing helix chain 'V' and resid 471 through 484 removed outlier: 4.571A pdb=" N ARG V 479 " --> pdb=" O GLU V 475 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU V 484 " --> pdb=" O LEU V 480 " (cutoff:3.500A) Processing helix chain 'V' and resid 494 through 506 removed outlier: 3.775A pdb=" N VAL V 499 " --> pdb=" O GLU V 495 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA V 500 " --> pdb=" O ARG V 496 " (cutoff:3.500A) Processing helix chain 'V' and resid 514 through 527 removed outlier: 3.920A pdb=" N ILE V 517 " --> pdb=" O VAL V 514 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N VAL V 518 " --> pdb=" O GLN V 515 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU V 521 " --> pdb=" O VAL V 518 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN V 527 " --> pdb=" O VAL V 524 " (cutoff:3.500A) Processing helix chain 'V' and resid 531 through 539 Processing helix chain 'V' and resid 546 through 554 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 189 through 200 Processing helix chain 'X' and resid 217 through 229 Processing helix chain 'X' and resid 236 through 241 removed outlier: 3.524A pdb=" N ARG X 239 " --> pdb=" O GLY X 236 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N GLY X 240 " --> pdb=" O ALA X 237 " (cutoff:3.500A) Processing helix chain 'X' and resid 255 through 259 Processing helix chain 'X' and resid 261 through 274 Processing helix chain 'X' and resid 287 through 298 removed outlier: 3.523A pdb=" N GLN X 292 " --> pdb=" O ARG X 289 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU X 296 " --> pdb=" O ALA X 293 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL X 297 " --> pdb=" O ASN X 294 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER X 298 " --> pdb=" O SER X 295 " (cutoff:3.500A) Processing helix chain 'X' and resid 314 through 324 removed outlier: 4.321A pdb=" N ARG X 324 " --> pdb=" O GLY X 320 " (cutoff:3.500A) Processing helix chain 'X' and resid 342 through 344 No H-bonds generated for 'chain 'X' and resid 342 through 344' Processing helix chain 'X' and resid 349 through 357 removed outlier: 3.628A pdb=" N THR X 354 " --> pdb=" O ALA X 350 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ALA X 356 " --> pdb=" O ALA X 352 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N HIS X 357 " --> pdb=" O THR X 353 " (cutoff:3.500A) Processing helix chain 'X' and resid 366 through 371 Processing helix chain 'X' and resid 389 through 392 No H-bonds generated for 'chain 'X' and resid 389 through 392' Processing helix chain 'X' and resid 396 through 418 removed outlier: 4.419A pdb=" N ASP X 415 " --> pdb=" O LYS X 411 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ILE X 416 " --> pdb=" O ASN X 412 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA X 418 " --> pdb=" O GLN X 414 " (cutoff:3.500A) Processing helix chain 'X' and resid 431 through 443 Processing helix chain 'X' and resid 451 through 454 No H-bonds generated for 'chain 'X' and resid 451 through 454' Processing helix chain 'X' and resid 463 through 475 removed outlier: 3.533A pdb=" N SER X 468 " --> pdb=" O ALA X 464 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY X 469 " --> pdb=" O ASP X 465 " (cutoff:3.500A) removed outlier: 3.654A 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 506 removed outlier: 3.824A pdb=" N LYS X 496 " --> pdb=" O ILE X 492 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N GLU X 497 " --> pdb=" O LYS X 493 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASP X 500 " --> pdb=" O LYS X 496 " (cutoff:3.500A) Processing helix chain 'X' and resid 527 through 533 removed outlier: 3.628A pdb=" N VAL X 531 " --> pdb=" O LEU X 527 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU X 533 " --> pdb=" O LYS X 529 " (cutoff:3.500A) Processing helix chain 'Y' and resid 115 through 117 No H-bonds generated for 'chain 'Y' and resid 115 through 117' Processing helix chain 'Y' and resid 165 through 169 Processing helix chain 'Y' and resid 189 through 203 Processing helix chain 'Y' and resid 217 through 229 Processing helix chain 'Y' and resid 238 through 241 Processing helix chain 'Y' and resid 255 through 274 removed outlier: 4.838A pdb=" N ALA Y 262 " --> pdb=" O ARG Y 258 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N LEU Y 263 " --> pdb=" O ALA Y 259 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE Y 272 " --> pdb=" O VAL Y 268 " (cutoff:3.500A) Processing helix chain 'Y' and resid 287 through 300 Processing helix chain 'Y' and resid 314 through 322 removed outlier: 3.816A pdb=" N LEU Y 321 " --> pdb=" O ASP Y 317 " (cutoff:3.500A) Processing helix chain 'Y' and resid 342 through 344 No H-bonds generated for 'chain 'Y' and resid 342 through 344' Processing helix chain 'Y' and resid 349 through 354 Processing helix chain 'Y' and resid 366 through 370 Processing helix chain 'Y' and resid 393 through 419 removed outlier: 4.540A pdb=" N ASP Y 415 " --> pdb=" O LYS Y 411 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ILE Y 416 " --> pdb=" O ASN Y 412 " (cutoff:3.500A) Processing helix chain 'Y' and resid 431 through 442 removed outlier: 4.096A pdb=" N LYS Y 438 " --> pdb=" O ALA Y 434 " (cutoff:3.500A) Processing helix chain 'Y' and resid 448 through 454 removed outlier: 4.686A pdb=" N VAL Y 452 " --> pdb=" O VAL Y 449 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR Y 454 " --> pdb=" O GLU Y 451 " (cutoff:3.500A) Processing helix chain 'Y' and resid 463 through 475 removed outlier: 3.912A pdb=" N VAL Y 473 " --> pdb=" O GLY Y 469 " (cutoff:3.500A) Processing helix chain 'Y' and resid 483 through 485 No H-bonds generated for 'chain 'Y' and resid 483 through 485' Processing helix chain 'Y' and resid 493 through 509 removed outlier: 4.004A pdb=" N GLU Y 497 " --> pdb=" O LYS Y 493 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS Y 504 " --> pdb=" O ASP Y 500 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ASP Y 505 " --> pdb=" O LYS Y 501 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ILE Y 506 " --> pdb=" O MET Y 502 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ALA Y 507 " --> pdb=" O ALA Y 503 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N SER Y 508 " --> pdb=" O LYS Y 504 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG Y 509 " --> pdb=" O ASP Y 505 " (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 533 removed outlier: 3.669A pdb=" N SER Y 532 " --> pdb=" O ASP Y 528 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU Y 533 " --> pdb=" O LYS Y 529 " (cutoff:3.500A) Processing helix chain 'Y' and resid 545 through 553 removed outlier: 4.081A pdb=" N LYS Y 550 " --> pdb=" O GLU Y 546 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU Y 552 " --> pdb=" O ASP Y 548 " (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 150 through 152 No H-bonds generated for 'chain 'Z' and resid 150 through 152' Processing helix chain 'Z' and resid 165 through 170 Processing helix chain 'Z' and resid 189 through 203 removed outlier: 4.543A pdb=" N LYS Z 202 " --> pdb=" O ASN Z 198 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA Z 203 " --> pdb=" O ASN Z 199 " (cutoff:3.500A) Processing helix chain 'Z' and resid 217 through 230 Processing helix chain 'Z' and resid 236 through 241 removed outlier: 3.651A pdb=" N ARG Z 239 " --> pdb=" O GLY Z 236 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLY Z 240 " --> pdb=" O ALA Z 237 " (cutoff:3.500A) Processing helix chain 'Z' and resid 255 through 274 removed outlier: 3.642A pdb=" N ARG Z 260 " --> pdb=" O GLY Z 256 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ALA Z 262 " --> pdb=" O ARG Z 258 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N LEU Z 263 " --> pdb=" O ALA Z 259 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE Z 272 " --> pdb=" O VAL Z 268 " (cutoff:3.500A) Processing helix chain 'Z' and resid 288 through 298 Processing helix chain 'Z' and resid 314 through 324 removed outlier: 4.418A pdb=" N ARG Z 324 " --> pdb=" O GLY Z 320 " (cutoff:3.500A) Processing helix chain 'Z' and resid 349 through 357 removed outlier: 4.413A pdb=" N ALA Z 356 " --> pdb=" O ALA Z 352 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N HIS Z 357 " --> pdb=" O THR Z 353 " (cutoff:3.500A) Processing helix chain 'Z' and resid 366 through 370 Processing helix chain 'Z' and resid 394 through 420 removed outlier: 3.507A pdb=" N LEU Z 413 " --> pdb=" O ASP Z 409 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ASP Z 415 " --> pdb=" O LYS Z 411 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ILE Z 416 " --> pdb=" O ASN Z 412 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA Z 418 " --> pdb=" O GLN Z 414 " (cutoff:3.500A) Processing helix chain 'Z' and resid 422 through 424 No H-bonds generated for 'chain 'Z' and resid 422 through 424' Processing helix chain 'Z' and resid 427 through 442 removed outlier: 3.707A pdb=" N LEU Z 431 " --> pdb=" O GLU Z 427 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG Z 441 " --> pdb=" O ARG Z 437 " (cutoff:3.500A) Processing helix chain 'Z' and resid 451 through 454 No H-bonds generated for 'chain 'Z' and resid 451 through 454' Processing helix chain 'Z' and resid 463 through 475 Processing helix chain 'Z' and resid 483 through 485 No H-bonds generated for 'chain 'Z' and resid 483 through 485' Processing helix chain 'Z' and resid 492 through 499 removed outlier: 3.702A pdb=" N LYS Z 496 " --> pdb=" O ILE Z 492 " (cutoff:3.500A) Processing helix chain 'Z' and resid 501 through 507 removed outlier: 3.970A pdb=" N ILE Z 506 " --> pdb=" O MET Z 502 " (cutoff:3.500A) Processing helix chain 'Z' and resid 528 through 532 removed outlier: 3.520A pdb=" N SER Z 532 " --> pdb=" O ASP Z 528 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 528 through 532' Processing sheet with id= A, first strand: chain '1' and resid 183 through 185 removed outlier: 4.459A pdb=" N VAL 1 226 " --> pdb=" O ALA 1 185 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '2' and resid 369 through 372 Processing sheet with id= C, first strand: chain '7' and resid 36 through 38 removed outlier: 3.574A pdb=" N VAL 7 61 " --> pdb=" O ALA 7 46 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL 7 48 " --> pdb=" O THR 7 59 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR 7 59 " --> pdb=" O VAL 7 48 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'P' and resid 155 through 158 Processing sheet with id= E, first strand: chain 'Q' and resid 45 through 49 Processing sheet with id= F, first strand: chain 'R' and resid 96 through 100 removed outlier: 3.865A pdb=" N THR R 88 " --> pdb=" O HIS R 119 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL R 115 " --> pdb=" O PRO R 92 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY R 114 " --> pdb=" O VAL R 129 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'R' and resid 107 through 110 Processing sheet with id= H, first strand: chain 'S' and resid 203 through 211 removed outlier: 5.262A pdb=" N ASN S 195 " --> pdb=" O VAL S 105 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ASP S 136 " --> pdb=" O SER S 100 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N VAL S 102 " --> pdb=" O ASP S 136 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N VAL S 138 " --> pdb=" O VAL S 102 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N ALA S 104 " --> pdb=" O VAL S 138 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL S 140 " --> pdb=" O ALA S 104 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN S 159 " --> pdb=" O VAL S 139 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N SER S 141 " --> pdb=" O GLN S 159 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ALA S 161 " --> pdb=" O SER S 141 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'T' and resid 85 through 91 removed outlier: 6.718A pdb=" N ARG T 96 " --> pdb=" O LEU T 88 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N VAL T 90 " --> pdb=" O ILE T 94 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE T 94 " --> pdb=" O VAL T 90 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN T 121 " --> pdb=" O GLY T 128 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL T 130 " --> pdb=" O ALA T 119 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N ALA T 119 " --> pdb=" O VAL T 130 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N PHE T 132 " --> pdb=" O GLY T 117 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N GLY T 117 " --> pdb=" O PHE T 132 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLU T 107 " --> pdb=" O ALA T 119 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'T' and resid 152 through 155 Processing sheet with id= K, first strand: chain 'T' and resid 404 through 408 removed outlier: 3.680A pdb=" N LEU T 222 " --> pdb=" O GLY T 404 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'T' and resid 376 through 381 removed outlier: 3.549A pdb=" N VAL T 262 " --> pdb=" O ASP T 325 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'U' and resid 85 through 91 removed outlier: 6.677A pdb=" N ARG U 96 " --> pdb=" O LEU U 88 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N VAL U 90 " --> pdb=" O ILE U 94 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE U 94 " --> pdb=" O VAL U 90 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN U 121 " --> pdb=" O GLY U 128 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N VAL U 130 " --> pdb=" O ALA U 119 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N ALA U 119 " --> pdb=" O VAL U 130 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N PHE U 132 " --> pdb=" O GLY U 117 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N GLY U 117 " --> pdb=" O PHE U 132 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU U 107 " --> pdb=" O ALA U 119 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'U' and resid 152 through 155 Processing sheet with id= O, first strand: chain 'U' and resid 404 through 408 Processing sheet with id= P, first strand: chain 'U' and resid 285 through 290 removed outlier: 8.544A pdb=" N ILE U 286 " --> pdb=" O VAL U 255 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N CYS U 257 " --> pdb=" O ILE U 286 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N VAL U 288 " --> pdb=" O CYS U 257 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N TYR U 259 " --> pdb=" O VAL U 288 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ALA U 290 " --> pdb=" O TYR U 259 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ALA U 261 " --> pdb=" O ALA U 290 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N HIS U 319 " --> pdb=" O TYR U 256 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N VAL U 258 " --> pdb=" O HIS U 319 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU U 321 " --> pdb=" O VAL U 258 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N VAL U 260 " --> pdb=" O LEU U 321 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE U 323 " --> pdb=" O VAL U 260 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL U 262 " --> pdb=" O ILE U 323 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASP U 325 " --> pdb=" O VAL U 262 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N SER U 376 " --> pdb=" O GLY U 320 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ILE U 322 " --> pdb=" O SER U 376 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N THR U 378 " --> pdb=" O ILE U 322 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N TYR U 324 " --> pdb=" O THR U 378 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N PHE U 380 " --> pdb=" O TYR U 324 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'V' and resid 143 through 145 removed outlier: 6.481A pdb=" N ARG V 96 " --> pdb=" O LEU V 88 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VAL V 90 " --> pdb=" O ILE V 94 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ILE V 94 " --> pdb=" O VAL V 90 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL V 130 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ALA V 119 " --> pdb=" O VAL V 130 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU V 107 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N GLN V 149 " --> pdb=" O LEU V 108 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N CYS V 110 " --> pdb=" O THR V 147 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N THR V 147 " --> pdb=" O CYS V 110 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'V' and resid 152 through 155 Processing sheet with id= S, first strand: chain 'V' and resid 404 through 408 Processing sheet with id= T, first strand: chain 'V' and resid 285 through 290 removed outlier: 8.749A pdb=" N ILE V 286 " --> pdb=" O VAL V 255 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N CYS V 257 " --> pdb=" O ILE V 286 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N VAL V 288 " --> pdb=" O CYS V 257 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N TYR V 259 " --> pdb=" O VAL V 288 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N ALA V 290 " --> pdb=" O TYR V 259 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ALA V 261 " --> pdb=" O ALA V 290 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N HIS V 319 " --> pdb=" O TYR V 256 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N VAL V 258 " --> pdb=" O HIS V 319 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LEU V 321 " --> pdb=" O VAL V 258 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N VAL V 260 " --> pdb=" O LEU V 321 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ILE V 323 " --> pdb=" O VAL V 260 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL V 262 " --> pdb=" O ILE V 323 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ASP V 325 " --> pdb=" O VAL V 262 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N SER V 376 " --> pdb=" O GLY V 320 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N ILE V 322 " --> pdb=" O SER V 376 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N THR V 378 " --> pdb=" O ILE V 322 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N TYR V 324 " --> pdb=" O THR V 378 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N PHE V 380 " --> pdb=" O TYR V 324 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'X' and resid 38 through 44 removed outlier: 6.468A pdb=" N ASP X 49 " --> pdb=" O SER X 41 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N VAL X 43 " --> pdb=" O VAL X 47 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL X 47 " --> pdb=" O VAL X 43 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE X 88 " --> pdb=" O VAL X 76 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N VAL X 76 " --> pdb=" O ILE X 88 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LEU X 72 " --> pdb=" O VAL X 65 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'X' and resid 158 through 160 removed outlier: 4.754A pdb=" N GLU X 158 " --> pdb=" O ARG X 175 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N TYR X 173 " --> pdb=" O LEU X 160 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'X' and resid 360 through 363 removed outlier: 7.683A pdb=" N ILE X 179 " --> pdb=" O ILE X 333 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N SER X 335 " --> pdb=" O ILE X 179 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N LEU X 181 " --> pdb=" O SER X 335 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLN X 337 " --> pdb=" O LEU X 181 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N GLY X 183 " --> pdb=" O GLN X 337 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N VAL X 339 " --> pdb=" O GLY X 183 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'X' and resid 559 through 561 Processing sheet with id= Y, first strand: chain 'Y' and resid 38 through 44 removed outlier: 6.359A pdb=" N ASP Y 49 " --> pdb=" O SER Y 41 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N VAL Y 43 " --> pdb=" O VAL Y 47 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL Y 47 " --> pdb=" O VAL Y 43 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE Y 88 " --> pdb=" O VAL Y 76 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N VAL Y 76 " --> pdb=" O ILE Y 88 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'Y' and resid 110 through 113 removed outlier: 3.547A pdb=" N ASP Y 139 " --> pdb=" O VAL Y 113 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'Y' and resid 360 through 363 removed outlier: 8.355A pdb=" N ILE Y 179 " --> pdb=" O ILE Y 333 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N SER Y 335 " --> pdb=" O ILE Y 179 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LEU Y 181 " --> pdb=" O SER Y 335 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLN Y 337 " --> pdb=" O LEU Y 181 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'Z' and resid 101 through 103 removed outlier: 6.641A pdb=" N ASP Z 49 " --> pdb=" O SER Z 41 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N VAL Z 43 " --> pdb=" O VAL Z 47 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL Z 47 " --> pdb=" O VAL Z 43 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE Z 88 " --> pdb=" O VAL Z 76 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N VAL Z 76 " --> pdb=" O ILE Z 88 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N SER Z 61 " --> pdb=" O VAL Z 76 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N SER Z 107 " --> pdb=" O SER Z 62 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N GLU Z 64 " --> pdb=" O THR Z 105 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N THR Z 105 " --> pdb=" O GLU Z 64 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'Z' and resid 110 through 113 Processing sheet with id= AD, first strand: chain 'Z' and resid 360 through 363 removed outlier: 7.491A pdb=" N ILE Z 179 " --> pdb=" O ILE Z 333 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N SER Z 335 " --> pdb=" O ILE Z 179 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N LEU Z 181 " --> pdb=" O SER Z 335 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N GLN Z 337 " --> pdb=" O LEU Z 181 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N GLY Z 183 " --> pdb=" O GLN Z 337 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL Z 339 " --> pdb=" O GLY Z 183 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N PHE Z 207 " --> pdb=" O LEU Z 281 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N PHE Z 283 " --> pdb=" O PHE Z 207 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL Z 209 " --> pdb=" O PHE Z 283 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ASP Z 285 " --> pdb=" O VAL Z 209 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ALA Z 211 " --> pdb=" O ASP Z 285 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'Z' and resid 559 through 561 2464 hydrogen bonds defined for protein. 6717 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: 17.00 Time building geometry restraints manager: 17.16 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: 16612 1.34 - 1.45: 7554 1.45 - 1.57: 30253 1.57 - 1.69: 21 1.69 - 1.81: 254 Bond restraints: 54694 Sorted by residual: 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 6.04e+01 bond pdb=" C4 ATP T1001 " pdb=" C5 ATP T1001 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.95e+01 bond pdb=" C4 ATP U1001 " pdb=" C5 ATP U1001 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.91e+01 bond pdb=" C5 ATP U1001 " pdb=" C6 ATP U1001 " ideal model delta sigma weight residual 1.409 1.477 -0.068 1.00e-02 1.00e+04 4.62e+01 bond pdb=" C5 ATP V1001 " pdb=" C6 ATP V1001 " ideal model delta sigma weight residual 1.409 1.476 -0.067 1.00e-02 1.00e+04 4.53e+01 ... (remaining 54689 not shown) Histogram of bond angle deviations from ideal: 97.20 - 104.99: 962 104.99 - 112.78: 29347 112.78 - 120.57: 25070 120.57 - 128.35: 18524 128.35 - 136.14: 269 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 139.87 121.46 18.41 1.00e+00 1.00e+00 3.39e+02 angle pdb=" PB ATP U1001 " pdb=" O3B ATP U1001 " pdb=" PG ATP U1001 " ideal model delta sigma weight residual 139.87 122.38 17.49 1.00e+00 1.00e+00 3.06e+02 angle pdb=" PB ATP T1001 " pdb=" O3B ATP T1001 " pdb=" PG ATP T1001 " ideal model delta sigma weight residual 139.87 122.53 17.34 1.00e+00 1.00e+00 3.01e+02 angle pdb=" PA ATP U1001 " pdb=" O3A ATP U1001 " pdb=" PB ATP U1001 " ideal model delta sigma weight residual 136.83 121.18 15.65 1.00e+00 1.00e+00 2.45e+02 angle pdb=" PA ATP T1001 " pdb=" O3A ATP T1001 " pdb=" PB ATP T1001 " ideal model delta sigma weight residual 136.83 122.20 14.63 1.00e+00 1.00e+00 2.14e+02 ... (remaining 74167 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.89: 32199 31.89 - 63.78: 748 63.78 - 95.67: 78 95.67 - 127.56: 1 127.56 - 159.46: 4 Dihedral angle restraints: 33030 sinusoidal: 12669 harmonic: 20361 Sorted by residual: 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 -126.90 -53.10 0 5.00e+00 4.00e-02 1.13e+02 dihedral pdb=" CA ALA X 307 " pdb=" C ALA X 307 " pdb=" N VAL X 308 " pdb=" CA VAL X 308 " ideal model delta harmonic sigma weight residual -180.00 -128.33 -51.67 0 5.00e+00 4.00e-02 1.07e+02 dihedral pdb=" CA ALA Y 307 " pdb=" C ALA Y 307 " pdb=" N VAL Y 308 " pdb=" CA VAL Y 308 " ideal model delta harmonic sigma weight residual 180.00 -128.88 -51.12 0 5.00e+00 4.00e-02 1.05e+02 ... (remaining 33027 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 6875 0.061 - 0.123: 1558 0.123 - 0.184: 232 0.184 - 0.245: 20 0.245 - 0.306: 5 Chirality restraints: 8690 Sorted by residual: chirality pdb=" CB VAL V 180 " pdb=" CA VAL V 180 " pdb=" CG1 VAL V 180 " pdb=" CG2 VAL V 180 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CB ILE H 95 " pdb=" CA ILE H 95 " pdb=" CG1 ILE H 95 " pdb=" CG2 ILE H 95 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CB ILE S 183 " pdb=" CA ILE S 183 " pdb=" CG1 ILE S 183 " pdb=" CG2 ILE S 183 " both_signs ideal model delta sigma weight residual False 2.64 2.92 -0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 8687 not shown) Planarity restraints: 9512 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA X 503 " -0.033 2.00e-02 2.50e+03 6.36e-02 4.05e+01 pdb=" C ALA X 503 " 0.110 2.00e-02 2.50e+03 pdb=" O ALA X 503 " -0.041 2.00e-02 2.50e+03 pdb=" N LYS X 504 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA Z 503 " 0.031 2.00e-02 2.50e+03 6.07e-02 3.68e+01 pdb=" C ALA Z 503 " -0.105 2.00e-02 2.50e+03 pdb=" O ALA Z 503 " 0.039 2.00e-02 2.50e+03 pdb=" N LYS Z 504 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR 1 92 " 0.052 5.00e-02 4.00e+02 7.99e-02 1.02e+01 pdb=" N PRO 1 93 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO 1 93 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO 1 93 " 0.044 5.00e-02 4.00e+02 ... (remaining 9509 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 7924 2.76 - 3.29: 51072 3.29 - 3.83: 93274 3.83 - 4.36: 113375 4.36 - 4.90: 191380 Nonbonded interactions: 457025 Sorted by model distance: nonbonded pdb=" OG1 THR T 232 " pdb="MG MG T1002 " model vdw 2.220 2.170 nonbonded pdb=" OG1 THR V 232 " pdb="MG MG V1002 " model vdw 2.224 2.170 nonbonded pdb=" O3G ATP U1001 " pdb="MG MG U1002 " model vdw 2.230 2.170 nonbonded pdb=" OH TYR 5 62 " pdb=" O PHE 6 146 " model vdw 2.233 2.440 nonbonded pdb=" OG1 THR U 232 " pdb="MG MG U1002 " model vdw 2.241 2.170 ... (remaining 457020 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.850 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: 23.570 Check model and map are aligned: 0.600 Set scattering table: 0.380 Process input model: 116.110 Find NCS groups from input model: 2.570 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 150.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 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 0.084 54694 Z= 0.372 Angle : 0.856 18.411 74172 Z= 0.494 Chirality : 0.053 0.306 8690 Planarity : 0.007 0.080 9512 Dihedral : 14.207 159.456 19942 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.38 % Favored : 95.50 % Rotamer: Outliers : 0.14 % Allowed : 4.99 % Favored : 94.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.82 (0.08), residues: 7039 helix: -2.81 (0.06), residues: 3808 sheet: -1.52 (0.20), residues: 564 loop : -2.02 (0.10), residues: 2667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP Z 141 HIS 0.008 0.001 HIS R 104 PHE 0.028 0.002 PHE A 122 TYR 0.025 0.002 TYR 4 211 ARG 0.009 0.001 ARG U 217 *********************** 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 1248 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1240 time to evaluate : 5.520 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: 0 40 LYS cc_start: 0.8622 (ttpt) cc_final: 0.7768 (tptt) REVERT: 1 32 THR cc_start: 0.8971 (p) cc_final: 0.8750 (p) REVERT: 1 212 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7405 (mp0) REVERT: 1 438 GLN cc_start: 0.8381 (tp-100) cc_final: 0.8118 (tp40) REVERT: 1 503 SER cc_start: 0.8549 (t) cc_final: 0.8142 (m) REVERT: 2 190 LYS cc_start: 0.8218 (mppt) cc_final: 0.7468 (tptt) REVERT: 2 192 THR cc_start: 0.8185 (m) cc_final: 0.7969 (p) REVERT: 3 276 GLU cc_start: 0.7509 (tp30) cc_final: 0.7000 (tp30) REVERT: 3 279 GLU cc_start: 0.7764 (pt0) cc_final: 0.7488 (pt0) REVERT: 8 5 GLU cc_start: 0.7595 (tt0) cc_final: 0.7305 (tt0) REVERT: A 81 MET cc_start: 0.7765 (ttp) cc_final: 0.7380 (ttp) REVERT: A 97 LYS cc_start: 0.8704 (mmmt) cc_final: 0.8319 (pttp) REVERT: C 60 LYS cc_start: 0.8097 (mttp) cc_final: 0.7510 (mttp) REVERT: C 81 MET cc_start: 0.8660 (ttp) cc_final: 0.8379 (ttm) REVERT: C 94 ASN cc_start: 0.8371 (p0) cc_final: 0.8052 (m110) REVERT: C 126 PHE cc_start: 0.6790 (m-80) cc_final: 0.6583 (m-10) REVERT: E 60 LYS cc_start: 0.7777 (mttp) cc_final: 0.7158 (mtpt) REVERT: G 94 ASN cc_start: 0.8529 (t0) cc_final: 0.8311 (t0) REVERT: H 81 MET cc_start: 0.8277 (ttp) cc_final: 0.7982 (ttp) REVERT: I 60 LYS cc_start: 0.8066 (mttp) cc_final: 0.7537 (mtpt) REVERT: I 91 ARG cc_start: 0.8200 (ttm110) cc_final: 0.7760 (ttm-80) REVERT: J 122 PHE cc_start: 0.7311 (m-10) cc_final: 0.6422 (t80) REVERT: P 75 TYR cc_start: 0.8115 (m-80) cc_final: 0.7150 (m-80) REVERT: P 206 ARG cc_start: 0.7996 (ttp80) cc_final: 0.7719 (ttp-170) REVERT: P 220 ASN cc_start: 0.8924 (m110) cc_final: 0.8705 (m-40) REVERT: Q 35 PHE cc_start: 0.6948 (m-80) cc_final: 0.6738 (m-80) REVERT: Q 40 GLN cc_start: 0.8196 (pm20) cc_final: 0.7991 (mm-40) REVERT: Q 42 ARG cc_start: 0.7362 (ptp90) cc_final: 0.7025 (ptp-170) REVERT: Q 48 ARG cc_start: 0.8450 (ptt-90) cc_final: 0.8028 (ptt-90) REVERT: R 54 TYR cc_start: 0.8173 (m-80) cc_final: 0.7431 (m-80) REVERT: R 117 GLU cc_start: 0.7659 (tt0) cc_final: 0.7379 (tt0) REVERT: S 271 MET cc_start: 0.7809 (ttp) cc_final: 0.7605 (ttp) REVERT: S 275 GLU cc_start: 0.7032 (tp30) cc_final: 0.6788 (tp30) REVERT: T 294 ASP cc_start: 0.6938 (m-30) cc_final: 0.6646 (m-30) REVERT: U 53 PHE cc_start: 0.6782 (p90) cc_final: 0.6030 (p90) REVERT: U 559 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.6852 (pp) REVERT: X 386 MET cc_start: 0.7053 (mmm) cc_final: 0.6763 (mmp) REVERT: Y 168 ASP cc_start: 0.7559 (m-30) cc_final: 0.7246 (m-30) REVERT: Y 345 ASP cc_start: 0.8012 (t0) cc_final: 0.7751 (t0) REVERT: Y 382 SER cc_start: 0.8637 (m) cc_final: 0.8331 (m) REVERT: Z 51 ARG cc_start: 0.7929 (ttm-80) cc_final: 0.7065 (ttm170) REVERT: Z 82 ASP cc_start: 0.7087 (t0) cc_final: 0.6687 (t0) REVERT: Z 215 GLU cc_start: 0.7393 (mm-30) cc_final: 0.7064 (mm-30) outliers start: 8 outliers final: 1 residues processed: 1243 average time/residue: 0.5796 time to fit residues: 1179.6051 Evaluate side-chains 689 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 687 time to evaluate : 4.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 188 VAL Chi-restraints excluded: chain U residue 559 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 589 optimal weight: 6.9990 chunk 529 optimal weight: 0.9990 chunk 293 optimal weight: 0.7980 chunk 180 optimal weight: 6.9990 chunk 356 optimal weight: 0.9980 chunk 282 optimal weight: 0.8980 chunk 547 optimal weight: 6.9990 chunk 211 optimal weight: 3.9990 chunk 332 optimal weight: 0.9980 chunk 407 optimal weight: 0.9990 chunk 633 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 48 ASN 1 100 GLN 1 166 ASN 1 257 HIS 1 285 GLN 1 298 GLN 1 316 ASN 1 365 GLN 1 394 GLN 1 428 HIS 1 430 GLN 1 482 ASN 1 587 ASN 1 590 HIS 2 122 ASN 2 243 GLN 2 432 GLN 3 206 ASN 3 229 ASN 4 240 GLN 5 107 ASN 6 40 ASN 6 74 GLN 7 24 GLN 7 123 HIS 7 170 HIS 7 184 ASN 8 26 HIS 9 35 GLN 9 41 HIS 9 60 ASN 9 80 GLN B 98 GLN F 94 ASN G 92 ASN H 87 ASN I 98 GLN J 98 GLN M 108 ASN M 163 ASN P 52 GLN P 59 GLN P 220 ASN P 223 ASN R 38 ASN R 73 ASN R 83 GLN R 85 GLN R 137 HIS R 154 GLN S 262 ASN T 64 GLN T 134 ASN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 244 ASN T 278 GLN T 358 HIS T 386 GLN ** T 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 441 GLN ** T 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 539 ASN U 60 GLN U 64 GLN ** U 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 241 HIS U 242 GLN U 248 GLN U 497 GLN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 139 HIS V 152 ASN V 219 GLN V 241 HIS V 242 GLN V 244 ASN V 435 GLN V 486 GLN ** V 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 123 ASN X 337 GLN Y 68 HIS Y 199 ASN Y 278 GLN Y 294 ASN Y 322 GLN Y 337 GLN Y 404 GLN ** Y 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 414 GLN Y 440 GLN Z 42 GLN Z 199 ASN Z 440 GLN Total number of N/Q/H flips: 87 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 54694 Z= 0.174 Angle : 0.538 10.767 74172 Z= 0.281 Chirality : 0.041 0.243 8690 Planarity : 0.005 0.063 9512 Dihedral : 6.699 152.634 7674 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.42 % Favored : 96.45 % Rotamer: Outliers : 1.74 % Allowed : 11.24 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.09), residues: 7039 helix: -1.03 (0.08), residues: 3820 sheet: -1.07 (0.20), residues: 596 loop : -1.49 (0.11), residues: 2623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 9 73 HIS 0.007 0.001 HIS U 61 PHE 0.020 0.001 PHE J 82 TYR 0.025 0.001 TYR U 453 ARG 0.005 0.000 ARG 1 453 *********************** 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 892 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 794 time to evaluate : 4.802 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: 0 40 LYS cc_start: 0.8574 (ttpt) cc_final: 0.7742 (tptt) REVERT: 1 32 THR cc_start: 0.8839 (p) cc_final: 0.8617 (p) REVERT: 1 212 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7365 (mp0) REVERT: 1 438 GLN cc_start: 0.8311 (tp-100) cc_final: 0.8034 (tp40) REVERT: 1 503 SER cc_start: 0.8542 (t) cc_final: 0.8254 (m) REVERT: 2 190 LYS cc_start: 0.8222 (mppt) cc_final: 0.7476 (tptt) REVERT: 3 93 GLU cc_start: 0.6040 (mp0) cc_final: 0.5720 (mp0) REVERT: 3 276 GLU cc_start: 0.7590 (tp30) cc_final: 0.7123 (tp30) REVERT: 3 279 GLU cc_start: 0.7951 (pt0) cc_final: 0.7617 (pt0) REVERT: 4 124 ASN cc_start: 0.7949 (m-40) cc_final: 0.7748 (m-40) REVERT: 6 76 LYS cc_start: 0.7818 (mtmt) cc_final: 0.7275 (mttm) REVERT: 8 5 GLU cc_start: 0.7630 (tt0) cc_final: 0.7366 (tt0) REVERT: C 60 LYS cc_start: 0.8004 (mttp) cc_final: 0.7672 (mttp) REVERT: C 81 MET cc_start: 0.8539 (ttp) cc_final: 0.8323 (ttm) REVERT: C 94 ASN cc_start: 0.8305 (p0) cc_final: 0.7981 (m110) REVERT: E 60 LYS cc_start: 0.7794 (mttp) cc_final: 0.7218 (mtpt) REVERT: H 116 PHE cc_start: 0.7540 (m-10) cc_final: 0.7134 (m-10) REVERT: I 60 LYS cc_start: 0.8010 (mttp) cc_final: 0.7580 (mtpt) REVERT: I 91 ARG cc_start: 0.8155 (ttm110) cc_final: 0.7651 (ttm-80) REVERT: J 122 PHE cc_start: 0.7339 (m-10) cc_final: 0.6398 (t80) REVERT: P 77 PHE cc_start: 0.8241 (m-80) cc_final: 0.8039 (m-80) REVERT: P 144 LEU cc_start: 0.8331 (mt) cc_final: 0.8006 (mp) REVERT: P 206 ARG cc_start: 0.8069 (ttp80) cc_final: 0.7664 (ttp-170) REVERT: P 220 ASN cc_start: 0.8827 (m-40) cc_final: 0.8602 (m-40) REVERT: R 31 LYS cc_start: 0.7480 (ptpp) cc_final: 0.7174 (mmmt) REVERT: R 37 TRP cc_start: 0.6728 (t60) cc_final: 0.6352 (t60) REVERT: R 117 GLU cc_start: 0.7764 (tt0) cc_final: 0.7434 (tt0) REVERT: R 171 GLN cc_start: 0.7336 (OUTLIER) cc_final: 0.6830 (pp30) REVERT: S 115 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7281 (mp) REVERT: T 541 LYS cc_start: 0.7370 (ttpt) cc_final: 0.6942 (tmtt) REVERT: T 546 LEU cc_start: 0.6769 (tp) cc_final: 0.6568 (tp) REVERT: U 53 PHE cc_start: 0.6620 (p90) cc_final: 0.6346 (p90) REVERT: V 483 MET cc_start: 0.6553 (tpp) cc_final: 0.5988 (tpp) REVERT: X 194 MET cc_start: 0.7120 (mmt) cc_final: 0.6755 (mmp) REVERT: X 386 MET cc_start: 0.7189 (mmm) cc_final: 0.6841 (mmp) REVERT: X 414 GLN cc_start: 0.6763 (mm-40) cc_final: 0.6444 (tp-100) REVERT: X 430 LYS cc_start: 0.7412 (OUTLIER) cc_final: 0.6992 (mtmt) REVERT: Y 278 GLN cc_start: 0.7230 (mt0) cc_final: 0.6789 (mt0) REVERT: Y 292 GLN cc_start: 0.7910 (tt0) cc_final: 0.7710 (tt0) REVERT: Y 345 ASP cc_start: 0.8152 (t0) cc_final: 0.7940 (t0) REVERT: Z 51 ARG cc_start: 0.7804 (ttm-80) cc_final: 0.7108 (ttm170) outliers start: 98 outliers final: 48 residues processed: 862 average time/residue: 0.5301 time to fit residues: 761.3328 Evaluate side-chains 699 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 648 time to evaluate : 4.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 188 VAL Chi-restraints excluded: chain 1 residue 258 GLU Chi-restraints excluded: chain 3 residue 116 THR Chi-restraints excluded: chain 5 residue 109 GLN Chi-restraints excluded: chain 5 residue 110 SER Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 7 residue 60 GLN Chi-restraints excluded: chain 7 residue 72 SER Chi-restraints excluded: chain 7 residue 175 SER Chi-restraints excluded: chain 7 residue 183 THR Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 9 residue 3 VAL Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain G residue 66 CYS Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain P residue 52 GLN Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain R residue 83 GLN Chi-restraints excluded: chain R residue 171 GLN Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain S residue 109 LYS Chi-restraints excluded: chain S residue 115 LEU Chi-restraints excluded: chain S residue 144 ASP Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 185 HIS Chi-restraints excluded: chain S residue 272 SER Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 102 SER Chi-restraints excluded: chain T residue 186 GLU Chi-restraints excluded: chain U residue 54 SER Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 473 VAL Chi-restraints excluded: chain U residue 559 LEU Chi-restraints excluded: chain V residue 169 GLN Chi-restraints excluded: chain V residue 220 ARG Chi-restraints excluded: chain X residue 235 LEU Chi-restraints excluded: chain X residue 247 VAL Chi-restraints excluded: chain X residue 274 ASP Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 430 LYS Chi-restraints excluded: chain Y residue 103 VAL Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Z residue 61 SER Chi-restraints excluded: chain Z residue 141 TRP Chi-restraints excluded: chain Z residue 390 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 352 optimal weight: 0.2980 chunk 196 optimal weight: 3.9990 chunk 527 optimal weight: 10.0000 chunk 431 optimal weight: 9.9990 chunk 174 optimal weight: 3.9990 chunk 635 optimal weight: 10.0000 chunk 685 optimal weight: 0.9980 chunk 565 optimal weight: 6.9990 chunk 629 optimal weight: 2.9990 chunk 216 optimal weight: 0.8980 chunk 509 optimal weight: 7.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 432 GLN 3 256 GLN 4 68 HIS 5 107 ASN 7 24 GLN 9 80 GLN F 94 ASN G 94 ASN P 59 GLN P 71 GLN ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 HIS R 178 GLN T 104 GLN T 134 ASN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 539 ASN U 64 GLN U 248 GLN U 452 GLN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 123 GLN V 452 GLN ** V 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 123 ASN X 241 ASN Y 144 HIS Y 278 GLN ** Y 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 54694 Z= 0.251 Angle : 0.557 12.307 74172 Z= 0.286 Chirality : 0.042 0.224 8690 Planarity : 0.004 0.059 9512 Dihedral : 6.369 155.074 7674 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.96 % Favored : 95.92 % Rotamer: Outliers : 2.52 % Allowed : 13.03 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.10), residues: 7039 helix: -0.41 (0.08), residues: 3813 sheet: -0.92 (0.20), residues: 617 loop : -1.18 (0.12), residues: 2609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 3 109 HIS 0.012 0.001 HIS Z 204 PHE 0.027 0.001 PHE J 107 TYR 0.026 0.001 TYR 4 211 ARG 0.005 0.000 ARG 1 453 *********************** 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 833 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 691 time to evaluate : 4.868 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: 0 40 LYS cc_start: 0.8582 (ttpt) cc_final: 0.7767 (tptt) REVERT: 1 32 THR cc_start: 0.8936 (p) cc_final: 0.8666 (p) REVERT: 1 212 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7287 (mt-10) REVERT: 1 438 GLN cc_start: 0.8342 (tp-100) cc_final: 0.8006 (tp40) REVERT: 1 503 SER cc_start: 0.8649 (t) cc_final: 0.8378 (m) REVERT: 1 578 ASP cc_start: 0.7549 (t0) cc_final: 0.7340 (t0) REVERT: 2 190 LYS cc_start: 0.8254 (mppt) cc_final: 0.7516 (tptt) REVERT: 3 93 GLU cc_start: 0.5996 (mp0) cc_final: 0.5727 (mp0) REVERT: 3 276 GLU cc_start: 0.7575 (tp30) cc_final: 0.7141 (tp30) REVERT: 3 279 GLU cc_start: 0.8043 (pt0) cc_final: 0.7683 (pt0) REVERT: 5 27 ASP cc_start: 0.8242 (m-30) cc_final: 0.7789 (m-30) REVERT: 6 76 LYS cc_start: 0.7839 (mtmt) cc_final: 0.7261 (mttm) REVERT: A 97 LYS cc_start: 0.8794 (mmmt) cc_final: 0.8394 (ptmm) REVERT: C 81 MET cc_start: 0.8555 (ttp) cc_final: 0.8344 (ttm) REVERT: C 94 ASN cc_start: 0.8227 (p0) cc_final: 0.7957 (m110) REVERT: E 60 LYS cc_start: 0.8052 (mttp) cc_final: 0.7848 (mttm) REVERT: E 61 MET cc_start: 0.8407 (mmm) cc_final: 0.8154 (mmt) REVERT: F 61 MET cc_start: 0.7542 (OUTLIER) cc_final: 0.7240 (mmt) REVERT: G 107 PHE cc_start: 0.7840 (t80) cc_final: 0.7525 (t80) REVERT: I 60 LYS cc_start: 0.8056 (mttp) cc_final: 0.7598 (mtpt) REVERT: I 91 ARG cc_start: 0.8256 (ttm110) cc_final: 0.7777 (ttm-80) REVERT: J 122 PHE cc_start: 0.7229 (m-10) cc_final: 0.6501 (t80) REVERT: M 271 VAL cc_start: 0.7557 (OUTLIER) cc_final: 0.7007 (t) REVERT: P 59 GLN cc_start: 0.8172 (mt0) cc_final: 0.7949 (mt0) REVERT: P 206 ARG cc_start: 0.8238 (ttp80) cc_final: 0.7707 (ttp-170) REVERT: P 220 ASN cc_start: 0.8842 (m-40) cc_final: 0.8639 (m-40) REVERT: R 31 LYS cc_start: 0.7446 (ptpp) cc_final: 0.7097 (mmmt) REVERT: R 171 GLN cc_start: 0.7355 (OUTLIER) cc_final: 0.6932 (pp30) REVERT: S 115 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7427 (mp) REVERT: T 541 LYS cc_start: 0.7601 (ttpt) cc_final: 0.7215 (tmtt) REVERT: X 386 MET cc_start: 0.7329 (mmm) cc_final: 0.7067 (mmp) REVERT: X 414 GLN cc_start: 0.6848 (mm-40) cc_final: 0.6473 (tp-100) REVERT: X 430 LYS cc_start: 0.7172 (OUTLIER) cc_final: 0.6967 (mtmt) REVERT: X 488 MET cc_start: 0.7226 (mmm) cc_final: 0.6859 (mmm) REVERT: Y 345 ASP cc_start: 0.8220 (t0) cc_final: 0.7984 (t0) REVERT: Z 51 ARG cc_start: 0.7959 (ttm-80) cc_final: 0.7113 (ttm170) REVERT: Z 82 ASP cc_start: 0.7329 (t0) cc_final: 0.7109 (t0) outliers start: 142 outliers final: 83 residues processed: 786 average time/residue: 0.5317 time to fit residues: 695.6268 Evaluate side-chains 695 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 607 time to evaluate : 4.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 188 VAL Chi-restraints excluded: chain 1 residue 258 GLU Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 549 ASP Chi-restraints excluded: chain 1 residue 572 ASP Chi-restraints excluded: chain 2 residue 385 SER Chi-restraints excluded: chain 3 residue 116 THR Chi-restraints excluded: chain 3 residue 256 GLN Chi-restraints excluded: chain 4 residue 19 ASP Chi-restraints excluded: chain 4 residue 133 ASP Chi-restraints excluded: chain 5 residue 109 GLN Chi-restraints excluded: chain 5 residue 110 SER Chi-restraints excluded: chain 6 residue 31 SER Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 7 residue 23 LEU Chi-restraints excluded: chain 7 residue 49 THR Chi-restraints excluded: chain 7 residue 60 GLN Chi-restraints excluded: chain 7 residue 72 SER Chi-restraints excluded: chain 7 residue 175 SER Chi-restraints excluded: chain 7 residue 183 THR Chi-restraints excluded: chain 9 residue 3 VAL Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain F residue 61 MET Chi-restraints excluded: chain G residue 66 CYS Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain M residue 254 LEU Chi-restraints excluded: chain M residue 257 MET Chi-restraints excluded: chain M residue 271 VAL Chi-restraints excluded: chain P residue 52 GLN Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain R residue 62 GLU Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 171 GLN Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 109 LYS Chi-restraints excluded: chain S residue 112 CYS Chi-restraints excluded: chain S residue 115 LEU Chi-restraints excluded: chain S residue 144 ASP Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 185 HIS Chi-restraints excluded: chain S residue 259 MET Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 186 GLU Chi-restraints excluded: chain U residue 54 SER Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 473 VAL Chi-restraints excluded: chain U residue 559 LEU Chi-restraints excluded: chain V residue 169 GLN Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain V residue 220 ARG Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 514 VAL Chi-restraints excluded: chain X residue 129 VAL Chi-restraints excluded: chain X residue 162 THR Chi-restraints excluded: chain X residue 165 LYS Chi-restraints excluded: chain X residue 233 ILE Chi-restraints excluded: chain X residue 235 LEU Chi-restraints excluded: chain X residue 247 VAL Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 430 LYS Chi-restraints excluded: chain Y residue 87 CYS Chi-restraints excluded: chain Y residue 103 VAL Chi-restraints excluded: chain Y residue 381 ASP Chi-restraints excluded: chain Z residue 61 SER Chi-restraints excluded: chain Z residue 87 CYS Chi-restraints excluded: chain Z residue 141 TRP Chi-restraints excluded: chain Z residue 162 THR Chi-restraints excluded: chain Z residue 390 ASN Chi-restraints excluded: chain Z residue 462 ASP Chi-restraints excluded: chain Z residue 497 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 627 optimal weight: 4.9990 chunk 477 optimal weight: 20.0000 chunk 329 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 303 optimal weight: 7.9990 chunk 426 optimal weight: 10.0000 chunk 637 optimal weight: 9.9990 chunk 674 optimal weight: 4.9990 chunk 332 optimal weight: 0.9990 chunk 603 optimal weight: 6.9990 chunk 181 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 256 GLN 5 107 ASN 7 24 GLN P 52 GLN P 83 GLN ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 GLN T 134 ASN T 278 GLN ** T 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 149 GLN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 440 GLN Z 408 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 54694 Z= 0.301 Angle : 0.575 13.524 74172 Z= 0.293 Chirality : 0.043 0.243 8690 Planarity : 0.004 0.058 9512 Dihedral : 6.359 156.857 7674 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.16 % Favored : 95.72 % Rotamer: Outliers : 2.81 % Allowed : 14.63 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.10), residues: 7039 helix: -0.20 (0.08), residues: 3825 sheet: -0.79 (0.21), residues: 632 loop : -1.01 (0.12), residues: 2582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP 3 109 HIS 0.007 0.001 HIS T 241 PHE 0.025 0.002 PHE J 107 TYR 0.024 0.002 TYR 4 211 ARG 0.004 0.000 ARG Q 48 *********************** 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 800 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 642 time to evaluate : 4.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 40 LYS cc_start: 0.8593 (ttpt) cc_final: 0.7771 (tptt) REVERT: 1 32 THR cc_start: 0.9003 (p) cc_final: 0.8737 (p) REVERT: 1 212 GLU cc_start: 0.7834 (tm-30) cc_final: 0.7215 (mt-10) REVERT: 1 503 SER cc_start: 0.8602 (t) cc_final: 0.8287 (m) REVERT: 1 578 ASP cc_start: 0.7582 (t0) cc_final: 0.7361 (t0) REVERT: 2 74 ASN cc_start: 0.7577 (t0) cc_final: 0.7298 (t0) REVERT: 2 190 LYS cc_start: 0.8279 (mppt) cc_final: 0.7491 (tptt) REVERT: 3 93 GLU cc_start: 0.6020 (mp0) cc_final: 0.5732 (mp0) REVERT: 3 276 GLU cc_start: 0.7568 (tp30) cc_final: 0.7196 (tp30) REVERT: 3 279 GLU cc_start: 0.8156 (pt0) cc_final: 0.7762 (pt0) REVERT: 5 27 ASP cc_start: 0.8317 (m-30) cc_final: 0.7785 (m-30) REVERT: 9 5 SER cc_start: 0.8697 (t) cc_final: 0.8222 (m) REVERT: 9 50 ASN cc_start: 0.8353 (m-40) cc_final: 0.8062 (m-40) REVERT: A 111 GLU cc_start: 0.7933 (tp30) cc_final: 0.7630 (mm-30) REVERT: C 60 LYS cc_start: 0.7967 (mttp) cc_final: 0.7499 (mttp) REVERT: C 81 MET cc_start: 0.8566 (ttp) cc_final: 0.8349 (ttm) REVERT: C 94 ASN cc_start: 0.8296 (p0) cc_final: 0.8024 (m110) REVERT: C 95 ILE cc_start: 0.8818 (pt) cc_final: 0.8605 (pt) REVERT: E 60 LYS cc_start: 0.8130 (mttp) cc_final: 0.7889 (mttm) REVERT: E 111 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7536 (tt0) REVERT: F 61 MET cc_start: 0.7575 (mmm) cc_final: 0.7324 (mmt) REVERT: I 60 LYS cc_start: 0.8116 (mttp) cc_final: 0.7625 (mtpt) REVERT: I 91 ARG cc_start: 0.8252 (ttm110) cc_final: 0.7799 (ttm-80) REVERT: I 97 LYS cc_start: 0.8033 (ptpp) cc_final: 0.7226 (mmmt) REVERT: J 122 PHE cc_start: 0.7211 (m-10) cc_final: 0.6640 (t80) REVERT: M 202 PHE cc_start: 0.6298 (OUTLIER) cc_final: 0.5464 (m-80) REVERT: M 231 PHE cc_start: 0.8564 (t80) cc_final: 0.8070 (t80) REVERT: M 271 VAL cc_start: 0.7591 (OUTLIER) cc_final: 0.7188 (t) REVERT: P 83 GLN cc_start: 0.8272 (mm-40) cc_final: 0.8001 (mm110) REVERT: P 206 ARG cc_start: 0.8255 (ttp80) cc_final: 0.8015 (ttp-170) REVERT: P 209 MET cc_start: 0.8613 (mmm) cc_final: 0.8341 (mmt) REVERT: P 220 ASN cc_start: 0.8881 (m-40) cc_final: 0.8644 (m-40) REVERT: R 31 LYS cc_start: 0.7371 (ptpp) cc_final: 0.7010 (mmmt) REVERT: R 171 GLN cc_start: 0.7349 (OUTLIER) cc_final: 0.6952 (pp30) REVERT: S 96 ASN cc_start: 0.7556 (p0) cc_final: 0.7338 (p0) REVERT: S 115 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7505 (mp) REVERT: S 227 SER cc_start: 0.8209 (t) cc_final: 0.7847 (p) REVERT: T 534 LYS cc_start: 0.8124 (mmtm) cc_final: 0.7685 (mptt) REVERT: U 73 TRP cc_start: 0.8021 (m-90) cc_final: 0.7034 (m-90) REVERT: U 277 THR cc_start: 0.8214 (OUTLIER) cc_final: 0.7903 (p) REVERT: U 559 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.7123 (pp) REVERT: X 386 MET cc_start: 0.7379 (mmm) cc_final: 0.7059 (mmp) REVERT: X 488 MET cc_start: 0.7123 (mmm) cc_final: 0.6843 (mmm) REVERT: Y 292 GLN cc_start: 0.7923 (tt0) cc_final: 0.7663 (tt0) REVERT: Y 345 ASP cc_start: 0.8233 (t0) cc_final: 0.7976 (t0) REVERT: Y 484 MET cc_start: 0.7278 (mmp) cc_final: 0.7053 (tpp) REVERT: Z 51 ARG cc_start: 0.8109 (ttm-80) cc_final: 0.7241 (ttm170) REVERT: Z 115 ARG cc_start: 0.8313 (ttm110) cc_final: 0.7912 (ttm-80) REVERT: Z 175 ARG cc_start: 0.6855 (tpp80) cc_final: 0.6638 (tpt90) REVERT: Z 276 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7653 (mm-30) outliers start: 158 outliers final: 113 residues processed: 752 average time/residue: 0.5480 time to fit residues: 694.6869 Evaluate side-chains 710 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 590 time to evaluate : 4.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 40 VAL Chi-restraints excluded: chain 1 residue 106 ASP Chi-restraints excluded: chain 1 residue 188 VAL Chi-restraints excluded: chain 1 residue 258 GLU Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 549 ASP Chi-restraints excluded: chain 1 residue 572 ASP Chi-restraints excluded: chain 2 residue 268 VAL Chi-restraints excluded: chain 2 residue 278 ASP Chi-restraints excluded: chain 2 residue 385 SER Chi-restraints excluded: chain 3 residue 116 THR Chi-restraints excluded: chain 4 residue 19 ASP Chi-restraints excluded: chain 4 residue 133 ASP Chi-restraints excluded: chain 4 residue 154 LEU Chi-restraints excluded: chain 4 residue 273 LYS Chi-restraints excluded: chain 5 residue 26 LEU Chi-restraints excluded: chain 5 residue 109 GLN Chi-restraints excluded: chain 5 residue 110 SER Chi-restraints excluded: chain 6 residue 31 SER Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 23 LEU Chi-restraints excluded: chain 7 residue 49 THR Chi-restraints excluded: chain 7 residue 60 GLN Chi-restraints excluded: chain 7 residue 72 SER Chi-restraints excluded: chain 7 residue 175 SER Chi-restraints excluded: chain 7 residue 183 THR Chi-restraints excluded: chain 8 residue 77 ILE Chi-restraints excluded: chain 9 residue 3 VAL Chi-restraints excluded: chain 9 residue 30 LEU Chi-restraints excluded: chain 9 residue 76 THR Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain G residue 66 CYS Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain M residue 202 PHE Chi-restraints excluded: chain M residue 254 LEU Chi-restraints excluded: chain M residue 257 MET Chi-restraints excluded: chain M residue 271 VAL Chi-restraints excluded: chain P residue 52 GLN Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain R residue 62 GLU Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 83 GLN Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 171 GLN Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 109 LYS Chi-restraints excluded: chain S residue 112 CYS Chi-restraints excluded: chain S residue 115 LEU Chi-restraints excluded: chain S residue 144 ASP Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 185 HIS Chi-restraints excluded: chain S residue 259 MET Chi-restraints excluded: chain S residue 272 SER Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 186 GLU Chi-restraints excluded: chain T residue 226 ASP Chi-restraints excluded: chain T residue 272 LEU Chi-restraints excluded: chain T residue 286 ILE Chi-restraints excluded: chain U residue 54 SER Chi-restraints excluded: chain U residue 187 VAL Chi-restraints excluded: chain U residue 277 THR Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 473 VAL Chi-restraints excluded: chain U residue 559 LEU Chi-restraints excluded: chain V residue 169 GLN Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain V residue 220 ARG Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 514 VAL Chi-restraints excluded: chain X residue 87 CYS Chi-restraints excluded: chain X residue 129 VAL Chi-restraints excluded: chain X residue 162 THR Chi-restraints excluded: chain X residue 165 LYS Chi-restraints excluded: chain X residue 233 ILE Chi-restraints excluded: chain X residue 235 LEU Chi-restraints excluded: chain X residue 247 VAL Chi-restraints excluded: chain X residue 274 ASP Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain Y residue 87 CYS Chi-restraints excluded: chain Y residue 103 VAL Chi-restraints excluded: chain Y residue 228 ILE Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 381 ASP Chi-restraints excluded: chain Y residue 440 GLN Chi-restraints excluded: chain Y residue 461 VAL Chi-restraints excluded: chain Z residue 61 SER Chi-restraints excluded: chain Z residue 87 CYS Chi-restraints excluded: chain Z residue 141 TRP Chi-restraints excluded: chain Z residue 162 THR Chi-restraints excluded: chain Z residue 204 HIS Chi-restraints excluded: chain Z residue 390 ASN Chi-restraints excluded: chain Z residue 462 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 561 optimal weight: 0.8980 chunk 382 optimal weight: 0.8980 chunk 9 optimal weight: 8.9990 chunk 502 optimal weight: 0.0370 chunk 278 optimal weight: 9.9990 chunk 575 optimal weight: 4.9990 chunk 466 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 344 optimal weight: 0.7980 chunk 605 optimal weight: 0.8980 chunk 170 optimal weight: 0.9990 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 256 GLN 5 107 ASN 7 24 GLN 9 60 ASN 9 80 GLN P 59 GLN Q 49 GLN ** T 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 452 GLN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 549 HIS ** V 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 539 ASN ** X 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 278 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 54694 Z= 0.149 Angle : 0.505 10.938 74172 Z= 0.258 Chirality : 0.040 0.248 8690 Planarity : 0.004 0.054 9512 Dihedral : 5.892 157.724 7674 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.45 % Favored : 96.43 % Rotamer: Outliers : 2.18 % Allowed : 15.86 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.10), residues: 7039 helix: 0.25 (0.09), residues: 3807 sheet: -0.66 (0.21), residues: 625 loop : -0.79 (0.12), residues: 2607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 4 206 HIS 0.005 0.001 HIS V 61 PHE 0.026 0.001 PHE J 107 TYR 0.023 0.001 TYR 4 211 ARG 0.007 0.000 ARG V 479 *********************** 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 817 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 694 time to evaluate : 4.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 40 LYS cc_start: 0.8544 (ttpt) cc_final: 0.7835 (tptt) REVERT: 1 32 THR cc_start: 0.8860 (p) cc_final: 0.8576 (p) REVERT: 1 212 GLU cc_start: 0.7842 (tm-30) cc_final: 0.7255 (mt-10) REVERT: 1 503 SER cc_start: 0.8563 (t) cc_final: 0.8327 (m) REVERT: 2 74 ASN cc_start: 0.7456 (t0) cc_final: 0.7187 (t0) REVERT: 2 187 ARG cc_start: 0.6093 (mtp85) cc_final: 0.5846 (mtp180) REVERT: 2 190 LYS cc_start: 0.8347 (mppt) cc_final: 0.7596 (tptt) REVERT: 3 93 GLU cc_start: 0.5967 (mp0) cc_final: 0.5716 (mp0) REVERT: 3 276 GLU cc_start: 0.7519 (tp30) cc_final: 0.7094 (tp30) REVERT: 3 279 GLU cc_start: 0.8048 (pt0) cc_final: 0.7724 (pt0) REVERT: 4 124 ASN cc_start: 0.7963 (m-40) cc_final: 0.7662 (m-40) REVERT: 6 76 LYS cc_start: 0.7856 (mtmt) cc_final: 0.7211 (mttm) REVERT: 8 5 GLU cc_start: 0.7760 (tt0) cc_final: 0.7376 (tt0) REVERT: A 97 LYS cc_start: 0.8781 (mmmt) cc_final: 0.8343 (ptmm) REVERT: C 60 LYS cc_start: 0.8006 (mttp) cc_final: 0.7546 (mttm) REVERT: C 81 MET cc_start: 0.8526 (ttp) cc_final: 0.8325 (ttm) REVERT: C 94 ASN cc_start: 0.8302 (p0) cc_final: 0.8098 (m110) REVERT: E 60 LYS cc_start: 0.8071 (mttp) cc_final: 0.7840 (mttm) REVERT: H 61 MET cc_start: 0.7615 (mmp) cc_final: 0.7277 (mmm) REVERT: H 115 LEU cc_start: 0.8019 (tt) cc_final: 0.7485 (mm) REVERT: I 60 LYS cc_start: 0.7962 (mttp) cc_final: 0.7582 (mtmt) REVERT: I 91 ARG cc_start: 0.8207 (ttm110) cc_final: 0.7844 (ttm-80) REVERT: J 120 VAL cc_start: 0.7394 (t) cc_final: 0.7192 (t) REVERT: J 122 PHE cc_start: 0.7208 (m-10) cc_final: 0.6789 (t80) REVERT: M 202 PHE cc_start: 0.6405 (OUTLIER) cc_final: 0.5656 (m-80) REVERT: M 231 PHE cc_start: 0.8477 (t80) cc_final: 0.8053 (t80) REVERT: M 271 VAL cc_start: 0.7472 (OUTLIER) cc_final: 0.7067 (t) REVERT: P 66 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.7396 (tt0) REVERT: P 83 GLN cc_start: 0.8214 (mm-40) cc_final: 0.7941 (mm110) REVERT: P 206 ARG cc_start: 0.8129 (ttp80) cc_final: 0.7648 (ttp-170) REVERT: P 209 MET cc_start: 0.8555 (mmm) cc_final: 0.8354 (mmt) REVERT: P 220 ASN cc_start: 0.8824 (m-40) cc_final: 0.8590 (m-40) REVERT: R 31 LYS cc_start: 0.7300 (ptpp) cc_final: 0.7016 (mmmt) REVERT: R 37 TRP cc_start: 0.6530 (t60) cc_final: 0.6099 (t60) REVERT: R 171 GLN cc_start: 0.7338 (OUTLIER) cc_final: 0.6927 (pp30) REVERT: S 115 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7487 (mp) REVERT: S 227 SER cc_start: 0.8158 (t) cc_final: 0.7809 (p) REVERT: U 73 TRP cc_start: 0.7941 (m-90) cc_final: 0.7409 (m-90) REVERT: U 213 VAL cc_start: 0.7847 (m) cc_final: 0.7492 (p) REVERT: U 393 TYR cc_start: 0.8502 (t80) cc_final: 0.8244 (t80) REVERT: U 496 ARG cc_start: 0.6653 (mtp180) cc_final: 0.6392 (mtp180) REVERT: U 559 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.7087 (pp) REVERT: X 49 ASP cc_start: 0.7435 (m-30) cc_final: 0.7205 (m-30) REVERT: X 80 MET cc_start: 0.8395 (mmm) cc_final: 0.8180 (mmm) REVERT: X 194 MET cc_start: 0.7356 (mmt) cc_final: 0.7151 (mmp) REVERT: X 386 MET cc_start: 0.7383 (mmm) cc_final: 0.7055 (mmp) REVERT: X 414 GLN cc_start: 0.6584 (mm-40) cc_final: 0.6126 (tp-100) REVERT: X 488 MET cc_start: 0.6955 (mmm) cc_final: 0.6675 (mmm) REVERT: Y 484 MET cc_start: 0.7297 (mmp) cc_final: 0.7059 (tpp) REVERT: Z 51 ARG cc_start: 0.8046 (ttm-80) cc_final: 0.7675 (tpp80) REVERT: Z 115 ARG cc_start: 0.8298 (ttm110) cc_final: 0.7174 (tpp-160) REVERT: Z 276 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7171 (mm-30) REVERT: Z 278 GLN cc_start: 0.7383 (mm-40) cc_final: 0.7166 (mt0) outliers start: 123 outliers final: 74 residues processed: 776 average time/residue: 0.5670 time to fit residues: 744.9123 Evaluate side-chains 691 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 611 time to evaluate : 4.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 40 VAL Chi-restraints excluded: chain 1 residue 171 THR Chi-restraints excluded: chain 1 residue 188 VAL Chi-restraints excluded: chain 1 residue 258 GLU Chi-restraints excluded: chain 2 residue 290 VAL Chi-restraints excluded: chain 3 residue 116 THR Chi-restraints excluded: chain 3 residue 256 GLN Chi-restraints excluded: chain 4 residue 19 ASP Chi-restraints excluded: chain 4 residue 133 ASP Chi-restraints excluded: chain 5 residue 109 GLN Chi-restraints excluded: chain 5 residue 110 SER Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 31 SER Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 23 LEU Chi-restraints excluded: chain 7 residue 60 GLN Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 8 residue 38 LYS Chi-restraints excluded: chain 9 residue 3 VAL Chi-restraints excluded: chain 9 residue 56 ASN Chi-restraints excluded: chain 9 residue 76 THR Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain G residue 66 CYS Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 202 PHE Chi-restraints excluded: chain M residue 257 MET Chi-restraints excluded: chain M residue 271 VAL Chi-restraints excluded: chain P residue 66 GLN Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain R residue 62 GLU Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 171 GLN Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 112 CYS Chi-restraints excluded: chain S residue 115 LEU Chi-restraints excluded: chain S residue 144 ASP Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 185 HIS Chi-restraints excluded: chain S residue 243 LEU Chi-restraints excluded: chain S residue 272 SER Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 186 GLU Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 559 LEU Chi-restraints excluded: chain V residue 169 GLN Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain X residue 227 MET Chi-restraints excluded: chain X residue 235 LEU Chi-restraints excluded: chain X residue 247 VAL Chi-restraints excluded: chain X residue 274 ASP Chi-restraints excluded: chain Y residue 103 VAL Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 440 GLN Chi-restraints excluded: chain Y residue 461 VAL Chi-restraints excluded: chain Z residue 61 SER Chi-restraints excluded: chain Z residue 87 CYS Chi-restraints excluded: chain Z residue 141 TRP Chi-restraints excluded: chain Z residue 162 THR Chi-restraints excluded: chain Z residue 228 ILE Chi-restraints excluded: chain Z residue 390 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 226 optimal weight: 2.9990 chunk 607 optimal weight: 7.9990 chunk 133 optimal weight: 0.1980 chunk 396 optimal weight: 5.9990 chunk 166 optimal weight: 2.9990 chunk 675 optimal weight: 0.9990 chunk 560 optimal weight: 4.9990 chunk 312 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 223 optimal weight: 0.7980 chunk 354 optimal weight: 5.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 256 GLN 5 107 ASN ** 7 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 60 ASN G 98 GLN ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 GLN S 267 HIS ** T 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 549 HIS V 539 ASN ** X 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 440 GLN Z 68 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 54694 Z= 0.205 Angle : 0.526 11.294 74172 Z= 0.267 Chirality : 0.041 0.269 8690 Planarity : 0.004 0.055 9512 Dihedral : 5.893 160.328 7674 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.71 % Favored : 96.18 % Rotamer: Outliers : 2.54 % Allowed : 16.50 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.10), residues: 7039 helix: 0.37 (0.09), residues: 3812 sheet: -0.60 (0.21), residues: 633 loop : -0.68 (0.13), residues: 2594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 4 206 HIS 0.005 0.001 HIS T 241 PHE 0.027 0.001 PHE J 107 TYR 0.021 0.001 TYR 4 211 ARG 0.007 0.000 ARG V 479 *********************** 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 786 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 643 time to evaluate : 5.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 40 LYS cc_start: 0.8550 (ttpt) cc_final: 0.7847 (tptt) REVERT: 1 32 THR cc_start: 0.8897 (p) cc_final: 0.8610 (p) REVERT: 1 212 GLU cc_start: 0.7869 (tm-30) cc_final: 0.7270 (mt-10) REVERT: 1 223 GLU cc_start: 0.7803 (mp0) cc_final: 0.7525 (mp0) REVERT: 1 493 LEU cc_start: 0.8396 (tp) cc_final: 0.8113 (tp) REVERT: 1 503 SER cc_start: 0.8661 (t) cc_final: 0.8413 (m) REVERT: 2 74 ASN cc_start: 0.7478 (t0) cc_final: 0.7193 (t0) REVERT: 2 187 ARG cc_start: 0.6199 (mtp85) cc_final: 0.5979 (mtp180) REVERT: 2 190 LYS cc_start: 0.8305 (mppt) cc_final: 0.7595 (tptt) REVERT: 3 93 GLU cc_start: 0.5962 (mp0) cc_final: 0.5752 (mp0) REVERT: 3 276 GLU cc_start: 0.7547 (tp30) cc_final: 0.7167 (tp30) REVERT: 3 279 GLU cc_start: 0.8105 (pt0) cc_final: 0.7827 (pt0) REVERT: 4 124 ASN cc_start: 0.8005 (m-40) cc_final: 0.7688 (m-40) REVERT: 5 27 ASP cc_start: 0.8263 (m-30) cc_final: 0.7807 (m-30) REVERT: 6 76 LYS cc_start: 0.7918 (mtmt) cc_final: 0.7272 (mttm) REVERT: 8 5 GLU cc_start: 0.7760 (tt0) cc_final: 0.7415 (tt0) REVERT: 9 50 ASN cc_start: 0.8292 (m-40) cc_final: 0.8087 (m-40) REVERT: A 97 LYS cc_start: 0.8768 (mmmt) cc_final: 0.8451 (pttp) REVERT: C 81 MET cc_start: 0.8538 (ttp) cc_final: 0.8328 (ttm) REVERT: E 60 LYS cc_start: 0.7992 (mttp) cc_final: 0.7671 (mttm) REVERT: H 61 MET cc_start: 0.7624 (mmp) cc_final: 0.7262 (mmm) REVERT: H 115 LEU cc_start: 0.8030 (tt) cc_final: 0.7497 (mm) REVERT: I 60 LYS cc_start: 0.7985 (mttp) cc_final: 0.7509 (mtpt) REVERT: I 91 ARG cc_start: 0.8233 (ttm110) cc_final: 0.7870 (ttm-80) REVERT: I 97 LYS cc_start: 0.7950 (ptpp) cc_final: 0.7215 (mmmt) REVERT: J 122 PHE cc_start: 0.7193 (m-10) cc_final: 0.6746 (t80) REVERT: M 110 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8699 (mm) REVERT: M 202 PHE cc_start: 0.6409 (OUTLIER) cc_final: 0.5720 (m-80) REVERT: M 231 PHE cc_start: 0.8525 (t80) cc_final: 0.8116 (t80) REVERT: M 271 VAL cc_start: 0.7467 (OUTLIER) cc_final: 0.7127 (t) REVERT: P 66 GLN cc_start: 0.7812 (OUTLIER) cc_final: 0.7508 (tt0) REVERT: P 206 ARG cc_start: 0.8171 (ttp80) cc_final: 0.7742 (ttt-90) REVERT: P 220 ASN cc_start: 0.8812 (m-40) cc_final: 0.8560 (m-40) REVERT: R 31 LYS cc_start: 0.7318 (ptpp) cc_final: 0.7012 (mmmt) REVERT: R 171 GLN cc_start: 0.7345 (OUTLIER) cc_final: 0.6951 (pp30) REVERT: S 115 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7572 (mp) REVERT: S 227 SER cc_start: 0.8214 (t) cc_final: 0.7863 (p) REVERT: T 557 VAL cc_start: 0.4850 (OUTLIER) cc_final: 0.4597 (p) REVERT: U 213 VAL cc_start: 0.8013 (m) cc_final: 0.7587 (p) REVERT: U 393 TYR cc_start: 0.8555 (t80) cc_final: 0.8310 (t80) REVERT: U 559 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.7098 (pp) REVERT: X 122 MET cc_start: 0.7269 (mtm) cc_final: 0.6943 (mtm) REVERT: X 386 MET cc_start: 0.7335 (mmm) cc_final: 0.7085 (mmp) REVERT: X 414 GLN cc_start: 0.6789 (mm-40) cc_final: 0.6318 (tp-100) REVERT: X 488 MET cc_start: 0.6861 (mmm) cc_final: 0.6605 (mmm) REVERT: Y 456 THR cc_start: 0.8257 (OUTLIER) cc_final: 0.7919 (m) REVERT: Z 115 ARG cc_start: 0.8318 (ttm110) cc_final: 0.7272 (tpp-160) REVERT: Z 276 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7295 (mm-30) outliers start: 143 outliers final: 100 residues processed: 748 average time/residue: 0.5150 time to fit residues: 648.6605 Evaluate side-chains 711 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 602 time to evaluate : 4.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 40 VAL Chi-restraints excluded: chain 1 residue 102 LEU Chi-restraints excluded: chain 1 residue 171 THR Chi-restraints excluded: chain 1 residue 188 VAL Chi-restraints excluded: chain 1 residue 256 VAL Chi-restraints excluded: chain 1 residue 258 GLU Chi-restraints excluded: chain 1 residue 378 GLU Chi-restraints excluded: chain 1 residue 476 VAL Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 2 residue 278 ASP Chi-restraints excluded: chain 2 residue 290 VAL Chi-restraints excluded: chain 3 residue 116 THR Chi-restraints excluded: chain 3 residue 256 GLN Chi-restraints excluded: chain 4 residue 19 ASP Chi-restraints excluded: chain 4 residue 133 ASP Chi-restraints excluded: chain 4 residue 212 THR Chi-restraints excluded: chain 5 residue 109 GLN Chi-restraints excluded: chain 5 residue 110 SER Chi-restraints excluded: chain 6 residue 31 SER Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 23 LEU Chi-restraints excluded: chain 7 residue 60 GLN Chi-restraints excluded: chain 7 residue 72 SER Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 7 residue 175 SER Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 8 residue 38 LYS Chi-restraints excluded: chain 9 residue 3 VAL Chi-restraints excluded: chain 9 residue 30 LEU Chi-restraints excluded: chain 9 residue 56 ASN Chi-restraints excluded: chain 9 residue 76 THR Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain G residue 66 CYS Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 202 PHE Chi-restraints excluded: chain M residue 257 MET Chi-restraints excluded: chain M residue 271 VAL Chi-restraints excluded: chain P residue 66 GLN Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain R residue 62 GLU Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 83 GLN Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 171 GLN Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 112 CYS Chi-restraints excluded: chain S residue 115 LEU Chi-restraints excluded: chain S residue 144 ASP Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 185 HIS Chi-restraints excluded: chain S residue 203 PHE Chi-restraints excluded: chain S residue 243 LEU Chi-restraints excluded: chain S residue 272 SER Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 186 GLU Chi-restraints excluded: chain T residue 272 LEU Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 559 LEU Chi-restraints excluded: chain V residue 115 VAL Chi-restraints excluded: chain V residue 169 GLN Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain V residue 220 ARG Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 87 CYS Chi-restraints excluded: chain X residue 162 THR Chi-restraints excluded: chain X residue 227 MET Chi-restraints excluded: chain X residue 235 LEU Chi-restraints excluded: chain X residue 247 VAL Chi-restraints excluded: chain X residue 274 ASP Chi-restraints excluded: chain Y residue 103 VAL Chi-restraints excluded: chain Y residue 281 LEU Chi-restraints excluded: chain Y residue 440 GLN Chi-restraints excluded: chain Y residue 456 THR Chi-restraints excluded: chain Y residue 461 VAL Chi-restraints excluded: chain Z residue 61 SER Chi-restraints excluded: chain Z residue 87 CYS Chi-restraints excluded: chain Z residue 141 TRP Chi-restraints excluded: chain Z residue 162 THR Chi-restraints excluded: chain Z residue 204 HIS Chi-restraints excluded: chain Z residue 228 ILE Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 390 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 651 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 384 optimal weight: 1.9990 chunk 493 optimal weight: 4.9990 chunk 382 optimal weight: 2.9990 chunk 568 optimal weight: 4.9990 chunk 377 optimal weight: 0.6980 chunk 672 optimal weight: 0.7980 chunk 421 optimal weight: 0.0170 chunk 410 optimal weight: 6.9990 chunk 310 optimal weight: 2.9990 overall best weight: 0.9020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 256 GLN 5 107 ASN ** 7 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 60 ASN 9 80 GLN G 98 GLN R 83 GLN S 159 GLN ** T 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 539 ASN U 386 GLN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 539 ASN ** X 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 440 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 54694 Z= 0.163 Angle : 0.510 10.535 74172 Z= 0.259 Chirality : 0.041 0.293 8690 Planarity : 0.004 0.053 9512 Dihedral : 5.770 166.452 7674 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.61 % Favored : 96.29 % Rotamer: Outliers : 2.49 % Allowed : 16.73 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.10), residues: 7039 helix: 0.52 (0.09), residues: 3810 sheet: -0.51 (0.21), residues: 635 loop : -0.59 (0.13), residues: 2594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 4 206 HIS 0.005 0.001 HIS V 61 PHE 0.031 0.001 PHE A 107 TYR 0.021 0.001 TYR 4 211 ARG 0.007 0.000 ARG V 479 *********************** 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 791 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 651 time to evaluate : 4.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 40 LYS cc_start: 0.8533 (ttpt) cc_final: 0.7843 (tptt) REVERT: 1 32 THR cc_start: 0.8827 (p) cc_final: 0.8570 (p) REVERT: 1 212 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7264 (mt-10) REVERT: 1 223 GLU cc_start: 0.7765 (mp0) cc_final: 0.7508 (mp0) REVERT: 1 503 SER cc_start: 0.8554 (t) cc_final: 0.8327 (m) REVERT: 2 74 ASN cc_start: 0.7472 (t0) cc_final: 0.7180 (t0) REVERT: 2 190 LYS cc_start: 0.8309 (mppt) cc_final: 0.7596 (tptt) REVERT: 3 276 GLU cc_start: 0.7544 (tp30) cc_final: 0.7208 (tp30) REVERT: 3 279 GLU cc_start: 0.8100 (pt0) cc_final: 0.7886 (pt0) REVERT: 6 76 LYS cc_start: 0.7837 (mtmt) cc_final: 0.7255 (mttm) REVERT: A 97 LYS cc_start: 0.8738 (mmmt) cc_final: 0.8389 (ptmm) REVERT: C 60 LYS cc_start: 0.7999 (mttp) cc_final: 0.7529 (mmtt) REVERT: C 81 MET cc_start: 0.8527 (ttp) cc_final: 0.8325 (ttm) REVERT: E 60 LYS cc_start: 0.7999 (mttp) cc_final: 0.7738 (mttm) REVERT: H 61 MET cc_start: 0.7677 (mmp) cc_final: 0.7350 (mmm) REVERT: H 81 MET cc_start: 0.7865 (ttm) cc_final: 0.7659 (ttp) REVERT: I 60 LYS cc_start: 0.7864 (mttp) cc_final: 0.7492 (mtpt) REVERT: I 91 ARG cc_start: 0.8096 (ttm110) cc_final: 0.7806 (ttm-80) REVERT: I 97 LYS cc_start: 0.7977 (ptpp) cc_final: 0.7240 (mmmt) REVERT: J 122 PHE cc_start: 0.7107 (m-10) cc_final: 0.6814 (t80) REVERT: M 110 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8573 (mm) REVERT: M 202 PHE cc_start: 0.6386 (OUTLIER) cc_final: 0.5649 (m-80) REVERT: M 231 PHE cc_start: 0.8497 (t80) cc_final: 0.8061 (t80) REVERT: M 271 VAL cc_start: 0.7412 (OUTLIER) cc_final: 0.7027 (t) REVERT: P 66 GLN cc_start: 0.7757 (OUTLIER) cc_final: 0.7469 (tt0) REVERT: P 206 ARG cc_start: 0.8143 (ttp80) cc_final: 0.7734 (ttt-90) REVERT: P 220 ASN cc_start: 0.8788 (m-40) cc_final: 0.8533 (m-40) REVERT: Q 52 TYR cc_start: 0.7467 (m-80) cc_final: 0.7152 (m-80) REVERT: R 31 LYS cc_start: 0.7319 (ptpp) cc_final: 0.7025 (mmmt) REVERT: R 37 TRP cc_start: 0.6590 (t60) cc_final: 0.6121 (t60) REVERT: R 171 GLN cc_start: 0.7353 (OUTLIER) cc_final: 0.6918 (pp30) REVERT: R 176 PHE cc_start: 0.8188 (t80) cc_final: 0.7979 (t80) REVERT: S 115 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7557 (mp) REVERT: S 227 SER cc_start: 0.8177 (t) cc_final: 0.7860 (p) REVERT: T 455 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7497 (pt0) REVERT: U 213 VAL cc_start: 0.7872 (m) cc_final: 0.7454 (p) REVERT: U 393 TYR cc_start: 0.8492 (t80) cc_final: 0.8281 (t80) REVERT: U 496 ARG cc_start: 0.6546 (mtp180) cc_final: 0.6266 (mtp180) REVERT: U 559 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.7099 (pp) REVERT: V 357 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.9091 (tp) REVERT: X 49 ASP cc_start: 0.7462 (m-30) cc_final: 0.7238 (m-30) REVERT: X 122 MET cc_start: 0.7232 (mtm) cc_final: 0.6908 (mtm) REVERT: X 386 MET cc_start: 0.7308 (mmm) cc_final: 0.7062 (mmp) REVERT: X 414 GLN cc_start: 0.6598 (mm-40) cc_final: 0.6136 (tp-100) REVERT: X 488 MET cc_start: 0.6833 (mmm) cc_final: 0.6568 (mmm) REVERT: Y 170 LEU cc_start: 0.8647 (mm) cc_final: 0.8404 (mt) REVERT: Y 456 THR cc_start: 0.8243 (OUTLIER) cc_final: 0.7918 (m) REVERT: Z 115 ARG cc_start: 0.8271 (ttm110) cc_final: 0.7172 (tpp-160) REVERT: Z 276 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7132 (mm-30) outliers start: 140 outliers final: 106 residues processed: 757 average time/residue: 0.5256 time to fit residues: 670.2734 Evaluate side-chains 723 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 608 time to evaluate : 4.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 40 VAL Chi-restraints excluded: chain 1 residue 102 LEU Chi-restraints excluded: chain 1 residue 171 THR Chi-restraints excluded: chain 1 residue 188 VAL Chi-restraints excluded: chain 1 residue 256 VAL Chi-restraints excluded: chain 1 residue 258 GLU Chi-restraints excluded: chain 1 residue 378 GLU Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 476 VAL Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 2 residue 278 ASP Chi-restraints excluded: chain 2 residue 290 VAL Chi-restraints excluded: chain 3 residue 116 THR Chi-restraints excluded: chain 3 residue 256 GLN Chi-restraints excluded: chain 4 residue 19 ASP Chi-restraints excluded: chain 4 residue 133 ASP Chi-restraints excluded: chain 5 residue 109 GLN Chi-restraints excluded: chain 5 residue 110 SER Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 31 SER Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 23 LEU Chi-restraints excluded: chain 7 residue 49 THR Chi-restraints excluded: chain 7 residue 60 GLN Chi-restraints excluded: chain 7 residue 72 SER Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 7 residue 175 SER Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 8 residue 38 LYS Chi-restraints excluded: chain 9 residue 3 VAL Chi-restraints excluded: chain 9 residue 56 ASN Chi-restraints excluded: chain 9 residue 76 THR Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain G residue 66 CYS Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 202 PHE Chi-restraints excluded: chain M residue 257 MET Chi-restraints excluded: chain M residue 271 VAL Chi-restraints excluded: chain P residue 66 GLN Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 144 LEU Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain R residue 62 GLU Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 83 GLN Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 171 GLN Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 112 CYS Chi-restraints excluded: chain S residue 115 LEU Chi-restraints excluded: chain S residue 144 ASP Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 185 HIS Chi-restraints excluded: chain S residue 203 PHE Chi-restraints excluded: chain S residue 243 LEU Chi-restraints excluded: chain S residue 272 SER Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 186 GLU Chi-restraints excluded: chain T residue 272 LEU Chi-restraints excluded: chain T residue 286 ILE Chi-restraints excluded: chain U residue 54 SER Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 559 LEU Chi-restraints excluded: chain V residue 115 VAL Chi-restraints excluded: chain V residue 169 GLN Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain V residue 220 ARG Chi-restraints excluded: chain V residue 357 LEU Chi-restraints excluded: chain V residue 509 LEU Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 87 CYS Chi-restraints excluded: chain X residue 227 MET Chi-restraints excluded: chain X residue 247 VAL Chi-restraints excluded: chain X residue 274 ASP Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain Y residue 103 VAL Chi-restraints excluded: chain Y residue 281 LEU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 440 GLN Chi-restraints excluded: chain Y residue 456 THR Chi-restraints excluded: chain Y residue 461 VAL Chi-restraints excluded: chain Z residue 61 SER Chi-restraints excluded: chain Z residue 87 CYS Chi-restraints excluded: chain Z residue 141 TRP Chi-restraints excluded: chain Z residue 162 THR Chi-restraints excluded: chain Z residue 204 HIS Chi-restraints excluded: chain Z residue 228 ILE Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 390 ASN Chi-restraints excluded: chain Z residue 462 ASP Chi-restraints excluded: chain Z residue 514 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 416 optimal weight: 7.9990 chunk 268 optimal weight: 3.9990 chunk 401 optimal weight: 10.0000 chunk 202 optimal weight: 0.0270 chunk 132 optimal weight: 9.9990 chunk 130 optimal weight: 7.9990 chunk 427 optimal weight: 5.9990 chunk 458 optimal weight: 0.4980 chunk 332 optimal weight: 0.8980 chunk 62 optimal weight: 0.2980 chunk 528 optimal weight: 0.0170 overall best weight: 0.3476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 256 GLN ** 4 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 184 ASN 9 60 ASN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN P 52 GLN P 83 GLN S 159 GLN S 195 ASN T 179 ASN ** T 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 539 ASN ** X 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 54694 Z= 0.129 Angle : 0.498 11.112 74172 Z= 0.252 Chirality : 0.040 0.348 8690 Planarity : 0.004 0.051 9512 Dihedral : 5.506 173.083 7674 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.44 % Favored : 96.45 % Rotamer: Outliers : 2.06 % Allowed : 17.33 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.10), residues: 7039 helix: 0.73 (0.09), residues: 3802 sheet: -0.38 (0.21), residues: 653 loop : -0.50 (0.13), residues: 2584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 1 583 HIS 0.006 0.001 HIS V 61 PHE 0.034 0.001 PHE J 107 TYR 0.022 0.001 TYR 4 211 ARG 0.008 0.000 ARG T 555 *********************** 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 817 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 701 time to evaluate : 4.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 40 LYS cc_start: 0.8545 (ttpt) cc_final: 0.7865 (tptt) REVERT: 1 32 THR cc_start: 0.8736 (p) cc_final: 0.8458 (p) REVERT: 1 212 GLU cc_start: 0.7720 (tm-30) cc_final: 0.7254 (mt-10) REVERT: 1 267 ARG cc_start: 0.8448 (mpt180) cc_final: 0.8027 (mpt180) REVERT: 1 548 MET cc_start: 0.8857 (mtm) cc_final: 0.8621 (mtp) REVERT: 2 74 ASN cc_start: 0.7425 (t0) cc_final: 0.7122 (t0) REVERT: 2 190 LYS cc_start: 0.8381 (mppt) cc_final: 0.7666 (tptt) REVERT: 3 276 GLU cc_start: 0.7527 (tp30) cc_final: 0.7249 (tp30) REVERT: 6 76 LYS cc_start: 0.7810 (mtmt) cc_final: 0.7226 (mttm) REVERT: C 60 LYS cc_start: 0.7977 (mttp) cc_final: 0.7514 (mttt) REVERT: C 81 MET cc_start: 0.8520 (ttp) cc_final: 0.8307 (ttp) REVERT: C 126 PHE cc_start: 0.6486 (m-80) cc_final: 0.6264 (m-10) REVERT: E 60 LYS cc_start: 0.7899 (mttp) cc_final: 0.7652 (mttm) REVERT: F 81 MET cc_start: 0.8208 (ttp) cc_final: 0.7957 (ttp) REVERT: H 61 MET cc_start: 0.7512 (mmp) cc_final: 0.7273 (mmm) REVERT: H 115 LEU cc_start: 0.8047 (tt) cc_final: 0.7550 (mm) REVERT: I 60 LYS cc_start: 0.7840 (mttp) cc_final: 0.7549 (mtpt) REVERT: I 91 ARG cc_start: 0.8031 (ttm110) cc_final: 0.7638 (ttm-80) REVERT: J 122 PHE cc_start: 0.7146 (m-10) cc_final: 0.6835 (t80) REVERT: M 110 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8431 (mm) REVERT: M 202 PHE cc_start: 0.6383 (OUTLIER) cc_final: 0.5804 (m-80) REVERT: M 230 THR cc_start: 0.9143 (t) cc_final: 0.8921 (m) REVERT: M 231 PHE cc_start: 0.8409 (t80) cc_final: 0.7991 (t80) REVERT: M 271 VAL cc_start: 0.7422 (OUTLIER) cc_final: 0.7058 (t) REVERT: P 66 GLN cc_start: 0.7628 (OUTLIER) cc_final: 0.7418 (tt0) REVERT: P 190 ILE cc_start: 0.8445 (pt) cc_final: 0.8178 (mm) REVERT: P 206 ARG cc_start: 0.8116 (ttp80) cc_final: 0.7700 (ttt-90) REVERT: P 220 ASN cc_start: 0.8727 (m-40) cc_final: 0.8459 (m-40) REVERT: Q 14 MET cc_start: 0.7547 (ttm) cc_final: 0.7286 (ttt) REVERT: Q 52 TYR cc_start: 0.7545 (m-80) cc_final: 0.7246 (m-80) REVERT: R 31 LYS cc_start: 0.7340 (ptpp) cc_final: 0.7034 (mmmt) REVERT: R 37 TRP cc_start: 0.6439 (t60) cc_final: 0.6151 (t60) REVERT: R 171 GLN cc_start: 0.7441 (OUTLIER) cc_final: 0.6976 (pp30) REVERT: R 176 PHE cc_start: 0.8172 (t80) cc_final: 0.7934 (t80) REVERT: S 115 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7496 (mp) REVERT: S 227 SER cc_start: 0.8159 (t) cc_final: 0.7852 (p) REVERT: U 213 VAL cc_start: 0.7818 (m) cc_final: 0.7454 (p) REVERT: U 496 ARG cc_start: 0.6571 (mtp180) cc_final: 0.6292 (mtp180) REVERT: U 559 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.7057 (pp) REVERT: V 357 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.9132 (tp) REVERT: V 483 MET cc_start: 0.6897 (tpp) cc_final: 0.5713 (tpp) REVERT: X 49 ASP cc_start: 0.7446 (m-30) cc_final: 0.7146 (m-30) REVERT: X 122 MET cc_start: 0.7190 (mtm) cc_final: 0.6857 (mtm) REVERT: X 386 MET cc_start: 0.7239 (mmm) cc_final: 0.6912 (mmp) REVERT: X 414 GLN cc_start: 0.6464 (mm-40) cc_final: 0.6054 (tp-100) REVERT: Y 345 ASP cc_start: 0.8276 (t0) cc_final: 0.8005 (t0) REVERT: Y 456 THR cc_start: 0.8135 (OUTLIER) cc_final: 0.7802 (m) REVERT: Z 115 ARG cc_start: 0.8281 (ttm110) cc_final: 0.7991 (ttm170) REVERT: Z 428 GLU cc_start: 0.6239 (mp0) cc_final: 0.6035 (mp0) outliers start: 116 outliers final: 82 residues processed: 778 average time/residue: 0.5652 time to fit residues: 746.0423 Evaluate side-chains 724 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 633 time to evaluate : 4.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 40 VAL Chi-restraints excluded: chain 1 residue 102 LEU Chi-restraints excluded: chain 1 residue 171 THR Chi-restraints excluded: chain 1 residue 188 VAL Chi-restraints excluded: chain 1 residue 258 GLU Chi-restraints excluded: chain 1 residue 378 GLU Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 2 residue 290 VAL Chi-restraints excluded: chain 3 residue 116 THR Chi-restraints excluded: chain 3 residue 256 GLN Chi-restraints excluded: chain 4 residue 19 ASP Chi-restraints excluded: chain 4 residue 133 ASP Chi-restraints excluded: chain 5 residue 110 SER Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 23 LEU Chi-restraints excluded: chain 7 residue 60 GLN Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 7 residue 175 SER Chi-restraints excluded: chain 7 residue 184 ASN Chi-restraints excluded: chain 8 residue 38 LYS Chi-restraints excluded: chain 9 residue 3 VAL Chi-restraints excluded: chain 9 residue 76 THR Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 202 PHE Chi-restraints excluded: chain M residue 257 MET Chi-restraints excluded: chain M residue 271 VAL Chi-restraints excluded: chain P residue 52 GLN Chi-restraints excluded: chain P residue 66 GLN Chi-restraints excluded: chain P residue 144 LEU Chi-restraints excluded: chain P residue 163 ASP Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain R residue 62 GLU Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 171 GLN Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 115 LEU Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 185 HIS Chi-restraints excluded: chain S residue 203 PHE Chi-restraints excluded: chain S residue 243 LEU Chi-restraints excluded: chain S residue 272 SER Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 186 GLU Chi-restraints excluded: chain T residue 272 LEU Chi-restraints excluded: chain U residue 54 SER Chi-restraints excluded: chain U residue 249 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 559 LEU Chi-restraints excluded: chain V residue 115 VAL Chi-restraints excluded: chain V residue 169 GLN Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain V residue 357 LEU Chi-restraints excluded: chain V residue 509 LEU Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 87 CYS Chi-restraints excluded: chain X residue 247 VAL Chi-restraints excluded: chain X residue 274 ASP Chi-restraints excluded: chain Y residue 103 VAL Chi-restraints excluded: chain Y residue 281 LEU Chi-restraints excluded: chain Y residue 456 THR Chi-restraints excluded: chain Y residue 461 VAL Chi-restraints excluded: chain Z residue 61 SER Chi-restraints excluded: chain Z residue 87 CYS Chi-restraints excluded: chain Z residue 141 TRP Chi-restraints excluded: chain Z residue 204 HIS Chi-restraints excluded: chain Z residue 390 ASN Chi-restraints excluded: chain Z residue 462 ASP Chi-restraints excluded: chain Z residue 514 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 611 optimal weight: 0.0060 chunk 644 optimal weight: 2.9990 chunk 588 optimal weight: 0.0040 chunk 626 optimal weight: 9.9990 chunk 377 optimal weight: 4.9990 chunk 273 optimal weight: 5.9990 chunk 492 optimal weight: 5.9990 chunk 192 optimal weight: 6.9990 chunk 566 optimal weight: 0.9990 chunk 592 optimal weight: 5.9990 chunk 624 optimal weight: 2.9990 overall best weight: 1.4014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 256 GLN ** 4 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 107 ASN ** 7 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 60 ASN G 98 GLN P 52 GLN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 539 ASN ** X 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 153 GLN ** X 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 54694 Z= 0.207 Angle : 0.536 10.799 74172 Z= 0.270 Chirality : 0.042 0.312 8690 Planarity : 0.004 0.053 9512 Dihedral : 5.439 137.900 7674 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.81 % Favored : 96.09 % Rotamer: Outliers : 2.01 % Allowed : 17.67 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.10), residues: 7039 helix: 0.70 (0.09), residues: 3811 sheet: -0.36 (0.21), residues: 647 loop : -0.48 (0.13), residues: 2581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP U 73 HIS 0.006 0.001 HIS V 61 PHE 0.051 0.001 PHE A 107 TYR 0.022 0.001 TYR 4 211 ARG 0.007 0.000 ARG 1 453 *********************** 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 743 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 630 time to evaluate : 4.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 40 LYS cc_start: 0.8527 (ttpt) cc_final: 0.7847 (tptt) REVERT: 1 32 THR cc_start: 0.8841 (p) cc_final: 0.8578 (p) REVERT: 1 212 GLU cc_start: 0.7838 (tm-30) cc_final: 0.7250 (mt-10) REVERT: 1 223 GLU cc_start: 0.7816 (mp0) cc_final: 0.7456 (mp0) REVERT: 2 74 ASN cc_start: 0.7517 (t0) cc_final: 0.7227 (t0) REVERT: 2 190 LYS cc_start: 0.8270 (mppt) cc_final: 0.7592 (tptt) REVERT: 4 6 VAL cc_start: 0.7534 (m) cc_final: 0.7218 (t) REVERT: 5 27 ASP cc_start: 0.8374 (m-30) cc_final: 0.7897 (m-30) REVERT: 6 76 LYS cc_start: 0.7841 (mtmt) cc_final: 0.7247 (mttm) REVERT: 9 22 GLU cc_start: 0.7697 (pp20) cc_final: 0.7352 (mm-30) REVERT: A 97 LYS cc_start: 0.8524 (ptmm) cc_final: 0.8144 (mmpt) REVERT: C 60 LYS cc_start: 0.8084 (mttp) cc_final: 0.7589 (mttt) REVERT: C 81 MET cc_start: 0.8538 (ttp) cc_final: 0.8313 (ttp) REVERT: E 60 LYS cc_start: 0.7921 (mttp) cc_final: 0.7671 (mttm) REVERT: H 61 MET cc_start: 0.7486 (mmp) cc_final: 0.7269 (mmm) REVERT: H 115 LEU cc_start: 0.8012 (tt) cc_final: 0.7484 (mm) REVERT: I 60 LYS cc_start: 0.7832 (mttp) cc_final: 0.7548 (mtpt) REVERT: I 91 ARG cc_start: 0.8060 (ttm110) cc_final: 0.7703 (ttm-80) REVERT: I 97 LYS cc_start: 0.8013 (ptpp) cc_final: 0.7368 (mmmt) REVERT: M 110 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8574 (mm) REVERT: M 202 PHE cc_start: 0.6312 (OUTLIER) cc_final: 0.5626 (m-80) REVERT: M 231 PHE cc_start: 0.8504 (t80) cc_final: 0.8104 (t80) REVERT: M 271 VAL cc_start: 0.7482 (OUTLIER) cc_final: 0.7103 (t) REVERT: P 66 GLN cc_start: 0.7812 (OUTLIER) cc_final: 0.7575 (tt0) REVERT: P 190 ILE cc_start: 0.8449 (pt) cc_final: 0.8177 (mm) REVERT: P 206 ARG cc_start: 0.8165 (ttp80) cc_final: 0.7794 (ttt-90) REVERT: P 220 ASN cc_start: 0.8748 (m-40) cc_final: 0.8458 (m-40) REVERT: Q 14 MET cc_start: 0.7600 (ttm) cc_final: 0.7300 (ttt) REVERT: Q 52 TYR cc_start: 0.7519 (m-80) cc_final: 0.7223 (m-80) REVERT: R 31 LYS cc_start: 0.7441 (ptpp) cc_final: 0.7065 (mmmt) REVERT: R 171 GLN cc_start: 0.7454 (OUTLIER) cc_final: 0.6968 (pp30) REVERT: R 176 PHE cc_start: 0.8188 (t80) cc_final: 0.7984 (t80) REVERT: S 115 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7569 (mp) REVERT: S 227 SER cc_start: 0.8182 (t) cc_final: 0.7867 (p) REVERT: U 213 VAL cc_start: 0.7926 (m) cc_final: 0.7531 (p) REVERT: U 471 GLN cc_start: 0.6433 (tm-30) cc_final: 0.6212 (tp40) REVERT: U 496 ARG cc_start: 0.6554 (mtp180) cc_final: 0.6286 (mtp180) REVERT: U 559 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.7142 (pp) REVERT: V 357 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.9079 (tp) REVERT: X 49 ASP cc_start: 0.7499 (m-30) cc_final: 0.7210 (m-30) REVERT: X 122 MET cc_start: 0.7168 (mtm) cc_final: 0.6810 (mtm) REVERT: X 386 MET cc_start: 0.7330 (mmm) cc_final: 0.6992 (mmp) REVERT: X 414 GLN cc_start: 0.6653 (mm-40) cc_final: 0.6172 (tp-100) REVERT: X 446 PRO cc_start: 0.7923 (Cg_exo) cc_final: 0.7694 (Cg_endo) REVERT: X 488 MET cc_start: 0.6668 (mmm) cc_final: 0.6210 (mmp) REVERT: Y 170 LEU cc_start: 0.8619 (mm) cc_final: 0.8417 (mt) REVERT: Y 345 ASP cc_start: 0.8280 (t0) cc_final: 0.8052 (t0) REVERT: Y 456 THR cc_start: 0.8167 (OUTLIER) cc_final: 0.7915 (m) outliers start: 113 outliers final: 93 residues processed: 713 average time/residue: 0.5144 time to fit residues: 616.2429 Evaluate side-chains 706 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 604 time to evaluate : 4.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 40 VAL Chi-restraints excluded: chain 1 residue 102 LEU Chi-restraints excluded: chain 1 residue 171 THR Chi-restraints excluded: chain 1 residue 188 VAL Chi-restraints excluded: chain 1 residue 258 GLU Chi-restraints excluded: chain 1 residue 378 GLU Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 476 VAL Chi-restraints excluded: chain 2 residue 278 ASP Chi-restraints excluded: chain 2 residue 290 VAL Chi-restraints excluded: chain 3 residue 116 THR Chi-restraints excluded: chain 3 residue 256 GLN Chi-restraints excluded: chain 4 residue 19 ASP Chi-restraints excluded: chain 4 residue 133 ASP Chi-restraints excluded: chain 5 residue 107 ASN Chi-restraints excluded: chain 5 residue 110 SER Chi-restraints excluded: chain 6 residue 31 SER Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 23 LEU Chi-restraints excluded: chain 7 residue 60 GLN Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 7 residue 175 SER Chi-restraints excluded: chain 8 residue 38 LYS Chi-restraints excluded: chain 9 residue 3 VAL Chi-restraints excluded: chain 9 residue 56 ASN Chi-restraints excluded: chain 9 residue 76 THR Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain G residue 66 CYS Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 202 PHE Chi-restraints excluded: chain M residue 257 MET Chi-restraints excluded: chain M residue 271 VAL Chi-restraints excluded: chain P residue 52 GLN Chi-restraints excluded: chain P residue 66 GLN Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 144 LEU Chi-restraints excluded: chain P residue 163 ASP Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain R residue 62 GLU Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 171 GLN Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 115 LEU Chi-restraints excluded: chain S residue 144 ASP Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 185 HIS Chi-restraints excluded: chain S residue 203 PHE Chi-restraints excluded: chain S residue 243 LEU Chi-restraints excluded: chain S residue 272 SER Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 186 GLU Chi-restraints excluded: chain T residue 272 LEU Chi-restraints excluded: chain U residue 54 SER Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 559 LEU Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain V residue 115 VAL Chi-restraints excluded: chain V residue 169 GLN Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 357 LEU Chi-restraints excluded: chain V residue 509 LEU Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 87 CYS Chi-restraints excluded: chain X residue 247 VAL Chi-restraints excluded: chain X residue 274 ASP Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain Y residue 103 VAL Chi-restraints excluded: chain Y residue 281 LEU Chi-restraints excluded: chain Y residue 456 THR Chi-restraints excluded: chain Y residue 461 VAL Chi-restraints excluded: chain Z residue 61 SER Chi-restraints excluded: chain Z residue 87 CYS Chi-restraints excluded: chain Z residue 141 TRP Chi-restraints excluded: chain Z residue 204 HIS Chi-restraints excluded: chain Z residue 390 ASN Chi-restraints excluded: chain Z residue 462 ASP Chi-restraints excluded: chain Z residue 514 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 411 optimal weight: 5.9990 chunk 662 optimal weight: 0.7980 chunk 404 optimal weight: 2.9990 chunk 314 optimal weight: 3.9990 chunk 460 optimal weight: 5.9990 chunk 695 optimal weight: 7.9990 chunk 640 optimal weight: 40.0000 chunk 553 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 427 optimal weight: 5.9990 chunk 339 optimal weight: 0.0980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 256 GLN ** 4 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 60 ASN G 98 GLN ** T 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 64 GLN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 539 ASN ** X 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 54694 Z= 0.282 Angle : 0.580 12.810 74172 Z= 0.292 Chirality : 0.043 0.314 8690 Planarity : 0.004 0.053 9512 Dihedral : 5.524 96.918 7674 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.99 % Favored : 95.89 % Rotamer: Outliers : 2.02 % Allowed : 17.86 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.10), residues: 7039 helix: 0.55 (0.09), residues: 3815 sheet: -0.43 (0.21), residues: 641 loop : -0.53 (0.13), residues: 2583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP U 73 HIS 0.005 0.001 HIS 4 233 PHE 0.040 0.002 PHE J 107 TYR 0.022 0.002 TYR 4 211 ARG 0.008 0.000 ARG 1 453 ********************** 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 713 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 599 time to evaluate : 4.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 40 LYS cc_start: 0.8586 (ttpt) cc_final: 0.7888 (tptt) REVERT: 1 32 THR cc_start: 0.8893 (p) cc_final: 0.8623 (p) REVERT: 1 212 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7518 (mm-30) REVERT: 1 223 GLU cc_start: 0.7890 (mp0) cc_final: 0.7569 (mp0) REVERT: 2 190 LYS cc_start: 0.8342 (mppt) cc_final: 0.7595 (tptt) REVERT: 3 256 GLN cc_start: 0.7211 (OUTLIER) cc_final: 0.7003 (mp10) REVERT: 4 6 VAL cc_start: 0.7637 (m) cc_final: 0.7323 (t) REVERT: 4 52 GLN cc_start: 0.8217 (mm110) cc_final: 0.7989 (mm110) REVERT: 5 27 ASP cc_start: 0.8306 (m-30) cc_final: 0.7801 (m-30) REVERT: 6 76 LYS cc_start: 0.7910 (mtmt) cc_final: 0.7296 (mttm) REVERT: 9 22 GLU cc_start: 0.7825 (pp20) cc_final: 0.7369 (mm-30) REVERT: A 97 LYS cc_start: 0.8556 (ptmm) cc_final: 0.8154 (mmpt) REVERT: C 81 MET cc_start: 0.8571 (ttp) cc_final: 0.8363 (ttm) REVERT: E 60 LYS cc_start: 0.7860 (mttp) cc_final: 0.7604 (mttm) REVERT: H 61 MET cc_start: 0.7570 (mmp) cc_final: 0.7350 (mmm) REVERT: I 60 LYS cc_start: 0.7893 (mttp) cc_final: 0.7574 (mtpt) REVERT: I 91 ARG cc_start: 0.8035 (ttm110) cc_final: 0.7615 (ttm-80) REVERT: I 97 LYS cc_start: 0.8043 (ptpp) cc_final: 0.7368 (mmtt) REVERT: M 110 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.8766 (mm) REVERT: M 202 PHE cc_start: 0.6293 (OUTLIER) cc_final: 0.5518 (m-80) REVERT: M 271 VAL cc_start: 0.7504 (OUTLIER) cc_final: 0.7145 (t) REVERT: P 66 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.7647 (tt0) REVERT: P 190 ILE cc_start: 0.8492 (pt) cc_final: 0.8177 (mm) REVERT: P 206 ARG cc_start: 0.8189 (ttp80) cc_final: 0.7837 (ttt-90) REVERT: P 209 MET cc_start: 0.8788 (mmm) cc_final: 0.8524 (mmt) REVERT: P 220 ASN cc_start: 0.8802 (m-40) cc_final: 0.8488 (m-40) REVERT: Q 14 MET cc_start: 0.7695 (ttm) cc_final: 0.7446 (ttt) REVERT: Q 52 TYR cc_start: 0.7490 (m-80) cc_final: 0.7172 (m-80) REVERT: R 31 LYS cc_start: 0.7345 (ptpp) cc_final: 0.7020 (mmmt) REVERT: R 83 GLN cc_start: 0.8236 (mt0) cc_final: 0.7846 (mm-40) REVERT: R 171 GLN cc_start: 0.7474 (OUTLIER) cc_final: 0.6987 (pp30) REVERT: R 176 PHE cc_start: 0.8283 (t80) cc_final: 0.8078 (t80) REVERT: S 115 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7644 (mp) REVERT: S 227 SER cc_start: 0.8223 (t) cc_final: 0.7921 (p) REVERT: T 118 MET cc_start: 0.8240 (ttt) cc_final: 0.7933 (ttt) REVERT: U 213 VAL cc_start: 0.8000 (m) cc_final: 0.7635 (p) REVERT: U 471 GLN cc_start: 0.6413 (tm-30) cc_final: 0.6193 (tp40) REVERT: U 496 ARG cc_start: 0.6673 (mtp180) cc_final: 0.6406 (mtp180) REVERT: U 559 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.7154 (pp) REVERT: V 357 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.9047 (tp) REVERT: X 49 ASP cc_start: 0.7502 (m-30) cc_final: 0.7266 (m-30) REVERT: X 122 MET cc_start: 0.7187 (mtm) cc_final: 0.6834 (mtm) REVERT: X 386 MET cc_start: 0.7374 (mmm) cc_final: 0.7034 (mmp) REVERT: X 446 PRO cc_start: 0.8015 (Cg_exo) cc_final: 0.7808 (Cg_endo) REVERT: X 488 MET cc_start: 0.6725 (mmm) cc_final: 0.6435 (mmm) REVERT: Y 170 LEU cc_start: 0.8615 (mm) cc_final: 0.8400 (mt) REVERT: Y 292 GLN cc_start: 0.7883 (tt0) cc_final: 0.7512 (tt0) REVERT: Y 456 THR cc_start: 0.8237 (OUTLIER) cc_final: 0.7959 (m) REVERT: Z 175 ARG cc_start: 0.6830 (tpp80) cc_final: 0.6613 (tpt170) outliers start: 114 outliers final: 100 residues processed: 687 average time/residue: 0.5226 time to fit residues: 603.4205 Evaluate side-chains 689 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 579 time to evaluate : 4.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 40 VAL Chi-restraints excluded: chain 1 residue 102 LEU Chi-restraints excluded: chain 1 residue 171 THR Chi-restraints excluded: chain 1 residue 188 VAL Chi-restraints excluded: chain 1 residue 258 GLU Chi-restraints excluded: chain 1 residue 378 GLU Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 476 VAL Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 2 residue 278 ASP Chi-restraints excluded: chain 2 residue 290 VAL Chi-restraints excluded: chain 3 residue 116 THR Chi-restraints excluded: chain 3 residue 256 GLN Chi-restraints excluded: chain 4 residue 19 ASP Chi-restraints excluded: chain 4 residue 133 ASP Chi-restraints excluded: chain 4 residue 212 THR Chi-restraints excluded: chain 6 residue 31 SER Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 23 LEU Chi-restraints excluded: chain 7 residue 49 THR Chi-restraints excluded: chain 7 residue 60 GLN Chi-restraints excluded: chain 7 residue 72 SER Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 7 residue 175 SER Chi-restraints excluded: chain 8 residue 38 LYS Chi-restraints excluded: chain 8 residue 77 ILE Chi-restraints excluded: chain 9 residue 3 VAL Chi-restraints excluded: chain 9 residue 27 ASN Chi-restraints excluded: chain 9 residue 76 THR Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain G residue 66 CYS Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 202 PHE Chi-restraints excluded: chain M residue 257 MET Chi-restraints excluded: chain M residue 271 VAL Chi-restraints excluded: chain P residue 52 GLN Chi-restraints excluded: chain P residue 66 GLN Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 144 LEU Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain R residue 62 GLU Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 171 GLN Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 115 LEU Chi-restraints excluded: chain S residue 144 ASP Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 185 HIS Chi-restraints excluded: chain S residue 243 LEU Chi-restraints excluded: chain S residue 272 SER Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 186 GLU Chi-restraints excluded: chain T residue 272 LEU Chi-restraints excluded: chain T residue 286 ILE Chi-restraints excluded: chain U residue 54 SER Chi-restraints excluded: chain U residue 192 ILE Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 559 LEU Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain V residue 115 VAL Chi-restraints excluded: chain V residue 169 GLN Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 357 LEU Chi-restraints excluded: chain V residue 509 LEU Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 87 CYS Chi-restraints excluded: chain X residue 162 THR Chi-restraints excluded: chain X residue 247 VAL Chi-restraints excluded: chain X residue 274 ASP Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain Y residue 103 VAL Chi-restraints excluded: chain Y residue 233 ILE Chi-restraints excluded: chain Y residue 281 LEU Chi-restraints excluded: chain Y residue 456 THR Chi-restraints excluded: chain Y residue 461 VAL Chi-restraints excluded: chain Z residue 61 SER Chi-restraints excluded: chain Z residue 87 CYS Chi-restraints excluded: chain Z residue 117 THR Chi-restraints excluded: chain Z residue 141 TRP Chi-restraints excluded: chain Z residue 204 HIS Chi-restraints excluded: chain Z residue 228 ILE Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 390 ASN Chi-restraints excluded: chain Z residue 462 ASP Chi-restraints excluded: chain Z residue 514 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 439 optimal weight: 0.5980 chunk 589 optimal weight: 5.9990 chunk 169 optimal weight: 0.7980 chunk 510 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 153 optimal weight: 9.9990 chunk 554 optimal weight: 0.0030 chunk 232 optimal weight: 2.9990 chunk 569 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 256 GLN ** 4 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 60 ASN G 98 GLN J 92 ASN P 52 GLN U 64 GLN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 539 ASN ** X 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 157 GLN Y 250 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.132582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.106692 restraints weight = 87188.940| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.07 r_work: 0.3081 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 54694 Z= 0.149 Angle : 0.523 11.662 74172 Z= 0.264 Chirality : 0.041 0.316 8690 Planarity : 0.004 0.060 9512 Dihedral : 5.127 81.406 7674 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.58 % Favored : 96.32 % Rotamer: Outliers : 1.74 % Allowed : 18.20 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.10), residues: 7039 helix: 0.79 (0.09), residues: 3810 sheet: -0.31 (0.21), residues: 642 loop : -0.38 (0.13), residues: 2587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP U 73 HIS 0.006 0.001 HIS V 61 PHE 0.040 0.001 PHE J 107 TYR 0.025 0.001 TYR Y 487 ARG 0.008 0.000 ARG 3 257 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12845.42 seconds wall clock time: 226 minutes 43.22 seconds (13603.22 seconds total)