Starting phenix.real_space_refine on Sun Mar 10 18:23:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdh_4818/03_2024/6rdh_4818_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdh_4818/03_2024/6rdh_4818.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdh_4818/03_2024/6rdh_4818.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdh_4818/03_2024/6rdh_4818.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdh_4818/03_2024/6rdh_4818_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdh_4818/03_2024/6rdh_4818_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 1.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 13 5.49 5 Mg 5 5.21 5 S 149 5.16 5 C 34297 2.51 5 N 9112 2.21 5 O 10171 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 106": "OD1" <-> "OD2" Residue "1 ARG 150": "NH1" <-> "NH2" Residue "1 ASP 172": "OD1" <-> "OD2" Residue "1 ARG 182": "NH1" <-> "NH2" Residue "1 GLU 212": "OE1" <-> "OE2" Residue "1 GLU 229": "OE1" <-> "OE2" Residue "1 GLU 235": "OE1" <-> "OE2" Residue "1 ARG 259": "NH1" <-> "NH2" Residue "1 GLU 281": "OE1" <-> "OE2" Residue "1 PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 329": "OE1" <-> "OE2" Residue "1 GLU 332": "OE1" <-> "OE2" Residue "1 GLU 350": "OE1" <-> "OE2" Residue "1 GLU 352": "OE1" <-> "OE2" Residue "1 GLU 355": "OE1" <-> "OE2" Residue "1 ARG 359": "NH1" <-> "NH2" Residue "1 GLU 378": "OE1" <-> "OE2" Residue "1 GLU 385": "OE1" <-> "OE2" Residue "1 ARG 387": "NH1" <-> "NH2" Residue "1 ASP 391": "OD1" <-> "OD2" Residue "1 GLU 409": "OE1" <-> "OE2" Residue "1 TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 422": "OD1" <-> "OD2" Residue "1 ARG 434": "NH1" <-> "NH2" Residue "1 PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 457": "OE1" <-> "OE2" Residue "1 GLU 496": "OE1" <-> "OE2" Residue "1 ASP 504": "OD1" <-> "OD2" Residue "1 ASP 508": "OD1" <-> "OD2" Residue "1 GLU 513": "OE1" <-> "OE2" Residue "1 GLU 577": "OE1" <-> "OE2" Residue "1 ARG 609": "NH1" <-> "NH2" Residue "2 ASP 31": "OD1" <-> "OD2" Residue "2 ARG 45": "NH1" <-> "NH2" Residue "2 GLU 86": "OE1" <-> "OE2" Residue "2 TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 154": "OD1" <-> "OD2" Residue "2 ARG 173": "NH1" <-> "NH2" Residue "2 GLU 205": "OE1" <-> "OE2" Residue "2 PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 258": "OD1" <-> "OD2" Residue "2 PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 281": "OE1" <-> "OE2" Residue "2 PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 346": "NH1" <-> "NH2" Residue "2 TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 426": "OD1" <-> "OD2" Residue "2 TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 149": "NH1" <-> "NH2" Residue "3 ASP 154": "OD1" <-> "OD2" Residue "3 PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 213": "NH1" <-> "NH2" Residue "3 ASP 217": "OD1" <-> "OD2" Residue "3 TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 233": "NH1" <-> "NH2" Residue "3 ARG 242": "NH1" <-> "NH2" Residue "3 ARG 257": "NH1" <-> "NH2" Residue "3 ASP 259": "OD1" <-> "OD2" Residue "3 PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 19": "OD1" <-> "OD2" Residue "4 TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 45": "OD1" <-> "OD2" Residue "4 GLU 48": "OE1" <-> "OE2" Residue "4 TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 84": "NH1" <-> "NH2" Residue "4 TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 148": "OE1" <-> "OE2" Residue "4 ASP 156": "OD1" <-> "OD2" Residue "4 ARG 176": "NH1" <-> "NH2" Residue "4 TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 193": "OE1" <-> "OE2" Residue "4 GLU 202": "OE1" <-> "OE2" Residue "4 TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 225": "OE1" <-> "OE2" Residue "4 ASP 231": "OD1" <-> "OD2" Residue "4 ARG 232": "NH1" <-> "NH2" Residue "4 ARG 255": "NH1" <-> "NH2" Residue "4 GLU 270": "OE1" <-> "OE2" Residue "4 ASP 271": "OD1" <-> "OD2" Residue "5 ARG 36": "NH1" <-> "NH2" Residue "5 ARG 50": "NH1" <-> "NH2" Residue "5 TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 112": "NH1" <-> "NH2" Residue "5 PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 91": "OD1" <-> "OD2" Residue "6 PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 81": "NH1" <-> "NH2" Residue "7 TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 164": "NH1" <-> "NH2" Residue "7 ARG 165": "NH1" <-> "NH2" Residue "7 ARG 166": "NH1" <-> "NH2" Residue "7 PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ARG 13": "NH1" <-> "NH2" Residue "8 ARG 65": "NH1" <-> "NH2" Residue "8 ASP 66": "OD1" <-> "OD2" 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 GLU 22": "OE1" <-> "OE2" 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 "C PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 111": "OE1" <-> "OE2" Residue "H PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 115": "NH1" <-> "NH2" Residue "M GLU 124": "OE1" <-> "OE2" Residue "M ARG 145": "NH1" <-> "NH2" Residue "M PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 225": "OE1" <-> "OE2" Residue "M ARG 232": "NH1" <-> "NH2" Residue "M ARG 239": "NH1" <-> "NH2" Residue "M PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 93": "OD1" <-> "OD2" Residue "P ASP 111": "OD1" <-> "OD2" Residue "P PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 127": "OD1" <-> "OD2" Residue "P GLU 136": "OE1" <-> "OE2" Residue "P GLU 142": "OE1" <-> "OE2" Residue "P PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 188": "OE1" <-> "OE2" 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 "Q ASP 54": "OD1" <-> "OD2" Residue "R PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 95": "OD1" <-> "OD2" Residue "R PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 143": "OD1" <-> "OD2" Residue "R ASP 153": "OD1" <-> "OD2" Residue "R GLU 186": "OE1" <-> "OE2" Residue "S ARG 46": "NH1" <-> "NH2" Residue "S ASP 83": "OD1" <-> "OD2" Residue "S ASP 91": "OD1" <-> "OD2" Residue "S ASP 108": "OD1" <-> "OD2" Residue "S ARG 147": "NH1" <-> "NH2" Residue "S ARG 152": "NH1" <-> "NH2" Residue "S ARG 157": "NH1" <-> "NH2" Residue "S TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 164": "OD1" <-> "OD2" Residue "S PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 181": "OE1" <-> "OE2" Residue "S TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 229": "OD1" <-> "OD2" Residue "S ASP 232": "OD1" <-> "OD2" Residue "S ASP 241": "OD1" <-> "OD2" Residue "S ARG 244": "NH1" <-> "NH2" Residue "S ASP 245": "OD1" <-> "OD2" Residue "S TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 306": "OE1" <-> "OE2" Residue "T ASP 41": "OD1" <-> "OD2" Residue "T ARG 49": "NH1" <-> "NH2" Residue "T ARG 86": "NH1" <-> "NH2" Residue "T ASP 142": "OD1" <-> "OD2" Residue "T ARG 162": "NH1" <-> "NH2" Residue "T ASP 172": "OD1" <-> "OD2" Residue "T ARG 195": "NH1" <-> "NH2" Residue "T ARG 199": "NH1" <-> "NH2" Residue "T PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 283": "NH1" <-> "NH2" Residue "T TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 325": "OD1" <-> "OD2" Residue "T PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 403": "OD1" <-> "OD2" Residue "T PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 429": "NH1" <-> "NH2" Residue "T PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 454": "NH1" <-> "NH2" Residue "T ASP 465": "OD1" <-> "OD2" Residue "T ASP 467": "OD1" <-> "OD2" Residue "T PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 555": "NH1" <-> "NH2" Residue "U ARG 49": "NH1" <-> "NH2" Residue "U TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 96": "NH1" <-> "NH2" Residue "U TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 112": "OD1" <-> "OD2" Residue "U TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 146": "NH1" <-> "NH2" Residue "U ARG 162": "NH1" <-> "NH2" Residue "U ARG 181": "NH1" <-> "NH2" Residue "U ARG 199": "NH1" <-> "NH2" Residue "U PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 221": "OE1" <-> "OE2" Residue "U ARG 227": "NH1" <-> "NH2" Residue "U 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 PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 449": "OE1" <-> "OE2" Residue "U ARG 454": "NH1" <-> "NH2" Residue "U PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 467": "OD1" <-> "OD2" Residue "U GLU 475": "OE1" <-> "OE2" Residue "U ARG 479": "NH1" <-> "NH2" Residue "U ARG 496": "NH1" <-> "NH2" Residue "U TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 513": "NH1" <-> "NH2" Residue "U PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 49": "NH1" <-> "NH2" Residue "V PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 112": "OD1" <-> "OD2" Residue "V PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 181": "NH1" <-> "NH2" Residue "V GLU 186": "OE1" <-> "OE2" Residue "V ARG 217": "NH1" <-> "NH2" Residue "V ARG 220": "NH1" <-> "NH2" Residue "V TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 266": "NH1" <-> "NH2" Residue "V PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 314": "NH1" <-> "NH2" Residue "V ARG 335": "NH1" <-> "NH2" Residue "V ARG 342": "NH1" <-> "NH2" Residue "V ARG 343": "NH1" <-> "NH2" Residue "V ARG 347": "NH1" <-> "NH2" Residue "V ARG 360": "NH1" <-> "NH2" Residue "V PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 403": "OD1" <-> "OD2" Residue "V GLU 409": "OE1" <-> "OE2" Residue "V PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 429": "NH1" <-> "NH2" Residue "V ARG 454": "NH1" <-> "NH2" Residue "V PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 467": "OD1" <-> "OD2" Residue "V ARG 476": "NH1" <-> "NH2" Residue "V PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 496": "NH1" <-> "NH2" Residue "V TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 510": "OD1" <-> "OD2" Residue "V ARG 513": "NH1" <-> "NH2" Residue "V ASP 516": "OD1" <-> "OD2" Residue "V GLU 553": "OE1" <-> "OE2" Residue "V ARG 555": "NH1" <-> "NH2" Residue "X TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 51": "NH1" <-> "NH2" Residue "X ASP 53": "OD1" <-> "OD2" Residue "X GLU 146": "OE1" <-> "OE2" Residue "X PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 215": "OE1" <-> "OE2" Residue "X ARG 218": "NH1" <-> "NH2" Residue "X GLU 219": "OE1" <-> "OE2" Residue "X ASP 222": "OD1" <-> "OD2" Residue "X ARG 225": "NH1" <-> "NH2" Residue "X ARG 239": "NH1" <-> "NH2" Residue "X TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 253": "OE1" <-> "OE2" Residue "X GLU 296": "OE1" <-> "OE2" Residue "X ASP 317": "OD1" <-> "OD2" Residue "X TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 378": "OD1" <-> "OD2" Residue "X ARG 385": "NH1" <-> "NH2" Residue "X TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 401": "NH1" <-> "NH2" Residue "X ASP 409": "OD1" <-> "OD2" Residue "X ASP 480": "OD1" <-> "OD2" Residue "X PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 494": "OE1" <-> "OE2" Residue "X ASP 505": "OD1" <-> "OD2" Residue "X ARG 509": "NH1" <-> "NH2" Residue "X ASP 523": "OD1" <-> "OD2" Residue "X GLU 533": "OE1" <-> "OE2" Residue "X GLU 541": "OE1" <-> "OE2" Residue "X GLU 547": "OE1" <-> "OE2" Residue "Y TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 53": "OD1" <-> "OD2" Residue "Y ARG 71": "NH1" <-> "NH2" Residue "Y ARG 86": "NH1" <-> "NH2" Residue "Y ARG 115": "NH1" <-> "NH2" Residue "Y ARG 120": "NH1" <-> "NH2" Residue "Y ARG 145": "NH1" <-> "NH2" Residue "Y PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 156": "OE1" <-> "OE2" Residue "Y ASP 168": "OD1" <-> "OD2" Residue "Y TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 215": "OE1" <-> "OE2" Residue "Y ASP 222": "OD1" <-> "OD2" Residue "Y ARG 258": "NH1" <-> "NH2" Residue "Y GLU 270": "OE1" <-> "OE2" Residue "Y ASP 279": "OD1" <-> "OD2" Residue "Y GLU 296": "OE1" <-> "OE2" Residue "Y TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 359": "OD1" <-> "OD2" Residue "Y ARG 366": "NH1" <-> "NH2" Residue "Y ASP 378": "OD1" <-> "OD2" Residue "Y ARG 385": "NH1" <-> "NH2" Residue "Y GLU 427": "OE1" <-> "OE2" Residue "Y ASP 429": "OD1" <-> "OD2" Residue "Y PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 491": "OD1" <-> "OD2" Residue "Y GLU 497": "OE1" <-> "OE2" Residue "Y ASP 500": "OD1" <-> "OD2" Residue "Y GLU 519": "OE1" <-> "OE2" Residue "Y ASP 528": "OD1" <-> "OD2" Residue "Y GLU 547": "OE1" <-> "OE2" Residue "Y PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 51": "NH1" <-> "NH2" Residue "Z ASP 53": "OD1" <-> "OD2" Residue "Z ARG 71": "NH1" <-> "NH2" Residue "Z ASP 82": "OD1" <-> "OD2" Residue "Z ARG 86": "NH1" <-> "NH2" Residue "Z ARG 98": "NH1" <-> "NH2" Residue "Z ARG 120": "NH1" <-> "NH2" Residue "Z GLU 127": "OE1" <-> "OE2" Residue "Z ASP 136": "OD1" <-> "OD2" Residue "Z PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 216": "NH1" <-> "NH2" Residue "Z GLU 226": "OE1" <-> "OE2" Residue "Z ARG 258": "NH1" <-> "NH2" Residue "Z GLU 270": "OE1" <-> "OE2" Residue "Z PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 289": "NH1" <-> "NH2" Residue "Z GLU 323": "OE1" <-> "OE2" Residue "Z PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 359": "OD1" <-> "OD2" Residue "Z GLU 370": "OE1" <-> "OE2" Residue "Z TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 381": "OD1" <-> "OD2" Residue "Z ARG 385": "NH1" <-> "NH2" Residue "Z ARG 401": "NH1" <-> "NH2" Residue "Z TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 415": "OD1" <-> "OD2" Residue "Z GLU 427": "OE1" <-> "OE2" Residue "Z ARG 435": "NH1" <-> "NH2" Residue "Z ARG 437": "NH1" <-> "NH2" Residue "Z PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 500": "OD1" <-> "OD2" Residue "Z ARG 509": "NH1" <-> "NH2" Residue "Z ASP 513": "OD1" <-> "OD2" Residue "Z GLU 520": "OE1" <-> "OE2" Residue "Z ASP 528": "OD1" <-> "OD2" Residue "Z ASP 548": "OD1" <-> "OD2" Residue "Z PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 53748 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: 4115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4115 Classifications: {'peptide': 542} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 517} Chain: "Y" Number of atoms: 3957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3957 Classifications: {'peptide': 521} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 498} Chain: "Z" Number of atoms: 4087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4087 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 513} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 21.67, per 1000 atoms: 0.40 Number of scatterers: 53748 At special positions: 0 Unit cell: (210.6, 132.678, 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 10171 8.00 N 9112 7.00 C 34297 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.34 Conformation dependent library (CDL) restraints added in 7.9 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 " 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13086 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 278 helices and 31 sheets defined 51.5% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.76 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 '1' and resid 46 through 72 Processing helix chain '1' and resid 104 through 141 removed outlier: 4.090A pdb=" N VAL 1 107 " --> pdb=" O ALA 1 104 " (cutoff:3.500A) Proline residue: 1 108 - end of helix removed outlier: 3.595A pdb=" N SER 1 116 " --> pdb=" O THR 1 113 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA 1 139 " --> pdb=" O GLU 1 136 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER 1 141 " --> pdb=" O GLU 1 138 " (cutoff:3.500A) Processing helix chain '1' and resid 164 through 177 removed outlier: 4.004A pdb=" N THR 1 169 " --> pdb=" O GLU 1 165 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA 1 177 " --> pdb=" O LYS 1 173 " (cutoff:3.500A) Processing helix chain '1' and resid 191 through 204 removed outlier: 3.783A pdb=" N ALA 1 196 " --> pdb=" O GLY 1 192 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL 1 204 " --> pdb=" O PHE 1 200 " (cutoff:3.500A) Processing helix chain '1' and resid 210 through 223 Processing helix chain '1' and resid 242 through 270 Processing helix chain '1' and resid 272 through 276 removed outlier: 3.607A pdb=" N ALA 1 275 " --> pdb=" O PRO 1 272 " (cutoff:3.500A) Processing helix chain '1' and resid 283 through 285 No H-bonds generated for 'chain '1' and resid 283 through 285' Processing helix chain '1' and resid 298 through 304 Processing helix chain '1' and resid 311 through 315 Processing helix chain '1' and resid 339 through 350 Processing helix chain '1' and resid 354 through 361 Processing helix chain '1' and resid 363 through 366 Processing helix chain '1' and resid 376 through 387 removed outlier: 3.799A pdb=" N VAL 1 382 " --> pdb=" O GLU 1 378 " (cutoff:3.500A) Processing helix chain '1' and resid 393 through 420 removed outlier: 3.696A pdb=" N GLU 1 415 " --> pdb=" O ALA 1 411 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N VAL 1 418 " --> pdb=" O GLU 1 414 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ILE 1 419 " --> pdb=" O GLU 1 415 " (cutoff:3.500A) Processing helix chain '1' and resid 426 through 431 Processing helix chain '1' and resid 436 through 459 removed outlier: 3.573A pdb=" N LYS 1 445 " --> pdb=" O PHE 1 441 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASN 1 446 " --> pdb=" O ASP 1 442 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N ALA 1 448 " --> pdb=" O LEU 1 444 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ALA 1 449 " --> pdb=" O LYS 1 445 " (cutoff:3.500A) Processing helix chain '1' and resid 464 through 477 Processing helix chain '1' and resid 480 through 482 No H-bonds generated for 'chain '1' and resid 480 through 482' Processing helix chain '1' and resid 486 through 489 No H-bonds generated for 'chain '1' and resid 486 through 489' Processing helix chain '1' and resid 491 through 515 removed outlier: 3.855A pdb=" N GLU 1 496 " --> pdb=" O GLN 1 492 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU 1 501 " --> pdb=" O LEU 1 497 " (cutoff:3.500A) removed outlier: 4.240A 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 578 through 587 Processing helix chain '1' and resid 589 through 591 No H-bonds generated for 'chain '1' and resid 589 through 591' Processing helix chain '1' and resid 593 through 605 Processing helix chain '1' and resid 611 through 613 No H-bonds generated for 'chain '1' and resid 611 through 613' Processing helix chain '2' and resid 8 through 19 Processing helix chain '2' and resid 26 through 38 Processing helix chain '2' and resid 45 through 57 Processing helix chain '2' and resid 63 through 76 Processing helix chain '2' and resid 81 through 93 removed outlier: 3.504A pdb=" N LEU 2 87 " --> pdb=" O THR 2 83 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA 2 88 " --> pdb=" O VAL 2 84 " (cutoff:3.500A) removed outlier: 4.872A 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: 3.690A 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 Processing helix chain '2' and resid 172 through 185 Processing helix chain '2' and resid 190 through 199 removed outlier: 4.044A pdb=" N ALA 2 195 " --> pdb=" O ALA 2 191 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER 2 199 " --> pdb=" O ALA 2 195 " (cutoff:3.500A) Processing helix chain '2' and resid 208 through 220 Processing helix chain '2' and resid 229 through 234 Processing helix chain '2' and resid 241 through 254 removed outlier: 4.238A pdb=" N GLU 2 246 " --> pdb=" O ALA 2 242 " (cutoff:3.500A) Processing helix chain '2' and resid 260 through 275 removed outlier: 3.780A pdb=" N VAL 2 268 " --> pdb=" O ALA 2 264 " (cutoff:3.500A) Proline residue: 2 271 - end of helix Processing helix chain '2' and resid 282 through 294 Processing helix chain '2' and resid 301 through 320 removed outlier: 3.641A pdb=" N SER 2 305 " --> pdb=" O ALA 2 301 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY 2 312 " --> pdb=" O ALA 2 308 " (cutoff:3.500A) Processing helix chain '2' and resid 326 through 338 Processing helix chain '2' and resid 346 through 355 Processing helix chain '2' and resid 397 through 409 removed outlier: 3.795A pdb=" N ALA 2 408 " --> pdb=" O LYS 2 404 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLN 2 409 " --> pdb=" O VAL 2 405 " (cutoff:3.500A) Processing helix chain '2' and resid 418 through 421 No H-bonds generated for 'chain '2' and resid 418 through 421' Processing helix chain '2' and resid 427 through 439 Processing helix chain '3' and resid 78 through 85 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 134 removed outlier: 4.330A pdb=" N LYS 3 123 " --> pdb=" O ASP 3 119 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS 3 129 " --> pdb=" O ALA 3 125 " (cutoff:3.500A) Proline residue: 3 130 - end of helix removed outlier: 5.273A pdb=" N ALA 3 133 " --> pdb=" O LYS 3 129 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ALA 3 134 " --> pdb=" O PRO 3 130 " (cutoff:3.500A) Processing helix chain '3' and resid 137 through 149 Processing helix chain '3' and resid 155 through 167 removed outlier: 3.991A pdb=" N GLY 3 160 " --> pdb=" O ASP 3 156 " (cutoff:3.500A) Processing helix chain '3' and resid 169 through 171 No H-bonds generated for 'chain '3' and resid 169 through 171' Processing helix chain '3' and resid 174 through 186 removed outlier: 4.071A 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: 4.153A pdb=" N THR 3 221 " --> pdb=" O ASP 3 217 " (cutoff:3.500A) Processing helix chain '3' and resid 234 through 243 removed outlier: 3.707A pdb=" N ARG 3 242 " --> pdb=" O ALA 3 238 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLY 3 243 " --> pdb=" O THR 3 239 " (cutoff:3.500A) Processing helix chain '3' and resid 246 through 250 Processing helix chain '3' and resid 254 through 271 removed outlier: 3.697A pdb=" N PHE 3 271 " --> pdb=" O ALA 3 267 " (cutoff:3.500A) Processing helix chain '3' and resid 276 through 286 removed outlier: 3.541A pdb=" N GLU 3 279 " --> pdb=" O GLU 3 276 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA 3 280 " --> pdb=" O SER 3 277 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE 3 282 " --> pdb=" O GLU 3 279 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY 3 283 " --> pdb=" O ALA 3 280 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU 3 286 " --> pdb=" O GLY 3 283 " (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 310 removed outlier: 3.649A 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 Processing helix chain '4' and resid 48 through 67 removed outlier: 4.239A pdb=" N GLN 4 61 " --> pdb=" O TYR 4 57 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL 4 62 " --> pdb=" O LEU 4 58 " (cutoff:3.500A) Proline residue: 4 65 - end of helix Processing helix chain '4' and resid 80 through 95 Processing helix chain '4' and resid 101 through 112 Processing helix chain '4' and resid 119 through 125 Processing helix chain '4' and resid 132 through 149 removed outlier: 3.728A pdb=" N ALA 4 137 " --> pdb=" O ASP 4 133 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL 4 141 " --> pdb=" O ALA 4 137 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU 4 148 " --> pdb=" O SER 4 144 " (cutoff:3.500A) Processing helix chain '4' and resid 160 through 176 removed outlier: 3.850A pdb=" N LYS 4 168 " --> pdb=" O LYS 4 164 " (cutoff:3.500A) removed outlier: 3.892A 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: 4.453A pdb=" N LYS 4 198 " --> pdb=" O ASP 4 194 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL 4 199 " --> pdb=" O ALA 4 195 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU 4 202 " --> pdb=" O LYS 4 198 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR 4 205 " --> pdb=" O LYS 4 201 " (cutoff:3.500A) Processing helix chain '4' and resid 238 through 258 removed outlier: 3.536A pdb=" N ALA 4 256 " --> pdb=" O LEU 4 252 " (cutoff:3.500A) Processing helix chain '4' and resid 263 through 283 Processing helix chain '5' and resid 8 through 29 Processing helix chain '5' and resid 31 through 58 removed outlier: 3.649A pdb=" N GLU 5 37 " --> pdb=" O THR 5 33 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N HIS 5 41 " --> pdb=" O GLU 5 37 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N LYS 5 49 " --> pdb=" O ALA 5 45 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ARG 5 50 " --> pdb=" O ALA 5 46 " (cutoff:3.500A) Processing helix chain '5' and resid 64 through 66 No H-bonds generated for 'chain '5' and resid 64 through 66' Processing helix chain '5' and resid 73 through 80 Processing helix chain '5' and resid 89 through 105 removed outlier: 3.986A pdb=" N LYS 5 101 " --> pdb=" O SER 5 97 " (cutoff:3.500A) Processing helix chain '6' and resid 31 through 40 Processing helix chain '6' and resid 51 through 57 Processing helix chain '6' and resid 73 through 93 Processing helix chain '6' and resid 99 through 119 removed outlier: 3.663A pdb=" N VAL 6 107 " --> pdb=" O LEU 6 103 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TRP 6 112 " --> pdb=" O LEU 6 108 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER 6 118 " --> pdb=" O ILE 6 114 " (cutoff:3.500A) Processing helix chain '6' and resid 122 through 129 Processing helix chain '7' and resid 63 through 66 No H-bonds generated for 'chain '7' and resid 63 through 66' Processing helix chain '7' and resid 69 through 71 No H-bonds generated for 'chain '7' and resid 69 through 71' Processing helix chain '7' and resid 84 through 103 removed outlier: 3.707A pdb=" N GLU 7 99 " --> pdb=" O SER 7 95 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU 7 103 " --> pdb=" O GLU 7 99 " (cutoff:3.500A) Processing helix chain '7' and resid 111 through 113 No H-bonds generated for 'chain '7' and resid 111 through 113' Processing helix chain '7' and resid 116 through 119 No H-bonds generated for 'chain '7' and resid 116 through 119' Processing helix chain '7' and resid 124 through 144 Processing helix chain '7' and resid 147 through 156 removed outlier: 3.584A pdb=" N LEU 7 150 " --> pdb=" O PHE 7 147 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N SER 7 151 " --> pdb=" O ASP 7 148 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER 7 155 " --> pdb=" O ALA 7 152 " (cutoff:3.500A) Processing helix chain '7' and resid 158 through 164 Processing helix chain '7' and resid 175 through 186 Processing helix chain '8' and resid 27 through 30 No H-bonds generated for 'chain '8' and resid 27 through 30' Processing helix chain '8' and resid 32 through 38 Processing helix chain '8' and resid 40 through 79 removed outlier: 3.642A pdb=" N TRP 8 45 " --> pdb=" O ILE 8 41 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N TYR 8 46 " --> pdb=" O PRO 8 42 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N LEU 8 47 " --> pdb=" O ARG 8 43 " (cutoff:3.500A) removed outlier: 4.043A 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 34 through 54 removed outlier: 3.542A pdb=" N ALA 9 38 " --> pdb=" O GLY 9 34 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL 9 42 " --> pdb=" O ALA 9 38 " (cutoff:3.500A) Processing helix chain '9' and resid 83 through 96 removed outlier: 4.126A pdb=" N LYS 9 95 " --> pdb=" O LYS 9 91 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER 9 96 " --> pdb=" O GLU 9 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 91 removed outlier: 4.640A pdb=" N MET A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ILE A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N ALA A 70 " --> pdb=" O CYS A 66 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N LEU A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ALA A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLY A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL A 74 " --> pdb=" O ALA A 70 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY A 75 " --> pdb=" O LEU A 71 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE A 86 " --> pdb=" O PHE A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 125 removed outlier: 3.633A pdb=" N ALA A 96 " --> pdb=" O PRO A 93 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N LYS A 97 " --> pdb=" O ASN A 94 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A 99 " --> pdb=" O ALA A 96 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL A 100 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA A 108 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLU A 111 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER A 112 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE A 113 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 118 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A 125 " --> pdb=" O PHE A 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 91 removed outlier: 3.727A pdb=" N MET B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N CYS B 66 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE B 69 " --> pdb=" O GLY B 65 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ALA B 70 " --> pdb=" O CYS B 66 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N LEU B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ALA B 72 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLY B 73 " --> pdb=" O ILE B 69 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL B 74 " --> pdb=" O ALA B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 125 removed outlier: 5.751A pdb=" N LYS B 97 " --> pdb=" O ASN B 94 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU B 99 " --> pdb=" O ALA B 96 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL B 100 " --> pdb=" O LYS B 97 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY B 106 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU B 111 " --> pdb=" O ALA B 108 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N SER B 112 " --> pdb=" O LEU B 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 91 removed outlier: 3.841A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE C 69 " --> pdb=" O GLY C 65 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ALA C 70 " --> pdb=" O CYS C 66 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N LEU C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ALA C 72 " --> pdb=" O THR C 68 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLY C 73 " --> pdb=" O ILE C 69 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 125 removed outlier: 3.502A pdb=" N ALA C 96 " --> pdb=" O PRO C 93 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N LYS C 97 " --> pdb=" O ASN C 94 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU C 99 " --> pdb=" O ALA C 96 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N VAL C 100 " --> pdb=" O LYS C 97 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY C 106 " --> pdb=" O ALA C 103 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER C 112 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE C 122 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU C 125 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 65 removed outlier: 4.205A pdb=" N MET D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 91 removed outlier: 3.508A pdb=" N PHE D 82 " --> pdb=" O GLY D 79 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU D 85 " --> pdb=" O PHE D 82 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY D 88 " --> pdb=" O LEU D 85 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG D 91 " --> pdb=" O GLY D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 125 removed outlier: 4.485A pdb=" N LYS D 97 " --> pdb=" O ASN D 94 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU D 99 " --> pdb=" O ALA D 96 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N VAL D 100 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER D 112 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ILE D 124 " --> pdb=" O VAL D 121 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU D 125 " --> pdb=" O PHE D 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 91 removed outlier: 3.533A pdb=" N CYS E 66 " --> pdb=" O VAL E 62 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE E 69 " --> pdb=" O GLY E 65 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ALA E 70 " --> pdb=" O CYS E 66 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N LEU E 71 " --> pdb=" O ALA E 67 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ALA E 72 " --> pdb=" O THR E 68 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLY E 73 " --> pdb=" O ILE E 69 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL E 74 " --> pdb=" O ALA E 70 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE E 86 " --> pdb=" O PHE E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 125 removed outlier: 3.609A pdb=" N LEU E 105 " --> pdb=" O GLY E 101 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER E 112 " --> pdb=" O ALA E 108 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ILE E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA E 114 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU E 125 " --> pdb=" O VAL E 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 91 removed outlier: 3.524A pdb=" N MET F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N CYS F 66 " --> pdb=" O VAL F 62 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ILE F 69 " --> pdb=" O GLY F 65 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ALA F 70 " --> pdb=" O CYS F 66 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N LEU F 71 " --> pdb=" O ALA F 67 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ALA F 72 " --> pdb=" O THR F 68 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLY F 73 " --> pdb=" O ILE F 69 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE F 86 " --> pdb=" O PHE F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 118 removed outlier: 5.174A pdb=" N LYS F 97 " --> pdb=" O ASN F 94 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL F 100 " --> pdb=" O LYS F 97 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR F 110 " --> pdb=" O PHE F 107 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER F 112 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE F 113 " --> pdb=" O THR F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 123 No H-bonds generated for 'chain 'F' and resid 120 through 123' Processing helix chain 'G' and resid 55 through 91 removed outlier: 4.111A pdb=" N MET G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE G 69 " --> pdb=" O GLY G 65 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ALA G 70 " --> pdb=" O CYS G 66 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N LEU G 71 " --> pdb=" O ALA G 67 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ALA G 72 " --> pdb=" O THR G 68 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLY G 73 " --> pdb=" O ILE G 69 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL G 80 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE G 86 " --> pdb=" O PHE G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 126 removed outlier: 5.334A pdb=" N LYS G 97 " --> pdb=" O ASN G 94 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU G 99 " --> pdb=" O ALA G 96 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY G 106 " --> pdb=" O ALA G 103 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER G 112 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE G 113 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE G 122 " --> pdb=" O LEU G 119 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ILE G 124 " --> pdb=" O VAL G 121 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU G 125 " --> pdb=" O PHE G 122 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE G 126 " --> pdb=" O LEU G 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 91 removed outlier: 3.819A pdb=" N THR H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ILE H 69 " --> pdb=" O GLY H 65 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N ALA H 70 " --> pdb=" O CYS H 66 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N LEU H 71 " --> pdb=" O ALA H 67 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ALA H 72 " --> pdb=" O THR H 68 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLY H 73 " --> pdb=" O ILE H 69 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL H 74 " --> pdb=" O ALA H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 126 removed outlier: 5.846A pdb=" N LYS H 97 " --> pdb=" O ASN H 94 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA H 108 " --> pdb=" O LEU H 105 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLU H 111 " --> pdb=" O ALA H 108 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N SER H 112 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU H 119 " --> pdb=" O PHE H 116 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N PHE H 126 " --> pdb=" O LEU H 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 66 Processing helix chain 'I' and resid 68 through 91 removed outlier: 3.557A pdb=" N PHE I 82 " --> pdb=" O GLY I 79 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU I 85 " --> pdb=" O PHE I 82 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY I 88 " --> pdb=" O LEU I 85 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 124 removed outlier: 3.612A pdb=" N ALA I 96 " --> pdb=" O PRO I 93 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LYS I 97 " --> pdb=" O ASN I 94 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU I 99 " --> pdb=" O ALA I 96 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL I 100 " --> pdb=" O LYS I 97 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU I 109 " --> pdb=" O GLY I 106 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU I 111 " --> pdb=" O ALA I 108 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER I 112 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU I 119 " --> pdb=" O PHE I 116 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL I 120 " --> pdb=" O SER I 117 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE I 124 " --> pdb=" O VAL I 121 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 89 removed outlier: 3.580A pdb=" N LYS J 60 " --> pdb=" O LEU J 56 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N MET J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL J 62 " --> pdb=" O ALA J 58 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE J 69 " --> pdb=" O GLY J 65 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ALA J 70 " --> pdb=" O CYS J 66 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N LEU J 71 " --> pdb=" O ALA J 67 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ALA J 72 " --> pdb=" O THR J 68 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLY J 73 " --> pdb=" O ILE J 69 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL J 74 " --> pdb=" O ALA J 70 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE J 86 " --> pdb=" O PHE J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 125 removed outlier: 3.541A pdb=" N ALA J 96 " --> pdb=" O PRO J 93 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N LYS J 97 " --> pdb=" O ASN J 94 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN J 98 " --> pdb=" O ILE J 95 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N GLU J 111 " --> pdb=" O ALA J 108 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N SER J 112 " --> pdb=" O LEU J 109 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU J 125 " --> pdb=" O PHE J 122 " (cutoff:3.500A) Processing helix chain 'M' and resid 105 through 118 Processing helix chain 'M' and resid 135 through 143 Processing helix chain 'M' and resid 148 through 167 removed outlier: 3.980A pdb=" N GLY M 166 " --> pdb=" O CYS M 162 " (cutoff:3.500A) removed outlier: 4.247A 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: 3.677A pdb=" N THR M 200 " --> pdb=" O GLY M 196 " (cutoff:3.500A) Processing helix chain 'M' and resid 221 through 229 Processing helix chain 'M' and resid 232 through 264 removed outlier: 3.796A pdb=" N GLY M 237 " --> pdb=" O ALA M 233 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY M 247 " --> pdb=" O ASN M 243 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N HIS M 248 " --> pdb=" O MET M 244 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA M 260 " --> pdb=" O GLY M 256 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEU M 261 " --> pdb=" O MET M 257 " (cutoff:3.500A) Proline residue: M 262 - end of helix Processing helix chain 'M' and resid 272 through 308 removed outlier: 3.874A pdb=" N VAL M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU M 280 " --> pdb=" O GLY M 276 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER M 296 " --> pdb=" O ALA M 292 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 61 Processing helix chain 'P' and resid 67 through 83 removed outlier: 3.708A pdb=" N GLN P 71 " --> pdb=" O LEU P 67 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP P 72 " --> pdb=" O ASP P 68 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU P 73 " --> pdb=" O LYS P 69 " (cutoff:3.500A) Processing helix chain 'P' and resid 85 through 92 removed outlier: 4.132A pdb=" N LEU P 90 " --> pdb=" O GLU P 86 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ALA P 91 " --> pdb=" O LEU P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 100 through 106 removed outlier: 4.025A pdb=" N ILE P 105 " --> pdb=" O ARG P 101 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER P 106 " --> pdb=" O THR P 102 " (cutoff:3.500A) Processing helix chain 'P' and resid 120 through 126 Processing helix chain 'P' and resid 130 through 148 removed outlier: 4.138A pdb=" N LEU P 135 " --> pdb=" O SER P 132 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N THR P 138 " --> pdb=" O LEU P 135 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL P 139 " --> pdb=" O GLU P 136 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN P 140 " --> pdb=" O VAL P 137 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU P 143 " --> pdb=" O ASN P 140 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LEU P 146 " --> pdb=" O GLU P 143 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA P 147 " --> pdb=" O LEU P 144 " (cutoff:3.500A) Processing helix chain 'P' and resid 166 through 176 removed outlier: 4.602A pdb=" N LYS P 176 " --> pdb=" O LYS P 172 " (cutoff:3.500A) Processing helix chain 'P' and resid 211 through 228 removed outlier: 4.302A pdb=" N LEU P 227 " --> pdb=" O ASN P 223 " (cutoff:3.500A) Processing helix chain 'Q' and resid 8 through 11 No H-bonds generated for 'chain 'Q' and resid 8 through 11' Processing helix chain 'Q' and resid 16 through 30 removed outlier: 3.769A pdb=" N VAL Q 30 " --> pdb=" O LEU Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 33 through 39 removed outlier: 3.579A pdb=" N ALA Q 37 " --> pdb=" O GLU Q 33 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N LYS Q 38 " --> pdb=" O PRO Q 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 30 through 39 removed outlier: 3.760A pdb=" N GLU R 35 " --> pdb=" O LYS R 31 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASN R 38 " --> pdb=" O THR R 34 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N LYS R 39 " --> pdb=" O GLU R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 154 No H-bonds generated for 'chain 'R' and resid 152 through 154' Processing helix chain 'R' and resid 159 through 167 Processing helix chain 'R' and resid 175 through 195 Processing helix chain 'S' and resid 42 through 78 removed outlier: 3.612A pdb=" N LYS S 69 " --> pdb=" O ALA S 65 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE S 73 " --> pdb=" O LYS S 69 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA S 74 " --> pdb=" O ASN S 70 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU S 76 " --> pdb=" O GLN S 72 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN S 77 " --> pdb=" O ILE S 73 " (cutoff:3.500A) Processing helix chain 'S' and resid 80 through 88 Proline residue: S 84 - end of helix Processing helix chain 'S' and resid 115 through 127 Processing helix chain 'S' and resid 144 through 147 No H-bonds generated for 'chain 'S' and resid 144 through 147' Processing helix chain 'S' and resid 150 through 153 No H-bonds generated for 'chain 'S' and resid 150 through 153' Processing helix chain 'S' and resid 172 through 184 Processing helix chain 'S' and resid 217 through 221 Processing helix chain 'S' and resid 239 through 312 removed outlier: 3.578A pdb=" N GLU S 248 " --> pdb=" O ARG S 244 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN S 263 " --> pdb=" O MET S 259 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER S 272 " --> pdb=" O ALA S 268 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU S 275 " --> pdb=" O MET S 271 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR S 278 " --> pdb=" O MET S 274 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE S 307 " --> pdb=" O GLU S 303 " (cutoff:3.500A) Processing helix chain 'T' and resid 59 through 75 Proline residue: T 68 - end of helix removed outlier: 3.577A 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 212 removed outlier: 3.552A pdb=" N LEU T 212 " --> pdb=" O ALA T 208 " (cutoff:3.500A) Processing helix chain 'T' and resid 231 through 246 removed outlier: 3.508A pdb=" N ALA T 235 " --> pdb=" O LYS T 231 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS T 243 " --> pdb=" O ILE T 239 " (cutoff:3.500A) Processing helix chain 'T' and resid 266 through 279 Processing helix chain 'T' and resid 281 through 284 Processing helix chain 'T' and resid 296 through 314 removed outlier: 3.726A pdb=" N LEU T 301 " --> pdb=" O PRO T 297 " (cutoff:3.500A) Proline residue: T 303 - end of helix removed outlier: 3.688A pdb=" N TYR T 312 " --> pdb=" O ALA T 308 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N PHE T 313 " --> pdb=" O MET T 309 " (cutoff:3.500A) Processing helix chain 'T' and resid 327 through 340 Processing helix chain 'T' and resid 352 through 364 removed outlier: 4.158A pdb=" N PHE T 355 " --> pdb=" O GLY T 352 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N SER T 359 " --> pdb=" O TYR T 356 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ARG T 360 " --> pdb=" O LEU T 357 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU T 362 " --> pdb=" O SER T 359 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLU T 363 " --> pdb=" O ARG T 360 " (cutoff:3.500A) Processing helix chain 'T' and resid 393 through 401 removed outlier: 3.688A pdb=" N SER T 400 " --> pdb=" O THR T 396 " (cutoff:3.500A) Processing helix chain 'T' and resid 410 through 414 Processing helix chain 'T' and resid 431 through 434 removed outlier: 3.931A pdb=" N ALA T 434 " --> pdb=" O GLY T 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 431 through 434' Processing helix chain 'T' and resid 437 through 440 No H-bonds generated for 'chain 'T' and resid 437 through 440' Processing helix chain 'T' and resid 446 through 459 removed outlier: 3.620A pdb=" N ALA T 451 " --> pdb=" O LYS T 447 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU T 455 " --> pdb=" O ALA T 451 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA T 458 " --> pdb=" O ARG T 454 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE T 459 " --> pdb=" O GLU T 455 " (cutoff:3.500A) Processing helix chain 'T' and resid 470 through 483 removed outlier: 3.692A pdb=" N ALA T 478 " --> pdb=" O LEU T 474 " (cutoff:3.500A) Processing helix chain 'T' and resid 495 through 505 removed outlier: 3.524A pdb=" N ALA T 504 " --> pdb=" O ALA T 500 " (cutoff:3.500A) Processing helix chain 'T' and resid 514 through 527 removed outlier: 4.001A pdb=" N ILE T 517 " --> pdb=" O VAL T 514 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N VAL T 518 " --> pdb=" O GLN T 515 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU T 521 " --> pdb=" O VAL T 518 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLU T 522 " --> pdb=" O ALA T 519 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL T 524 " --> pdb=" O GLU T 521 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLN T 527 " --> pdb=" O VAL T 524 " (cutoff:3.500A) Processing helix chain 'T' and resid 531 through 539 Processing helix chain 'T' and resid 544 through 553 removed outlier: 4.249A pdb=" N HIS T 549 " --> pdb=" O ALA T 545 " (cutoff:3.500A) Processing helix chain 'U' and resid 43 through 48 removed outlier: 4.914A pdb=" N LEU U 48 " --> pdb=" O ALA U 44 " (cutoff:3.500A) Processing helix chain 'U' and resid 59 through 62 No H-bonds generated for 'chain 'U' and resid 59 through 62' Processing helix chain 'U' and resid 66 through 72 Processing helix chain 'U' and resid 135 through 137 No H-bonds generated for 'chain 'U' and resid 135 through 137' Processing helix chain 'U' and resid 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 248 removed outlier: 3.819A pdb=" N ALA U 235 " --> pdb=" O LYS U 231 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU U 247 " --> pdb=" O LYS U 243 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N GLN U 248 " --> pdb=" O ASN U 244 " (cutoff:3.500A) Processing helix chain 'U' and resid 266 through 278 Processing helix chain 'U' and resid 281 through 283 No H-bonds generated for 'chain 'U' and resid 281 through 283' Processing helix chain 'U' and resid 296 through 315 Proline residue: U 303 - end of helix removed outlier: 3.639A pdb=" N TYR U 312 " --> pdb=" O ALA U 308 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) Processing helix chain 'U' and resid 327 through 340 removed outlier: 3.761A pdb=" N VAL U 332 " --> pdb=" O SER U 328 " (cutoff:3.500A) Processing helix chain 'U' and resid 354 through 364 removed outlier: 3.666A pdb=" N HIS U 358 " --> pdb=" O VAL U 354 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU U 361 " --> pdb=" O LEU U 357 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ARG U 364 " --> pdb=" O ARG U 360 " (cutoff:3.500A) Processing helix chain 'U' and resid 393 through 399 Processing helix chain 'U' and resid 410 through 414 Processing helix chain 'U' and resid 437 through 458 removed outlier: 3.630A pdb=" N VAL U 442 " --> pdb=" O GLY U 438 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY U 444 " --> pdb=" O LYS U 440 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N THR U 445 " --> pdb=" O GLN U 441 " (cutoff:3.500A) Processing helix chain 'U' and resid 470 through 484 removed outlier: 3.614A pdb=" N ALA U 478 " --> pdb=" O LEU U 474 " (cutoff:3.500A) Processing helix chain 'U' and resid 494 through 505 removed outlier: 3.523A pdb=" N ALA U 500 " --> pdb=" O ARG U 496 " (cutoff:3.500A) Processing helix chain 'U' and resid 517 through 527 Processing helix chain 'U' and resid 531 through 539 Processing helix chain 'U' and resid 544 through 555 removed outlier: 3.970A pdb=" N HIS U 549 " --> pdb=" O ALA U 545 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG U 555 " --> pdb=" O LYS U 551 " (cutoff:3.500A) Processing helix chain 'V' and resid 59 through 66 removed outlier: 3.553A pdb=" N GLN V 64 " --> pdb=" O GLN V 60 " (cutoff:3.500A) Processing helix chain 'V' and resid 135 through 137 No H-bonds generated for 'chain 'V' and resid 135 through 137' Processing helix chain 'V' and resid 157 through 159 No H-bonds generated for 'chain 'V' and resid 157 through 159' Processing helix chain 'V' and resid 207 through 211 Processing helix chain 'V' and resid 231 through 246 Processing helix chain 'V' and resid 266 through 279 Processing helix chain 'V' and resid 281 through 283 No H-bonds generated for 'chain 'V' and resid 281 through 283' Processing helix chain 'V' and resid 296 through 315 Proline residue: V 303 - end of helix removed outlier: 3.724A pdb=" N TYR V 312 " --> pdb=" O ALA V 308 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N PHE V 313 " --> pdb=" O MET V 309 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG V 314 " --> pdb=" O ALA V 310 " (cutoff:3.500A) Processing helix chain 'V' and resid 327 through 340 Processing helix chain 'V' and resid 352 through 364 removed outlier: 4.419A pdb=" N PHE V 355 " --> pdb=" O GLY V 352 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER V 359 " --> pdb=" O TYR V 356 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG V 360 " --> pdb=" O LEU V 357 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLU V 363 " --> pdb=" O ARG V 360 " (cutoff:3.500A) Processing helix chain 'V' and resid 370 through 372 No H-bonds generated for 'chain 'V' and resid 370 through 372' Processing helix chain 'V' and resid 393 through 401 Processing helix chain 'V' and resid 410 through 414 Processing helix chain 'V' and resid 431 through 434 removed outlier: 3.588A pdb=" N ALA V 434 " --> pdb=" O GLY V 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 431 through 434' Processing helix chain 'V' and resid 440 through 455 removed outlier: 3.880A pdb=" N GLY V 444 " --> pdb=" O LYS V 440 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N THR V 445 " --> pdb=" O GLN V 441 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU V 448 " --> pdb=" O GLY V 444 " (cutoff:3.500A) Processing helix chain 'V' and resid 470 through 481 Processing helix chain 'V' and resid 494 through 506 Processing helix chain 'V' and resid 514 through 516 No H-bonds generated for 'chain 'V' and resid 514 through 516' Processing helix chain 'V' and resid 522 through 525 No H-bonds generated for 'chain 'V' and resid 522 through 525' Processing helix chain 'V' and resid 532 through 539 Processing helix chain 'V' and resid 544 through 553 removed outlier: 4.317A pdb=" N LYS V 551 " --> pdb=" O ASP V 547 " (cutoff:3.500A) Processing helix chain 'X' and resid 115 through 117 No H-bonds generated for 'chain 'X' and resid 115 through 117' Processing helix chain 'X' and resid 165 through 170 Processing helix chain 'X' and resid 189 through 200 Processing helix chain 'X' and resid 217 through 228 Processing helix chain 'X' and resid 236 through 241 removed outlier: 4.835A pdb=" N GLY X 240 " --> pdb=" O ALA X 237 " (cutoff:3.500A) Processing helix chain 'X' and resid 255 through 258 No H-bonds generated for 'chain 'X' and resid 255 through 258' Processing helix chain 'X' and resid 261 through 274 removed outlier: 3.602A pdb=" N PHE X 272 " --> pdb=" O VAL X 268 " (cutoff:3.500A) Processing helix chain 'X' and resid 288 through 298 Processing helix chain 'X' and resid 314 through 322 Processing helix chain 'X' and resid 349 through 357 removed outlier: 4.677A pdb=" N ALA X 356 " --> pdb=" O ALA X 352 " (cutoff:3.500A) removed outlier: 4.494A 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 394 through 420 removed outlier: 4.691A pdb=" N ASP X 415 " --> pdb=" O LYS X 411 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ILE X 416 " --> pdb=" O ASN X 412 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE X 419 " --> pdb=" O ASP X 415 " (cutoff:3.500A) Processing helix chain 'X' and resid 422 through 424 No H-bonds generated for 'chain 'X' and resid 422 through 424' Processing helix chain 'X' and resid 427 through 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 Processing helix chain 'X' and resid 492 through 505 removed outlier: 3.921A pdb=" N LYS X 496 " --> pdb=" O ILE X 492 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP X 505 " --> pdb=" O LYS X 501 " (cutoff:3.500A) Processing helix chain 'X' and resid 527 through 533 removed outlier: 3.573A pdb=" N SER X 532 " --> pdb=" O ASP X 528 " (cutoff:3.500A) removed outlier: 3.801A 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 170 Processing helix chain 'Y' and resid 189 through 200 Processing helix chain 'Y' and resid 217 through 229 Processing helix chain 'Y' and resid 236 through 241 removed outlier: 4.510A pdb=" N GLY Y 240 " --> pdb=" O ALA Y 237 " (cutoff:3.500A) Processing helix chain 'Y' and resid 255 through 258 No H-bonds generated for 'chain 'Y' and resid 255 through 258' Processing helix chain 'Y' and resid 261 through 274 Processing helix chain 'Y' and resid 288 through 295 Processing helix chain 'Y' and resid 314 through 324 removed outlier: 4.443A pdb=" N ARG Y 324 " --> pdb=" O GLY Y 320 " (cutoff:3.500A) Processing helix chain 'Y' and resid 349 through 357 removed outlier: 4.536A pdb=" N ALA Y 356 " --> pdb=" O ALA Y 352 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N HIS Y 357 " --> pdb=" O THR Y 353 " (cutoff:3.500A) Processing helix chain 'Y' and resid 366 through 370 Processing helix chain 'Y' and resid 389 through 392 No H-bonds generated for 'chain 'Y' and resid 389 through 392' Processing helix chain 'Y' and resid 394 through 420 removed outlier: 4.134A pdb=" N ASP Y 415 " --> pdb=" O LYS Y 411 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE Y 416 " --> pdb=" O ASN Y 412 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE Y 419 " --> pdb=" O ASP Y 415 " (cutoff:3.500A) Processing helix chain 'Y' and resid 429 through 443 Processing helix chain 'Y' and resid 463 through 475 Processing helix chain 'Y' and resid 483 through 485 No H-bonds generated for 'chain 'Y' and resid 483 through 485' Processing helix chain 'Y' and resid 492 through 506 removed outlier: 3.593A pdb=" N ASP Y 500 " --> pdb=" O LYS Y 496 " (cutoff:3.500A) Processing helix chain 'Y' and resid 527 through 533 Processing helix chain 'Y' and resid 545 through 554 Processing helix chain 'Z' and resid 115 through 117 No H-bonds generated for 'chain 'Z' and resid 115 through 117' Processing helix chain 'Z' and resid 165 through 169 Processing helix chain 'Z' and resid 189 through 203 Processing helix chain 'Z' and resid 217 through 228 Processing helix chain 'Z' and resid 236 through 241 removed outlier: 4.594A pdb=" N GLY Z 240 " --> pdb=" O ALA Z 237 " (cutoff:3.500A) Processing helix chain 'Z' and resid 255 through 258 No H-bonds generated for 'chain 'Z' and resid 255 through 258' Processing helix chain 'Z' and resid 261 through 274 removed outlier: 3.715A pdb=" N PHE Z 272 " --> pdb=" O VAL Z 268 " (cutoff:3.500A) Processing helix chain 'Z' and resid 287 through 300 Processing helix chain 'Z' and resid 314 through 322 removed outlier: 3.827A pdb=" N LEU Z 321 " --> pdb=" O ASP Z 317 " (cutoff:3.500A) Processing helix chain 'Z' and resid 349 through 354 Processing helix chain 'Z' and resid 366 through 369 No H-bonds generated for 'chain 'Z' and resid 366 through 369' Processing helix chain 'Z' and resid 393 through 410 Processing helix chain 'Z' and resid 414 through 420 removed outlier: 4.610A pdb=" N ILE Z 419 " --> pdb=" O ASP Z 415 " (cutoff:3.500A) Processing helix chain 'Z' and resid 427 through 442 removed outlier: 3.611A pdb=" N LEU Z 431 " --> pdb=" O GLU Z 427 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS Z 438 " --> pdb=" O ALA Z 434 " (cutoff:3.500A) Processing helix chain 'Z' and resid 448 through 454 removed outlier: 3.700A pdb=" N GLU Z 451 " --> pdb=" O GLN Z 448 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N VAL Z 452 " --> pdb=" O VAL Z 449 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N THR Z 454 " --> pdb=" O GLU Z 451 " (cutoff:3.500A) Processing helix chain 'Z' and resid 463 through 475 Processing helix chain 'Z' and resid 492 through 508 removed outlier: 4.150A pdb=" N LYS Z 496 " --> pdb=" O ILE Z 492 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N GLU Z 497 " --> pdb=" O LYS Z 493 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ILE Z 506 " --> pdb=" O MET Z 502 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ALA Z 507 " --> pdb=" O ALA Z 503 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER Z 508 " --> pdb=" O LYS Z 504 " (cutoff:3.500A) Processing helix chain 'Z' and resid 527 through 533 removed outlier: 3.762A pdb=" N SER Z 532 " --> pdb=" O ASP Z 528 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU Z 533 " --> pdb=" O LYS Z 529 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain '2' and resid 369 through 372 Processing sheet with id= B, first strand: chain '2' and resid 379 through 382 removed outlier: 6.511A pdb=" N ALA 2 414 " --> pdb=" O GLN 2 380 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N VAL 2 382 " --> pdb=" O ALA 2 414 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VAL 2 416 " --> pdb=" O VAL 2 382 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain '7' and resid 36 through 41 removed outlier: 3.703A pdb=" N ASN 7 38 " --> pdb=" O THR 7 49 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA 7 52 " --> pdb=" O ALA 7 55 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA 7 55 " --> pdb=" O ALA 7 52 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'P' and resid 151 through 153 removed outlier: 6.485A pdb=" N LYS P 183 " --> pdb=" O VAL P 152 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'P' and resid 156 through 158 Processing sheet with id= F, first strand: chain 'Q' and resid 45 through 49 Processing sheet with id= G, first strand: chain 'R' and resid 72 through 75 removed outlier: 6.568A pdb=" N THR R 142 " --> pdb=" O ASN R 73 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N TYR R 75 " --> pdb=" O THR R 142 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE R 144 " --> pdb=" O TYR R 75 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'R' and resid 97 through 100 removed outlier: 3.957A pdb=" N THR R 88 " --> pdb=" O HIS R 119 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL R 115 " --> pdb=" O PRO R 92 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU R 125 " --> pdb=" O LEU R 118 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'S' and resid 203 through 211 removed outlier: 5.130A pdb=" N ASN S 195 " --> pdb=" O VAL S 105 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ASP S 136 " --> pdb=" O SER S 100 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N VAL S 102 " --> pdb=" O ASP S 136 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N VAL S 138 " --> pdb=" O VAL S 102 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ALA S 104 " --> pdb=" O VAL S 138 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL S 140 " --> pdb=" O ALA S 104 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N SER S 141 " --> pdb=" O GLN S 159 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ALA S 161 " --> pdb=" O SER S 141 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'T' and resid 84 through 86 removed outlier: 4.290A pdb=" N LYS T 116 " --> pdb=" O PHE T 132 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLY T 128 " --> pdb=" O LEU T 120 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N LEU T 122 " --> pdb=" O HIS T 126 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N HIS T 126 " --> pdb=" O LEU T 122 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N TYR T 98 " --> pdb=" O VAL T 87 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N VAL T 87 " --> pdb=" O TYR T 98 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'T' and resid 152 through 155 Processing sheet with id= L, first strand: chain 'T' and resid 404 through 408 removed outlier: 3.705A pdb=" N LEU T 222 " --> pdb=" O GLY T 404 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'T' and resid 285 through 290 removed outlier: 8.809A pdb=" N ILE T 286 " --> pdb=" O VAL T 255 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N CYS T 257 " --> pdb=" O ILE T 286 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N VAL T 288 " --> pdb=" O CYS T 257 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N TYR T 259 " --> pdb=" O VAL T 288 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ALA T 290 " --> pdb=" O TYR T 259 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA T 261 " --> pdb=" O ALA T 290 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N HIS T 319 " --> pdb=" O TYR T 256 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N VAL T 258 " --> pdb=" O HIS T 319 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU T 321 " --> pdb=" O VAL T 258 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N VAL T 260 " --> pdb=" O LEU T 321 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ILE T 323 " --> pdb=" O VAL T 260 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VAL T 262 " --> pdb=" O ILE T 323 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ASP T 325 " --> pdb=" O VAL T 262 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N SER T 376 " --> pdb=" O GLY T 320 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ILE T 322 " --> pdb=" O SER T 376 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N THR T 378 " --> pdb=" O ILE T 322 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N TYR T 324 " --> pdb=" O THR T 378 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N PHE T 380 " --> pdb=" O TYR T 324 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'U' and resid 85 through 91 removed outlier: 6.786A pdb=" N ARG U 96 " --> pdb=" O LEU U 88 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N VAL U 90 " --> pdb=" O ILE U 94 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE U 94 " --> pdb=" O VAL U 90 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL U 130 " --> pdb=" O ALA U 119 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ALA U 119 " --> pdb=" O VAL U 130 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N PHE U 132 " --> pdb=" O GLY U 117 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N GLY U 117 " --> pdb=" O PHE U 132 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'U' and resid 152 through 155 Processing sheet with id= P, first strand: chain 'U' and resid 404 through 408 Processing sheet with id= Q, first strand: chain 'U' and resid 285 through 290 removed outlier: 8.811A pdb=" N ILE U 286 " --> pdb=" O VAL U 255 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N CYS U 257 " --> pdb=" O ILE U 286 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N VAL U 288 " --> pdb=" O CYS U 257 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N TYR U 259 " --> pdb=" O VAL U 288 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ALA U 290 " --> pdb=" O TYR U 259 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ALA U 261 " --> pdb=" O ALA U 290 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N HIS U 319 " --> pdb=" O TYR U 256 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N VAL U 258 " --> pdb=" O HIS U 319 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU U 321 " --> pdb=" O VAL U 258 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N VAL U 260 " --> pdb=" O LEU U 321 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE U 323 " --> pdb=" O VAL U 260 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL U 262 " --> pdb=" O ILE U 323 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ASP U 325 " --> pdb=" O VAL U 262 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N SER U 376 " --> pdb=" O GLY U 320 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ILE U 322 " --> pdb=" O SER U 376 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N THR U 378 " --> pdb=" O ILE U 322 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N TYR U 324 " --> pdb=" O THR U 378 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N PHE U 380 " --> pdb=" O TYR U 324 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'V' and resid 85 through 89 removed outlier: 6.544A pdb=" N ARG V 96 " --> pdb=" O LEU V 88 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL V 130 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N ALA V 119 " --> pdb=" O VAL V 130 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU V 107 " --> pdb=" O ALA V 119 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'V' and resid 152 through 155 Processing sheet with id= T, first strand: chain 'V' and resid 404 through 408 Processing sheet with id= U, first strand: chain 'V' and resid 285 through 290 removed outlier: 8.819A pdb=" N ILE V 286 " --> pdb=" O VAL V 255 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N CYS V 257 " --> pdb=" O ILE V 286 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N VAL V 288 " --> pdb=" O CYS V 257 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N TYR V 259 " --> pdb=" O VAL V 288 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ALA V 290 " --> pdb=" O TYR V 259 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ALA V 261 " --> pdb=" O ALA V 290 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N HIS V 319 " --> pdb=" O TYR V 256 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N VAL V 258 " --> pdb=" O HIS V 319 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU V 321 " --> pdb=" O VAL V 258 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N VAL V 260 " --> pdb=" O LEU V 321 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE V 323 " --> pdb=" O VAL V 260 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL V 262 " --> pdb=" O ILE V 323 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ASP V 325 " --> pdb=" O VAL V 262 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N SER V 376 " --> pdb=" O GLY V 320 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ILE V 322 " --> pdb=" O SER V 376 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N THR V 378 " --> pdb=" O ILE V 322 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N TYR V 324 " --> pdb=" O THR V 378 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N PHE V 380 " --> pdb=" O TYR V 324 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'X' and resid 37 through 39 removed outlier: 4.756A pdb=" N LEU X 72 " --> pdb=" O VAL X 65 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ARG X 86 " --> pdb=" O ALA X 77 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N HIS X 79 " --> pdb=" O THR X 84 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N THR X 84 " --> pdb=" O HIS X 79 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ARG X 51 " --> pdb=" O VAL X 40 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N VAL X 40 " --> pdb=" O ARG X 51 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'X' and resid 110 through 113 removed outlier: 3.516A pdb=" N ASP X 139 " --> pdb=" O VAL X 113 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'X' and resid 360 through 363 removed outlier: 7.463A pdb=" N ILE X 179 " --> pdb=" O ILE X 333 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N SER X 335 " --> pdb=" O ILE X 179 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N LEU X 181 " --> pdb=" O SER X 335 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N GLN X 337 " --> pdb=" O LEU X 181 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N GLY X 183 " --> pdb=" O GLN X 337 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL X 339 " --> pdb=" O GLY X 183 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N PHE X 207 " --> pdb=" O LEU X 281 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N PHE X 283 " --> pdb=" O PHE X 207 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL X 209 " --> pdb=" O PHE X 283 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N ASP X 285 " --> pdb=" O VAL X 209 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ALA X 211 " --> pdb=" O ASP X 285 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'X' and resid 559 through 561 Processing sheet with id= Z, first strand: chain 'Y' and resid 38 through 44 removed outlier: 6.449A pdb=" N ASP Y 49 " --> pdb=" O SER Y 41 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N VAL Y 43 " --> pdb=" O VAL Y 47 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL Y 47 " --> pdb=" O VAL Y 43 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE Y 88 " --> pdb=" O VAL Y 76 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N VAL Y 76 " --> pdb=" O ILE Y 88 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N LEU Y 72 " --> pdb=" O VAL Y 65 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'Y' and resid 360 through 362 removed outlier: 7.428A pdb=" N ILE Y 179 " --> pdb=" O ILE Y 333 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N SER Y 335 " --> pdb=" O ILE Y 179 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N LEU Y 181 " --> pdb=" O SER Y 335 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N GLN Y 337 " --> pdb=" O LEU Y 181 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL Y 280 " --> pdb=" O THR Y 334 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N VAL Y 336 " --> pdb=" O VAL Y 280 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU Y 282 " --> pdb=" O VAL Y 336 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ALA Y 338 " --> pdb=" O LEU Y 282 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL Y 284 " --> pdb=" O ALA Y 338 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N PHE Y 207 " --> pdb=" O LEU Y 281 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N PHE Y 283 " --> pdb=" O PHE Y 207 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL Y 209 " --> pdb=" O PHE Y 283 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N ASP Y 285 " --> pdb=" O VAL Y 209 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ALA Y 211 " --> pdb=" O ASP Y 285 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'Z' and resid 38 through 44 removed outlier: 6.300A pdb=" N ASP Z 49 " --> pdb=" O SER Z 41 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL Z 43 " --> pdb=" O VAL Z 47 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL Z 47 " --> pdb=" O VAL Z 43 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE Z 88 " --> pdb=" O VAL Z 76 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N VAL Z 76 " --> pdb=" O ILE Z 88 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'Z' and resid 110 through 113 Processing sheet with id= AD, first strand: chain 'Z' and resid 360 through 362 removed outlier: 8.537A pdb=" N ILE Z 179 " --> pdb=" O ILE Z 333 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N SER Z 335 " --> pdb=" O ILE Z 179 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N LEU Z 181 " --> pdb=" O SER Z 335 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLN Z 337 " --> pdb=" O LEU Z 181 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL Z 284 " --> pdb=" O VAL Z 336 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL Z 213 " --> pdb=" O ASP Z 285 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'Z' and resid 559 through 561 2431 hydrogen bonds defined for protein. 6330 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: 18.32 Time building geometry restraints manager: 18.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 14002 1.33 - 1.45: 10098 1.45 - 1.57: 30311 1.57 - 1.69: 21 1.69 - 1.82: 254 Bond restraints: 54686 Sorted by residual: bond pdb=" C4 ATP U1001 " pdb=" C5 ATP U1001 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.18e+01 bond pdb=" C4 ATP T1001 " pdb=" C5 ATP T1001 " ideal model delta sigma weight residual 1.388 1.458 -0.070 1.00e-02 1.00e+04 4.94e+01 bond pdb=" C4 ATP V1001 " pdb=" C5 ATP V1001 " ideal model delta sigma weight residual 1.388 1.457 -0.069 1.00e-02 1.00e+04 4.77e+01 bond pdb=" C ILE V 67 " pdb=" N PRO V 68 " ideal model delta sigma weight residual 1.331 1.382 -0.051 7.90e-03 1.60e+04 4.11e+01 bond pdb=" C5 ATP U1001 " pdb=" C6 ATP U1001 " ideal model delta sigma weight residual 1.409 1.468 -0.059 1.00e-02 1.00e+04 3.45e+01 ... (remaining 54681 not shown) Histogram of bond angle deviations from ideal: 95.83 - 103.89: 759 103.89 - 111.95: 26062 111.95 - 120.01: 24384 120.01 - 128.07: 22619 128.07 - 136.13: 337 Bond angle restraints: 74161 Sorted by residual: angle pdb=" PB ATP U1001 " pdb=" O3B ATP U1001 " pdb=" PG ATP U1001 " ideal model delta sigma weight residual 139.87 119.51 20.36 1.00e+00 1.00e+00 4.14e+02 angle pdb=" PB ATP V1001 " pdb=" O3B ATP V1001 " pdb=" PG ATP V1001 " ideal model delta sigma weight residual 139.87 121.58 18.29 1.00e+00 1.00e+00 3.34e+02 angle pdb=" PB ATP T1001 " pdb=" O3B ATP T1001 " pdb=" PG ATP T1001 " ideal model delta sigma weight residual 139.87 123.32 16.55 1.00e+00 1.00e+00 2.74e+02 angle pdb=" PA ATP U1001 " pdb=" O3A ATP U1001 " pdb=" PB ATP U1001 " ideal model delta sigma weight residual 136.83 123.53 13.30 1.00e+00 1.00e+00 1.77e+02 angle pdb=" PA ATP V1001 " pdb=" O3A ATP V1001 " pdb=" PB ATP V1001 " ideal model delta sigma weight residual 136.83 125.38 11.45 1.00e+00 1.00e+00 1.31e+02 ... (remaining 74156 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.73: 32302 33.73 - 67.45: 679 67.45 - 101.18: 41 101.18 - 134.90: 1 134.90 - 168.63: 2 Dihedral angle restraints: 33025 sinusoidal: 12667 harmonic: 20358 Sorted by residual: dihedral pdb=" CA ALA X 307 " pdb=" C ALA X 307 " pdb=" N VAL X 308 " pdb=" CA VAL X 308 " ideal model delta harmonic sigma weight residual -180.00 -120.79 -59.21 0 5.00e+00 4.00e-02 1.40e+02 dihedral pdb=" CA ALA Y 307 " pdb=" C ALA Y 307 " pdb=" N VAL Y 308 " pdb=" CA VAL Y 308 " ideal model delta harmonic sigma weight residual -180.00 -124.14 -55.86 0 5.00e+00 4.00e-02 1.25e+02 dihedral pdb=" CA GLU V 348 " pdb=" C GLU V 348 " pdb=" N ALA V 349 " pdb=" CA ALA V 349 " ideal model delta harmonic sigma weight residual 180.00 124.84 55.16 0 5.00e+00 4.00e-02 1.22e+02 ... (remaining 33022 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 6755 0.071 - 0.141: 1694 0.141 - 0.212: 205 0.212 - 0.282: 29 0.282 - 0.353: 6 Chirality restraints: 8689 Sorted by residual: chirality pdb=" CB VAL Z 113 " pdb=" CA VAL Z 113 " pdb=" CG1 VAL Z 113 " pdb=" CG2 VAL Z 113 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" CB VAL U 180 " pdb=" CA VAL U 180 " pdb=" CG1 VAL U 180 " pdb=" CG2 VAL U 180 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CA PRO U 201 " pdb=" N PRO U 201 " pdb=" C PRO U 201 " pdb=" CB PRO U 201 " both_signs ideal model delta sigma weight residual False 2.72 2.39 0.33 2.00e-01 2.50e+01 2.71e+00 ... (remaining 8686 not shown) Planarity restraints: 9510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA Z 503 " 0.031 2.00e-02 2.50e+03 6.03e-02 3.64e+01 pdb=" C ALA Z 503 " -0.104 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=" CA MET Y 502 " 0.027 2.00e-02 2.50e+03 5.34e-02 2.85e+01 pdb=" C MET Y 502 " -0.092 2.00e-02 2.50e+03 pdb=" O MET Y 502 " 0.034 2.00e-02 2.50e+03 pdb=" N ALA Y 503 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA U 296 " 0.062 5.00e-02 4.00e+02 9.32e-02 1.39e+01 pdb=" N PRO U 297 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO U 297 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO U 297 " 0.052 5.00e-02 4.00e+02 ... (remaining 9507 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 542 2.60 - 3.17: 44671 3.17 - 3.75: 86400 3.75 - 4.32: 125648 4.32 - 4.90: 203814 Nonbonded interactions: 461075 Sorted by model distance: nonbonded pdb=" O2B ATP T1001 " pdb="MG MG T1002 " model vdw 2.025 2.170 nonbonded pdb=" OG1 THR V 232 " pdb="MG MG V1002 " model vdw 2.025 2.170 nonbonded pdb=" OE1 GLN U 228 " pdb=" NH1 ARG Z 385 " model vdw 2.044 2.520 nonbonded pdb=" OG1 THR U 232 " pdb="MG MG U1002 " model vdw 2.057 2.170 nonbonded pdb=" O2B ATP U1001 " pdb="MG MG U1002 " model vdw 2.084 2.170 ... (remaining 461070 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = (chain 'T' and (resid 43 through 562 or resid 1001 through 1002)) selection = (chain 'U' and (resid 43 through 561 or (resid 562 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1001 through 1002)) selection = (chain 'V' and (resid 43 through 561 or (resid 562 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1001 through 1002)) } ncs_group { reference = (chain 'X' and resid 37 through 556) selection = (chain 'Y' and resid 37 through 556) selection = (chain 'Z' and resid 37 through 556) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 23.660 Check model and map are aligned: 0.590 Set scattering table: 0.370 Process input model: 122.940 Find NCS groups from input model: 2.610 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:9.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 163.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.135 54686 Z= 0.666 Angle : 1.008 20.359 74161 Z= 0.569 Chirality : 0.062 0.353 8689 Planarity : 0.008 0.093 9510 Dihedral : 14.156 168.626 19939 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.00 % Favored : 94.77 % Rotamer: Outliers : 0.34 % Allowed : 7.26 % Favored : 92.40 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -3.87 (0.08), residues: 7038 helix: -2.82 (0.06), residues: 3862 sheet: -1.34 (0.19), residues: 654 loop : -2.14 (0.11), residues: 2522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP 7 107 HIS 0.013 0.002 HIS Y 79 PHE 0.036 0.003 PHE S 249 TYR 0.025 0.003 TYR 4 211 ARG 0.010 0.001 ARG Z 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 923 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 904 time to evaluate : 4.566 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 34 GLU cc_start: 0.7587 (pm20) cc_final: 0.7334 (pm20) REVERT: 1 195 LYS cc_start: 0.7265 (mmtm) cc_final: 0.6826 (mmmm) REVERT: 1 456 LYS cc_start: 0.8529 (tttt) cc_final: 0.8168 (tptm) REVERT: 2 316 ASP cc_start: 0.7893 (p0) cc_final: 0.7675 (p0) REVERT: 3 129 LYS cc_start: 0.8211 (mttt) cc_final: 0.8004 (mttp) REVERT: 3 262 LEU cc_start: 0.8020 (mt) cc_final: 0.7809 (mp) REVERT: 4 158 LYS cc_start: 0.7630 (mppt) cc_final: 0.7156 (mptt) REVERT: 4 255 ARG cc_start: 0.8022 (ttm170) cc_final: 0.7473 (mtm-85) REVERT: 9 85 LYS cc_start: 0.7350 (tptm) cc_final: 0.7090 (tppp) REVERT: B 60 LYS cc_start: 0.7426 (mtmt) cc_final: 0.7054 (mttp) REVERT: B 81 MET cc_start: 0.8755 (ttp) cc_final: 0.8444 (ttp) REVERT: C 94 ASN cc_start: 0.8590 (m110) cc_final: 0.8364 (t0) REVERT: F 81 MET cc_start: 0.7985 (ttp) cc_final: 0.7769 (ttp) REVERT: G 82 PHE cc_start: 0.8270 (m-80) cc_final: 0.7891 (m-10) REVERT: G 92 ASN cc_start: 0.8060 (p0) cc_final: 0.7638 (p0) REVERT: G 95 ILE cc_start: 0.8512 (mm) cc_final: 0.8204 (mm) REVERT: G 116 PHE cc_start: 0.7515 (m-10) cc_final: 0.7248 (m-10) REVERT: I 97 LYS cc_start: 0.8580 (mppt) cc_final: 0.8241 (mtpt) REVERT: I 124 ILE cc_start: 0.8158 (mm) cc_final: 0.7828 (mp) REVERT: J 84 SER cc_start: 0.8766 (m) cc_final: 0.8427 (p) REVERT: J 98 GLN cc_start: 0.8494 (tt0) cc_final: 0.8284 (tt0) REVERT: P 59 GLN cc_start: 0.8339 (mt0) cc_final: 0.8089 (mm-40) REVERT: P 72 ASP cc_start: 0.7646 (p0) cc_final: 0.7406 (t70) REVERT: P 205 ARG cc_start: 0.8375 (ttp-110) cc_final: 0.7941 (ttp80) REVERT: Q 15 SER cc_start: 0.8759 (m) cc_final: 0.8550 (p) REVERT: S 45 GLN cc_start: 0.7642 (pt0) cc_final: 0.7354 (pp30) REVERT: S 68 MET cc_start: 0.7981 (ttp) cc_final: 0.7604 (tmm) REVERT: S 275 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7623 (tm-30) REVERT: T 65 LYS cc_start: 0.8348 (mmtt) cc_final: 0.8138 (mmpt) REVERT: T 440 LYS cc_start: 0.8298 (ttpt) cc_final: 0.8032 (ttmt) REVERT: T 471 GLN cc_start: 0.7846 (tm-30) cc_final: 0.7398 (tm-30) REVERT: T 535 ILE cc_start: 0.8841 (mt) cc_final: 0.8620 (mp) REVERT: T 539 ASN cc_start: 0.8250 (m-40) cc_final: 0.8036 (m-40) REVERT: T 555 ARG cc_start: 0.7545 (mtt-85) cc_final: 0.7099 (mmt90) REVERT: U 472 TYR cc_start: 0.7244 (t80) cc_final: 0.6960 (t80) REVERT: U 553 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7435 (mm-30) REVERT: V 50 LYS cc_start: 0.8083 (tppt) cc_final: 0.7873 (tptt) REVERT: V 518 VAL cc_start: 0.8790 (m) cc_final: 0.8433 (t) REVERT: X 484 MET cc_start: 0.8334 (mmt) cc_final: 0.8107 (mmm) REVERT: Y 227 MET cc_start: 0.8827 (mtp) cc_final: 0.8603 (mtt) REVERT: Y 414 GLN cc_start: 0.8582 (mt0) cc_final: 0.8361 (tt0) REVERT: Z 292 GLN cc_start: 0.7906 (mt0) cc_final: 0.7669 (mt0) REVERT: Z 430 LYS cc_start: 0.7293 (tppp) cc_final: 0.6802 (mttp) outliers start: 19 outliers final: 12 residues processed: 923 average time/residue: 1.3989 time to fit residues: 1616.1692 Evaluate side-chains 612 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 600 time to evaluate : 4.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 24 LEU Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 3 residue 316 VAL Chi-restraints excluded: chain 4 residue 122 VAL Chi-restraints excluded: chain 9 residue 3 VAL Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain J residue 69 ILE Chi-restraints excluded: chain T residue 300 PHE Chi-restraints excluded: chain U residue 48 LEU Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain Y residue 50 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 589 optimal weight: 0.9980 chunk 529 optimal weight: 3.9990 chunk 293 optimal weight: 0.7980 chunk 180 optimal weight: 4.9990 chunk 356 optimal weight: 2.9990 chunk 282 optimal weight: 0.6980 chunk 547 optimal weight: 0.7980 chunk 211 optimal weight: 0.7980 chunk 332 optimal weight: 0.0980 chunk 407 optimal weight: 0.9990 chunk 633 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 100 GLN 1 166 ASN 1 285 GLN 1 298 GLN 1 316 ASN 1 365 GLN 1 587 ASN 1 590 HIS 2 122 ASN 2 243 GLN 2 289 HIS 2 427 GLN 3 79 GLN 3 189 HIS 3 206 ASN 3 229 ASN 3 231 HIS 3 256 GLN 4 38 GLN 4 52 GLN 4 111 GLN 4 240 GLN ** 4 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 29 GLN 5 107 ASN 6 40 ASN 6 74 GLN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 123 HIS 7 170 HIS 7 184 ASN 9 27 ASN 9 35 GLN 9 80 GLN A 87 ASN I 98 GLN J 98 GLN M 108 ASN M 131 ASN M 163 ASN P 65 ASN P 71 GLN P 140 ASN P 220 ASN Q 40 GLN Q 43 GLN Q 46 HIS R 73 ASN R 119 HIS R 137 HIS S 188 GLN S 297 GLN T 64 GLN T 78 GLN T 104 GLN T 196 GLN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 386 GLN T 435 GLN T 441 GLN T 461 GLN T 497 GLN U 134 ASN U 149 GLN U 179 ASN U 241 HIS U 246 ASN U 319 HIS U 386 GLN U 441 GLN U 497 GLN U 539 ASN V 60 GLN V 139 HIS ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 242 GLN V 244 ASN V 246 ASN V 271 GLN V 461 GLN V 486 GLN ** V 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 199 ASN X 241 ASN X 278 GLN X 322 GLN X 337 GLN X 398 ASN X 414 GLN Y 123 ASN Y 144 HIS Y 174 GLN Y 278 GLN Z 144 HIS Z 199 ASN Z 250 GLN Z 278 GLN Z 294 ASN Z 390 ASN Total number of N/Q/H flips: 94 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 54686 Z= 0.167 Angle : 0.560 10.796 74161 Z= 0.293 Chirality : 0.041 0.163 8689 Planarity : 0.005 0.065 9510 Dihedral : 6.788 179.392 7687 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.71 % Favored : 96.12 % Rotamer: Outliers : 2.42 % Allowed : 13.48 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.90 (0.09), residues: 7038 helix: -0.99 (0.08), residues: 3860 sheet: -1.20 (0.20), residues: 639 loop : -1.46 (0.12), residues: 2539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP 9 93 HIS 0.004 0.001 HIS 7 123 PHE 0.030 0.001 PHE C 122 TYR 0.025 0.001 TYR 4 211 ARG 0.005 0.000 ARG 1 387 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 880 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 744 time to evaluate : 4.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 34 GLU cc_start: 0.7430 (pm20) cc_final: 0.7198 (pm20) REVERT: 1 195 LYS cc_start: 0.7231 (mmtm) cc_final: 0.7026 (mmmm) REVERT: 1 456 LYS cc_start: 0.8531 (tttt) cc_final: 0.8145 (tptm) REVERT: 2 7 ASP cc_start: 0.5600 (OUTLIER) cc_final: 0.5340 (p0) REVERT: 2 299 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7790 (pp) REVERT: 3 129 LYS cc_start: 0.8286 (mttt) cc_final: 0.8057 (mttp) REVERT: 3 309 ASN cc_start: 0.6838 (p0) cc_final: 0.5954 (m-40) REVERT: 4 158 LYS cc_start: 0.7479 (mppt) cc_final: 0.6984 (mptt) REVERT: 4 255 ARG cc_start: 0.8057 (ttm170) cc_final: 0.7731 (mtm-85) REVERT: 5 28 THR cc_start: 0.9101 (m) cc_final: 0.8821 (m) REVERT: 8 41 ILE cc_start: 0.9138 (OUTLIER) cc_final: 0.8899 (mm) REVERT: 8 69 LYS cc_start: 0.8696 (mttt) cc_final: 0.7245 (tmtt) REVERT: B 124 ILE cc_start: 0.8293 (mt) cc_final: 0.8071 (mm) REVERT: C 61 MET cc_start: 0.7877 (mmt) cc_final: 0.7609 (mmt) REVERT: C 84 SER cc_start: 0.8301 (m) cc_final: 0.8031 (p) REVERT: C 94 ASN cc_start: 0.8616 (m110) cc_final: 0.8409 (t0) REVERT: D 59 SER cc_start: 0.7909 (m) cc_final: 0.7396 (p) REVERT: G 116 PHE cc_start: 0.7155 (m-10) cc_final: 0.6911 (m-10) REVERT: I 97 LYS cc_start: 0.8496 (mppt) cc_final: 0.8171 (ttpt) REVERT: I 109 LEU cc_start: 0.8378 (mp) cc_final: 0.8127 (tp) REVERT: I 124 ILE cc_start: 0.8146 (mm) cc_final: 0.7883 (mp) REVERT: J 84 SER cc_start: 0.8654 (m) cc_final: 0.8448 (p) REVERT: M 124 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.6622 (mp0) REVERT: P 59 GLN cc_start: 0.8419 (mt0) cc_final: 0.8079 (mm-40) REVERT: P 68 ASP cc_start: 0.8749 (t0) cc_final: 0.8495 (t0) REVERT: P 72 ASP cc_start: 0.7592 (p0) cc_final: 0.7091 (t70) REVERT: P 134 LEU cc_start: 0.8778 (tp) cc_final: 0.8556 (tp) REVERT: P 205 ARG cc_start: 0.8215 (ttp-110) cc_final: 0.7938 (ttp-110) REVERT: S 45 GLN cc_start: 0.7566 (pt0) cc_final: 0.7326 (pp30) REVERT: S 68 MET cc_start: 0.7855 (ttp) cc_final: 0.7478 (ttp) REVERT: S 198 ARG cc_start: 0.6790 (mmm160) cc_final: 0.6579 (mmm160) REVERT: S 275 GLU cc_start: 0.7627 (tm-30) cc_final: 0.7310 (tm-30) REVERT: T 440 LYS cc_start: 0.8244 (ttpt) cc_final: 0.7944 (ttmt) REVERT: T 471 GLN cc_start: 0.7849 (tm-30) cc_final: 0.7515 (tm-30) REVERT: T 496 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7932 (mtt90) REVERT: T 535 ILE cc_start: 0.8790 (mt) cc_final: 0.8477 (mp) REVERT: T 539 ASN cc_start: 0.8243 (m-40) cc_final: 0.7951 (m-40) REVERT: T 549 HIS cc_start: 0.6869 (OUTLIER) cc_final: 0.6513 (t70) REVERT: U 553 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7467 (mm-30) REVERT: V 50 LYS cc_start: 0.7988 (tppt) cc_final: 0.7680 (tptt) REVERT: V 429 ARG cc_start: 0.8119 (mtt-85) cc_final: 0.7768 (mtt-85) REVERT: X 471 GLN cc_start: 0.7689 (tt0) cc_final: 0.7426 (tp-100) REVERT: X 484 MET cc_start: 0.8415 (mmt) cc_final: 0.8195 (mmm) REVERT: Y 215 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.8042 (mm-30) REVERT: Y 227 MET cc_start: 0.8787 (mtp) cc_final: 0.8535 (mtt) REVERT: Y 414 GLN cc_start: 0.8297 (mt0) cc_final: 0.8043 (tt0) REVERT: Y 441 ARG cc_start: 0.7836 (mmt-90) cc_final: 0.7623 (mpt-90) REVERT: Z 88 ILE cc_start: 0.9020 (OUTLIER) cc_final: 0.8777 (pt) REVERT: Z 430 LYS cc_start: 0.7253 (tppp) cc_final: 0.6858 (mttp) outliers start: 136 outliers final: 39 residues processed: 837 average time/residue: 1.2584 time to fit residues: 1361.9710 Evaluate side-chains 644 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 597 time to evaluate : 5.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 1 residue 24 LEU Chi-restraints excluded: chain 1 residue 217 LEU Chi-restraints excluded: chain 1 residue 227 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 2 residue 7 ASP Chi-restraints excluded: chain 2 residue 74 ASN Chi-restraints excluded: chain 2 residue 125 SER Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 2 residue 299 LEU Chi-restraints excluded: chain 2 residue 391 THR Chi-restraints excluded: chain 4 residue 122 VAL Chi-restraints excluded: chain 7 residue 39 VAL Chi-restraints excluded: chain 7 residue 146 GLU Chi-restraints excluded: chain 8 residue 41 ILE Chi-restraints excluded: chain 9 residue 3 VAL Chi-restraints excluded: chain 9 residue 91 LYS Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain M residue 124 GLU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain Q residue 10 ARG Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 107 THR Chi-restraints excluded: chain S residue 76 GLU Chi-restraints excluded: chain S residue 127 LEU Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 496 ARG Chi-restraints excluded: chain T residue 549 HIS Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 409 GLU Chi-restraints excluded: chain V residue 554 LEU Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 466 THR Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Y residue 70 VAL Chi-restraints excluded: chain Y residue 215 GLU Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain Z residue 113 VAL Chi-restraints excluded: chain Z residue 417 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 352 optimal weight: 0.9980 chunk 196 optimal weight: 1.9990 chunk 527 optimal weight: 0.8980 chunk 431 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 chunk 635 optimal weight: 4.9990 chunk 685 optimal weight: 7.9990 chunk 565 optimal weight: 1.9990 chunk 629 optimal weight: 3.9990 chunk 216 optimal weight: 9.9990 chunk 509 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 256 GLN 4 52 GLN 4 240 GLN 5 59 ASN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 86 HIS ** 9 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 80 GLN C 98 GLN G 98 GLN ** P 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 220 ASN Q 29 ASN Q 43 GLN ** R 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 185 HIS T 140 GLN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 83 HIS ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 539 ASN U 549 HIS V 152 ASN ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 244 ASN V 358 HIS V 461 GLN X 83 ASN X 198 ASN Y 123 ASN Y 204 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 54686 Z= 0.283 Angle : 0.586 12.037 74161 Z= 0.303 Chirality : 0.043 0.200 8689 Planarity : 0.005 0.060 9510 Dihedral : 6.662 170.068 7678 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.35 % Favored : 95.47 % Rotamer: Outliers : 2.98 % Allowed : 15.68 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.10), residues: 7038 helix: -0.42 (0.08), residues: 3867 sheet: -1.00 (0.20), residues: 630 loop : -1.19 (0.12), residues: 2541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP 9 93 HIS 0.012 0.001 HIS Y 204 PHE 0.033 0.001 PHE 2 165 TYR 0.025 0.002 TYR 4 211 ARG 0.007 0.000 ARG S 124 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 817 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 649 time to evaluate : 4.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 34 GLU cc_start: 0.7436 (pm20) cc_final: 0.7201 (pm20) REVERT: 1 195 LYS cc_start: 0.7285 (mmtm) cc_final: 0.6973 (mmmm) REVERT: 1 456 LYS cc_start: 0.8468 (tttt) cc_final: 0.8170 (tptm) REVERT: 2 7 ASP cc_start: 0.5527 (OUTLIER) cc_final: 0.5260 (p0) REVERT: 2 299 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7834 (pp) REVERT: 3 129 LYS cc_start: 0.8394 (mttt) cc_final: 0.8160 (mttm) REVERT: 4 158 LYS cc_start: 0.7486 (mppt) cc_final: 0.7026 (mptt) REVERT: 4 255 ARG cc_start: 0.8057 (ttm170) cc_final: 0.7523 (mtm-85) REVERT: 5 112 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7267 (ptm-80) REVERT: 6 146 PHE cc_start: 0.8587 (OUTLIER) cc_final: 0.7741 (t80) REVERT: 7 37 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7592 (tt) REVERT: 8 69 LYS cc_start: 0.8744 (mttt) cc_final: 0.7319 (tmtt) REVERT: 9 91 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7855 (mtmt) REVERT: B 60 LYS cc_start: 0.7343 (mtmt) cc_final: 0.7016 (mttp) REVERT: B 81 MET cc_start: 0.8574 (ttm) cc_final: 0.8249 (ttm) REVERT: C 119 LEU cc_start: 0.7558 (mt) cc_final: 0.7157 (tm) REVERT: D 59 SER cc_start: 0.7995 (m) cc_final: 0.7316 (p) REVERT: F 78 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7494 (tp) REVERT: F 81 MET cc_start: 0.7775 (ttp) cc_final: 0.7565 (ttp) REVERT: G 82 PHE cc_start: 0.8063 (m-10) cc_final: 0.7799 (m-10) REVERT: G 92 ASN cc_start: 0.7843 (p0) cc_final: 0.7623 (p0) REVERT: G 95 ILE cc_start: 0.8583 (mm) cc_final: 0.8324 (mm) REVERT: G 116 PHE cc_start: 0.7149 (m-10) cc_final: 0.6886 (m-10) REVERT: I 97 LYS cc_start: 0.8558 (mppt) cc_final: 0.8200 (ttpt) REVERT: I 98 GLN cc_start: 0.8267 (tt0) cc_final: 0.7917 (tm130) REVERT: I 124 ILE cc_start: 0.8165 (mm) cc_final: 0.7912 (mp) REVERT: J 84 SER cc_start: 0.8836 (m) cc_final: 0.8446 (p) REVERT: M 124 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6824 (mp0) REVERT: M 159 ILE cc_start: 0.8971 (mt) cc_final: 0.8751 (mt) REVERT: M 254 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8546 (tt) REVERT: M 314 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8254 (tmtm) REVERT: P 59 GLN cc_start: 0.8383 (mt0) cc_final: 0.8032 (mm-40) REVERT: P 68 ASP cc_start: 0.8752 (t0) cc_final: 0.8496 (t0) REVERT: P 72 ASP cc_start: 0.7401 (p0) cc_final: 0.7197 (t70) REVERT: P 134 LEU cc_start: 0.8788 (tp) cc_final: 0.8579 (tp) REVERT: P 205 ARG cc_start: 0.8286 (ttp-110) cc_final: 0.7896 (ttp80) REVERT: R 117 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7400 (mp0) REVERT: S 68 MET cc_start: 0.7839 (ttp) cc_final: 0.7351 (tmm) REVERT: S 275 GLU cc_start: 0.7649 (tm-30) cc_final: 0.7327 (tm-30) REVERT: T 149 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7562 (pt0) REVERT: T 169 GLN cc_start: 0.7885 (mt0) cc_final: 0.7643 (mp10) REVERT: T 411 GLU cc_start: 0.7633 (pm20) cc_final: 0.7334 (mp0) REVERT: T 439 MET cc_start: 0.9130 (ttp) cc_final: 0.8619 (ttp) REVERT: T 440 LYS cc_start: 0.8435 (ttpt) cc_final: 0.8111 (ttmt) REVERT: T 471 GLN cc_start: 0.7921 (tm-30) cc_final: 0.7558 (tm-30) REVERT: T 496 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.8067 (mtt90) REVERT: T 535 ILE cc_start: 0.8694 (mt) cc_final: 0.8357 (mp) REVERT: T 539 ASN cc_start: 0.8292 (m-40) cc_final: 0.7970 (m-40) REVERT: T 549 HIS cc_start: 0.6812 (OUTLIER) cc_final: 0.6458 (t70) REVERT: U 75 LYS cc_start: 0.8158 (mmmt) cc_final: 0.7951 (mttp) REVERT: U 472 TYR cc_start: 0.7320 (t80) cc_final: 0.7095 (t80) REVERT: U 553 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7469 (mm-30) REVERT: V 50 LYS cc_start: 0.8044 (tppt) cc_final: 0.7729 (tptt) REVERT: V 287 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.8057 (mtp) REVERT: X 484 MET cc_start: 0.8421 (mmt) cc_final: 0.8138 (mmm) REVERT: Y 227 MET cc_start: 0.8798 (mtp) cc_final: 0.8592 (mtt) REVERT: Y 414 GLN cc_start: 0.8293 (mt0) cc_final: 0.8047 (tt0) REVERT: Y 441 ARG cc_start: 0.7985 (mmt-90) cc_final: 0.7779 (mpt-90) REVERT: Z 430 LYS cc_start: 0.7164 (tppp) cc_final: 0.6729 (mttp) REVERT: Z 451 GLU cc_start: 0.8010 (pt0) cc_final: 0.7797 (pt0) outliers start: 168 outliers final: 75 residues processed: 755 average time/residue: 1.2197 time to fit residues: 1184.6950 Evaluate side-chains 678 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 588 time to evaluate : 4.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 1 residue 24 LEU Chi-restraints excluded: chain 1 residue 217 LEU Chi-restraints excluded: chain 1 residue 227 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 302 SER Chi-restraints excluded: chain 1 residue 308 ASN Chi-restraints excluded: chain 1 residue 389 THR Chi-restraints excluded: chain 1 residue 426 VAL Chi-restraints excluded: chain 2 residue 7 ASP Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 2 residue 299 LEU Chi-restraints excluded: chain 3 residue 192 VAL Chi-restraints excluded: chain 3 residue 311 LEU Chi-restraints excluded: chain 3 residue 316 VAL Chi-restraints excluded: chain 4 residue 122 VAL Chi-restraints excluded: chain 4 residue 209 SER Chi-restraints excluded: chain 5 residue 27 ASP Chi-restraints excluded: chain 5 residue 112 ARG Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 35 ILE Chi-restraints excluded: chain 7 residue 37 LEU Chi-restraints excluded: chain 7 residue 39 VAL Chi-restraints excluded: chain 7 residue 146 GLU Chi-restraints excluded: chain 9 residue 3 VAL Chi-restraints excluded: chain 9 residue 26 LEU Chi-restraints excluded: chain 9 residue 91 LYS Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain M residue 124 GLU Chi-restraints excluded: chain M residue 172 GLU Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 254 LEU Chi-restraints excluded: chain M residue 296 SER Chi-restraints excluded: chain M residue 313 ASP Chi-restraints excluded: chain M residue 314 LYS Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 66 GLN Chi-restraints excluded: chain P residue 93 ASP Chi-restraints excluded: chain P residue 195 LEU Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 107 THR Chi-restraints excluded: chain R residue 117 GLU Chi-restraints excluded: chain S residue 127 LEU Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 283 GLU Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 149 GLN Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 481 THR Chi-restraints excluded: chain T residue 496 ARG Chi-restraints excluded: chain T residue 518 VAL Chi-restraints excluded: chain T residue 549 HIS Chi-restraints excluded: chain U residue 41 ASP Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 226 ASP Chi-restraints excluded: chain U residue 326 ASP Chi-restraints excluded: chain U residue 550 LEU Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain V residue 102 SER Chi-restraints excluded: chain V residue 113 SER Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 287 MET Chi-restraints excluded: chain V residue 360 ARG Chi-restraints excluded: chain V residue 411 GLU Chi-restraints excluded: chain V residue 554 LEU Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 341 VAL Chi-restraints excluded: chain X residue 466 THR Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Y residue 70 VAL Chi-restraints excluded: chain Y residue 166 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain Z residue 113 VAL Chi-restraints excluded: chain Z residue 415 ASP Chi-restraints excluded: chain Z residue 416 ILE Chi-restraints excluded: chain Z residue 439 ILE Chi-restraints excluded: chain Z residue 559 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 627 optimal weight: 5.9990 chunk 477 optimal weight: 20.0000 chunk 329 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 303 optimal weight: 9.9990 chunk 426 optimal weight: 3.9990 chunk 637 optimal weight: 6.9990 chunk 674 optimal weight: 1.9990 chunk 332 optimal weight: 0.6980 chunk 603 optimal weight: 3.9990 chunk 181 optimal weight: 5.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 256 GLN 4 38 GLN 4 52 GLN 4 95 GLN 4 240 GLN 5 59 ASN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 60 ASN ** G 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN I 94 ASN J 98 GLN P 65 ASN P 66 GLN Q 43 GLN ** R 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 435 GLN U 121 ASN U 539 ASN V 461 GLN ** V 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 123 ASN Y 250 GLN Z 396 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 54686 Z= 0.400 Angle : 0.637 12.009 74161 Z= 0.328 Chirality : 0.046 0.232 8689 Planarity : 0.005 0.061 9510 Dihedral : 6.845 163.568 7678 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.73 % Favored : 95.07 % Rotamer: Outliers : 3.94 % Allowed : 16.43 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.05 (0.10), residues: 7038 helix: -0.28 (0.08), residues: 3883 sheet: -0.97 (0.20), residues: 646 loop : -1.07 (0.12), residues: 2509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP 9 93 HIS 0.008 0.001 HIS 4 233 PHE 0.030 0.002 PHE C 122 TYR 0.026 0.002 TYR 4 211 ARG 0.005 0.001 ARG T 479 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 833 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 611 time to evaluate : 5.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 34 GLU cc_start: 0.7451 (pm20) cc_final: 0.7234 (pm20) REVERT: 1 195 LYS cc_start: 0.7258 (mmtm) cc_final: 0.6953 (mmmm) REVERT: 1 438 GLN cc_start: 0.7132 (OUTLIER) cc_final: 0.6741 (tm-30) REVERT: 1 456 LYS cc_start: 0.8505 (tttt) cc_final: 0.8143 (tptm) REVERT: 1 572 ASP cc_start: 0.8258 (p0) cc_final: 0.7964 (p0) REVERT: 2 7 ASP cc_start: 0.5551 (OUTLIER) cc_final: 0.5294 (p0) REVERT: 3 129 LYS cc_start: 0.8396 (mttt) cc_final: 0.8139 (mttm) REVERT: 3 309 ASN cc_start: 0.6872 (p0) cc_final: 0.6461 (p0) REVERT: 4 255 ARG cc_start: 0.8078 (ttm170) cc_final: 0.7591 (mtm-85) REVERT: 5 119 LYS cc_start: 0.7949 (mmmm) cc_final: 0.7658 (mmmt) REVERT: 6 146 PHE cc_start: 0.8625 (OUTLIER) cc_final: 0.7926 (t80) REVERT: 7 37 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7573 (tt) REVERT: 8 69 LYS cc_start: 0.8777 (mttt) cc_final: 0.7270 (tmtt) REVERT: 9 91 LYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7841 (mtmt) REVERT: B 81 MET cc_start: 0.8596 (ttm) cc_final: 0.8257 (ttm) REVERT: C 84 SER cc_start: 0.8386 (m) cc_final: 0.8100 (p) REVERT: C 119 LEU cc_start: 0.7519 (mt) cc_final: 0.7142 (tm) REVERT: F 81 MET cc_start: 0.7903 (ttp) cc_final: 0.7666 (ttp) REVERT: G 82 PHE cc_start: 0.8171 (m-10) cc_final: 0.7942 (m-10) REVERT: G 92 ASN cc_start: 0.7931 (p0) cc_final: 0.7597 (p0) REVERT: I 97 LYS cc_start: 0.8447 (mppt) cc_final: 0.8109 (ttpt) REVERT: I 98 GLN cc_start: 0.8341 (tt0) cc_final: 0.8003 (tm130) REVERT: I 109 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8131 (tp) REVERT: I 124 ILE cc_start: 0.8129 (mm) cc_final: 0.7786 (mp) REVERT: J 84 SER cc_start: 0.8874 (m) cc_final: 0.8388 (p) REVERT: M 124 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.6853 (mp0) REVERT: M 254 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8533 (tt) REVERT: P 59 GLN cc_start: 0.8341 (mt0) cc_final: 0.7880 (mt0) REVERT: P 205 ARG cc_start: 0.8266 (ttp-110) cc_final: 0.7911 (ttp80) REVERT: Q 42 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.7049 (ptt90) REVERT: R 117 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7518 (mp0) REVERT: S 68 MET cc_start: 0.7909 (ttp) cc_final: 0.7492 (tmm) REVERT: S 220 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.7690 (mm) REVERT: S 275 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7365 (tm-30) REVERT: T 149 GLN cc_start: 0.7859 (OUTLIER) cc_final: 0.7594 (pt0) REVERT: T 169 GLN cc_start: 0.7951 (mt0) cc_final: 0.7668 (mp10) REVERT: T 411 GLU cc_start: 0.7661 (pm20) cc_final: 0.7384 (mp0) REVERT: T 439 MET cc_start: 0.9140 (ttp) cc_final: 0.8862 (ttp) REVERT: T 440 LYS cc_start: 0.8452 (ttpt) cc_final: 0.8201 (ttmt) REVERT: T 471 GLN cc_start: 0.7914 (tm-30) cc_final: 0.7632 (tm-30) REVERT: T 496 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.8077 (mtt90) REVERT: T 535 ILE cc_start: 0.8735 (mt) cc_final: 0.8398 (mp) REVERT: T 539 ASN cc_start: 0.8238 (m-40) cc_final: 0.7902 (m-40) REVERT: T 549 HIS cc_start: 0.6836 (OUTLIER) cc_final: 0.6530 (t70) REVERT: U 75 LYS cc_start: 0.8179 (mmmt) cc_final: 0.7970 (mttp) REVERT: U 553 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7458 (mm-30) REVERT: V 50 LYS cc_start: 0.8039 (tppt) cc_final: 0.7720 (tptt) REVERT: V 429 ARG cc_start: 0.8234 (mtt-85) cc_final: 0.7866 (mtt-85) REVERT: X 276 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7380 (mt-10) REVERT: Y 55 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.6610 (mp0) REVERT: Z 430 LYS cc_start: 0.7229 (tppp) cc_final: 0.6875 (mttp) REVERT: Z 451 GLU cc_start: 0.7996 (pt0) cc_final: 0.7771 (pt0) REVERT: Z 542 ASP cc_start: 0.5938 (OUTLIER) cc_final: 0.5690 (p0) outliers start: 222 outliers final: 105 residues processed: 767 average time/residue: 1.2177 time to fit residues: 1207.3416 Evaluate side-chains 690 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 568 time to evaluate : 4.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 1 residue 24 LEU Chi-restraints excluded: chain 1 residue 47 VAL Chi-restraints excluded: chain 1 residue 188 VAL Chi-restraints excluded: chain 1 residue 217 LEU Chi-restraints excluded: chain 1 residue 227 VAL Chi-restraints excluded: chain 1 residue 233 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 302 SER Chi-restraints excluded: chain 1 residue 308 ASN Chi-restraints excluded: chain 1 residue 389 THR Chi-restraints excluded: chain 1 residue 426 VAL Chi-restraints excluded: chain 1 residue 438 GLN Chi-restraints excluded: chain 1 residue 512 LEU Chi-restraints excluded: chain 1 residue 596 ILE Chi-restraints excluded: chain 2 residue 7 ASP Chi-restraints excluded: chain 2 residue 125 SER Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 2 residue 391 THR Chi-restraints excluded: chain 3 residue 96 VAL Chi-restraints excluded: chain 3 residue 137 THR Chi-restraints excluded: chain 3 residue 192 VAL Chi-restraints excluded: chain 3 residue 311 LEU Chi-restraints excluded: chain 3 residue 316 VAL Chi-restraints excluded: chain 4 residue 64 GLU Chi-restraints excluded: chain 4 residue 115 THR Chi-restraints excluded: chain 4 residue 122 VAL Chi-restraints excluded: chain 4 residue 199 VAL Chi-restraints excluded: chain 4 residue 209 SER Chi-restraints excluded: chain 5 residue 1 MET Chi-restraints excluded: chain 5 residue 27 ASP Chi-restraints excluded: chain 5 residue 61 SER Chi-restraints excluded: chain 6 residue 119 LEU Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 35 ILE Chi-restraints excluded: chain 7 residue 37 LEU Chi-restraints excluded: chain 7 residue 39 VAL Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 71 LYS Chi-restraints excluded: chain 9 residue 1 MET Chi-restraints excluded: chain 9 residue 3 VAL Chi-restraints excluded: chain 9 residue 26 LEU Chi-restraints excluded: chain 9 residue 91 LYS Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain M residue 124 GLU Chi-restraints excluded: chain M residue 172 GLU Chi-restraints excluded: chain M residue 182 THR Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 254 LEU Chi-restraints excluded: chain M residue 274 THR Chi-restraints excluded: chain M residue 296 SER Chi-restraints excluded: chain M residue 313 ASP Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 66 GLN Chi-restraints excluded: chain P residue 93 ASP Chi-restraints excluded: chain P residue 195 LEU Chi-restraints excluded: chain Q residue 42 ARG Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain R residue 60 VAL Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 107 THR Chi-restraints excluded: chain R residue 117 GLU Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain S residue 63 VAL Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 283 GLU Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 149 GLN Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 353 ASP Chi-restraints excluded: chain T residue 481 THR Chi-restraints excluded: chain T residue 496 ARG Chi-restraints excluded: chain T residue 518 VAL Chi-restraints excluded: chain T residue 549 HIS Chi-restraints excluded: chain U residue 41 ASP Chi-restraints excluded: chain U residue 48 LEU Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 326 ASP Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 532 VAL Chi-restraints excluded: chain U residue 550 LEU Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain V residue 102 SER Chi-restraints excluded: chain V residue 113 SER Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 267 SER Chi-restraints excluded: chain V residue 411 GLU Chi-restraints excluded: chain V residue 517 ILE Chi-restraints excluded: chain V residue 554 LEU Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 276 GLU Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 341 VAL Chi-restraints excluded: chain X residue 466 THR Chi-restraints excluded: chain X residue 491 ASP Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Y residue 55 GLU Chi-restraints excluded: chain Y residue 70 VAL Chi-restraints excluded: chain Y residue 166 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Z residue 69 SER Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain Z residue 113 VAL Chi-restraints excluded: chain Z residue 280 VAL Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 416 ILE Chi-restraints excluded: chain Z residue 439 ILE Chi-restraints excluded: chain Z residue 456 THR Chi-restraints excluded: chain Z residue 542 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 561 optimal weight: 0.0470 chunk 382 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 502 optimal weight: 3.9990 chunk 278 optimal weight: 0.9990 chunk 575 optimal weight: 2.9990 chunk 466 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 344 optimal weight: 3.9990 chunk 605 optimal weight: 4.9990 chunk 170 optimal weight: 0.3980 overall best weight: 0.8082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 394 GLN ** 1 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 527 GLN 2 74 ASN ** 2 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 256 GLN 4 52 GLN 4 95 GLN 4 240 GLN ** 4 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 59 ASN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 35 GLN ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN P 65 ASN P 220 ASN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 262 ASN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 435 GLN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 539 ASN V 104 GLN ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 461 GLN ** V 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 123 ASN Y 414 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 54686 Z= 0.175 Angle : 0.537 12.583 74161 Z= 0.276 Chirality : 0.041 0.232 8689 Planarity : 0.004 0.059 9510 Dihedral : 6.056 123.921 7678 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.86 % Favored : 95.96 % Rotamer: Outliers : 3.16 % Allowed : 18.22 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.55 (0.10), residues: 7038 helix: 0.16 (0.09), residues: 3862 sheet: -0.86 (0.20), residues: 640 loop : -0.85 (0.13), residues: 2536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP 9 93 HIS 0.004 0.001 HIS 4 233 PHE 0.033 0.001 PHE F 107 TYR 0.024 0.001 TYR 4 211 ARG 0.006 0.000 ARG Y 51 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 835 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 657 time to evaluate : 4.681 Fit side-chains revert: symmetry clash REVERT: 0 41 GLU cc_start: 0.5206 (OUTLIER) cc_final: 0.3274 (pm20) REVERT: 1 34 GLU cc_start: 0.7418 (pm20) cc_final: 0.7202 (pm20) REVERT: 1 195 LYS cc_start: 0.7197 (mmtm) cc_final: 0.6888 (mmmm) REVERT: 1 352 GLU cc_start: 0.7499 (mm-30) cc_final: 0.7107 (mp0) REVERT: 1 456 LYS cc_start: 0.8478 (tttt) cc_final: 0.8133 (tptm) REVERT: 3 129 LYS cc_start: 0.8373 (mttt) cc_final: 0.8131 (mttm) REVERT: 4 158 LYS cc_start: 0.7389 (OUTLIER) cc_final: 0.6887 (tptt) REVERT: 4 255 ARG cc_start: 0.8025 (ttm170) cc_final: 0.7517 (mtm-85) REVERT: 5 28 THR cc_start: 0.9013 (m) cc_final: 0.8753 (m) REVERT: 5 119 LYS cc_start: 0.7844 (mmmm) cc_final: 0.7578 (mmmt) REVERT: 6 71 TYR cc_start: 0.6102 (m-80) cc_final: 0.5842 (m-80) REVERT: 6 146 PHE cc_start: 0.8579 (OUTLIER) cc_final: 0.7874 (t80) REVERT: 7 37 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7574 (tt) REVERT: 8 69 LYS cc_start: 0.8707 (mttt) cc_final: 0.7280 (tmtt) REVERT: 9 91 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7818 (mtmt) REVERT: B 81 MET cc_start: 0.8554 (ttm) cc_final: 0.8239 (ttm) REVERT: B 97 LYS cc_start: 0.8368 (mmtt) cc_final: 0.7936 (mmtt) REVERT: C 119 LEU cc_start: 0.7454 (mt) cc_final: 0.7139 (tm) REVERT: D 61 MET cc_start: 0.7820 (ptp) cc_final: 0.7591 (ptm) REVERT: E 61 MET cc_start: 0.8168 (mmp) cc_final: 0.7823 (mpt) REVERT: F 78 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7546 (tp) REVERT: F 81 MET cc_start: 0.7861 (ttp) cc_final: 0.7611 (ttp) REVERT: G 95 ILE cc_start: 0.8639 (mm) cc_final: 0.8301 (mm) REVERT: G 107 PHE cc_start: 0.7134 (t80) cc_final: 0.6916 (t80) REVERT: I 97 LYS cc_start: 0.8464 (mppt) cc_final: 0.8126 (ttpt) REVERT: I 98 GLN cc_start: 0.8213 (tt0) cc_final: 0.7989 (tm130) REVERT: I 109 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8173 (tp) REVERT: I 124 ILE cc_start: 0.8141 (mm) cc_final: 0.7861 (mp) REVERT: J 84 SER cc_start: 0.8854 (m) cc_final: 0.8455 (p) REVERT: J 92 ASN cc_start: 0.8339 (p0) cc_final: 0.8138 (p0) REVERT: M 124 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.6668 (mp0) REVERT: M 254 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8533 (tt) REVERT: M 314 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8115 (ttpm) REVERT: P 66 GLN cc_start: 0.8353 (pt0) cc_final: 0.8124 (pt0) REVERT: P 205 ARG cc_start: 0.8229 (ttp-110) cc_final: 0.7846 (ttp80) REVERT: Q 42 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.7006 (ptt180) REVERT: S 68 MET cc_start: 0.7825 (ttp) cc_final: 0.7390 (tmm) REVERT: S 198 ARG cc_start: 0.6723 (mmm160) cc_final: 0.6434 (mmm160) REVERT: S 275 GLU cc_start: 0.7578 (tm-30) cc_final: 0.7265 (tm-30) REVERT: S 283 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.7162 (mp0) REVERT: T 149 GLN cc_start: 0.7730 (OUTLIER) cc_final: 0.7447 (pt0) REVERT: T 411 GLU cc_start: 0.7655 (pm20) cc_final: 0.7387 (mp0) REVERT: T 439 MET cc_start: 0.9100 (OUTLIER) cc_final: 0.8891 (ttp) REVERT: T 440 LYS cc_start: 0.8403 (ttpt) cc_final: 0.8069 (ttmt) REVERT: T 487 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.8082 (mtmt) REVERT: T 496 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.8085 (mtt90) REVERT: T 535 ILE cc_start: 0.8631 (mt) cc_final: 0.8208 (mp) REVERT: T 539 ASN cc_start: 0.8282 (m-40) cc_final: 0.7954 (m-40) REVERT: T 549 HIS cc_start: 0.6966 (OUTLIER) cc_final: 0.6573 (t70) REVERT: T 555 ARG cc_start: 0.7688 (mtt-85) cc_final: 0.7289 (mmt90) REVERT: U 75 LYS cc_start: 0.8163 (mmmt) cc_final: 0.7956 (mttp) REVERT: U 553 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7460 (mm-30) REVERT: V 50 LYS cc_start: 0.7892 (tppt) cc_final: 0.7510 (tptt) REVERT: V 429 ARG cc_start: 0.8238 (mtt-85) cc_final: 0.7965 (mtt-85) REVERT: Y 215 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7705 (mm-30) REVERT: Y 441 ARG cc_start: 0.7902 (mmt-90) cc_final: 0.7651 (mpt-90) REVERT: Z 430 LYS cc_start: 0.7142 (tppp) cc_final: 0.6774 (mttp) REVERT: Z 451 GLU cc_start: 0.7986 (pt0) cc_final: 0.7765 (pt0) outliers start: 178 outliers final: 81 residues processed: 774 average time/residue: 1.2410 time to fit residues: 1251.3242 Evaluate side-chains 693 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 595 time to evaluate : 4.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 0 residue 41 GLU Chi-restraints excluded: chain 1 residue 24 LEU Chi-restraints excluded: chain 1 residue 188 VAL Chi-restraints excluded: chain 1 residue 227 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 258 GLU Chi-restraints excluded: chain 1 residue 389 THR Chi-restraints excluded: chain 1 residue 426 VAL Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 2 residue 391 THR Chi-restraints excluded: chain 3 residue 121 PHE Chi-restraints excluded: chain 3 residue 144 THR Chi-restraints excluded: chain 4 residue 115 THR Chi-restraints excluded: chain 4 residue 122 VAL Chi-restraints excluded: chain 4 residue 158 LYS Chi-restraints excluded: chain 4 residue 178 LEU Chi-restraints excluded: chain 4 residue 199 VAL Chi-restraints excluded: chain 4 residue 209 SER Chi-restraints excluded: chain 5 residue 27 ASP Chi-restraints excluded: chain 5 residue 111 LYS Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 31 LEU Chi-restraints excluded: chain 7 residue 35 ILE Chi-restraints excluded: chain 7 residue 37 LEU Chi-restraints excluded: chain 7 residue 39 VAL Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 7 residue 146 GLU Chi-restraints excluded: chain 9 residue 3 VAL Chi-restraints excluded: chain 9 residue 91 LYS Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain M residue 124 GLU Chi-restraints excluded: chain M residue 182 THR Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 254 LEU Chi-restraints excluded: chain M residue 274 THR Chi-restraints excluded: chain M residue 296 SER Chi-restraints excluded: chain M residue 313 ASP Chi-restraints excluded: chain M residue 314 LYS Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain Q residue 42 ARG Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain R residue 60 VAL Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 107 THR Chi-restraints excluded: chain S residue 127 LEU Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 283 GLU Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 149 GLN Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 439 MET Chi-restraints excluded: chain T residue 487 LYS Chi-restraints excluded: chain T residue 496 ARG Chi-restraints excluded: chain T residue 518 VAL Chi-restraints excluded: chain T residue 549 HIS Chi-restraints excluded: chain U residue 41 ASP Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 226 ASP Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 532 VAL Chi-restraints excluded: chain U residue 550 LEU Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain V residue 102 SER Chi-restraints excluded: chain V residue 113 SER Chi-restraints excluded: chain V residue 152 ASN Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 411 GLU Chi-restraints excluded: chain V residue 482 GLU Chi-restraints excluded: chain V residue 554 LEU Chi-restraints excluded: chain X residue 44 ILE Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 341 VAL Chi-restraints excluded: chain X residue 466 THR Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Y residue 70 VAL Chi-restraints excluded: chain Y residue 166 VAL Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 365 SER Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain Z residue 113 VAL Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 415 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 226 optimal weight: 4.9990 chunk 607 optimal weight: 7.9990 chunk 133 optimal weight: 9.9990 chunk 396 optimal weight: 4.9990 chunk 166 optimal weight: 0.5980 chunk 675 optimal weight: 0.0970 chunk 560 optimal weight: 0.3980 chunk 312 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 chunk 223 optimal weight: 5.9990 chunk 354 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 256 GLN 4 52 GLN 4 240 GLN ** 4 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 59 ASN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN G 98 GLN Q 43 GLN ** R 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 253 GLN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 539 ASN ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 241 HIS V 461 GLN ** V 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 123 ASN Y 198 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 54686 Z= 0.155 Angle : 0.527 12.697 74161 Z= 0.270 Chirality : 0.041 0.183 8689 Planarity : 0.004 0.058 9510 Dihedral : 5.613 106.532 7678 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.98 % Favored : 95.88 % Rotamer: Outliers : 2.86 % Allowed : 19.27 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.10), residues: 7038 helix: 0.45 (0.09), residues: 3855 sheet: -0.78 (0.20), residues: 661 loop : -0.72 (0.13), residues: 2522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP 9 93 HIS 0.003 0.001 HIS 4 233 PHE 0.062 0.001 PHE 3 121 TYR 0.025 0.001 TYR 4 211 ARG 0.006 0.000 ARG T 199 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 655 time to evaluate : 4.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 34 GLU cc_start: 0.7467 (pm20) cc_final: 0.7265 (pm20) REVERT: 1 195 LYS cc_start: 0.7156 (mmtm) cc_final: 0.6849 (mmtm) REVERT: 1 352 GLU cc_start: 0.7380 (mm-30) cc_final: 0.6993 (mp0) REVERT: 1 438 GLN cc_start: 0.7186 (OUTLIER) cc_final: 0.6803 (tm-30) REVERT: 1 456 LYS cc_start: 0.8378 (tttt) cc_final: 0.8003 (tptm) REVERT: 2 7 ASP cc_start: 0.5770 (OUTLIER) cc_final: 0.5453 (p0) REVERT: 3 129 LYS cc_start: 0.8362 (mttt) cc_final: 0.8128 (mttm) REVERT: 3 309 ASN cc_start: 0.6625 (p0) cc_final: 0.6225 (p0) REVERT: 4 255 ARG cc_start: 0.8026 (ttm170) cc_final: 0.7593 (mtm-85) REVERT: 5 28 THR cc_start: 0.9008 (m) cc_final: 0.8768 (m) REVERT: 5 112 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7532 (ptm-80) REVERT: 5 119 LYS cc_start: 0.7780 (mmmm) cc_final: 0.7552 (mmmt) REVERT: 7 37 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7601 (tt) REVERT: 8 69 LYS cc_start: 0.8642 (mttt) cc_final: 0.6521 (tmtt) REVERT: B 81 MET cc_start: 0.8596 (ttm) cc_final: 0.8294 (ttm) REVERT: B 97 LYS cc_start: 0.8299 (mmtt) cc_final: 0.7865 (mmtt) REVERT: E 61 MET cc_start: 0.8151 (mmp) cc_final: 0.7900 (mpt) REVERT: F 78 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7559 (tp) REVERT: F 81 MET cc_start: 0.7798 (ttp) cc_final: 0.7551 (ttp) REVERT: G 116 PHE cc_start: 0.7288 (m-10) cc_final: 0.6981 (m-10) REVERT: I 97 LYS cc_start: 0.8478 (mppt) cc_final: 0.8116 (ttpt) REVERT: I 124 ILE cc_start: 0.8120 (mm) cc_final: 0.7851 (mp) REVERT: J 84 SER cc_start: 0.8768 (m) cc_final: 0.8424 (p) REVERT: J 92 ASN cc_start: 0.8244 (p0) cc_final: 0.7952 (p0) REVERT: M 124 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.6708 (mp0) REVERT: M 314 LYS cc_start: 0.8538 (tmtm) cc_final: 0.8331 (tptt) REVERT: P 194 LEU cc_start: 0.7710 (mp) cc_final: 0.7360 (mp) REVERT: Q 42 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.7033 (ptt90) REVERT: R 176 PHE cc_start: 0.8173 (t80) cc_final: 0.7865 (t80) REVERT: S 68 MET cc_start: 0.7777 (ttp) cc_final: 0.7308 (tmm) REVERT: S 275 GLU cc_start: 0.7543 (tm-30) cc_final: 0.7230 (tm-30) REVERT: T 149 GLN cc_start: 0.7591 (OUTLIER) cc_final: 0.7322 (pt0) REVERT: T 411 GLU cc_start: 0.7642 (pm20) cc_final: 0.7407 (mp0) REVERT: T 439 MET cc_start: 0.9063 (ttp) cc_final: 0.8796 (ttp) REVERT: T 440 LYS cc_start: 0.8388 (ttpt) cc_final: 0.8095 (ttmt) REVERT: T 496 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.8043 (mtt90) REVERT: T 535 ILE cc_start: 0.8610 (mt) cc_final: 0.8241 (mp) REVERT: T 539 ASN cc_start: 0.8241 (m-40) cc_final: 0.7961 (m-40) REVERT: T 549 HIS cc_start: 0.6938 (OUTLIER) cc_final: 0.6530 (t70) REVERT: T 555 ARG cc_start: 0.7705 (mtt-85) cc_final: 0.7291 (mmt90) REVERT: U 75 LYS cc_start: 0.8195 (mmmt) cc_final: 0.7994 (mttp) REVERT: U 253 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.8082 (mt0) REVERT: U 553 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7435 (mm-30) REVERT: V 50 LYS cc_start: 0.8033 (tppt) cc_final: 0.7713 (tptt) REVERT: V 429 ARG cc_start: 0.8164 (mtt-85) cc_final: 0.7909 (mtt-85) REVERT: Y 441 ARG cc_start: 0.7830 (mmt-90) cc_final: 0.7576 (mpt-90) REVERT: Z 430 LYS cc_start: 0.7085 (tppp) cc_final: 0.6760 (mttp) REVERT: Z 451 GLU cc_start: 0.7992 (pt0) cc_final: 0.7723 (pt0) REVERT: Z 542 ASP cc_start: 0.6152 (OUTLIER) cc_final: 0.5868 (p0) outliers start: 161 outliers final: 84 residues processed: 765 average time/residue: 1.2450 time to fit residues: 1234.4287 Evaluate side-chains 687 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 591 time to evaluate : 4.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 1 residue 24 LEU Chi-restraints excluded: chain 1 residue 188 VAL Chi-restraints excluded: chain 1 residue 227 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 426 VAL Chi-restraints excluded: chain 1 residue 438 GLN Chi-restraints excluded: chain 2 residue 7 ASP Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 2 residue 391 THR Chi-restraints excluded: chain 3 residue 144 THR Chi-restraints excluded: chain 4 residue 115 THR Chi-restraints excluded: chain 4 residue 122 VAL Chi-restraints excluded: chain 4 residue 178 LEU Chi-restraints excluded: chain 4 residue 199 VAL Chi-restraints excluded: chain 5 residue 59 ASN Chi-restraints excluded: chain 5 residue 61 SER Chi-restraints excluded: chain 5 residue 112 ARG Chi-restraints excluded: chain 7 residue 31 LEU Chi-restraints excluded: chain 7 residue 35 ILE Chi-restraints excluded: chain 7 residue 37 LEU Chi-restraints excluded: chain 7 residue 39 VAL Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain M residue 124 GLU Chi-restraints excluded: chain M residue 182 THR Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 274 THR Chi-restraints excluded: chain M residue 313 ASP Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 93 ASP Chi-restraints excluded: chain Q residue 42 ARG Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain R residue 60 VAL Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 107 THR Chi-restraints excluded: chain S residue 127 LEU Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 283 GLU Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 149 GLN Chi-restraints excluded: chain T residue 167 LEU Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 494 ILE Chi-restraints excluded: chain T residue 496 ARG Chi-restraints excluded: chain T residue 518 VAL Chi-restraints excluded: chain T residue 549 HIS Chi-restraints excluded: chain U residue 41 ASP Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 198 VAL Chi-restraints excluded: chain U residue 253 GLN Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 532 VAL Chi-restraints excluded: chain U residue 550 LEU Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 113 SER Chi-restraints excluded: chain V residue 152 ASN Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 409 GLU Chi-restraints excluded: chain V residue 554 LEU Chi-restraints excluded: chain X residue 44 ILE Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Y residue 70 VAL Chi-restraints excluded: chain Y residue 193 ILE Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 365 SER Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain Z residue 113 VAL Chi-restraints excluded: chain Z residue 140 ILE Chi-restraints excluded: chain Z residue 251 MET Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 386 MET Chi-restraints excluded: chain Z residue 415 ASP Chi-restraints excluded: chain Z residue 416 ILE Chi-restraints excluded: chain Z residue 456 THR Chi-restraints excluded: chain Z residue 542 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 651 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 384 optimal weight: 5.9990 chunk 493 optimal weight: 2.9990 chunk 382 optimal weight: 2.9990 chunk 568 optimal weight: 2.9990 chunk 377 optimal weight: 4.9990 chunk 672 optimal weight: 3.9990 chunk 421 optimal weight: 4.9990 chunk 410 optimal weight: 1.9990 chunk 310 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 48 ASN ** 1 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 256 GLN 4 52 GLN ** 4 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN G 98 GLN I 98 GLN P 66 GLN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 78 HIS R 104 HIS ** R 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 293 ASN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 539 ASN V 219 GLN V 461 GLN ** V 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 123 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 54686 Z= 0.384 Angle : 0.636 13.093 74161 Z= 0.325 Chirality : 0.046 0.223 8689 Planarity : 0.005 0.071 9510 Dihedral : 6.148 111.633 7677 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.70 % Favored : 95.11 % Rotamer: Outliers : 3.46 % Allowed : 19.71 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.44 (0.10), residues: 7038 helix: 0.23 (0.08), residues: 3877 sheet: -0.79 (0.20), residues: 640 loop : -0.79 (0.13), residues: 2521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP 9 93 HIS 0.008 0.001 HIS 4 233 PHE 0.039 0.002 PHE F 107 TYR 0.024 0.002 TYR 4 211 ARG 0.016 0.001 ARG P 167 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 779 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 584 time to evaluate : 4.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 34 GLU cc_start: 0.7411 (pm20) cc_final: 0.7195 (pm20) REVERT: 1 195 LYS cc_start: 0.7274 (mmtm) cc_final: 0.6902 (mmmm) REVERT: 1 352 GLU cc_start: 0.7533 (mm-30) cc_final: 0.7112 (mp0) REVERT: 1 456 LYS cc_start: 0.8305 (tttt) cc_final: 0.7943 (tptm) REVERT: 2 7 ASP cc_start: 0.5931 (OUTLIER) cc_final: 0.5648 (p0) REVERT: 3 129 LYS cc_start: 0.8381 (mttt) cc_final: 0.8153 (mttm) REVERT: 4 255 ARG cc_start: 0.8061 (ttm170) cc_final: 0.7587 (mtm-85) REVERT: 5 112 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7626 (ptm-80) REVERT: 5 119 LYS cc_start: 0.7963 (mmmm) cc_final: 0.7703 (mmmt) REVERT: 6 71 TYR cc_start: 0.6405 (m-80) cc_final: 0.6172 (m-80) REVERT: 6 146 PHE cc_start: 0.8587 (OUTLIER) cc_final: 0.7778 (t80) REVERT: 7 37 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7601 (tt) REVERT: 8 69 LYS cc_start: 0.8761 (mttt) cc_final: 0.6451 (tmtt) REVERT: 9 52 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8146 (mm) REVERT: B 81 MET cc_start: 0.8627 (ttm) cc_final: 0.8284 (ttm) REVERT: B 97 LYS cc_start: 0.8497 (mmtt) cc_final: 0.8001 (mmtt) REVERT: F 81 MET cc_start: 0.7902 (ttp) cc_final: 0.7614 (ttp) REVERT: G 92 ASN cc_start: 0.7834 (p0) cc_final: 0.7541 (p0) REVERT: G 95 ILE cc_start: 0.8687 (mm) cc_final: 0.8405 (mm) REVERT: I 97 LYS cc_start: 0.8517 (mppt) cc_final: 0.8159 (ttpt) REVERT: I 98 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.8280 (tm-30) REVERT: J 84 SER cc_start: 0.8865 (m) cc_final: 0.8404 (p) REVERT: J 92 ASN cc_start: 0.8486 (p0) cc_final: 0.8215 (p0) REVERT: M 124 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6867 (mp0) REVERT: M 314 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8206 (tttm) REVERT: P 68 ASP cc_start: 0.8764 (t0) cc_final: 0.8306 (t0) REVERT: Q 42 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7087 (ptt180) REVERT: S 68 MET cc_start: 0.7852 (ttp) cc_final: 0.7418 (tmm) REVERT: S 275 GLU cc_start: 0.7672 (tm-30) cc_final: 0.7400 (tm-30) REVERT: T 149 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.7510 (pt0) REVERT: T 411 GLU cc_start: 0.7603 (pm20) cc_final: 0.7348 (mp0) REVERT: T 440 LYS cc_start: 0.8461 (ttpt) cc_final: 0.8204 (ttmt) REVERT: T 496 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.8082 (mtt90) REVERT: T 522 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6900 (mp0) REVERT: T 535 ILE cc_start: 0.8656 (mt) cc_final: 0.8298 (mp) REVERT: T 539 ASN cc_start: 0.8282 (m-40) cc_final: 0.7939 (m-40) REVERT: T 549 HIS cc_start: 0.7073 (OUTLIER) cc_final: 0.6643 (t70) REVERT: U 553 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7472 (mm-30) REVERT: V 50 LYS cc_start: 0.8042 (tppt) cc_final: 0.7719 (tptt) REVERT: X 276 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7364 (mt-10) REVERT: Y 441 ARG cc_start: 0.8206 (mmt-90) cc_final: 0.7988 (mpt-90) REVERT: Z 430 LYS cc_start: 0.7179 (tppp) cc_final: 0.6759 (mttp) REVERT: Z 451 GLU cc_start: 0.7977 (pt0) cc_final: 0.7739 (pt0) REVERT: Z 542 ASP cc_start: 0.6221 (OUTLIER) cc_final: 0.5937 (p0) outliers start: 195 outliers final: 101 residues processed: 720 average time/residue: 1.2548 time to fit residues: 1167.0852 Evaluate side-chains 684 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 568 time to evaluate : 4.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 1 residue 24 LEU Chi-restraints excluded: chain 1 residue 188 VAL Chi-restraints excluded: chain 1 residue 217 LEU Chi-restraints excluded: chain 1 residue 227 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 302 SER Chi-restraints excluded: chain 1 residue 308 ASN Chi-restraints excluded: chain 1 residue 389 THR Chi-restraints excluded: chain 1 residue 394 GLN Chi-restraints excluded: chain 1 residue 426 VAL Chi-restraints excluded: chain 2 residue 7 ASP Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 2 residue 391 THR Chi-restraints excluded: chain 3 residue 96 VAL Chi-restraints excluded: chain 3 residue 137 THR Chi-restraints excluded: chain 3 residue 144 THR Chi-restraints excluded: chain 3 residue 192 VAL Chi-restraints excluded: chain 3 residue 316 VAL Chi-restraints excluded: chain 4 residue 115 THR Chi-restraints excluded: chain 4 residue 122 VAL Chi-restraints excluded: chain 4 residue 199 VAL Chi-restraints excluded: chain 4 residue 209 SER Chi-restraints excluded: chain 5 residue 1 MET Chi-restraints excluded: chain 5 residue 27 ASP Chi-restraints excluded: chain 5 residue 61 SER Chi-restraints excluded: chain 5 residue 112 ARG Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 31 LEU Chi-restraints excluded: chain 7 residue 35 ILE Chi-restraints excluded: chain 7 residue 37 LEU Chi-restraints excluded: chain 7 residue 39 VAL Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 6 VAL Chi-restraints excluded: chain 9 residue 52 LEU Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 98 GLN Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain M residue 124 GLU Chi-restraints excluded: chain M residue 172 GLU Chi-restraints excluded: chain M residue 182 THR Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 274 THR Chi-restraints excluded: chain M residue 296 SER Chi-restraints excluded: chain M residue 313 ASP Chi-restraints excluded: chain M residue 314 LYS Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 66 GLN Chi-restraints excluded: chain P residue 93 ASP Chi-restraints excluded: chain P residue 195 LEU Chi-restraints excluded: chain Q residue 42 ARG Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain R residue 60 VAL Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 107 THR Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain S residue 63 VAL Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 283 GLU Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 149 GLN Chi-restraints excluded: chain T residue 167 LEU Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 496 ARG Chi-restraints excluded: chain T residue 515 GLN Chi-restraints excluded: chain T residue 518 VAL Chi-restraints excluded: chain T residue 522 GLU Chi-restraints excluded: chain T residue 549 HIS Chi-restraints excluded: chain U residue 41 ASP Chi-restraints excluded: chain U residue 48 LEU Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain U residue 115 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 198 VAL Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 532 VAL Chi-restraints excluded: chain U residue 550 LEU Chi-restraints excluded: chain V residue 102 SER Chi-restraints excluded: chain V residue 113 SER Chi-restraints excluded: chain V residue 152 ASN Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain V residue 554 LEU Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 159 ILE Chi-restraints excluded: chain X residue 227 MET Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 276 GLU Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 341 VAL Chi-restraints excluded: chain X residue 466 THR Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Y residue 70 VAL Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 365 SER Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain Z residue 113 VAL Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 416 ILE Chi-restraints excluded: chain Z residue 417 ILE Chi-restraints excluded: chain Z residue 456 THR Chi-restraints excluded: chain Z residue 542 ASP Chi-restraints excluded: chain Z residue 573 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 416 optimal weight: 1.9990 chunk 268 optimal weight: 0.6980 chunk 401 optimal weight: 1.9990 chunk 202 optimal weight: 0.3980 chunk 132 optimal weight: 7.9990 chunk 130 optimal weight: 0.7980 chunk 427 optimal weight: 2.9990 chunk 458 optimal weight: 0.6980 chunk 332 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 528 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 256 GLN 4 52 GLN 4 240 GLN ** 4 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 59 ASN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 121 ASN ** P 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 253 GLN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 539 ASN V 219 GLN V 461 GLN ** V 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 123 ASN Y 414 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 54686 Z= 0.167 Angle : 0.552 13.804 74161 Z= 0.280 Chirality : 0.041 0.176 8689 Planarity : 0.004 0.073 9510 Dihedral : 5.569 108.522 7677 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.72 % Favored : 96.14 % Rotamer: Outliers : 2.36 % Allowed : 20.97 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.10 (0.10), residues: 7038 helix: 0.54 (0.09), residues: 3855 sheet: -0.69 (0.21), residues: 646 loop : -0.67 (0.13), residues: 2537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP 9 93 HIS 0.003 0.001 HIS 4 233 PHE 0.039 0.001 PHE F 107 TYR 0.024 0.001 TYR 4 211 ARG 0.019 0.000 ARG P 167 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 769 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 636 time to evaluate : 4.796 Fit side-chains revert: symmetry clash REVERT: 1 195 LYS cc_start: 0.7148 (mmtm) cc_final: 0.6857 (mmtm) REVERT: 1 352 GLU cc_start: 0.7364 (mm-30) cc_final: 0.6986 (mp0) REVERT: 1 438 GLN cc_start: 0.7095 (OUTLIER) cc_final: 0.6878 (tm-30) REVERT: 1 456 LYS cc_start: 0.8341 (tttt) cc_final: 0.7999 (tptm) REVERT: 2 7 ASP cc_start: 0.6016 (OUTLIER) cc_final: 0.5699 (p0) REVERT: 2 16 ASP cc_start: 0.7768 (t0) cc_final: 0.7519 (t0) REVERT: 3 129 LYS cc_start: 0.8354 (mttt) cc_final: 0.8112 (mttm) REVERT: 3 309 ASN cc_start: 0.6525 (p0) cc_final: 0.5637 (m-40) REVERT: 4 255 ARG cc_start: 0.8077 (ttm170) cc_final: 0.7651 (mtm-85) REVERT: 5 28 THR cc_start: 0.9011 (m) cc_final: 0.8766 (m) REVERT: 5 112 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7429 (ptm-80) REVERT: 6 146 PHE cc_start: 0.8535 (OUTLIER) cc_final: 0.7724 (t80) REVERT: 7 37 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7580 (tt) REVERT: 8 69 LYS cc_start: 0.8677 (mttt) cc_final: 0.7316 (tmtt) REVERT: B 81 MET cc_start: 0.8600 (ttm) cc_final: 0.8279 (ttm) REVERT: B 97 LYS cc_start: 0.8322 (mmtt) cc_final: 0.7877 (mmtt) REVERT: D 98 GLN cc_start: 0.7871 (tt0) cc_final: 0.7150 (tp-100) REVERT: E 61 MET cc_start: 0.7839 (mpt) cc_final: 0.7584 (mpm) REVERT: F 78 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7476 (tp) REVERT: F 81 MET cc_start: 0.7891 (ttp) cc_final: 0.7641 (ttp) REVERT: G 95 ILE cc_start: 0.8620 (mm) cc_final: 0.8364 (mm) REVERT: I 97 LYS cc_start: 0.8478 (mppt) cc_final: 0.8100 (mtpt) REVERT: I 98 GLN cc_start: 0.8492 (tm130) cc_final: 0.8126 (tm-30) REVERT: J 84 SER cc_start: 0.8848 (m) cc_final: 0.8459 (p) REVERT: J 92 ASN cc_start: 0.8304 (p0) cc_final: 0.7975 (p0) REVERT: M 124 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.6866 (mp0) REVERT: M 314 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8341 (tptt) REVERT: P 194 LEU cc_start: 0.7650 (mp) cc_final: 0.7328 (mp) REVERT: R 75 TYR cc_start: 0.8097 (m-80) cc_final: 0.7595 (m-10) REVERT: R 176 PHE cc_start: 0.8131 (t80) cc_final: 0.7788 (t80) REVERT: S 68 MET cc_start: 0.7810 (ttp) cc_final: 0.7361 (tmm) REVERT: S 198 ARG cc_start: 0.6703 (mmm160) cc_final: 0.6414 (mmm160) REVERT: S 275 GLU cc_start: 0.7516 (tm-30) cc_final: 0.7222 (tm-30) REVERT: T 149 GLN cc_start: 0.7642 (OUTLIER) cc_final: 0.7363 (pt0) REVERT: T 411 GLU cc_start: 0.7582 (pm20) cc_final: 0.7347 (mp0) REVERT: T 440 LYS cc_start: 0.8394 (ttpt) cc_final: 0.8108 (ttmt) REVERT: T 496 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.8018 (mtt90) REVERT: T 535 ILE cc_start: 0.8616 (mt) cc_final: 0.8197 (mp) REVERT: T 539 ASN cc_start: 0.8301 (m-40) cc_final: 0.8032 (m-40) REVERT: T 549 HIS cc_start: 0.6925 (OUTLIER) cc_final: 0.6506 (t70) REVERT: U 253 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.8026 (mt0) REVERT: U 553 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7409 (mm-30) REVERT: V 50 LYS cc_start: 0.8007 (tppt) cc_final: 0.7708 (tptt) REVERT: V 559 LEU cc_start: 0.8342 (mt) cc_final: 0.8106 (mt) REVERT: Y 386 MET cc_start: 0.8334 (tpp) cc_final: 0.8102 (mmm) REVERT: Y 441 ARG cc_start: 0.7831 (mmt-90) cc_final: 0.7591 (mpt-90) REVERT: Z 430 LYS cc_start: 0.7209 (tppp) cc_final: 0.6801 (mttp) REVERT: Z 451 GLU cc_start: 0.8003 (pt0) cc_final: 0.7729 (pt0) REVERT: Z 542 ASP cc_start: 0.6109 (OUTLIER) cc_final: 0.5816 (p0) outliers start: 133 outliers final: 79 residues processed: 726 average time/residue: 1.2588 time to fit residues: 1186.9692 Evaluate side-chains 687 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 595 time to evaluate : 4.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 24 LEU Chi-restraints excluded: chain 1 residue 188 VAL Chi-restraints excluded: chain 1 residue 227 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 389 THR Chi-restraints excluded: chain 1 residue 426 VAL Chi-restraints excluded: chain 1 residue 438 GLN Chi-restraints excluded: chain 2 residue 7 ASP Chi-restraints excluded: chain 2 residue 19 VAL Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 2 residue 391 THR Chi-restraints excluded: chain 3 residue 144 THR Chi-restraints excluded: chain 4 residue 122 VAL Chi-restraints excluded: chain 4 residue 199 VAL Chi-restraints excluded: chain 5 residue 61 SER Chi-restraints excluded: chain 5 residue 112 ARG Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 31 LEU Chi-restraints excluded: chain 7 residue 35 ILE Chi-restraints excluded: chain 7 residue 37 LEU Chi-restraints excluded: chain 7 residue 39 VAL Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 7 residue 146 GLU Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain M residue 124 GLU Chi-restraints excluded: chain M residue 182 THR Chi-restraints excluded: chain M residue 313 ASP Chi-restraints excluded: chain M residue 314 LYS Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain R residue 60 VAL Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 283 GLU Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 149 GLN Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 353 ASP Chi-restraints excluded: chain T residue 496 ARG Chi-restraints excluded: chain T residue 518 VAL Chi-restraints excluded: chain T residue 549 HIS Chi-restraints excluded: chain U residue 41 ASP Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 198 VAL Chi-restraints excluded: chain U residue 226 ASP Chi-restraints excluded: chain U residue 253 GLN Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 532 VAL Chi-restraints excluded: chain U residue 550 LEU Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 113 SER Chi-restraints excluded: chain V residue 152 ASN Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 267 SER Chi-restraints excluded: chain V residue 482 GLU Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain V residue 554 LEU Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 466 THR Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Y residue 70 VAL Chi-restraints excluded: chain Y residue 193 ILE Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 318 LEU Chi-restraints excluded: chain Y residue 475 THR Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain Z residue 113 VAL Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 415 ASP Chi-restraints excluded: chain Z residue 416 ILE Chi-restraints excluded: chain Z residue 417 ILE Chi-restraints excluded: chain Z residue 456 THR Chi-restraints excluded: chain Z residue 542 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 611 optimal weight: 0.9980 chunk 644 optimal weight: 0.6980 chunk 588 optimal weight: 7.9990 chunk 626 optimal weight: 2.9990 chunk 377 optimal weight: 4.9990 chunk 273 optimal weight: 10.0000 chunk 492 optimal weight: 4.9990 chunk 192 optimal weight: 10.0000 chunk 566 optimal weight: 0.0070 chunk 592 optimal weight: 0.3980 chunk 624 optimal weight: 8.9990 overall best weight: 1.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 44 ASN 2 74 ASN ** 2 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 256 GLN 4 52 GLN 4 240 GLN ** 4 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 59 ASN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 184 ASN G 98 GLN I 98 GLN P 65 ASN ** P 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 GLN ** R 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 253 GLN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 539 ASN V 461 GLN ** V 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 123 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 54686 Z= 0.201 Angle : 0.565 13.475 74161 Z= 0.288 Chirality : 0.042 0.190 8689 Planarity : 0.004 0.072 9510 Dihedral : 5.546 106.170 7677 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.04 % Favored : 95.81 % Rotamer: Outliers : 2.33 % Allowed : 21.47 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.10), residues: 7038 helix: 0.60 (0.09), residues: 3857 sheet: -0.61 (0.21), residues: 641 loop : -0.64 (0.13), residues: 2540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP 9 93 HIS 0.004 0.001 HIS 4 233 PHE 0.038 0.001 PHE G 107 TYR 0.024 0.001 TYR 4 211 ARG 0.017 0.000 ARG P 167 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 605 time to evaluate : 4.735 Fit side-chains revert: symmetry clash REVERT: 1 195 LYS cc_start: 0.7178 (mmtm) cc_final: 0.6880 (mmtm) REVERT: 1 352 GLU cc_start: 0.7364 (mm-30) cc_final: 0.6982 (mp0) REVERT: 1 445 LYS cc_start: 0.7714 (tmmt) cc_final: 0.7500 (pttm) REVERT: 1 456 LYS cc_start: 0.8334 (tttt) cc_final: 0.7994 (tptm) REVERT: 2 7 ASP cc_start: 0.6000 (OUTLIER) cc_final: 0.5693 (p0) REVERT: 2 16 ASP cc_start: 0.7716 (t0) cc_final: 0.7479 (t0) REVERT: 2 223 LYS cc_start: 0.5758 (tptt) cc_final: 0.5490 (ttpt) REVERT: 3 129 LYS cc_start: 0.8358 (mttt) cc_final: 0.8121 (mttm) REVERT: 4 255 ARG cc_start: 0.8056 (ttm170) cc_final: 0.7633 (mtm-85) REVERT: 5 28 THR cc_start: 0.9037 (m) cc_final: 0.8780 (m) REVERT: 5 112 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7515 (ptm-80) REVERT: 6 146 PHE cc_start: 0.8547 (OUTLIER) cc_final: 0.7739 (t80) REVERT: 7 37 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7590 (tt) REVERT: 8 69 LYS cc_start: 0.8661 (mttt) cc_final: 0.6480 (tmtt) REVERT: B 81 MET cc_start: 0.8616 (ttm) cc_final: 0.8301 (ttm) REVERT: B 97 LYS cc_start: 0.8328 (mmtt) cc_final: 0.7922 (mmtt) REVERT: E 61 MET cc_start: 0.7809 (mpt) cc_final: 0.7497 (mpm) REVERT: F 81 MET cc_start: 0.7826 (ttp) cc_final: 0.7545 (ttp) REVERT: G 95 ILE cc_start: 0.8633 (mm) cc_final: 0.8380 (mm) REVERT: I 97 LYS cc_start: 0.8493 (mppt) cc_final: 0.8156 (ttpt) REVERT: I 98 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8241 (tm-30) REVERT: J 84 SER cc_start: 0.8841 (m) cc_final: 0.8454 (p) REVERT: J 92 ASN cc_start: 0.8269 (p0) cc_final: 0.7927 (p0) REVERT: M 124 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.6888 (mp0) REVERT: M 314 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8305 (tptt) REVERT: R 176 PHE cc_start: 0.8096 (t80) cc_final: 0.7677 (t80) REVERT: R 196 GLU cc_start: 0.6775 (OUTLIER) cc_final: 0.5505 (mp0) REVERT: S 68 MET cc_start: 0.7802 (ttp) cc_final: 0.7349 (tmm) REVERT: S 198 ARG cc_start: 0.6711 (mmm160) cc_final: 0.6434 (mmm160) REVERT: S 275 GLU cc_start: 0.7536 (tm-30) cc_final: 0.7233 (tm-30) REVERT: T 149 GLN cc_start: 0.7615 (OUTLIER) cc_final: 0.7338 (pt0) REVERT: T 411 GLU cc_start: 0.7644 (pm20) cc_final: 0.7388 (mp0) REVERT: T 440 LYS cc_start: 0.8401 (ttpt) cc_final: 0.8123 (ttmt) REVERT: T 535 ILE cc_start: 0.8622 (mt) cc_final: 0.8185 (mp) REVERT: T 539 ASN cc_start: 0.8247 (m-40) cc_final: 0.7961 (m-40) REVERT: T 549 HIS cc_start: 0.6938 (OUTLIER) cc_final: 0.6511 (t70) REVERT: U 253 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.8004 (mt0) REVERT: U 553 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7442 (mm-30) REVERT: V 50 LYS cc_start: 0.8023 (tppt) cc_final: 0.7705 (tptt) REVERT: V 559 LEU cc_start: 0.8364 (mt) cc_final: 0.8127 (mt) REVERT: X 531 VAL cc_start: 0.7717 (t) cc_final: 0.7225 (p) REVERT: Y 441 ARG cc_start: 0.7887 (mmt-90) cc_final: 0.7648 (mpt-90) REVERT: Z 430 LYS cc_start: 0.7185 (tppp) cc_final: 0.6775 (mttp) REVERT: Z 451 GLU cc_start: 0.7977 (pt0) cc_final: 0.7708 (pt0) REVERT: Z 542 ASP cc_start: 0.6104 (OUTLIER) cc_final: 0.5790 (p0) REVERT: Z 573 LYS cc_start: 0.6432 (OUTLIER) cc_final: 0.5889 (mmpt) outliers start: 131 outliers final: 89 residues processed: 695 average time/residue: 1.2794 time to fit residues: 1159.4988 Evaluate side-chains 684 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 582 time to evaluate : 4.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 24 LEU Chi-restraints excluded: chain 1 residue 188 VAL Chi-restraints excluded: chain 1 residue 227 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 389 THR Chi-restraints excluded: chain 1 residue 426 VAL Chi-restraints excluded: chain 2 residue 7 ASP Chi-restraints excluded: chain 2 residue 19 VAL Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 2 residue 391 THR Chi-restraints excluded: chain 3 residue 96 VAL Chi-restraints excluded: chain 3 residue 132 VAL Chi-restraints excluded: chain 3 residue 144 THR Chi-restraints excluded: chain 4 residue 115 THR Chi-restraints excluded: chain 4 residue 122 VAL Chi-restraints excluded: chain 4 residue 199 VAL Chi-restraints excluded: chain 5 residue 59 ASN Chi-restraints excluded: chain 5 residue 61 SER Chi-restraints excluded: chain 5 residue 112 ARG Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 31 LEU Chi-restraints excluded: chain 7 residue 35 ILE Chi-restraints excluded: chain 7 residue 37 LEU Chi-restraints excluded: chain 7 residue 39 VAL Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 7 residue 146 GLU Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 8 residue 6 VAL Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain I residue 98 GLN Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain M residue 124 GLU Chi-restraints excluded: chain M residue 182 THR Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 313 ASP Chi-restraints excluded: chain M residue 314 LYS Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 93 ASP Chi-restraints excluded: chain P residue 195 LEU Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain R residue 60 VAL Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 83 GLN Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain R residue 196 GLU Chi-restraints excluded: chain S residue 127 LEU Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 283 GLU Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 149 GLN Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 353 ASP Chi-restraints excluded: chain T residue 515 GLN Chi-restraints excluded: chain T residue 518 VAL Chi-restraints excluded: chain T residue 549 HIS Chi-restraints excluded: chain U residue 41 ASP Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 198 VAL Chi-restraints excluded: chain U residue 253 GLN Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 483 MET Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 532 VAL Chi-restraints excluded: chain U residue 550 LEU Chi-restraints excluded: chain V residue 113 SER Chi-restraints excluded: chain V residue 152 ASN Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 267 SER Chi-restraints excluded: chain V residue 482 GLU Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain V residue 554 LEU Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 466 THR Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Y residue 70 VAL Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 318 LEU Chi-restraints excluded: chain Y residue 365 SER Chi-restraints excluded: chain Y residue 475 THR Chi-restraints excluded: chain Z residue 69 SER Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain Z residue 113 VAL Chi-restraints excluded: chain Z residue 158 GLU Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 416 ILE Chi-restraints excluded: chain Z residue 417 ILE Chi-restraints excluded: chain Z residue 456 THR Chi-restraints excluded: chain Z residue 542 ASP Chi-restraints excluded: chain Z residue 573 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 411 optimal weight: 3.9990 chunk 662 optimal weight: 7.9990 chunk 404 optimal weight: 0.7980 chunk 314 optimal weight: 0.8980 chunk 460 optimal weight: 2.9990 chunk 695 optimal weight: 10.0000 chunk 640 optimal weight: 0.0980 chunk 553 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 427 optimal weight: 0.8980 chunk 339 optimal weight: 9.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 482 ASN ** 2 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 256 GLN 4 52 GLN 4 240 GLN ** 4 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 ASN I 98 GLN ** P 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 HIS R 83 GLN R 85 GLN R 171 GLN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 253 GLN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 539 ASN V 461 GLN ** V 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 123 ASN Y 414 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 54686 Z= 0.176 Angle : 0.560 13.862 74161 Z= 0.284 Chirality : 0.041 0.239 8689 Planarity : 0.004 0.069 9510 Dihedral : 5.424 102.222 7677 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.77 % Favored : 96.09 % Rotamer: Outliers : 2.13 % Allowed : 22.00 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.10 (0.10), residues: 7038 helix: 0.69 (0.09), residues: 3862 sheet: -0.63 (0.21), residues: 650 loop : -0.57 (0.13), residues: 2526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP 9 93 HIS 0.003 0.001 HIS 4 233 PHE 0.039 0.001 PHE G 107 TYR 0.024 0.001 TYR 4 211 ARG 0.016 0.000 ARG P 167 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 723 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 603 time to evaluate : 4.677 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 195 LYS cc_start: 0.7155 (mmtm) cc_final: 0.6676 (mmtm) REVERT: 1 352 GLU cc_start: 0.7313 (mm-30) cc_final: 0.6942 (mp0) REVERT: 1 456 LYS cc_start: 0.8329 (tttt) cc_final: 0.7989 (tptm) REVERT: 2 7 ASP cc_start: 0.6014 (OUTLIER) cc_final: 0.5702 (p0) REVERT: 2 16 ASP cc_start: 0.7702 (t0) cc_final: 0.7462 (t0) REVERT: 2 223 LYS cc_start: 0.5853 (tptt) cc_final: 0.5469 (ttpp) REVERT: 2 391 THR cc_start: 0.5217 (OUTLIER) cc_final: 0.4933 (m) REVERT: 3 129 LYS cc_start: 0.8343 (mttt) cc_final: 0.8112 (mttm) REVERT: 3 152 TYR cc_start: 0.7784 (t80) cc_final: 0.7478 (t80) REVERT: 4 255 ARG cc_start: 0.8049 (ttm170) cc_final: 0.7620 (mtm-85) REVERT: 5 28 THR cc_start: 0.9023 (m) cc_final: 0.8777 (m) REVERT: 6 146 PHE cc_start: 0.8529 (OUTLIER) cc_final: 0.7740 (t80) REVERT: 7 37 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7634 (tt) REVERT: 8 69 LYS cc_start: 0.8650 (mttt) cc_final: 0.6519 (tmtt) REVERT: B 81 MET cc_start: 0.8624 (ttm) cc_final: 0.8301 (ttm) REVERT: B 97 LYS cc_start: 0.8320 (mmtt) cc_final: 0.7920 (mmtt) REVERT: C 61 MET cc_start: 0.8036 (mmt) cc_final: 0.7676 (mtt) REVERT: D 98 GLN cc_start: 0.7746 (tt0) cc_final: 0.7061 (tp-100) REVERT: E 61 MET cc_start: 0.7700 (mpt) cc_final: 0.7447 (mpm) REVERT: F 81 MET cc_start: 0.7834 (ttp) cc_final: 0.7581 (ttp) REVERT: G 95 ILE cc_start: 0.8665 (mm) cc_final: 0.8410 (mm) REVERT: G 116 PHE cc_start: 0.7267 (m-10) cc_final: 0.6909 (m-10) REVERT: I 98 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.8366 (tm-30) REVERT: J 84 SER cc_start: 0.8763 (m) cc_final: 0.8419 (p) REVERT: J 92 ASN cc_start: 0.8254 (p0) cc_final: 0.7869 (p0) REVERT: M 124 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.6899 (mp0) REVERT: M 314 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8319 (tptt) REVERT: P 68 ASP cc_start: 0.8578 (t0) cc_final: 0.8144 (t0) REVERT: R 176 PHE cc_start: 0.8003 (t80) cc_final: 0.7707 (t80) REVERT: R 196 GLU cc_start: 0.6770 (OUTLIER) cc_final: 0.5506 (mp0) REVERT: S 68 MET cc_start: 0.7789 (ttp) cc_final: 0.7328 (tmm) REVERT: S 198 ARG cc_start: 0.6673 (mmm160) cc_final: 0.6408 (mmm160) REVERT: S 275 GLU cc_start: 0.7537 (tm-30) cc_final: 0.7189 (tm-30) REVERT: T 149 GLN cc_start: 0.7583 (OUTLIER) cc_final: 0.7289 (pt0) REVERT: T 411 GLU cc_start: 0.7629 (pm20) cc_final: 0.7371 (mp0) REVERT: T 440 LYS cc_start: 0.8373 (ttpt) cc_final: 0.8084 (ttmt) REVERT: T 535 ILE cc_start: 0.8624 (mt) cc_final: 0.8197 (mp) REVERT: T 539 ASN cc_start: 0.8245 (m-40) cc_final: 0.7964 (m-40) REVERT: T 549 HIS cc_start: 0.6954 (OUTLIER) cc_final: 0.6540 (t70) REVERT: U 553 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7435 (mm-30) REVERT: V 50 LYS cc_start: 0.8096 (tppt) cc_final: 0.7768 (tptt) REVERT: V 559 LEU cc_start: 0.8342 (mt) cc_final: 0.8123 (mt) REVERT: X 531 VAL cc_start: 0.7662 (t) cc_final: 0.7179 (p) REVERT: Y 441 ARG cc_start: 0.7796 (mmt-90) cc_final: 0.7545 (mpt-90) REVERT: Z 430 LYS cc_start: 0.6987 (tppp) cc_final: 0.6637 (mttp) REVERT: Z 451 GLU cc_start: 0.7969 (pt0) cc_final: 0.7653 (pt0) REVERT: Z 542 ASP cc_start: 0.6108 (OUTLIER) cc_final: 0.5792 (p0) outliers start: 120 outliers final: 86 residues processed: 687 average time/residue: 1.2559 time to fit residues: 1122.2931 Evaluate side-chains 675 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 578 time to evaluate : 5.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 24 LEU Chi-restraints excluded: chain 1 residue 227 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 389 THR Chi-restraints excluded: chain 1 residue 426 VAL Chi-restraints excluded: chain 2 residue 7 ASP Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 2 residue 391 THR Chi-restraints excluded: chain 3 residue 96 VAL Chi-restraints excluded: chain 3 residue 132 VAL Chi-restraints excluded: chain 3 residue 137 THR Chi-restraints excluded: chain 3 residue 144 THR Chi-restraints excluded: chain 4 residue 115 THR Chi-restraints excluded: chain 4 residue 122 VAL Chi-restraints excluded: chain 4 residue 199 VAL Chi-restraints excluded: chain 5 residue 61 SER Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 31 LEU Chi-restraints excluded: chain 7 residue 35 ILE Chi-restraints excluded: chain 7 residue 37 LEU Chi-restraints excluded: chain 7 residue 39 VAL Chi-restraints excluded: chain 7 residue 78 GLU Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 7 residue 146 GLU Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 8 residue 6 VAL Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 98 GLN Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain M residue 124 GLU Chi-restraints excluded: chain M residue 182 THR Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 202 PHE Chi-restraints excluded: chain M residue 313 ASP Chi-restraints excluded: chain M residue 314 LYS Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 195 LEU Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain R residue 60 VAL Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 83 GLN Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain R residue 196 GLU Chi-restraints excluded: chain S residue 164 ASP Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 283 GLU Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 149 GLN Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 353 ASP Chi-restraints excluded: chain T residue 494 ILE Chi-restraints excluded: chain T residue 518 VAL Chi-restraints excluded: chain T residue 549 HIS Chi-restraints excluded: chain U residue 41 ASP Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 198 VAL Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain U residue 532 VAL Chi-restraints excluded: chain U residue 550 LEU Chi-restraints excluded: chain V residue 113 SER Chi-restraints excluded: chain V residue 152 ASN Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 267 SER Chi-restraints excluded: chain V residue 482 GLU Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain V residue 554 LEU Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 466 THR Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Y residue 70 VAL Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 318 LEU Chi-restraints excluded: chain Y residue 365 SER Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 475 THR Chi-restraints excluded: chain Z residue 69 SER Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain Z residue 113 VAL Chi-restraints excluded: chain Z residue 158 GLU Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 416 ILE Chi-restraints excluded: chain Z residue 417 ILE Chi-restraints excluded: chain Z residue 456 THR Chi-restraints excluded: chain Z residue 542 ASP Chi-restraints excluded: chain Z residue 573 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 439 optimal weight: 0.7980 chunk 589 optimal weight: 0.0980 chunk 169 optimal weight: 0.8980 chunk 510 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 153 optimal weight: 0.0870 chunk 554 optimal weight: 4.9990 chunk 232 optimal weight: 4.9990 chunk 569 optimal weight: 0.9980 chunk 70 optimal weight: 0.2980 chunk 102 optimal weight: 9.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 74 ASN ** 2 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 256 GLN ** 4 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN I 98 GLN ** P 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 21 ASN Q 43 GLN R 83 GLN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 253 GLN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 539 ASN V 219 GLN V 461 GLN ** V 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 250 GLN Y 123 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.138056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.108571 restraints weight = 77516.618| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.67 r_work: 0.3165 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 54686 Z= 0.155 Angle : 0.553 13.766 74161 Z= 0.280 Chirality : 0.041 0.164 8689 Planarity : 0.004 0.078 9510 Dihedral : 5.232 94.182 7677 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.84 % Favored : 96.04 % Rotamer: Outliers : 1.92 % Allowed : 22.38 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.24 (0.10), residues: 7038 helix: 0.80 (0.09), residues: 3865 sheet: -0.60 (0.21), residues: 654 loop : -0.49 (0.13), residues: 2519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP 9 93 HIS 0.003 0.001 HIS R 66 PHE 0.038 0.001 PHE G 107 TYR 0.025 0.001 TYR 4 211 ARG 0.019 0.000 ARG P 167 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18303.47 seconds wall clock time: 319 minutes 12.36 seconds (19152.36 seconds total)